Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Research Publications

This bibliography contains publications from research funded by the Genomic Science Program. Most publications are from FY 2021 and beyond, though older publications appear in some cases. If you are a GSP-funded researcher and don’t see your publications listed below, contact Marissa Mills (millsmd@ornl.gov) to get your publications added.

 

YearDOIAuthorsTitleJournalVolume/Pages
202310.1002/anie.202212440Zhou, Y., E. N. Mirts, S. Yook, M. Waugh, R. Martini, Y.-S. Jin and Y. LuReshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of PolyketidesAngewandte Chemie International Edition62(5) e202212440
202310.1021/acs.analchem.2c04845Zhou, S., Z. Fatma, P. Xue, S. Mishra, M. Cao, H. Zhao and J. V. SweedlerMass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid CultureAnalytical Chemistry95(8) 4067–76
202310.1016/j.ijbiomac.2023.124743Zhou, F., H. Wu, Y. Chen, M. Wang, G. A. Tuskan and T. YinFunction and molecular mechanism of a poplar placenta limited MIXTA gene in regulating differentiation of plant epidermal cellsInternational Journal of Biological Macromolecules242 124743
202310.1111/gcbb.13021Zhang, N., B. P. Sharma and M. KhannaDetermining spatially varying profit-maximizing management practices for miscanthus and switchgrass production in the rainfed United StatesGCB Bioenergy15(3) 271–82
202310.1016/j.copbio.2022.102870Zha, J., Z. Zhao, Z. Xiao, T. Eng, A. Mukhopadhyay, M. A. G. Koffas and Y. J. TangBiosystem design of Corynebacterium glutamicum for bioproductionCurrent Opinion in Biotechnology79 102870
202310.3390/plants12081657Yuan, G., Y. Liu, T. Yao, W. Muchero, J.-G. Chen, G. A. Tuskan and X. YangeYGFPuv-Assisted Transgenic Selection in Populus deltoides WV94 and Multiplex Genome Editing in Protoplasts of P. trichocarpa x P. deltoides Clone ’52-225’Plants12(8) 1657
202310.1128/aem.01753-22Yayo, J., T. Rydzak, T. Kuil, A. Karlsson, D. J. Harding, A. M. Guss and A. J. A. v. MarisThe Roles of Nicotinamide Adenine Dinucleotide Phosphate Reoxidation and Ammonium Assimilation in the Secretion of Amino Acids as Byproducts of Clostridium thermocellumApplied and Environmental Microbiology89(1) e01753-22
202310.1093/hr/uhad085Yao, T., G. Yuan, H. Lu, Y. Liu, J. Zhang, G. A. Tuskan, W. Muchero, J.-G. Chen and X. YangCRISPR/Cas9-based gene activation and base editing in PopulusHorticulture Researchuhad085
202310.1186/s13068-023-02302-6Yang, J., T. Sooksa-nguan, B. Kannan, S. Cano-Alfanar, H. Liu, A. Kent, J. Shanklin, F. Altpeter and A. HoweMicrobiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy productionBiotechnology for Biofuels and Bioproducts16(1) 56
202310.1016/j.ymben.2023.01.003Yan, Q., T. B. Jacobson, Z. Ye, Y. R. Cortés-Pena, S. S. Bhagwat, S. Hubbard, W. T. Cordell, R. E. Oleniczak, F. V. Gambacorta, J. R. Vazquez, E. V. Shusta, D. Amador-Noguez, J. S. Guest and B. F. PflegerEvaluation of 1,2-diacyl-3-acetyl triacylglycerol production in Yarrowia lipolyticaMetabolic Engineering76 18–28
2023US11629356B2Xie, M., W. Muchero, J.-G. Chen and G. A. TuskanRegulating lignin biosynthesis and sugar release in plantsUnited States PatentUT Battelle LLC
202310.1016/j.mec.2023.e00220Wu, Z.-Y., W. Sun, Y. Shen, J. Pratas, P. F. Suthers, P.-H. Hsieh, S. Dwaraknath, J. D. Rabinowitz, C. D. Maranas, Z. Shao and Y. YoshikuniMetabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalateMetabolic Engineering Communications16 e00220
202310.1128/aem.00500-23Wu, X., S. Gushgari-Doyle, L. M. Lui, A. J. Hendrickson, Y. Liu, S. Jagadamma, T. N. Nielsen, N. B. Justice, T. Simmons, N. J. Hess, D. C. Joyner, T. C. Hazen, A. P. Arkin and R. ChakrabortyDistinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical ZoneApplied and Environmental Microbiologye00500-23
202310.1016/j.engmic.2023.100074Wei, H., W. Wang, Y.-C. Chou, M. E. Himmel, X. Chen, Y. J. Bomble and M. ZhangProspects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO2 and H2Engineering Microbiology3(2) 100074
202310.1021/acs.est.2c06674Wang, Y., N. R. Baral, M. Yang and C. D. ScownCo-Processing Agricultural Residues and Wet Organic Waste Can Produce Lower-Cost Carbon-Negative Fuels and BioplasticsEnvironmental Science & Technology57(7) 2958–69
202310.1016/j.biortech.2022.128216Walls, L. E., P. Otoupal, R. Ledesma-Amaro, S. B. Velasquez-Orta, J. M. Gladden and L. Rios-SolisBioconversion of cellulose into bisabolene using Ruminococcus flavefaciens and Rhodosporidium toruloidesBioresource Technology368 128216
202310.1021/acs.chemrev.2c00403Volk, M. J., V. G. Tran, S.-I. Tan, S. Mishra, Z. Fatma, A. Boob, H. Li, P. Xue, T. A. Martin and H. ZhaoMetabolic Engineering: Methodologies and ApplicationsChemical Reviews123(9) 5521–70
202310.1111/nph.18734Vigneaud, J., A. Kohler, M. D. Sow, A. Delaunay, L. Fauchery, et al.DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungusNew Phytologist238(6) 2561–77
202310.1002/bit.28337VanArsdale, E., A. Navid, M. J. Chu, T. M. Halvorsen, G. F. Payne, Y. Jiao, W. E. Bentley and M. C. YungElectrogenetic signaling and information propagation for controlling microbial consortia via programmed lysisBiotechnology and Bioengineering120(5) 1366–81
202310.1017/S1473550423000058Trubl, G., K. M. Stedman, K. F. Bywaters, E. E. Matula, P. Sommers, et al.Astrovirology: how viruses enhance our understanding of life in the UniverseInternational Journal of Astrobiology1–25
2023Tibocha-Bonilla, J. D., R. Santibáñez-Palominos and K. ZenglerCoralME - An automated tool for next-generation metabolic model design and optimizationMetabolic Engineering 15
202310.3389/fpls.2022.1023571Tejera-Nieves, M., M. Abraha, J. Chen, S. K. Hamilton, G. P. Robertson and B. J. WalkerSeasonal decline in leaf photosynthesis in perennial switchgrass explained by sink limitations and water deficitFrontiers in Plant Science13
202310.1021/acssuschemeng.2c06876Tan, L., H. L. Scott, M. D. Smith, S. V. Pingali, H. M. O’Neill, J. L. Morrell-Falvey, J. Katsaras, J. C. Smith, B. H. Davison, J. G. Elkins and J. D. NickelsAmphiphilic Co-Solvents Modulate the Structure of Membrane DomainsACS Sustainable Chemistry & Engineering11(4) 1598–609
202310.1016/j.ces.2022.118406Taifan, G. S. P. and C. T. MaraveliasIntegrated membrane material design and system synthesisChemical Engineering Science269 118406
2023Suzuki, Y. and J. C. Venter20 Years of the Minimal Cell’s Rise from Theory to PracticeKeiko SFC Journal22(2) 42–53
2023Suzuki, Y., A. Murao, J. Sebesta, B. Yang, D. H. Hernandez, et al.IMAGINE BioSecurity: Genome-Scale Engineering and Modeling for Secure Biosystems DesignDOE Genomic Sciences Program Annual Meeting
202310.1021/acssuschemeng.2c05199Sumer, Z. and R. C. Van LehnHeuristic Computational Model for Predicting Lignin Solubility in Tailored Organic SolventsACS Sustainable Chemistry & Engineering11(1) 187–98
202310.1038/s41396-022-01354-0Stone, B. W. G., P. Dijkstra, B. K. Finley, R. Fitzpatrick, M. M. Foley, et al.Life history strategies among soil bacteria—dichotomy for few, continuum for manyThe ISME Journal17(4) 611–9
202310.1007/s00442-023-05322-zStone, B. W., S. J. Blazewicz, B. J. Koch, P. Dijkstra, M. Hayer, K. S. Hofmockel, X. J. A. Liu, R. L. Mau, J. Pett-Ridge, E. Schwartz and B. A. HungateNutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial communityOecologia201(3) 771–82
202310.1021/acs.est.2c07936Stewart, D. W., Y. R. Cortés-Peña, Y. Li, A. S. Stillwell, M. Khanna and J. S. GuestImplications of Biorefinery Policy Incentives and Location-Specific Economic Parameters for the Financial Viability of BiofuelsEnvironmental Science & Technology57(6) 2262–71
202310.1002/ijch.202200083Stephens, K. and W. E. BentleyQuorum Sensing from Two Engineers’ PerspectivesIsrael Journal of Chemistrye202200083
202310.1007/s00438-022-01987-ySrivastava, S., S. Bombaywala, S. J. Jakhesara, N. V. Patil, C. G. Joshi, H. J. Purohit and N. A. DafalePotential of camel rumen derived Bacillus subtilis and Bacillus velezensis strains for application in plant biomass hydrolysisMolecular Genetics and Genomics298(2) 361–74
202310.1007/s10482-022-01801-0Sreya, P., G. Suresh, A. Rai, B. Ria, L. Vighnesh, V. C. Agre, U. Jagadeeshwari, C. Sasikala and C. V. RamanaRevisiting the taxonomy of the genus Rhodopirellula with the proposal for reclassification of the genus to Rhodopirellula sensu stricto, Aporhodopirellula gen. nov., Allorhodopirellula gen. nov. and Neorhodopirellula gen. novAntonie van Leeuwenhoek116(3) 243–64
202310.1039/D2NP00077FSirirungruang, S., C. R. Barnum, S. N. Tang and P. M. ShihPlant glycosyltransferases for expanding bioactive glycoside diversityNatural Product Reports
202310.1002/bbb.2427Singh, R., S. S. Bhagwat, M. B. Viswanathan, Y. R. Cortés-Peña, K. K. Eilts, G. McDonough, M. Cao, J. S. Guest, H. Zhao and V. SinghAdsorptive separation and recovery of triacetic acid lactone from fermentation brothBiofuels, Bioproducts and Biorefining17(1) 109–20
202310.1111/gcb.16609Silverstein, M. R., D. Segrè and J. M. BhatnagarEnvironmental microbiome engineering for the mitigation of climate changeGlobal Change Biology29(8) 2050–66
202310.3390/cells12071082Shrestha, H., T. Yao, Z. Qiao, W. Muchero, R. L. Hettich, J.-G. Chen and P. E. AbrahamLectin Receptor-like Kinase Signaling during Engineered Ectomycorrhiza ColonizationCells12(7) 1082
202310.1128/aem.00406-23Sharma, B. D., D. G. Olson, R. J. Giannone, R. L. Hettich and L. R. LyndCharacterization and Amelioration of Filtration Difficulties Encountered in Metabolomic Studies of Clostridium thermocellum at Elevated Sugar ConcentrationsApplied and Environmental Microbiology89(4) e00406-23
202310.1016/j.mib.2022.102263Shade, A.Microbiome rescue: directing resilience of environmental microbial communitiesCurrent Opinion in Microbiology72 102263
202310.1016/j.scitotenv.2022.159496Semedo, M. and B. SongSediment metagenomics reveals the impacts of poultry industry wastewater on antibiotic resistance and nitrogen cycling genes in tidal creek ecosystemsScience of The Total Environment857(Part 2) 159496
2023Sebesta, J., C. Pastore, H. Hou and J. YuBiocontainment of genetically modified Synechocystis sp. PCC 6803The 2023 Alabama State University STEM Research Symposium
2023Sebesta, J., M. Cantrell, E. Schaedig, H. Hou, C. Pastore, K. Chou, W. Xiong, M. Guarnieri and J. YuPolyphosphate kinase deletion in Synechocystis sp. PCC6803 increases productivity in controlled conditions but decreases tolerance to a variety of stress conditionsGorden Conference Photosynthesis
202310.1016/j.ymben.2023.04.003Schroeder, W. L., T. Kuil, A. J. A. van Maris, D. G. Olson, L. R. Lynd and C. D. MaranasA detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysisMetabolic Engineering77 306–22
202310.3389/fmicb.2023.1219318Schaedig, E., M. Cantrell, C. Urban, X. Zhao, D. Greene, J. Dancer, M. Gross, J. Sebesta, K. J. Chou, J. Grabowy, M. Gross, K. Kumar and J. YuIsolation of phosphorus-hyperaccumulating microalgae from revolving algal biofilm (RAB) wastewater treatment systemsFrontiers in Microbiology14
202310.1007/s10482-022-01804-xSaticioglu, I. B., H. Ay, S. Altun, E. Karakaya, E. S. Gunduz, D. Aydogdu, D. Yarim, N. Erkek and M. DumanGenomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss)Antonie van Leeuwenhoek116(3) 291–302
202310.1128/jb.00338-22Riley, L. A., I. C. Payne, M. Tumen-Velasquez and A. M. GussSimple and Rapid Site-Specific Integration of Multiple Heterologous DNAs into the Escherichia coli ChromosomeJournal of Bacteriology205(2) e00338-22
202310.1016/j.jaridenv.2022.104876Reeve, S., B. Palmer, P. Cobb, N. Pietrasiak and D. A. LipsonFacilitating restoration of degraded biological soil crusts using mixed culture inoculationJournal of Arid Environments208 104876
202310.1038/s41559-022-01936-3Price, M.Erroneous predictions of auxotrophies by CarveMeNature Ecology & Evolution7(2) 194–95
202310.1038/s41477-023-01358-4Prabhakar, P. K., J. H. Pereira, R. Taujale, W. Shao, V. S. Bharadwaj, D. Chapla, J.-Y. Yang, Y. J. Bomble, K. W. Moremen, N. Kannan, M. Hammel, P. D. Adams, H. V. Scheller and B. R. UrbanowiczStructural and biochemical insight into a modular _-1,4-galactan synthase in plantsNature Plants9(3) 486–500
202310.1016/j.copbio.2022.102869Ploessl, D., Y. Zhao and Z. ShaoEngineering of non-model eukaryotes for bioenergy and biochemical productionCurrent Opinion in Biotechnology79 102869
202310.1016/j.copbio.2023.102913Pfleger, B. F. and R. TakorsRecent progress in the synthesis of advanced biofuel and bioproductsCurrent Opinion in Biotechnology80 102913
2023Pastore, C.Evaluating the inability to store polyphosphate as a biocontainment strategy in genetically modified microalgaeDOE Office of Science’s Science Undergraduate Laboratory Internship Program Final Report
202310.1111/1462-2920.16296Park, M.-R., R. Gauttam, B. Fong, Y. Chen, H. G. Lim, A. M. Feist, A. Mukhopadhyay, C. J. Petzold, B. A. Simmons and S. W. SingerRevealing oxidative pentose metabolism in new Pseudomonas putida isolatesEnvironmental Microbiology25(2) 493–504
202310.1038/s41467-023-39010-6Pang, C., J. Chai, P. Zhu, J. Shanklin and Q. LiuStructural mechanism of intracellular autoregulation of zinc uptake in ZIP transportersNature Communications14(1) 3404
202310.1007/s00248-022-02137-yPalmer, B., D. Lawson and D. A. LipsonYears After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal GrasslandMicrobial Ecology85(3) 1028–44
202310.1111/nph.18624Ortega, M. A., R. Zhou, M. S. S. Chen, W. P. Bewg, B. Simon and C.-J. TsaiIn vitro floral development in poplar: insights into seed trichome regulation and trimonoecyNew Phytologist237(4) 1078–81
202310.1128/mra.00359-22O’Toole, P., R. A. Daly, R. K. Afshar, M. Shaffer, K. C. Wrighton and B. B. McGivernDraft Metagenome-Assembled Genome Sequence of a Novel Citricoccus Species from Agricultural Soil in Western ColoradoMicrobiology Resource Announcements12(1) e00359-22
202310.1093/plphys/kiac580O’Leary, B. M., A. P. Scafaro and L. M. YorkHigh-throughput, dynamic, multi-dimensional: an expanding repertoire of plant respiration measurementsPlant Physiology191(4) 2070–83
202310.3389/frmbi.2023.1078024Naylor, D., K. Naasko, M. Smith, S. Couvillion, C. Nicora, J. Trejo, S. Fransen, R. Danczak, R. McClure, K. S. Hofmockel and J. K. JanssonInteractive effects of depth and differential irrigation on soil microbiome composition and functioningFrontiers in Microbiomes2
202310.1111/nph.18518Mottiar, Y., R. A. Smith, S. D. Karlen, J. Ralph and S. D. MansfieldEvolution of p-coumaroylated lignin in eudicots provides new tools for cell wall engineeringNew Phytologist237(1) 251–64
202310.1111/pbi.13935Mottiar, Y., S. D. Karlen, R. E. Goacher, J. Ralph and S. D. MansfieldMetabolic engineering of p-hydroxybenzoate in poplar ligninPlant Biotechnology Journal21(1) 176–88
202310.1021/acssuschemeng.3c00624Mohan, M., M. D. Smith, O. N. Demerdash, B. A. Simmons, S. Singh, M. K. Kidder and J. C. SmithQuantum Chemistry-Driven Machine Learning Approach for the Prediction of the Surface Tension and Speed of Sound in Ionic LiquidsACS Sustainable Chemistry & Engineering11(20) 7809–21
202310.1038/s41598-022-25372-2Mohan, M., B. A. Simmons, K. L. Sale and S. SinghMultiscale molecular simulations for the solvation of lignin in ionic liquidsScientific Reports13(1) 271
202310.1039/D2GC04425KMohan, M., O. Demerdash, B. A. Simmons, J. C. Smith, M. K. Kidder and S. SinghAccurate prediction of carbon dioxide capture by deep eutectic solvents using quantum chemistry and a neural networkGreen Chemistry25(9) 3475–92
202310.1094/pbiomes-08-22-0046-fiMechan, M., J. Mullet and A. ShadePhyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilagePhytobiomes Journal
202310.1016/j.ymben.2023.02.006McNaught, K. J., E. Kuatsjah, M. Zahn, É. T. Prates, H. Shao, et al.Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440Metabolic Engineering76 193–203
202310.1038/s41467-023-37164-xMcLaughlin, S., K. Zhalnina, S. Kosina, T. R. Northen and J. SasseThe core metabolome and root exudation dynamics of three phylogenetically distinct plant speciesNature Communications14(1) 1649
202310.1002/eap.2784McDaniel, M. D., J. A. Bird, J. Pett-Ridge, E. Marin-Spiotta, T. M. Schmidt and A. S. GrandyDiversifying and perennializing plants in agroecosystems alters retention of new C and N from crop residuesEcological Applications33(2) e2784
202310.3389/fmicb.2022.1046661McClure, R., M. Garcia, S. Couvillion, Y. Farris and K. S. HofmockelRemoval of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancyFrontiers in Microbiology13
202310.1002/tpg2.20298May, D., K. Paldi and F. AltpeterTargeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospectsThe Plant Genomee20298
202310.1016/j.copbio.2022.102881Martin, H. G., T. Radivojevic, J. Zucker, K. Bouchard, J. Sustarich, et al.Perspectives for self-driving labs in synthetic biologyCurrent Opinion in Biotechnology79 102881
202310.1016/j.scitotenv.2022.158863Loiola, M., A. E. T. Silva, M. Krull, F. A. Barbosa, E. H. Galvão, V. F. Patire, I. C. S. Cruz, F. Barros, V. Hatje and P. M. MeirellesMangrove microbial community recovery and their role in early stages of forest recolonization within shrimp pondsScience of The Total Environment855 158863
202310.1093/plphys/kiad076Liu, Y., G. Yuan, B. Hyden, G. A. Tuskan, P. E. Abraham and X. YangExpanding the application of anti-CRISPR proteins in plants for tunable genome editingPlant Physiology192(1) 60–4
202310.1039/D3RA01546GLi, Y., X. Meng, R. Meng, T. Cai, Y. Pu, Z.-M. Zhao and A. J. RagauskasValorization of homogeneous linear catechyl lignin: opportunities and challengesRSC Advances13(19) 12750–9
202310.1021/acssuschemeng.2c07139Li, Y., G. A. Kontos, D. V. Cabrera, N. M. Avila, T. W. Parkinson, M. B. Viswanathan, V. Singh, F. Altpeter, R. A. Labatut and J. S. GuestDesign of a High-Rate Wastewater Treatment Process for Energy and Water Recovery at BiorefineriesACS Sustainable Chemistry & Engineering11(9) 3861–72
202310.1038/s41467-023-38096-2Li, M., T. Yao, W. Lin, W. E. Hinckley, M. Galli, W. Muchero, A. Gallavotti, J.-G. Chen and S.-s. C. HuangDouble DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factorsNature Communications14(1) 2600
202310.1016/j.xplc.2023.100594Li, C., W. Huang, X. Han, G. Zhao, W. Zhang, et al.Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesisPlant Communications100594
202310.1016/j.cej.2022.138886Lee, J. W., S. S. Bhagwat, N. Kuanyshev, Y. B. Cho, L. Sun, Y.-G. Lee, Y. R. Cortés-Peña, Y. Li, C. V. Rao, J. S. Guest and Y.-S. JinRewiring yeast metabolism for producing 2,3-butanediol and two downstream applications: Techno-economic analysis and life cycle assessment of methyl ethyl ketone (MEK) and agricultural biostimulant productionChemical Engineering Journal451 138886
202310.1002/biot.202200535Lane, S., T. L. Turner and Y.-S. JinGlucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiaeBiotechnology Journal18(4) 2200535
202310.1007/978-1-0716-2784-6_27Ko, D. K. and F. BrandizziCoexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress ResponsesPlant Proteostasis: Methods and Protocols2581 385–401
202310.1186/s13068-023-02291-6Kim, S.-K., Y. J. Bomble and J. WestphelingSimultaneous expression of an endogenous spermidine synthase and a butanol dehydrogenase from Thermoanaerobacter pseudethanolicus in Clostridium thermocellum results in increased resistance to acetic acid and furans, increased ethanol production and an increase in thermotoleranceBiotechnology for Biofuels and Bioproducts16(1) 46
202310.1007/978-1-0716-2639-9_4Kim, S.-J. and F. BrandizziMicroscopy and Immunocytochemistry-Based Methods to Study Cell Wall Biosynthetic Enzymes in the GolgiGolgi: Methods and Protocols2557 39–51
202310.1111/gcbb.13024Kim, S., B. E. Dale, R. Martinez-Feria, B. Basso, K. Thelen, C. T. Maravelias, D. Landis, T. J. Lark and G. P. RobertsonGlobal warming intensity of biofuel derived from switchgrass grown on marginal land in MichiganGCB Bioenergy15(3) 319–31
202310.1021/acssuschemeng.3c00115Kenny, J. K., J. W. Medlin and G. T. BeckhamQuantification of Phenolic Hydroxyl Groups in Lignin via 19F NMR SpectroscopyACS Sustainable Chemistry & Engineering11(14) 5644–55
202310.1038/s41564-023-01361-7Kelliher, J. M., M. Rudolph, P. Vangay, A. Abbas, M. A. Borton, et al.Cohort-based learning for microbiome research community standardsNature Microbiology8(5) 751–3
202310.1016/j.mtbio.2023.100560Jo, C., J. Zhang, J. M. Tam, G. M. Church, A. S. Khalil, D. Segrè and T.-C. TangUnlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainabilityMaterials Today Bio19 100560
202310.1128/msystems.00017-21Jo, C., D. B. Bernstein, N. Vaisman, H. M. Frydman and D. SegrèConstruction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial InteractionsmSystems8(2) e00017-21
202310.1016/j.ymben.2023.02.012Jindra, M. A., K. Choe, R. Chowdhury, R. Kong, S. Ghaffari, J. V. Sweedler and B. F. PflegerEvaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acidsMetabolic Engineering77 21–31
202310.1016/j.biortech.2023.128630Jia, Y., S. Maitra and V. SinghChemical-free production of multiple high-value bioproducts from metabolically engineered transgenic sugarcane ‘oilcane’ bagasse and their recovery using nanofiltrationBioresource Technology371 128630
202310.1038/s41579-022-00811-zJansson, J. K. and R. WuSoil viral diversity, ecology and climate changeNature Reviews Microbiology21(5) 296–311
202310.3389/fgeed.2023.1074641Illa-Berenguer, E., P. R. LaFayette and W. A. ParrottEditing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in riceFrontiers in Genome Editing5
202310.1111/gcbb.13020Hussain, M. Z., S. K. Hamilton and G. P. RobertsonSoil phosphorus drawdown by perennial bioenergy cropping systems in the Midwestern USGCB Bioenergy15(2) 254–63
202310.1016/j.biortech.2022.128528Huntington, T., N. R. Baral, M. Yang, E. Sundstrom and C. D. ScownMachine learning for surrogate process models of bioproduction pathwaysBioresource Technology370 128528
202310.1016/j.ymben.2023.01.001Hu, M., H. V. Dinh, Y. Shen, P. F. Suthers, C. J. Foster, C. M. Call, X. Ye, J. Pratas, Z. Fatma, H. Zhao, J. D. Rabinowitz and C. D. MaranasComparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scaleMetabolic Engineering76 1–17
202310.1038/s41467-023-36515-yHowe, A., N. Stopnisek, S. K. Dooley, F. Yang, K. L. Grady and A. ShadeSeasonal activities of the phyllosphere microbiome of perennial cropsNature Communications14(1) 1039
2023Hou, H. J. M., J. Sebesta, C. Pastore and J. YuProbing CO2 uptake of genetically engineered microalgae using MIMSThe 2023 Alabama State University STEM Research Symposium
2023Hou, H. J. M., J. Sebesta, A. Deshpande, C. Pastore, L. Laurens and J. YuCarbon metabolism of a polyphosphate synthase mutant in cyanobacteriaGorden Conference Photosynthesis
2023Higgins, R. C., K. L. Arnolds, N. Lamb, G. Li, J. G. Linger and M. T. GuarnieriDigital droplet PCR for the targeted detection and assessment of Saccharomyces cerevisiae in the soil microbiomeFront Range Microbiome Symposium
202310.1038/s41598-023-29220-9Herring, C. D., M. P. Ajie and L. R. LyndGrowth-uncoupled propanediol production in a Thermoanaerobacterium thermosaccharolyticum strain engineered for high ethanol yieldScientific Reports13(1) 2394
202310.1186/s13068-023-02287-2Harman-Ware, A. E., M. Z. Martin, N. L. Engle, C. Doeppke and T. J. TschaplinskiRapid screening of secondary aromatic metabolites in Populus trichocarpa leavesBiotechnology for Biofuels and Bioproducts16(1) 41
202310.1016/j.jbc.2022.102782Hall, B. W., C. A. Bingman, B. G. Fox, D. R. Noguera and T. J. DonohueA broad specificity _-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including _-valerolactoneJournal of Biological Chemistry299(1) 102782
202310.1038/s41396-022-01351-3Goff, J. L., Y. Chen, M. P. Thorgersen, L. T. Hoang, F. L. Poole, E. G. Szink, G. Siuzdak, C. J. Petzold and M. W. W. AdamsMixed heavy metal stress induces global iron starvation responseThe ISME Journal17(3) 382–92
202310.1111/1751-7915.14205Gauttam, R., T. Eng, Z. Zhao, Q. ul ain Rana, B. A. Simmons, Y. Yoshikuni, A. Mukhopadhyay and S. W. SingerDevelopment of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putidaMicrobial Biotechnology16(3) 645–61
202310.1038/s41477-022-01294-9Fu, X., L. M. Gregory, S. E. Weise and B. J. WalkerIntegrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespirationNature Plants9(1) 169–78
202310.1128/mra.00824-22Fraccascia, D., R. M. Chanyi, E. Altermann, N. C. Roy, S. H. Flint and W. C. McNabbComplete Genome Sequences of Eight Faecalibacterium sp. Strains Isolated from Healthy Human StoolMicrobiology Resource Announcements12(1) e00824-22
202310.1016/j.soilbio.2022.108886Foley, M. M., S. J. Blazewicz, K. J. McFarlane, A. Greenlon, M. Hayer, J. A. Kimbrel, B. J. Koch, V. L. Monsaint-Queeney, K. Morrison, E. Morrissey, B. A. Hungate and J. Pett-RidgeActive populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslandsSoil Biology and Biochemistry177 108886
202310.1111/irv.13057Faleye, T. O. C., A. Elyaderani, P. Skidmore, S. Adhikari, A. Smith, N. Kaiser, H. Sandrolini, S. Finnerty, R. U. Halden, A. Varsani and M. ScotchSurveillance of rhinovirus diversity among a university community identifies multiple types from all three species including an unassigned rhinovirus A genotypeInfluenza and Other Respiratory Viruses17(1) e13057
202310.1126/sciadv.ade1285Elmore, J. R., G. N. Dexter, H. Baldino, J. D. Huenemann, R. Francis, G. L. Peabody, J. Martinez-Baird, L. A. Riley, T. Simmons, D. Coleman-Derr, A. M. Guss and R. G. EgbertHigh-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integrationScience Advances9(10) eade1285
202310.1002/cssc.202201441Dong, X., H. B. Mayes, K. Morreel, R. Katahira, Y. Li, J. Ralph, B. A. Black and G. T. BeckhamEnergy-Resolved Mass Spectrometry as a Tool for Identification of Lignin Depolymerization ProductsChemSusChem16(1) e202201441
202310.1021/acssynbio.2c00658Dinglasan, J. L. N., T. T. Sword, J. W. Barker, M. J. Doktycz and C. B. BaileyInvestigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter SystemACS Synthetic Biology12(5) 1447–60
202310.1093/synbio/ysad007Dinglasan, J. L. N. and M. J. DoktyczRewiring cell-free metabolic flux in E. coli lysates using a block—push—pull approachSynthetic Biology8(1) ysad007
202310.1016/j.xplc.2022.100512Di, X., D. Ortega-Alarcon, R. Kakumanu, J. Iglesias-Fernandez, L. Diaz, E. E. K. Baidoo, A. Velazquez-Campoy, M. Rodríguez-Concepción and J. Perez-GilMEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supplyPlant Communications4(3) 100512
202310.3390/fermentation9010005Deshavath, N. N., B. S. Dien, P. J. Slininger, Y.-S. Jin and V. SinghA Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery ApproachFermentation9(1) 5
202310.1016/j.ab.2022.114997Deng, K., X. Wang, N. Ing, P. Opgenorth, M. de Raad, J. Kim, B. A. Simmons, P. D. Adams, A. K. Singh, T. S. Lee and T. R. NorthenRapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS)Analytical Biochemistry662 114997
202310.1016/j.jbc.2023.102939de Raad, M., K. Koper, K. Deng, B. P. Bowen, H. A. Maeda and T. R. NorthenMass spectrometry imaging-based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzymeJournal of Biological Chemistry299(3)
202310.3390/metabo13020140Dahal, S., G. B. Hurst, K. Chourey, N. L. Engle, L. H. Burdick, J. L. Morrell-Falvey, T. J. Tschaplinski, M. J. Doktycz and D. A. PelletierMechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas—Rahnella Co-CultureMetabolites13(2) 140
202310.1016/j.tcsw.2023.100101Curry, T. M., M. J. Peña and B. R. UrbanowiczAn update on xylan structure, biosynthesis, and potential commercial applicationsThe Cell Surface9 100101
202310.1186/s40168-022-01427-4Couvillion, S. P., R. E. Danczak, D. Naylor, M. L. Smith, K. G. Stratton, et al.Rapid remodeling of the soil lipidome in response to a drying-rewetting eventMicrobiome11(1) 34
202310.1016/j.csbj.2022.12.052Cope, K. R., E. T. Prates, J. I. Miller, O. N. A. Demerdash, M. Shah, et al.Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop PopulusComputational and Structural Biotechnology Journal21 1122–39
202310.1016/j.soilbio.2022.108935Chuckran, P. F., C. Flagg, J. Propster, W. A. Rutherford, E. T. Sieradzki, S. J. Blazewicz, B. Hungate, J. Pett-Ridge, E. Schwartz and P. DijkstraEdaphic controls on genome size and GC content of bacteria in soil microbial communitiesSoil Biology and Biochemistry178 108935
202310.1002/chem.202300330Choudhary, H., L. Das, J. G. Pelton, L. Sheps, B. A. Simmons, J. M. Gladden and S. SinghFunneled Depolymerization of Ionic Liquid-Based Biorefinery “Heterogeneous” Lignin into Guaiacols over Reusable Palladium CatalystChemistry – A European Journal29(27) e202300330
202310.3390/molecules28031427Choi, J., A. Rodriguez, B. A. Simmons and J. M. GladdenValorization of Hemp-Based Packaging Waste with One-Pot Ionic Liquid TechnologyMolecules28(3) 1427
202310.1038/s41596-022-00747-xChivian, D., S. P. Jungbluth, P. S. Dehal, E. M. Wood-Charlson, R. S. Canon, et al.Metagenome-assembled genome extraction and analysis from microbiomes using KBaseNature Protocols18(1) 208–38
2023Chiarelli, D., D. Olson and L. LyndExpression and characterization of glycolytic enzymes from Thermoanaerobacterium saccharolyticum and Zymomonas mobilis in Clostridium thermocellumSBFC: Symposium on Biomaterials, Fuels and Chemicals
202310.1039/D2GC03446HCheng, F., S. Liu, S. D. Karlen, H. Kim, F. Lu, J. Ralph, L. M. Vázquez Ramos, G. W. Huber and J. A. DumesicPoplar lignin structural changes during extraction in _-valerolactone (GVL)Green Chemistry25(1) 336–47
202310.1093/bioadv/vbad005Chang, C. H., W. C. Nelson, A. Jerger, A. T. Wright, R. G. Egbert and J. E. McDermottSnekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recodingBioinformatics Advances3(1)
202310.1007/s12155-022-10513-2Casler, M. D., D. Lee, R. B. Mitchell, K. J. Moore, P. R. Adler, et al.Biomass Quality Responses to Selection for Increased Biomass Yield in Perennial Energy GrassesBioEnergy Research16(2) 877–85
202310.1099/ijsem.0.005628Carro, L. and A. OrenDescriptions of Micromonospora grosourdyae nom. nov., Micromonospora sonchi comb. nov. and Micromonospora thawaii sp. nov. to resolve problems with the taxonomy and nomenclature of strains named Micromonospora endophyticaInternational Journal of Systematic and Evolutionary Microbiology72(12)
202310.1016/j.virusres.2023.199121Buivydait_, _., L. Aryal, F. B. Corrêa, T. Chen, V. Langlois, et al.Meeting report: The first soil viral workshop 2022Virus Research331 199121
202310.3389/fpls.2023.1153113Bryant, N., J. Zhang, K. Feng, M. Shu, R. Ployet, J.-G. Chen, W. Muchero, C. G. Yoo, T. J. Tschaplinski, Y. Pu and A. J. RagauskasNovel candidate genes for lignin structure identified through genome-wide association study of naturally varying Populus trichocarpaFrontiers in Plant Science14
202310.1002/prot.26422Boorla, V. S., R. Chowdhury, R. Ramasubramanian, B. Ameglio, R. Frick, J. J. Gray and C. D. MaranasDe novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)Proteins: Structure, Function, and Bioinformatics91(2) 196–208
202310.1016/B978-0-12-821430-5.00002-XBlaby-Haas, C. E. and S. S. MerchantTrace metal nutrition and response to deficiencyThe Chlamydomonas Sourcebook (Third Edition)2 167–203
202310.2489/jswc.2023.00069Bell, S. L., A. E. Zimmerman and K. S. HofmockelCropping system drives microbial community response to simulated climate change and plant inputsJournal of Soil and Water Conservation78(2) 178–92
202310.1002/yea.3837Barros, K. O., F. B. M. Alvarenga, G. Magni, G. F. L. Souza, M. A. Abegg, F. Palladino, S. S. da Silva, R. C. L. B. Rodrigues, T. K. Sato, C. T. Hittinger and C. A. RosaThe Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast speciesYeast40(2) 84–101
202310.1016/j.eti.2022.102977Banerjee, S., R. Singh and V. SinghBioenergy crops as alternative feedstocks for recovery of anthocyanins: A reviewEnvironmental Technology & Innovation29 102977
202310.1039/D2SU00066KBanerjee, D. and A. MukhopadhyayPerspectives in growth production trade-off in microbial bioproductionRSC Sustainability1(2) 224–33
202310.1038/s41467-022-35677-5Ascensao, J. A., K. M. Wetmore, B. H. Good, A. P. Arkin and O. HallatschekQuantifying the local adaptive landscape of a nascent bacterial communityNature Communications14(1) 248
2023Arnolds, K., R. C. Higgins, G. Li, J. G. Linger and M. T. GuarnieriIMAGINE BioSecurity: Mesocosm-based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native EcosystemsDOE Genomic Sciences Program Annual Meeting
2023Arnolds, K., R. C. Higgins, N. Lamb, G. Li, J. G. Linger and M. T. GuarnieriIMAGINE BioSecurity: Mesocosm-based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native EcosystemsCenter for Microbiome Innovation International Microbiome Meeting
202310.1007/s11104-023-05988-7Andrews, H. B., M. Z. Martin, A. M. Wymore and U. C. KalluriRapid in situ nutrient element distribution in plants and soils using laser-induced breakdown spectroscopy (LIBS)Plant and Soil
202310.1002/chem.202203941Álvarez-Martínez, I., C. Ruprecht, D. Senf, H.-t. Wang, B. R. Urbanowicz and F. PfrengleChemo-Enzymatic Synthesis of Long-Chain Oligosaccharides for Studying Xylan-Modifying EnzymesChemistry – A European Journal29(26) e202203941
202310.3390/md21010034Almeida, J. F., M. Marques, V. Oliveira, C. Egas, D. Mil-Homens, R. Viana, D. F. R. Cleary, Y. M. Huang, A. M. Fialho, M. C. Teixeira, N. C. M. Gomes, R. Costa and T. Keller-CostaMarine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human PathogensMarine Drugs21(1) 34
202310.1038/s41589-023-01269-7Adler, B. A., K. Chamakura, H. Carion, J. Krog, A. M. Deutschbauer, R. Young, V. K. Mutalik and A. P. ArkinMulticopy suppressor screens reveal convergent evolution of single-gene lysis proteinsNature Chemical Biology19(6) 759–66
202310.1038/s43705-023-00265-1Acharya, S. M., M. O. Yee, S. Diamond, P. F. Andeer, N. F. Baig, O. T. Aladesanmi, T. R. Northen, J. F. Banfield and R. ChakrabortyFine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant rootsISME Communications3(1) 54
202210.1016/j.isci.2022.104562Zomorrodi, A. R., C. Hemez, P. Arranz-Gibert, T. Wu, F. J. Isaacs and D. SegrèComputational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanineiScience25(7) 104562
202210.1126/sciadv.abm8145Zhuo, C., X. Wang, M. Docampo-Palacios, B. C. Sanders, N. L. Engle, T. J. Tschaplinski, J. I. Hendry, C. D. Maranas, F. Chen and R. A. DixonDevelopmental changes in lignin composition are driven by both monolignol supply and laccase specificityScience Advances8(10) eabm8145
202210.1093/plcell/koab251Zhu, F., S. Alseekh, K. Koper, H. Tong, Z. Nikoloski, T. Naake, H. Liu, J. Yan, Y. Brotman, W. Wen, H. Maeda, Y. Cheng and A. R. FernieGenome-wide association of the metabolic shifts underpinning dark-induced senescence in ArabidopsisPlant Cell34(1) 557-578
202210.1038/s41467-022-29555-3Zhou, Y., G. E. Klinger, E. L. Hegg, C. M. Saffron and J. E. JacksonSkeletal Ni electrode-catalyzed C-O cleavage of diaryl ethers entails direct elimination via benzyne intermediatesNature Communications13(1) 2050
202210.1002/jaa2.23Zhong, J. and M. KhannaAssessing the efficiency implications of renewable fuel policy design in the United StatesJournal of the Agricultural and Applied Economics Association1(3) 222–35
202210.1126/science.abm1483Zheng, W., S. Zhao, Y. Yin, H. Zhang, D. M. Needham, E. D. Evans, C. L. Dai, P. J. Lu, E. J. Alm and D. A. WeitzHigh-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiomeScience376(6597) eabm1483
202210.1016/j.geoderma.2021.115565Zheng, H., A. K. Guber, Y. Kuzyakov, W. Zhang and A. N. KravchenkoPlant species and plant neighbor identity affect associations between plant assimilated C inputs and soil poresGeoderma407 115565
202210.1002/biot.202000427Zheng, A. O., A. Sher, D. Fridman, C. J. Musante and J. D. YoungPool size measurements improve precision of flux estimates but increase sensitivity to unmodeled reactions outside the core network in isotopically nonstationary metabolic flux analysis (INST-MFA)Biotechnology Journal17(3) 2000427
202210.1016/j.biortech.2021.126367Zhao, Z.-M., X. Meng, B. Scheidemantle, Y. Pu, Z.-H. Liu, B.-Z. Li, C. E. Wyman, C. M. Cai and A. J. RagauskasCosolvent enhanced lignocellulosic fractionation tailoring lignin chemistry and enhancing lignin bioconversionBioresource Technology347 126367
202210.3390/ijms23105581Zhao, Y., Y. Zhang, W. Zhang, Y. Shi, C. Jiang, X. Song, G. A. Tuskan, W. Zeng, J. Zhang and M. LuThe PagKNAT2/6b-PagBOP1/2a Regulatory Module Controls Leaf Morphogenesis in PopulusInternational Journal of Molecular Sciences23(10) 5581
202210.1016/j.pbi.2022.102222Zhao, K. and S. Y. RheeOmics-guided metabolic pathway discovery in plants: Resources, approaches, and opportunitiesCurrent Opinion in Plant Biology67
202210.1021/acscatal.1c04518Zhang, Z., C. E. Berdugo-Díaz, D. T. Bregante, H. Zhang and D. W. FlahertyAldol Condensation and Esterification over Ti-Substituted *BEA Zeolite: Mechanisms and Effects of Pore HydrophobicityACS Catalysis12(2) 1481–96
202210.1128/mra.00564-22Zhang, Y., K. S. Myers, M. Place, J. Serate, D. Xie, E. Pohlmann, A. L. Reau, R. Landick and T. K. SatoTranscriptomic Data Sets for Zymomonas mobilis 2032 during Fermentation of Ammonia Fiber Expansion (AFEX)-Pretreated Corn Stover and Switchgrass HydrolysatesMicrobiology Resource Announcements11(9) e00564-22
202210.1038/s41467-021-27852-xZhang, Y., J. D. Cortez, S. K. Hammer, C. Carrasco-López, S. Á. García Echauri, J. B. Wiggins, W. Wang and J. L. AvalosBiosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol productionNature Communications13(1)
202210.1002/cssc.202201230Zhang, X., J. Zhang, H. Yang, C. He, Y. Ke, S. Singh and G. ChengDetermination of the Structures of Lignin Subunits and Nanoparticles in Solution by Small-Angle Neutron Scattering: Towards Improving Lignin ValorizationChemSusChem15(19) e202201230
202210.1186/s13059-022-02711-0Zhang, R., R. Kuo, M. Coulter, C. P. G. Calixto, J. C. Entizne, et al.A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysisGenome Biology23(1)
202210.1007/s00122-022-04096-xZhang, L., A. MacQueen, X. Weng, K. D. Behrman, J. Bonnette, J. L. Reilley, F. M. Rouquette, P. A. Fay, Y. Wu, F. B. Fritschi, R. B. Mitchell, D. B. Lowry, A. R. Boe and T. E. JuengerThe genetic basis for panicle trait variation in switchgrass (Panicum virgatum)Theoretical and Applied Genetics135(8) 2577–92
202210.1002/advs.202203887Zhang, J., J. Shin, N. Tague, H. Lin, M. Zhang, X. Ge, W. Wong, M. J. Dunlop and J. X. ChengVisualization of a limonene synthesis metabolon inside living bacteria by hyperspectral SRS microscopyAdvanced Science
202210.1016/j.fgb.2022.103673Zhang, J., L. Meng Markillie, H. D. Mitchell, M. J. Gaffrey, G. Orr and J. S. SchillingDistinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placentaFungal Genetics and Biology159
202210.7150/thno.72581Zhang, H., X. Su, S. K. Burley and X. F. Steven ZhengmTOR regulates aerobic glycolysis through NEAT1 and nuclear paraspeckle-mediated mechanism in hepatocellular carcinomaTheranostics12(8) 3518-3533
202210.1038/s41565-021-01018-8Zhang, H., N. S. Goh, J. W. Wang, R. L. Pinals, E. González-Grandío, G. S. Demirer, S. Butrus, S. C. Fakra, A. Del Rio Flores, R. Zhai, B. Zhao, S. J. Park and M. P. LandryNanoparticle cellular internalization is not required for RNA delivery to mature plant leavesNature Nanotechnology17(2) 197-205
202210.1111/nph.17940Zhang, F., A. Labourel, M. Haon, M. Kemppainen, E. Da Silva Machado, N. Brouilly, C. Veneault-Fourrey, A. Kohler, M.-N. Rosso, A. Pardo, B. Henrissat, J.-G. Berrin and F. MartinThe ectomycorrhizal basidiomycete Laccaria bicolor releases a GH28 polygalacturonase that plays a key role in symbiosis establishmentNew Phytologist233(6) 2534–47
202210.1016/j.jbc.2022.101761Zhang, B., G. R. Munske, V. I. Timokhin, J. Ralph, D. R. Davydov, W. Vermerris, S. E. Sattler and C. KangFunctional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin compositionJournal of Biological Chemistry298(4) 101761
202210.1109/TGRS.2022.3141907Zarei, A., E. Gonzalez, N. Merchant, D. Pauli, E. Lyons and K. BarnardMegaStitch: Robust Large-Scale Image StitchingIEEE Transactions on Geoscience and Remote Sensing60
202210.1002/pro.4200Zardecki, C., S. Dutta, D. S. Goodsell, R. Lowe, M. Voigt and S. K. BurleyPDB-101: Educational resources supporting molecular explorations through biology and medicineProtein Science31(1) 129-140
202210.1111/gcbb.12903Zahorec, A., M. L. Reid, L. K. Tiemann and D. A. LandisPerennial grass bioenergy cropping systems: Impacts on soil fauna and implications for soil carbon accrualGCB Bioenergy14(1) 4–23
202210.1016/j.copbio.2022.102709Yunus, I. S. and T. S. LeeApplications of targeted proteomics in metabolic engineering: advances and opportunitiesCurrent Opinion in Biotechnology75 102709
202210.1039/D2RE00160HYun, D., Z. Zhang and D. W. FlahertyCatalyst and reactor design considerations for selective production of acids by oxidative cleavage of alkenes and unsaturated fatty acids with H2O2Reaction Chemistry & Engineering7 2054–65
202210.3390/cells11162467Yuan, G., S. Martin, M. M. Hassan, G. A. Tuskan and X. YangPARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR TechnologiesCells11(16) 2467
202210.1093/hr/uhac077Yuan, G., H. Lu, D. J. Weston, S. Jawdy, T. J. Tschaplinski, G. A. Tuskan and X. YangReporter genes confer new-to-nature ornamental traits in plantsHorticulture Research9 uhac077
202210.1021/acssynbio.1c00507Yuan, G., H. Lu, K. De, M. M. Hassan, Y. Liu, Y. Li, W. Muchero, P. E. Abraham, G. A. Tuskan and X. YangAn Intein-Mediated Split–nCas9 System for Base Editing in PlantsACS Synthetic Biology11(7) 2513–7
202210.1111/tpj.15960Yu, K. M. J., J. Oliver, B. McKinley, B. Weers, H. T. Fabich, N. Evetts, M. S. Conradi, S. A. Altobelli, A. Marshall-Colon and J. MulletBioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysisThe Plant Journal112(2) 476–92
202210.1128/aem.02109-21Yu, H., D. R. Speth, S. A. Connon, D. Goudeau, R. R. Malmstrom, T. Woyke and V. J. OrphanCommunity Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane SeepApplied and Environmental Microbiology88(11)
202210.1038/s41396-021-01047-0Yu, H., C. T. Skennerton, G. L. Chadwick, A. O. Leu, M. Aoki, G. W. Tyson and V. J. OrphanSulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaeaISME Journal16(1) 168-177
202210.1093/plphys/kiac154Young, D. Y., N. Pang and Y. Shachar-Hill13C-labeling reveals how membrane lipid components contribute to triacylglycerol accumulation in ChlamydomonasPlant Physiology189(3) 1326-1344
202210.1016/j.copbio.2022.102682York, L. M., M. Griffiths and T. M. MaazWhole-plant phenotypic engineering: moving beyond ratios for multi-objective optimization of nutrient use efficiencyCurrent Opinion in Biotechnology75 102682
202210.1002/ppj2.20028York, L. M., J. R. Cumming, A. Trusiak, G. Bonito, A. C. von Haden, et al.Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop productionThe Plant Phenome Journal5(1) e20028
202210.1002/tpg2.20209Yoon, S., J. Bragg, S. Aucar-Yamato, L. Chanbusarakum, K. Dluge, P. Cheng, E. Blumwald, Y. Gu and C. M. TobiasHaploidy and aneuploidy in switchgrass mediated by misexpression of CENH3Plant Genome
202210.1038/s41929-022-00836-wYilmaz, S., A. Nyerges, J. van der Oost, G. M. Church and N. J. ClaassensTowards next-generation cell factories by rational genome-scale engineeringNature Catalysis5(9) 751-765
202210.1128/mra.00360-22Yerlan, A., R. A. Daly, R. K. Afshar, M. Shaffer, K. C. Wrighton and B. B. McGivernDraft Metagenome-Assembled Genome Sequences of Three Novel Ammonia-Oxidizing Nitrososphaera Strains Recovered from Agricultural Soils in Western ColoradoMicrobiology Resource Announcements11(9) e00360-22
202210.1016/j.foodres.2022.111190Yasir, M., I. A. Al-Zahrani, F. Bibi, M. Abd El Ghany and E. I. AzharNew insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteriaFood Research International157 111190
2022Yarbrough, J., D. Stich, D. Chung, N. Hengge, T. Vinzant, S. Huang, Y. Zeng, B. Donohoe, M. Himmel, Y. Bomble and G. A. TuskanLeveraging Super High Optical Resolution Microscopy to Probe the Interaction Zone Between Clostridium thermocellum and BiomassIntegration 2020: Visualizing the Proteome
202210.3389/fenrg.2021.804086Yao, L., H. Yang, X. Meng and A. J. RagauskasToward a Fundamental Understanding of the Role of Lignin in the Biorefinery ProcessFrontiers in Energy Research9
202210.1021/acssuschemeng.1c06276Yang, Z., M. B. Foston, H. O’Neill, V. S. Urban, A. Ragauskas, B. R. Evans, B. H. Davison and S. V. PingaliStructural Reorganization of Noncellulosic Polymers Observed In Situ during Dilute Acid Pretreatment by Small-Angle Neutron ScatteringACS Sustainable Chemistry & Engineering10(1) 314–22
202210.1128/msphere.00931-21Yang, Y., T. Schubert, Y. Lv, X. Li and J. YanComparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum StrainsmSphere7(1) e00931-21
202210.1016/j.molcel.2022.03.001Yang, Y., S. Liu, S. Egloff, C. D. Eichhorn, T. Hadjian, J. Zhen, T. Kiss, Z. H. Zhou and J. FeigonStructural basis of RNA conformational switching in the transcriptional regulator 7SK RNPMolecular Cell82(9) 1724-1736.e7
202210.1016/j.tibtech.2022.09.007Yang, Y., T. A. Chaffin, A. H. Ahkami, E. Blumwald and C. N. Stewart, Jr.Plant synthetic biology innovations for biofuels and bioproductsTrends in Biotechnology40(12) 1454–68
202210.1021/acs.est.1c07747Yang, P., X. Piao and X. CaiWater Availability for Biorefineries in the Contiguous United States and the Implications for Bioenergy Production DistributionEnvironmental Science & Technology56(6) 3748–57
202210.1016/j.rser.2022.112745Yang, P., X. Cai, X. Hu, Q. Zhao, Y. Lee, M. Khanna, Y. R. Cortés-Peña, J. S. Guest, J. Kent, T. W. Hudiburg, E. Du, S. John and F. IutziAn agent-based modeling tool supporting bioenergy and bio-product community communication regarding cellulosic bioeconomy developmentRenewable and Sustainable Energy Reviews167 112745
202210.1094/pbiomes-09-21-0054-aYang, P., N. Bokros, S. Debolt, Z. Zhao and Y. XiaGenome Sequence Source of Bacillus amyloliquefaciens Strain GD4a, a Bacterial Endophyte Associated with Switchgrass PlantsPhytobiomes Journal6(4) 354–7
202210.1073/pnas.2122309119Yang, M., D. Liu, N. R. Baral, C.-Y. Lin, B. A. Simmons, J. M. Gladden, A. Eudes and C. D. ScownComparing in planta accumulation with microbial routes to set targets for a cost-competitive bioeconomyProceedings of the National Academy of Sciences119(30) e2122309119
202210.1515/hf-2021-0224Yang, L., J. Wang, C. Wang, F. Yue and F. LuA tailored fast thioacidolysis method incorporating multi-reaction monitoring mode of GC-MS for higher sensitivity on lignin monomer quantificationHolzforschung76(7) 604-610
202210.1128/spectrum.02116-21Yang, J., J. Lee, J. Choi, L. Ma, E. A. Heaton and A. HoweResponse of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus _ Giganteus Cultivated Soil to Different Nitrogen Fertilization RatesMicrobiology Spectrum10(1) e0211621
202210.1007/s11783-023-1650-zYan, X., X. Shen, J. Wang, J. Zhuang, Y. Wang, J. Yao, H. Liu, Y. Liu, J. P. Shapleigh and W. LiHigher N2O production in sequencing batch reactors compared to continuous stirred tank reactors: effect of feast-famine cyclesFrontiers of Environmental Science & Engineering17(4) 50
202210.1038/s41467-022-29218-3Yan, Q., W. T. Cordell, M. A. Jindra, D. K. Courtney, M. K. Kuckuk, X. Chen and B. F. PflegerMetabolic engineering strategies to produce medium-chain oleochemicals via acyl-ACP:CoA transacylase activityNature Communications13(1) 1619
202210.1111/nph.18053Yan, H., J. Lee, Q. Song, Q. Li, J. Schiefelbein, B. Zhao and S. LiIdentification of new marker genes from plant single-cell RNA-seq data using interpretable machine learning methodsNew Phytologist234(4) 1507-1520
202210.1128/mra.00453-21Yamamoto, K., Y. Yoneda, A. Makino, Y. Tanaka, X.-Y. Meng, et al.Draft Genome Sequence of Bryobacteraceae Strain F-183Microbiology Resource Announcements11(1) e00453-21
202210.1128/mra.00455-21Yamamoto, K., Y. Yoneda, A. Makino, Y. Tanaka, X.-Y. Meng, et al.Complete Genome Sequence of Luteitalea sp. Strain TBR-22Microbiology Resource Announcements11(2) e00455-21
202210.1038/s41598-022-06530-yXue, S., S. Pattathil, L. da Costa Sousa, B. Ubanwa, B. Dale, A. D. Jones and V. BalanUnderstanding the structure and composition of recalcitrant oligosaccharides in hydrolysate using high-throughput biotin-based glycome profiling and mass spectrometryScientific Reports12(1)
202210.34133/2022/9879610Xu, Z., L. M. York, A. Seethepalli, B. Bucciarelli, H. Cheng and D. A. SamacObjective Phenotyping of Root System Architecture Using Image Augmentation and Machine Learning in Alfalfa (Medicago sativa L.)Plant Phenomics2022 9879610
202210.1186/s13068-022-02214-xXu, Z., B. Peng, R. B. Kitata, C. D. Nicora, K. K. Weitz, Y. Pu, T. Shi, J. R. Cort, A. J. Ragauskas and B. YangUnderstanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysisBiotechnology for Biofuels and Bioproducts15(1) 117
202210.1093/jxb/erac003Xu, C. and J. FanLinks between autophagy and lipid droplet dynamicsJournal of Experimental Botany73(9) 2848–58
2022US11473086B2Xie, M., J.-G. Chen, L. E. Gunter, S. S. Jawdy, W. Muchero, G. Tuskan and J. ZhangLoss of function alleles of PtEPSP-TF and its regulatory targets in riceUnited States PatentU.S. Department of Energy, UT Battelle LLC
202210.1038/s41589-022-01091-7Xiao, T., A. Khan, Y. Shen, L. Chen and J. D. RabinowitzGlucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeastNature Chemical Biology18(12) 1380–7
202210.1073/pnas.2109995119Xiao, N., A. Zhou, M. L. Kempher, B. Y. Zhou, Z. J. Shi, M. Yuan, X. Guo, L. Wu, D. Ning, J. V. Nostrand, M. K. Firestone and J. ZhouDisentangling direct from indirect relationships in association networksProceedings of the National Academy of Sciences119(2) e2109995119
202210.1016/j.oneear.2022.03.010Wu, R., G. Trubl, N. Ta_ and J. K. JanssonPermafrost as a potential pathogen reservoirOne Earth5(4) 351–60
202210.1038/s41467-022-32993-8Wu, R., C. A. Smith, G. W. Buchko, I. K. Blaby, D. Paez-Espino, N. C. Kyrpides, Y. Yoshikuni, J. E. McDermott, K. S. Hofmockel, J. R. Cort and J. K. JanssonStructural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanaseNature Communications13(1) 5485
202210.1038/s41564-022-01147-3Wu, L., Y. Zhang, X. Guo, D. Ning, X. Zhou, et al.Reduction of microbial diversity in grassland soil is driven by long-term climate warmingNature Microbiology7(7) 1054-1062
202210.1111/mec.16319Wu, L., F. Yang, J. Feng, X. Tao, Q. Qi, C. Wang, E. A. G. Schuur, R. Bracho, Y. Huang, J. R. Cole, J. M. Tiedje and J. ZhouPermafrost thaw with warming reduces microbial metabolic capacities in subsurface soilsMolecular Ecology31(5) 1403-1415
202210.1016/j.agrformet.2022.109046Wu, G., K. Guan, C. Jiang, H. Kimm, G. Miao, C. J. Bernacchi, C. E. Moore, E. A. Ainsworth, X. Yang, J. A. Berry, C. Frankenberg and M. ChenAttributing differences of solar-induced chlorophyll fluorescence (SIF)-gross primary production (GPP) relationships between two C4 crops: corn and miscanthusAgricultural and Forest Meteorology323 109046
202210.1021/acssynbio.1c00189Wu, C., J. Yu, M. Guarnieri and W. XiongComputational Framework for Machine-Learning-Enabled 13C FluxomicsACS Synthetic Biology11(1) 103–15
202210.1021/acssynbio.1c00189Wu, C., J. Yu, M. Guarnieri and W. XiongComputational Framework for Machine-Learning-Enabled 13C FluxomicsACS Synthetic Biology11(1) 103–15
202210.1093/femsec/fiac069Woolet, J., E. Whitman, M. A. Parisien, D. K. Thompson, M. D. Flannigan and T. WhitmanEffects of short-interval reburns in the boreal forest on soil bacterial communities compared to long-interval reburnsFEMS Microbiology Ecology98(8)
202210.3390/metabo12080767Wong, T. M., J. H. Sullivan and E. EisensteinAcclimation and Compensating Metabolite Responses to UV-B Radiation in Natural and Transgenic Populus spp. Defective in Lignin BiosynthesisMetabolites12(8)
202210.1128/mbio.02949-21Wong, E. O.-Y., E. J. E. Brownlie, K. M. Ng, S. Kathirgamanathan, F. B. Yu, B. D. Merrill, K. C. Huang, A. Martin, C. Tropini and W. W. NavarreThe CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine GutmBio13(2) e02949-21
202210.1093/femsec/fiac091Windler, M., R. Stuart, J. S. Deutzmann, X. Mayali, A. Navid, P. D'haeseleer, O. E. Marcu, M. Lipton, C. Nicora and A. M. SpormannBacterial exometabolites influence Chlamydomonas cell cycle and double algal productivityFEMS Microbiology Ecology98(9) fiac091
202210.1016/j.scitotenv.2021.152757Wilson, R. M., M. A. Hough, B. A. Verbeke, S. B. Hodgkins, G. Tyson, et al.Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatlandScience of the Total Environment820
202210.1111/ppl.13812Willick, I. R. and D. B. LowryCold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiodPhysiologia Plantarum174(6) e13812
202210.1016/j.soilbio.2021.108472Wilhelm, R. C., H. M. van Es and D. H. BuckleyPredicting measures of soil health using the microbiome and supervised machine learningSoil Biology and Biochemistry164
202210.1016/j.soilbio.2022.108681Wilhelm, R. C., L. Lynch, T. M. Webster, S. Schweizer, T. M. Inagaki, M. M. Tfaily, R. Kukkadapu, C. Hoeschen, D. H. Buckley and J. LehmannSusceptibility of new soil organic carbon to mineralization during dry-wet cycling in soils from contrasting ends of a precipitation gradientSoil Biology and Biochemistry169
202210.1016/j.soilbio.2022.108755Whitman, T., J. Woolet, M. Sikora, D. B. Johnson and E. WhitmanResilience in soil bacterial communities of the boreal forest from one to five years after wildfire across a severity gradientSoil Biology and Biochemistry172
202210.1007/s00248-021-01836-2Whitaker, B. K., H. Giauque, C. Timmerman, N. Birk and C. V. HawkesLocal Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 GrassMicrobial Ecology84(1) 122–30
202210.1111/gcb.16413Whalen, E. D., A. S. Grandy, N. W. Sokol, M. Keiluweit, J. Ernakovich, R. G. Smith and S. D. FreyClarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understandingGlobal Change Biology28(24) 7167–85
202210.1016/j.jmb.2022.167599Westbrook, J. D., J. Y. Young, C. Shao, Z. Feng, V. Guranovic, et al.PDBx/mmCIF Ecosystem: Foundational semantic tools for structural biology: PDBx/mmCIF ecosystem: Foundational semantic toolsJournal of Molecular Biology434(11)
2022West, C. G., S. E. Honig, L. M. Lui and L. RaschkeIntegration of Authentic STEM Practices in Real-World Education and Research Environments: Lessons from the PDPLeaders in Effective and Inclusive STEM: Twenty Years of the Institute for Scientist & Engineer Educators 341–58
202210.1371/journal.pcbi.1009906Wendering, P. and Z. NikoloskiCOMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructionsPLoS Computational Biology18(3) e1009906
202210.1016/j.aca.2021.339400Wei, B., M. A. Zenaidee, C. Lantz, R. R. Ogorzalek Loo and J. A. LooTowards understanding the formation of internal fragments generated by collisionally activated dissociation for top-down mass spectrometryAnalytica Chimica Acta1194
202210.1016/j.cbpa.2022.102207Wegner, S. A., R. M. Barocio-Galindo and J. L. AvalosThe bright frontiers of microbial metabolic optogeneticsCurrent Opinion in Chemical Biology71
202210.3389/fmicb.2022.914472Wang, Y., R. C. Wilhelm, T. L. Swenson, A. Silver, P. F. Andeer, A. Golini, S. M. Kosina, B. P. Bowen, D. H. Buckley and T. R. NorthenSubstrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History StrategiesFrontiers in Microbiology13 914472
202210.1111/nph.18485Wang, Y., S. S. Stutz, C. J. Bernacchi, R. A. Boyd, D. R. Ort and S. P. LongIncreased bundle-sheath leakiness of CO2 during photosynthetic induction shows a lack of coordination between the C4 and C3 cyclesNew Phytologist236(5) 1661–75
202210.1186/s13068-022-02235-6Wang, X., E. E. K. Baidoo, R. Kakumanu, S. Xie, A. Mukhopadhyay and T. S. LeeEngineering isoprenoids production in metabolically versatile microbial host Pseudomonas putidaBiotechnology for Biofuels and Bioproducts15(1) 137
202210.1038/s41559-022-01795-yWang, W., K. Tang, P. Wang, Z. Zeng, T. Xu, W. Zhan, T. Liu, Y. Wang and X. WangThe coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage inductionNature Ecology & Evolution6(8) 1132–44
202210.1016/j.pbi.2021.102171Wang, P., A. M. Schumacher and S.-H. ShiuComputational prediction of plant metabolic pathwaysCurrent Opinion in Plant Biology66 102171
202210.1111/nph.18056Wang, P., F. Meng, P. Donaldson, S. Horan, N. L. Panchy, E. Vischulis, E. Winship, J. K. Conner, P. J. Krysan, S.-H. Shiu and M. D. Lehti-ShiuHigh-throughput measurement of plant fitness traits with an object detection method using Faster R-CNNNew Phytologist234(4) 1521–33
202210.1016/j.vetmic.2022.109379Wang, H., L. Zhang, L. Cao, X. Zeng, B. Gillespie and J. LinIsolation and characterization of Escherichia albertii originated from the broiler farms in Mississippi and AlabamaVeterinary Microbiology267 109379
202210.1111/gcb.16036Wang, G., Q. Gao, Y. Yang, S. E. Hobbie, P. B. Reich and J. ZhouSoil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modelingGlobal Change Biology28(5) 1935-1950
202210.1021/acs.analchem.1c05338Wang, B. and J. D. Young13C-Isotope-Assisted Assessment of Metabolic Quenching during Sample Collection from Suspension Cell CulturesAnalytical Chemistry94(22) 7787-7794
202210.3389/fevo.2022.841824Wang, B. and S. D. AllisonClimate-Driven Legacies in Simulated Microbial Communities Alter Litter Decomposition RatesFrontiers in Ecology and Evolution10
202210.1021/jasms.2c00081Walton, C. L., M. Khalid, A. N. Bible, V. Kertesz, S. T. Retterer, J. Morrell-Falvey and J. F. CahillIn Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass SpectrometryJournal of the American Society for Mass Spectrometry33(9) 1615–25
202210.1038/s41396-022-01269-wWalters, K. E., J. K. Capocchi, M. B. N. Albright, Z. Hao, E. L. Brodie and J. B. H. MartinyRoutes and rates of bacterial dispersal impact surface soil microbiome composition and functioningISME Journal16(10) 2295-2304
202210.1128/mra.00293-22Walters, K. A., K. S. Myers, H. Wang, N. W. Fortney, A. T. Ingle, M. J. Scarborough, T. J. Donohue and D. R. NogueraMetagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk PermeateMicrobiology Resource Announcements11(7) e00293-22
202210.1128/msystems.00348-22Walker, C., S. Ryu, S. Garcia, D. Dooley, B. Mendoza and C. T. TrinhGene Coexpression Connectivity Predicts Gene Targets Underlying High Ionic-Liquid Tolerance in Yarrowia lipolyticamSystems7(4)
202210.1016/j.csbj.2022.06.037Walker, A. M., A. Cliff, J. Romero, M. B. Shah, P. Jones, J. G. Felipe Machado Gazolla, D. A. Jacobson and D. KainerEvaluating the performance of random forest and iterative random forest based methods when applied to gene expression dataComputational and Structural Biotechnology Journal20 3372–86
202210.1111/mec.16640Wagner, R., L. Montoya, C. Gao, J. R. Head, J. Remais and J. W. TaylorThe air mycobiome is decoupled from the soil mycobiome in the California San Joaquin ValleyMolecular Ecology
202210.1186/s13068-022-02168-0Wadler, C. S., J. F. Wolters, N. W. Fortney, K. O. Throckmorton, Y. Zhang, C. R. Miller, R. M. Schneider, E. Wendt-Pienkowski, C. R. Currie, T. J. Donohue, D. R. Noguera, C. T. Hittinger and M. G. ThomasUtilization of lignocellulosic biofuel conversion residue by diverse microorganismsBiotechnology for Biofuels and Bioproducts15(1) 70
202210.1126/science.abb3634Volland, J.-M., S. Gonzalez-Rizzo, O. Gros, T. Tyml, N. Ivanova, et al.A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organellesScience376(6600) 1453–8
202210.1038/s41467-022-30571-6Vögeli, B., L. Schulz, S. Garg, K. Tarasava, J. M. Clomburg, et al.Cell-free prototyping enables implementation of optimized reverse _-oxidation pathways in heterotrophic and autotrophic bacteriaNature Communications13(1)
202210.1089/ast.2021.0137Vishnivetskaya, T. A., V. A. Mironov, A. A. Abramov, V. A. Shcherbakova and E. M. RivkinaBiogeochemical Characteristics of Earth's Volcanic Permafrost: An Analog of Extraterrestrial EnvironmentsAstrobiology22(7) 812-828
202210.3389/ffunb.2022.808578Villalobos Solis, M. I., N. L. Engle, M. K. Spangler, S. Cottaz, S. Fort, J. Maeda, J.-M. Ané, T. J. Tschaplinski, J. L. Labbé, R. L. Hettich, P. E. Abraham and T. A. RushExpanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and DevelopmentFrontiers in Fungal Biology3
202210.1186/s13068-022-02125-xVillalobos Solis, M. I., P. Chirania and R. L. HettichIn silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactorsBiotechnology for Biofuels and Bioproducts15(1) 32
202210.1038/s41396-022-01220-zViacava, K., J. Qiao, A. Janowczyk, S. Poudel, N. Jacquemin, K. L. Meibom, H. K. Shrestha, M. C. Reid, R. L. Hettich and R. Bernier-LatmaniMeta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacteriumThe ISME Journal16(7) 1740–9
202210.1016/j.jbc.2022.102627Vermaas, J. V., M. F. Crowley and G. T. BeckhamMolecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranesJournal of Biological Chemistry298(12)
202210.1099/mgen.0.000853Venturini, A. M., J. B. Gontijo, J. A. Mandro, F. S. Paula, C. A. Yoshiura, A. G. da França and S. M. TsaiGenome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soilsMicrobial Genomics8(7)
202210.1021/acs.est.2c03566Vega, M. A. P., R. C. Scholes, A. R. Brady, R. A. Daly, A. B. Narrowe, L. B. Bosworth, K. C. Wrighton, D. L. Sedlak and J. O. SharpPharmaceutical biotransformation is influenced by photosynthesis and microbial nitrogen cycling in a benthic wetland biomatEnvironmental Science and Technology
202210.1093/nar/gkac025Vasileva, Delyana P., Jared C. Streich, Leah H. Burdick, Dawn M. Klingeman, H. B. Chhetri, Christa M. Brelsford, J. C. Ellis, D. M. Close, Daniel A. Jacobson and Joshua K. MichenerProtoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombinationNucleic Acids Research50(11) 6211–23
202210.1098/rsta.2021.0022Varner, R. K., P. M. Crill, S. Frolking, C. K. McCalley, S. A. Burke, J. P. Chanton, M. E. Holmes, S. Saleska and M. W. PalacePermafrost thaw driven changes in hydrology and vegetation cover increase trace gas emissions and climate forcing in Stordalen Mire from 1970 to 2014Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences380(2215)
202210.3390/rs14215333Varela, S., X. Zheng, J. N. Njuguna, E. J. Sacks, D. P. Allen, J. Ruhter and A. D. B. LeakeyDeep Convolutional Neural Networks Exploit High-Spatial- and -Temporal-Resolution Aerial Imagery to Phenotype Key Traits in MiscanthusRemote Sensing14(21) 5333
202210.3390/rs14030733Varela, S., T. L. Pederson and A. D. B. LeakeyImplementing Spatio-Temporal 3D-Convolution Neural Networks and UAV Time Series Imagery to Better Predict Lodging Damage in SorghumRemote Sensing14(3) 733
202210.1016/j.pbi.2021.102152VanWallendael, A., D. B. Lowry and J. A. HamiltonOne hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systemsCurrent Opinion in Plant Biology66 102152
202210.1371/journal.pbio.3001681VanWallendael, A., G. M. N. Benucci, P. B. da Costa, L. Fraser, A. Sreedasyam, F. Fritschi, T. E. Juenger, J. T. Lovell, G. Bonito and D. B. LowryHost genotype controls ecological change in the leaf fungal microbiomePLoS Biology20(8) e3001681
202210.1021/acssynbio.1c00522VanArsdale, E., J. Pitzer, S. Wang, K. Stephens, C.-y. Chen, G. F. Payne and W. E. BentleyElectrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, TyrosineACS Synthetic Biology11(2) 877–87
202210.1093/femsyr/foac036Vanacloig-Pedros, E., K. J. Fisher, L. Liu, D. J. Debrauske, M. K. M. Young, M. Place, C. T. Hittinger, T. K. Sato and A. P. GaschComparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributionsFEMS Yeast Research22(1) foac036
202210.3389/frai.2022.959470van Dijk, A. D. J., S.-H. Shiu and D. de RidderEditorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and GeneticsFrontiers in Artificial Intelligence5
202210.1038/s42003-022-04336-2Valencia, L. E., M. R. Incha, M. Schmidt, A. N. Pearson, M. G. Thompson, J. B. Roberts, M. Mehling, K. Yin, N. Sun, A. Oka, P. M. Shih, L. M. Blank, J. Gladden and J. D. KeaslingEngineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical productionCommunications Biology5(1) 1363
202210.1139/facets-2021-0109Valadez-Cano, C., K. Hawkes, R. Calvaruso, A. Reyes-Prieto and J. LawrenceAmplicon-based and metagenomic approaches provide insights into toxigenic potential in understudied Atlantic Canadian lakesFACETS7 194–214
202210.15252/msb.202110785Vaiana, C. A., H. Kim, J. Cottet, K. Oai, Z. Ge, K. Conforti, A. M. King, A. J. Meyer, H. Chen, C. A. Voigt and C. R. BuieCharacterizing chemical signaling between engineered “microbial sentinels” in porous microplatesMolecular Systems Biology18(3) e10785
202210.1111/nph.18136Unda, F., Y. Mottiar, E. L. Mahon, S. D. Karlen, K. H. Kim, D. Loqué, A. Eudes, J. Ralph and S. D. MansfieldA new approach to zip-lignin: 3,4-dihydroxybenzoate is compatible with lignificationNew Phytologist235(1) 234–46
202210.3389/fceng.2022.1036084Umana, G. E., J. M. Perez, F. Unda, C.-Y. Lin, C. Sener, S. D. Karlen, S. D. Mansfield, A. Eudes, J. Ralph, T. J. Donohue and D. R. NogueraBiological funneling of phenolics from transgenic plants engineered to express the bacterial 3-dehydroshikimate dehydratase (qsuB) geneFrontiers in Chemical Engineering4
202210.1016/j.soilbio.2022.108753Ulbrich, T. C., A. Rivas-Ubach, L. K. Tiemann, M. L. Friesen and S. E. EvansPlant root exudates and rhizosphere bacterial communities shift with neighbor contextSoil Biology and Biochemistry172 108753
202210.1126/sciadv.ade5155Uchiyama, T., T. Uchihashi, T. Ishida, A. Nakamura, J. V. Vermaas, M. F. Crowley, M. Samejima, G. T. Beckham and K. IgarashiLytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surfaceScience Advances8(51) eade5155
202210.1016/j.scitotenv.2022.155492Trutschel, L. R., G. L. Chadwick, B. Kruger, J. G. Blank, W. J. Brazelton, E. R. Dart and A. R. RoweInvestigation of microbial metabolisms in an extremely high pH marine-like terrestrial serpentinizing system: Ney SpringsScience of The Total Environment836 155492
202210.1021/acs.analchem.1c03243Trujillo, E. A., A. S. Hebert, J. C. Rivera Vazquez, D. R. Brademan, M. Tatli, D. Amador-Noguez, J. G. Meyer and J. J. CoonRapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM)Analytical Chemistry94(4) 1965–73
202210.1128/mra.00938-21Trubitsyn, V., E. Rivkina and V. ShcherbakovaDraft Genome Sequence of a Methanogenic Archaeon from West Spitsbergen PermafrostMicrobiology Resource Announcements11(2) e00938-21
202210.1093/plphys/kiab447Triozzi, P. M., T. B. Irving, H. W. Schmidt, Z. P. Keyser, S. Chakraborty, K. Balmant, W. J. Pereira, C. Dervinis, K. S. Mysore, J. Wen, J. M. Ané, M. Kirst and D. CondeSpatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule developmentPlant Physiology188(1) 560-575
202210.1186/s13068-022-02241-8Trieu, A., M. B. Belaffif, P. Hirannaiah, S. Manjunatha, R. Wood, Y. Bathula, R. L. Billingsley, A. Arpan, E. J. Sacks, T. E. Clemente, S. P. Moose, N. A. Reichert and K. SwaminathanTransformation and gene editing in the bioenergy grass MiscanthusBiotechnology for Biofuels and Bioproducts15(1) 148
202210.1038/s41467-022-30118-9Treen, D. G. C., M. Wang, S. Xing, K. B. Louie, T. Huan, P. C. Dorrestein, T. R. Northen and B. P. BowenSIMILE enables alignment of tandem mass spectra with statistical significanceNature Communications13(1) 2510
202210.1093/plphys/kiac579Toma_, _., M. Petek, T. Lukan, K. Poga_ar, K. Stare, et al.A mini-TGA protein modulates gene expression through heterogeneous association with transcription factorsPlant Physiology191(3) 1934–52
202210.1186/s40168-022-01377-xTom, L. M., M. Aulitto, Y.-W. Wu, K. Deng, Y. Gao, et al.Low-abundance populations distinguish microbiome performance in plant cell wall deconstructionMicrobiome10(1) 183
202210.1128/spectrum.00049-22Tinker, K., D. Lipus, J. Gardiner, M. Stuckman and D. GulliverThe Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing MicroorganismsMicrobiology Spectrum10(4) e00049-22
202210.1002/glr2.12007Tilhou, N. W., S. M. Kaeppler and M. D. CaslerStrong parallel evidence of selection during switchgrass sward establishment in hybrid and lowland ecotypesGrassland Research1(1) 31–42
202210.1111/gcbb.12983Tilhou, N. W. and M. D. CaslerBiomass yield improvement in switchgrass through genomic prediction of flowering timeGCB Bioenergy14(9) 1023–34
202210.1007/s10722-021-01282-6Tilhou, N. W. and M. D. CaslerSurveying Grassland Islands: the genetics and performance of Appalachian switchgrass (Panicum virgatum L.) collectionsGenetic Resources and Crop Evolution69(3) 1039–55
202210.1002/glr2.12035Tilhou, N. W. and M. D. CaslerSwitchgrass sward establishment selection is consistent across multiple environments and fertilization levelsGrassland Research1(4) 252–61
202210.1002/csc2.20767Tilhou, N. W. and M. CaslerGenetic correlations between switchgrass performance in sward conditions and surrogate measuresCrop Science62(4) 1511–21
202210.1111/nph.18443Tiedge, K., X. Li, A. T. Merrill, D. Davisson, Y. Chen, P. Yu, D. J. Tantillo, R. L. Last and P. ZerbeComparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum)New Phytologist236(4) 1393–408
202210.1186/s13007-022-00903-0Tiedge, K., J. Destremps, J. Solano-Sanchez, M. L. Arce-Rodriguez and P. ZerbeFoxtail mosaic virus-induced gene silencing (VIGS) in switchgrass (Panicum virgatum L.)Plant Methods18(1)
202210.1038/s41540-022-00259-0Tibocha-Bonilla, J. D., C. Zuñiga, A. Lekbua, C. Lloyd, K. Rychel, K. Short and K. ZenglerPredicting stress response and improved protein overproduction in Bacillus subtilisnpj Systems Biology and Applications8(1) 50
2022Tibocha-Bonilla, J. D., R. Santibanez, B. Estefan, B. Arianpour, K. Patel, C. Zuniga and K. ZenglerIMAGINE BioSecurity: Modeling Bacterial Metabolism and Expression To Develop Biocontainment StrategiesDOE Genomic Sciences Program Annual Meeting
202210.1021/acssuschemeng.2c01160Tian, Y., M. Yang, C.-Y. Lin, J.-H. Park, C.-Y. Wu, et al.Expression of Dehydroshikimate Dehydratase in Sorghum Improves Biomass Yield, Accumulation of Protocatechuate, and Biorefinery EconomicsACS Sustainable Chemistry & Engineering10(38) 12520–8
202210.3390/microorganisms10051055Thomas, P. E., C. Gates, W. Campodonico-Burnett and J. C. CameronZam is a redox-regulated member of the RNB-family required for optimal photosynthesis in cyanobacteriaMicroorganisms10(5)
202210.1016/j.tplants.2021.11.005Therby-Vale, R., B. Lacombe, S. Y. Rhee, L. Nussaume and H. RouachedMineral nutrient signaling controls photosynthesis: focus on iron deficiency-induced chlorosisTrends in Plant Science27(5) 502-509
202210.1094/pbiomes-05-21-0033-mrThe Inter-BRC Microbiome Workshop Consortium, A. Howe, G. Bonito, M.-Y. Chou, M. A. Cregger, A. Fedders, J. L. Field, H. G. Martin, J. L. Labbé, M. E. Mechan-Llontop, T. R. Northen, A. Shade and T. J. TschaplinskiFrontiers and Opportunities in Bioenergy Crop Microbiome Research NetworksPhytobiomes Journal6(2) 118–26
202210.1186/s40168-022-01229-8ter Horst, A. M., C. Santos-Medellín, J. W. Sorensen, L. A. Zinke, R. M. Wilson, E. R. Johnston, G. Trubl, J. Pett-Ridge, S. J. Blazewicz, P. J. Hanson, J. P. Chanton, C. W. Schadt, J. E. Kostka and J. B. EmersonCorrection to: Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations (Microbiome, (2021), 9, 1, (233), 10.1186/s40168-021-01156-0)Microbiome10(1)
202210.1093/jxb/erac382Tejera, M., N. N. Boersma, S. V. Archontoulis, F. E. Miguez, A. VanLoocke and E. A. HeatonPhotosynthetic decline in aging perennial grass is not fully explained by leaf nitrogenJournal of Experimental Botany73(22) 7582–95
202210.7554/eLife.76523Tatli, M., S. Moraïs, O. E. Tovar-Herrera, Y. J. Bomble, E. A. Bayer, O. Medalia and I. MizrahiNanoscale resolution of microbial fiber degradation in actioneLife11 e76523
202210.1093/nar/gkac1075Tao, X. B., S. LaFrance, Y. Xing, A. A. Nava, Hector G. Martin, Jay D. Keasling and Tyler W. H. BackmanClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase designNucleic Acids Research51(D1) D532–8
202210.1128/aem.00401-22Tao, X., A. Zhou, M. L. Kempher, J. Liu, M. Peng, Y. Li, J. P. Michael, R. Chakraborty, A. M. Deutschbauer, A. P. Arkin and J. ZhouDevelopment of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificansApplied and Environmental Microbiology88(14) e00401-22
202210.1093/femsyr/foac032Tan, L.-R., J.-J. Liu, A. Deewan, J. W. Lee, P.-F. Xia, C. V. Rao, Y.-S. Jin and S.-G. WangGenome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxideFEMS Yeast Research22(1) foac032
202210.1016/j.ces.2022.117482Taifan, G. S. P. and C. T. MaraveliasGeneralized optimization-based synthesis of membrane systems for multicomponent gas mixture separationChemical Engineering Science252 117482
202210.1002/btpr.3276Suthers, P. F. and C. D. MaranasExamining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modelingBiotechnology Progress38(5) e3276
202210.1038/s41477-022-01139-5Sun, Y., D. H. Oh, L. Duan, P. Ramachandran, A. Ramirez, A. Bartlett, K. N. Tran, G. Wang, M. Dassanayake and J. R. DinnenyDivergence in the ABA gene regulatory network underlies differential growth controlNature Plants8(5) 549-560
202210.1021/acssuschemeng.2c01375Sumer, Z. and R. C. Van LehnData-Centric Development of Lignin Structure–Solubility Relationships in Deep Eutectic Solvents Using Molecular SimulationsACS Sustainable Chemistry & Engineering10(31) 10144–56
202210.1111/tpj.15948Strenkert, D., A. Yildirim, J. Yan, Y. Yoshinaga, M. Pellegrini, R. C. O'Malley, S. S. Merchant and J. G. UmenThe landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cyclePlant Journal
202210.1002/pld3.392Strenkert, D., M. Mingay, S. Schmollinger, C. Chen, R. C. O'Malley and S. S. MerchantAn optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensisPlant Direct6(3)
202210.1016/j.joule.2022.08.005Stone, M. L., M. S. Webber, W. P. Mounfield, III, D. C. Bell, E. Christensen, A. R. C. Morais, Y. Li, E. M. Anderson, J. S. Heyne, G. T. Beckham and Y. Román-LeshkovContinuous hydrodeoxygenation of lignin to jet-range aromatic hydrocarbonsJoule6(10) 2324–37
202210.1111/nph.18407Steindorff, A. S., K. Seong, A. Carver, S. Calhoun, M. S. Fischer, et al.Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual developmentNew Phytologist236(3) 1154-1167
202210.1126/sciadv.abn0105Steenwyk, J. L., M. A. Phillips, F. Yang, S. S. Date, T. R. Graham, J. Berman, C. T. Hittinger and A. RokasAn orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and functionScience Advances8(18) eabn0105
202210.1021/acssuschemeng.1c05916Starace, A. K., D. D. Lee, K. T. Hietala, Y. Kim, S. Kim, A. E. Harman-Ware and D. L. CarpenterPredicting Catalytic Pyrolysis Aromatic Selectivity from Pyrolysis Vapor Composition Using Mass Spectra Coupled with Statistical AnalysisACS Sustainable Chemistry & Engineering10(1) 234–44
202210.1111/gcb.16321Sridhar, B., R. C. Wilhelm, S. J. Debenport, T. J. Fahey, D. H. Buckley and C. L. GoodaleMicrobial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soilsGlobal Change Biology28(18) 5399-5415
202210.1111/1462-2920.16119Sridhar, B., G. B. Lawrence, S. J. Debenport, T. J. Fahey, D. H. Buckley, R. C. Wilhelm and C. L. GoodaleWatershed-scale liming reveals the short- and long-term effects of pH on the forest soil microbiome and carbon cyclingEnvironmental Microbiology
202210.1002/yea.3679Spurley, W. J., K. J. Fisher, Q. K. Langdon, K. V. Buh, M. Jarzyna, et al.Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolatesYeast39(1–2) 55–68
202210.1038/s41396-022-01222-xSpeth, D. R., F. B. Yu, S. A. Connon, S. Lim, J. S. Magyar, M. E. Peña-Salinas, S. R. Quake and V. J. OrphanMicrobial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophilyISME Journal16(7) 1750-1764
202210.1525/elementa.2021.00076Sorouri, B. and S. D. AllisonMicrobial extracellular enzyme activity with simulated climate changeElementa10(1)
202210.1007/s10570-022-04551-4Song, Y., X. Meng, W. Jiang, B. R. Evans, H. Ben, Y. Zhang, Y. Pu, S. V. Pingali, B. H. Davison, S. Zhang, G. Han and A. J. RagauskasDeuterium incorporation into cellulose: a mini-review of biological and chemical methodsCellulose29(8) 4269–86
202210.1002/prot.26269Soltanikazemi, E., F. Quadir, R. S. Roy, Z. Guo and J. ChengDistance-based reconstruction of protein quaternary structures from inter-chain contactsProteins: Structure, Function and Bioinformatics90(3) 720-731
202210.1111/1365-2435.14040Sokol, N. W., E. D. Whalen, A. Jilling, C. Kallenbach, J. Pett-Ridge and K. GeorgiouGlobal distribution, formation and fate of mineral-associated soil organic matter under a changing climate: A trait-based perspectiveFunctional Ecology36(6) 1411–29
202210.1038/s41579-022-00695-zSokol, N. W., E. Slessarev, G. L. Marschmann, A. Nicolas, S. J. Blazewicz, et al.Life and death in the soil microbiome: how ecological processes influence biogeochemistryNature Reviews Microbiology20(7) 415–30
202210.1186/s40793-022-00440-2Smrhova, T., K. Jani, P. Pajer, G. Kapinusova, T. Vylita, J. Suman, M. Strejcek and O. UhlikProkaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysisEnvironmental Microbiome17(1) 48
202210.1093/pcp/pcac031Smith, R. A., F. Lu, F. Muro-Villanueva, J. C. Cusumano, C. Chapple and J. RalphManipulation of Lignin Monomer Composition Combined with the Introduction of Monolignol Conjugate Biosynthesis Leads to Synergistic Changes in Lignin StructurePlant and Cell Physiology63(6) 744–54
202210.1093/plphys/kiac035Smith, R. A., E. T. Beebe, C. A. Bingman, K. Vander Meulen, A. Eugene, A. J. Steiner, S. D. Karlen, J. Ralph and B. G. FoxIdentification and characterization of a set of monocot BAHD monolignol transferasesPlant Physiology189(1) 37–48
202210.1021/acsmaterialsau.2c00006Smith, P. J., T. M. Curry, J.-Y. Yang, W. J. Barnes, S. J. Ziegler, A. Mittal, K. W. Moremen, W. S. York, Y. J. Bomble, M. J. Peña and B. R. UrbanowiczEnzymatic Synthesis of Xylan Microparticles with Tunable MorphologiesACS Materials Au
202210.1128/mra.00337-22Smith, A., N. Kaiser, A. Yanez, T. Perleberg, A. Elyaderani, P. Skidmore, S. Adhikari, E. M. Driver, R. U. Halden, A. Varsani, M. Scotch and T. O. C. FaleyeGenome Sequence of a Microvirus Recovered from Wastewater in Arizona, USA, in October 2020, Encodes a Previously Undescribed DNA-Binding ProteinMicrobiology Resource Announcements11(10) e00337-22
202210.1007/s10533-021-00859-8Slessarev, E. W., O. A. Chadwick, N. W. Sokol, E. E. Nuccio and J. Pett-RidgeRock weathering controls the potential for soil carbon storage at a continental scaleBiogeochemistry157(1) 1–13
202210.1039/D2NP00017BSirirungruang, S., K. Markel and P. M. ShihPlant-based engineering for production of high-valued natural productsNatural Product Reports39(7) 1492–509
202210.1128/mra.00201-22Sipes, K., R. Paul, T. C. Onstott, T. A. Vishnivetskaya and K. G. LloydDraft Genome Sequences of 10 Pseudomonas sp. Isolates from the Active Layer of Permafrost in Ny Ålesund, Svalbard, NorwayMicrobiology Resource Announcements11(6) e00201-22
202210.3389/fmicb.2021.757812Sipes, K., R. Paul, A. Fine, P. Li, R. Liang, J. Boike, T. C. Onstott, T. A. Vishnivetskaya, S. Schaeffer and K. G. LloydPermafrost active layer microbes from Ny Ålesund, Svalbard (79°N) show autotrophic and heterotrophic metabolisms with diverse carbon-degrading enzymesFrontiers in Microbiology12
202210.1002/aocs.12633Singh, R., B. S. Dien and V. SinghSolvent-free enzymatic esterification of free fatty acids with glycerol for biodiesel application: Optimized using the Taguchi experimental methodJournal of the American Oil Chemists' Society99(9) 781–90
202210.1016/j.fgb.2021.103655Singh, P., S. Y. Huang, A. G. Hernandez, P. Adhikari, T. M. Jamann and S. X. MiderosGenomic regions associated with virulence in Setosphaeria turcica identified by linkage mapping in a biparental populationFungal Genetics and Biology159
202210.1007/s00294-022-01247-xSingh, A. K., M. Kumari, N. Sharma, A. K. Rai and S. P. SinghMetagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potentialCurrent Genetics68(5) 565–79
202210.1007/s11274-022-03311-7Singh, A. K., R. K. Gupta, H. J. Purohit and A. A. KhardenavisGenomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soilWorld Journal of Microbiology and Biotechnology38(8) 140
202210.3390/genes13010022Singer, E., E. M. Carpenter, J. Bonnette, T. Woyke and T. E. JuengerImpact of harvest on switchgrass leaf microbial communitiesGenes13(1)
202210.1016/bs.mie.2022.07.039Simpson, J. and C. ChappleTag you're it: Application of stable isotope labeling and LC-MS to identify the precursors of specialized metabolites in plantsMethods in Enzymology676 279-303
202210.1016/j.rse.2022.112938Shuai, G. and B. BassoSubfield maize yield prediction improves when in-season crop water deficit is included in remote sensing imagery-based modelsRemote Sensing of Environment272 112938
202210.3389/fpls.2022.893610Shrestha, V., H. B. Chhetri, D. Kainer, Y. Xu, L. Hamilton, C. Piasecki, B. Wolfe, X. Wang, M. Saha, D. Jacobson, R. J. Millwood, M. Mazarei and C. N. StewartThe Genetic Architecture of Nitrogen Use Efficiency in Switchgrass (Panicum virgatum L.)Frontiers in Plant Science13
202210.3389/fpls.2022.908649Shrestha, H. K., Y. Fichman, N. L. Engle, T. J. Tschaplinski, R. Mittler, R. A. Dixon, R. L. Hettich, J. Barros and P. E. AbrahamMulti-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effectsFrontiers in Plant Science13 908649
202210.1016/j.agrformet.2022.109175Shirkey, G., R. John, J. Chen, K. Dahlin, M. Abraha, P. Sciusco, C. Lei and D. E. ReedFine resolution remote sensing spectra improves estimates of gross primary production of croplandsAgricultural and Forest Meteorology326 109175
202210.1021/acsomega.2c00483Shin, J., E. J. South and M. J. DunlopTranscriptional tuning of mevalonate pathway enzymes to identify the impact on limonene production in Escherichia coliACS Omega7(22) 18331-18338
202210.3389/fpls.2022.805101Sheng, X., C. Y. Hsu, C. Ma and A. M. BrunnerFunctional Diversification of Populus FLOWERING LOCUS D-LIKE3 Transcription Factor and Two Paralogs in Shoot Ontogeny, Flowering, and Vegetative PhenologyFrontiers in Plant Science13
202210.1016/j.jenvman.2022.114569Sharma, N., R. Kumari, M. Thakur, A. K. Rai and S. P. SinghMolecular dissemination of emerging antibiotic, biocide, and metal co-resistomes in the Himalayan hot springsJournal of Environmental Management307 114569
202210.1111/gcbb.12929Sharma, B. P., N. Zhang, D. Lee, E. Heaton, E. H. Delucia, E. J. Sacks, I. B. Kantola, N. N. Boersma, S. P. Long, T. B. Voigt and M. KhannaResponsiveness of miscanthus and switchgrass yields to stand age and nitrogen fertilization: A meta-regression analysisGCB Bioenergy14(5) 539–57
202210.1007/s40820-022-00922-5Sharifi, S., N. N. Mahmoud, E. Voke, M. P. Landry and M. MahmoudiImportance of Standardizing Analytical Characterization Methodology for Improved Reliability of the Nanomedicine LiteratureNano-Micro Letters14(1)
202210.1016/j.str.2021.10.003Shao, C., J. D. Westbrook, C. Lu, C. Bhikadiya, E. Peisach, J. Y. Young, J. M. Duarte, R. Lowe, S. Wang, Y. Rose, Z. Feng and S. K. BurleySimplified quality assessment for small-molecule ligands in the Protein Data BankStructure30(2) 252-262.e4
202210.1016/j.str.2022.08.004Shao, C., S. Bittrich, S. Wang and S. K. BurleyAssessing PDB macromolecular crystal structure confidence at the individual amino acid residue levelStructure30(10) 1385-1394.e3
202210.1002/pro.4257Shahpasand-Kroner, H., J. Portillo, C. Lantz, P. M. Seidler, N. Sarafian, J. A. Loo and G. BitanThree-repeat and four-repeat tau isoforms form different oligomersProtein Science31(3) 613-627
202210.1016/j.gca.2022.04.028Shabtai, I. A., S. Das, T. M. Inagaki, B. Azimzadeh, B. Richards, C. E. Martínez, I. Kögel-Knabner and J. LehmannSoil organic carbon accrual due to more efficient microbial utilization of plant inputs at greater long-term soil moistureGeochimica et Cosmochimica Acta327 170-185
202210.1007/s10534-021-00359-0Sen, S., N. Mondal, W. Ghosh and R. ChakrabortyInducible boron resistance via active efflux in Lysinibacillus and Enterococcus isolates from boron-contaminated agricultural soilBioMetals35(2) 215–28
202210.1128/aem.00226-22Seitz, V. A., B. B. McGivern, R. A. Daly, J. M. Chaparro, M. A. Borton, A. M. Sheflin, S. Kresovich, L. Shields, M. E. Schipanski, K. C. Wrighton and J. E. PrenniVariation in root exudate composition influences soil microbiome membership and functionApplied and Environmental Microbiology88(11)
202210.1093/bioinformatics/btac317Segura, J., Y. Rose, S. Bittrich, S. K. Burley and J. M. DuarteRCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assembliesBioinformatics38(12) 3304-3305
202210.1039/D2CY00288DSeemala, B. and C. E. WymanRelationship between ZSM-5 pore modifications and gallium proximity and liquid hydrocarbon number distribution from ethanol oligomerizationCatalysis Science & Technology12(15) 4903–16
202210.1111/gcb.16073See, C. R., A. B. Keller, S. E. Hobbie, P. G. Kennedy, P. K. Weber and J. Pett-RidgeHyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilizationGlobal Change Biology28(8) 2527–40
202210.3389/fpls.2022.839446Sebesta, J., W. Xiong, M. T. Guarnieri and J. YuBiocontainment of Genetically Engineered AlgaeFrontiers in Plant Science13
202210.3389/fpls.2022.839446Sebesta, J., W. Xiong, M. T. Guarnieri and J. YuBiocontainment of Genetically Engineered AlgaeFrontiers in Plant Science13
202210.1038/s41587-022-01248-8Scown, C. D. and J. D. KeaslingSustainable manufacturing with synthetic biologyNature Biotechnology40(3) 304–7
202210.1016/j.tibtech.2022.09.004Scown, C. D.Prospects for carbon-negative biomanufacturingTrends in Biotechnology40(12) 1415–24
202210.1111/tpj.15878Scott, S., E. B. Cahoon and L. BustaVariation on a Theme: The Structures and Biosynthesis of Specialized Fatty Acid Natural Products in PlantsThe Plant Journal11(4)
202210.3390/land11020283Sciusco, P., J. Chen, V. Giannico, M. Abraha, C. Lei, G. Shirkey, J. Yuan and G. P. RobertsonAlbedo-Induced Global Warming Impact at Multiple Temporal Scales within an Upper Midwest USA WatershedLand11(2) 283
202210.1038/s41522-022-00267-2Schweitzer, H. D., H. J. Smith, E. P. Barnhart, L. J. McKay, R. Gerlach, A. B. Cunningham, R. R. Malmstrom, D. Goudeau and M. W. FieldsSubsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomicsnpj Biofilms and Microbiomes8(1) 7
202210.1146/annurev-arplant-072221-092913Schwechheimer, C., P. M. Schröder and C. E. Blaby-HaasPlant GATA Factors: Their Biology, Phylogeny, and PhylogenomicsAnnual Review of Plant Biology73 123–48
202210.1186/s12934-022-01750-3Schultz, J. C., S. Mishra, E. Gaither, A. Mejia, H. Dinh, C. Maranas and H. ZhaoMetabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic mediaMicrobial Cell Factories21(1) 26
202210.1038/s41893-021-00827-ySchulte, L. A., B. E. Dale, S. Bozzetto, M. Liebman, G. M. Souza, N. Haddad, T. L. Richard, B. Basso, R. C. Brown, J. A. Hilbert and J. G. ArbuckleMeeting global challenges with regenerative agriculture producing food and energyNature Sustainability5(5) 384–8
2022Schroeder, W., D. Olson and C. D. MaranasBuilding Bottom-up Kinetic Models for Optimizing Cell-Free Lignocellulose Degradation SystemsAIChE Annual Meeting
2022Schroeder, W., T. Kuil, D. Olson and C. D. MaranasTracking Pyrophosphate Metabolism and Evaluating Its Significance in the Bioprocessing of Lignocellulosic Biomass By Clostridium ThermocellumAIChE Annual Meeting
202210.1111/nph.18390Scholz, P., K. D. Chapman, R. T. Mullen and T. IschebeckFinding new friends and revisiting old ones – how plant lipid droplets connect with other subcellular structuresNew Phytologist236(3) 833-838
202210.1128/aem.02430-21Schmidt, M., A. N. Pearson, M. R. Incha, M. G. Thompson, E. E. K. Baidoo, R. Kakumanu, A. Mukhopadhyay, P. M. Shih, A. M. Deutschbauer, L. M. Blank and J. D. KeaslingNitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon SequencingApplied and Environmental Microbiology88(7) e02430-21
202210.1007/s12155-021-10272-6Schetter, A., C. H. Lin, C. Zumpf, C. Jang, L. Hoffmann, W. Rooney and D. K. LeeGenotype-Environment-Management Interactions in Biomass Yield and Feedstock Composition of Photoperiod-Sensitive Energy SorghumBioEnergy Research15(2) 1017–32
202210.1128/mra.01151-21Scarborough, M. J., K. S. Myers, N. W. Fortney, A. T. Ingle, T. J. Donohue and D. R. NogueraMetagenome-Assembled Genomes from a Microbiome Converting Xylose to Medium-Chain Carboxylic AcidsMicrobiology Resource Announcements11(4) e01151-21
202210.1128/aem.02429-21Scales, N. C., A. B. Chase, S. S. Finks, A. A. Malik, C. Weihe, S. D. Allison, A. C. Martiny and J. B. H. MartinyDifferential Response of Bacterial Microdiversity to Simulated Global ChangeApplied and Environmental Microbiology88(6)
202210.1007/10_2022_213Sattayawat, P., I. S. Yunus and P. R. JonesProduction of Fatty Acids and Derivatives Using CyanobacteriaCyanobacteria in Biotechnology 145–69
202210.1016/j.ymben.2022.01.005Sasaki, Y. and Y. YoshikuniMetabolic engineering for valorization of macroalgae biomassMetabolic Engineering71 42-61
202210.1016/j.geoderma.2022.115854Sanford, G. R., R. D. Jackson, Y. Rui and C. J. KucharikLand use-land cover gradient demonstrates the importance of perennial grasslands with intact soils for building soil carbon in the fertile Mollisols of the North Central USGeoderma418 115854
202210.1016/j.jmb.2022.167556Sanchez-Garcia, R., J. R. Macias, C. O. S. Sorzano, J. M. Carazo and J. SeguraBIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site PredictionJournal of Molecular Biology434(11)
202210.1002/cbic.202200396Samanta, N., Y. B. Ruiz-Blanco, Z. Fetahaj, D. Gnutt, C. Lantz, J. A. Loo, E. Sanchez-Garcia and S. EbbinghausSuperoxide Dismutase 1 folding stability as a target for molecular tweezers in SOD1-Related Amyotrophic Lateral SclerosisChemBioChem
202210.1016/j.fuel.2022.124638Sakai, S. and D. RothamerRelative particle emission tendencies of 2-methyl-3-buten-2-ol–gasoline, isobutanol–gasoline, and ethanol–gasoline blends from premixed combustion in a spark-ignition engineFuel324(Part C) 124638
202210.1128/mra.00246-22Saito, D., L. N. Lemos, A. T. R. N. Ferreira, C. P. B. Saito, R. F. d. Oliveira, F. d. S. Cannavan and S. M. TsaiDraft Genome Sequences of Five Putatively Novel Saccharibacteria Species Assembled from the Human Oral MetagenomeMicrobiology Resource Announcements11(7) e00246-22
202210.3390/microorganisms10010080Saini, M. K., S. Yoshida, A. Sebastian, E. Hara, H. Tamaki, N. T. Soulier, I. Albert, S. Hanada, M. Tank and D. A. BryantElioraea tepida, sp. nov., a Moderately Thermophilic Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Mat Community of an Alkaline Siliceous Hot Spring in Yellowstone National Park, WY, USAMicroorganisms10(1) 80
202210.1021/acs.chemrev.1c00879Saha, A., S. S. Nia and J. A. RodríguezElectron Diffraction of 3D Molecular CrystalsChemical Reviews122(17) 13883-13914
202210.1002/eco.2475Saha, A., E. H. Boughton, H. Li, G. Sonniér, N. Gomez-Casanovas, N. McMillan and X. ZhangEvapotranspiration in a subtropical wetland savanna using low-cost lysimeter, eddy covariance and modelling approachesEcohydrology
202210.1186/s40643-021-00491-2Sacko, O., N. L. Engle, T. J. Tschaplinski, S. Kumar and J. W. LeeOzonized biochar filtrate effects on the growth of Pseudomonas putida and cyanobacteria Synechococcus elongatus PCC 7942Bioresources and Bioprocessing9(1) 2
202210.1093/nar/gkac142Rybnicky, G. A., N. A. Fackler, A. S. Karim, M. Köpke and M. C. JewettSpacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequencesNucleic Acids Research50(6) 3523-3534
202210.1021/acssynbio.1c00503Rybnicky, G. A., R. A. Dixon, R. M. Kuhn, A. S. Karim and M. C. JewettDevelopment of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science ClassroomACS Synthetic Biology11(2) 835-842
202210.1128/msystems.01052-22Rush, T. A., J. Tannous, M. J. Lane, M. G. Meena, A. A. Carrell, et al.Lipo-Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial GrowthmSystems7(6) e01052-22
202210.1038/s41564-021-01014-7Rubin, B. E., S. Diamond, B. F. Cress, A. Crits-Christoph, Y. C. Lou, et al.Species- and site-specific genome editing in complex bacterial communitiesNature Microbiology7(1) 34–47
202210.1021/acssynbio.2c00385Rostain, W., T. Zaplana, M. Boutard, C. Baum, S. Tabuteau, M. Sanitha, M. Ramya, A. Guss, L. Ettwiller and A. C. TolonenTuning of Gene Expression in Clostridium phytofermentans Using Synthetic Promoters and CRISPRiACS Synthetic Biology11(12) 4077–88
202210.1038/s41564-022-01208-7Rosconi, F., E. Rudmann, J. Li, D. Surujon, J. Anthony, M. Frank, D. S. Jones, C. Rock, J. W. Rosch, C. D. Johnston and T. van OpijnenA bacterial pan-genome makes gene essentiality strain-dependent and evolvableNature Microbiology7(10) 1580–92
202210.1080/00275514.2022.2031780Romero-Jiménez, M.-J., J. A. Rudgers, A. Jumpponen, J. Herrera, M. Hutchinson, C. Kuske, J. Dunbar, D. G. Knapp, G. M. Kovács and A. Porras-AlfaroDarksidea phi, sp. nov., a dark septate root-associated fungus in foundation grasses in North American Great PlainsMycologia114(2) 254–69
202210.1099/ijsem.0.005294Roldán, D. M., A. Costa, S. Králová, H.-J. Busse, V. Amarelle, E. Fabiano and R. J. MenesPaenibacillus farraposensis sp. nov., isolated from a root nodule of Arachis villosaInternational Journal of Systematic and Evolutionary Microbiology72(3)
202210.1038/s41396-022-01331-7Rogers, T. J., J. Buongiorno, G. L. Jessen, M. O. Schrenk, J. A. Fordyce, J. M. de Moor, C. J. Ramírez, P. H. Barry, M. Yücel, M. Selci, A. Cordone, D. Giovannelli and K. G. LloydChemolithoautotroph distributions across the subsurface of a convergent marginISME Journal
202210.1016/j.anaerobe.2022.102519Rodríguez-Pallares, S., P. Fernández-Palacios, E. Jurado-Tarifa, F. Arroyo, M. A. Rodríguez-Iglesias and F. Galán-SánchezTransmission of toxigenic Clostridiodes difficile between a pet dog with diarrhea and a 10-month-old infantAnaerobe74 102519
202210.3389/fmicb.2022.847964Rocca, J. D., A. Yammine, M. Simonin and J. P. GibertProtist predation influences the temperature response of bacterial communitiesFrontiers in Microbiology13
202210.3389/fgene.2021.821715Robinson, A. J., H. E. Daligault, J. M. Kelliher, E. S. LeBrun and P. S. G. ChainMultiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast GenomesFrontiers in Genetics12
202210.1111/gcb.16267Robertson, G. P., S. K. Hamilton, K. Paustian and P. SmithLand-based climate solutions for the United StatesGlobal Change Biology28(16) 4912–9
202210.1093/nar/gkac985Roberts, A., M. A. Nethery and R. BarrangouFunctional characterization of diverse type I-F CRISPR-associated transposonsNucleic Acids Research50(20) 11670–81
202210.1099/ijsem.0.005680Riesco, R., M. Ortúzar, B. Román-Ponce, F. Sánchez-Juanes, J. M. Igual and M. E. TrujilloSix novel Micromonospora species associated with the phyllosphere and roots of leguminous plants: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov., and Micromonospora trifolii sp. novInternational Journal of Systematic and Evolutionary Microbiology72(11)
202210.1016/j.soilbio.2022.108857Ridgeway, J. R., E. M. Morrissey and E. R. BrzostekPlant litter traits control microbial decomposition and drive soil carbon stabilizationSoil Biology and Biochemistry175 108857
202210.3389/fpls.2022.739133Razar, R. M., P. Qi, K. M. Devos and A. M. MissaouiGenotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass F1 Populations (Lowland x Coastal and Coastal x Upland)Frontiers in Plant Science13 739133
202210.1007/978-1-0716-1998-8_12Rasor, B. J., B. Vögeli, M. C. Jewett and A. S. KarimCell-Free Protein Synthesis for High-Throughput Biosynthetic Pathway PrototypingMethods in Molecular Biology2433 199-215
202210.3389/fpls.2022.998400Ranaweera, T., B. N. I. Brown, P. Wang and S.-H. ShiuTemporal regulation of cold transcriptional response in switchgrassFrontiers in Plant Science13
202210.7717/peerj.12632Ramnarine, S., J. Jayaraman and A. RamsubhagComparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profilesPeerJ9 e12632
202210.1016/j.fuel.2021.122459Rahaman, M. S., S. Tulaphol, M. A. Hossain, J. B. Jasinski, N. Sun, A. George, B. A. Simmons, T. Maihom, M. Crocker and N. SathitsuksanohCooperative Brønsted-Lewis acid sites created by phosphotungstic acid encapsulated metal–organic frameworks for selective glucose conversion to 5-hydroxymethylfurfuralFuel310 122459
202210.1128/mra.00041-22Quintela, I. A., A. Hwang, T. Vasse, A. Salvador, Y. Zhang, Y.-T. Liao and V. C. H. WuWhole-Genome Analysis of Escherichia Phage vB_EcoM-S1P5QW, Isolated from Manures Collected from Cattle Farms in MaineMicrobiology Resource Announcements11(4) e00041-22
202210.1038/s41396-022-01245-4Qi, M., J. C. Berry, K. W. Veley, L. O’Connor, O. M. Finkel, et al.Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisonsISME Journal16(8) 1957-1969
202210.3389/fenvs.2021.821882Putt, A. D., E. R. Kelly, K. A. Lowe, M. Rodriguez and T. C. HazenEffects of Cone Penetrometer Testing on Shallow Hydrogeology at a Contaminated SiteFrontiers in Environmental Science9
202210.1016/j.ymben.2021.11.003Purdy, H. M., B. F. Pfleger and J. L. ReedIntroduction of NADH-dependent nitrate assimilation in Synechococcus sp. PCC 7002 improves photosynthetic production of 2-methyl-1-butanol and isobutanolMetabolic Engineering69 87-97
202210.1371/journal.pgen.1010156Price, M. N., A. M. Deutschbauer and A. P. ArkinFilling gaps in bacterial catabolic pathways with computation and high-throughput geneticsPLoS Genetics18(4) e1010156
202210.1128/msystems.00705-22Price, M. N. and A. P. ArkinInteractive Analysis of Functional Residues in Protein FamiliesmSystems7(6) e00705-22
202210.1016/j.jbc.2021.101396Pollard, M. and Y. Shachar-HillKinetic complexities of triacylglycerol accumulation in developing embryos from Camelina sativa provide evidence for multiple biosynthetic systemsJournal of Biological Chemistry298(1)
202210.1111/1462-2920.16115Plett, J. M., J. Sabotic, E. Vogt, F. Snijders, A. Kohler, U. N. Nielsen, M. Kunzler, F. Martin and C. Veneault-FourreyMycorrhiza-induced mycocypins of Laccaria bicolor are potent protease inhibitors with nematotoxic and collembola antifeedant activityEnvironmental Microbiology24(10) 4607–22
202210.3390/metabo12040303Placido, D., N. Dong, B. Amer, C. Dong, G. Ponciano, T. Kahlon, M. Whalen, E. E. K. Baidoo and C. McMahanDownregulation of Squalene Synthase Broadly Impacts Isoprenoid Biosynthesis in GuayuleMetabolites12(4) 303
202210.3390/cancers14215369Pietrzak, B., K. Tomela, A. Olejnik-Schmidt, _. Galus, J. Mackiewicz, M. Kaczmarek, A. Mackiewicz and M. SchmidtA Clinical Outcome of the Anti-PD-1 Therapy of Melanoma in Polish Patients Is Mediated by Population-Specific Gut Microbiome CompositionCancers14(21) 5369
202210.3389/fenrg.2022.863153Pham, L. T. M., H. Choudhary, R. Gauttam, S. W. Singer, J. M. Gladden, B. A. Simmons, S. Singh and K. L. SaleRevisiting Theoretical Tools and Approaches for the Valorization of Recalcitrant Lignocellulosic Biomass to Value-Added ChemicalsFrontiers in Energy Research10
202210.1038/s41592-021-01339-5Petras, D., V. V. Phelan, D. Acharya, A. E. Allen, A. T. Aron, et al.GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browserNature Methods19(2) 134–6
202210.1002/fes3.421Perlo, V., A. Furtado, F. C. Botha, G. R. A. Margarido, K. Hodgson-Kratky, H. Choudhary, J. Gladden, B. Simmons and R. J. HenryTranscriptome and metabolome integration in sugarcane through culm developmentFood and Energy Security11(4) e421
202210.1039/D1GC03774APérez Pimienta, J. A., G. Papa, J. Sun, V. Stavila, A. Sanchez, J. M. Gladden and B. A. SimmonsOne-pot ethanol production under optimized pretreatment conditions using agave bagasse at high solids loading with low-cost biocompatible protic ionic liquidGreen Chemistry24(1) 207–17
202210.1039/D1GC03592DPerez, J. M., C. Sener, S. Misra, G. E. Umana, J. Coplien, D. Haak, Y. Li, C. T. Maravelias, S. D. Karlen, J. Ralph, T. J. Donohue and D. R. NogueraIntegrating lignin depolymerization with microbial funneling processes using agronomically relevant feedstocksGreen Chemistry24(7) 2795–811
202210.1111/nph.18006Pereira, W. J., S. Knaack, S. Chakraborty, D. Conde, R. A. Folk, P. M. Triozzi, K. M. Balmant, C. Dervinis, H. W. Schmidt, J. M. Ané, S. Roy and M. KirstFunctional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing cladeNew Phytologist234(2) 634-649
202210.1128/AEM.01793-21Peng, P., C. S. Kang-Yun, J. Chang, W. Gu, A. A. Dispirito and J. D. SemrauTwo TonB-dependent transporters in Methylosinus trichosporium OB3b are responsible for uptake of different forms of methanobactin and are involved in the canonical "copper switch"Applied and Environmental Microbiology88(1)
202210.1128/spectrum.02591-21Peng, M., D. Wang, L. M. Lui, T. Nielsen, R. Tian, et al.Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated AquiferMicrobiology Spectrum10(1) e02591-21
202210.1016/j.watres.2021.117933Pelivano, B., S. Bryson, K. A. Hunt, M. Denecke, D. A. Stahl and M. WinklerApplication of pyritic sludge with an anaerobic granule consortium for nitrate removal in low carbon systemsWater Research209 117933
202210.3389/fmicb.2022.1060160Pelicaen, R., S. Weckx, D. Gonze and L. De VuystApplication of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848T and Acetobacter senegalensis 108B cocoa strainsFrontiers in Microbiology13
202210.1002/pld3.419Payyavula, R. S., R. Badmi, S. S. Jawdy, M. Rodriguez Jr, L. Gunter, R. W. Sykes, K. A. Winkeler, C. M. Collins, W. H. Rottmann, J.-G. Chen, X. Yang, G. A. Tuskan and U. C. KalluriBiomass formation and sugar release efficiency of Populus modified by altered expression of a NAC transcription factorPlant Direct6(8) e419
202210.1016/j.ymben.2022.01.015Pavan, M., K. Reinmets, S. Garg, A. P. Mueller, E. Marcellin, M. Köpke and K. ValgepeaAdvances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economyMetabolic Engineering71 117-141
202210.1186/s12859-022-04593-2Paul, H. M., D. D. Istanto, J. Heldenbrand and M. E. HudsonCROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validationBMC Bioinformatics23(1) 74
202210.1111/nph.18427Pathare, V. S., R. J. DiMario, N. Koteyeva and A. B. CousinsMesophyll conductance response to short-term changes in pCO2 is related to leaf anatomy and biochemistry in diverse C4 grassesNew Phytologist236(4) 1281-1295
202210.1016/j.celrep.2022.110834Pasquini, M., N. Grosjean, K. K. Hixson, C. D. Nicora, E. F. Yee, M. Lipton, I. K. Blaby, J. D. Haley and C. E. Blaby-HaasZng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidaseCell Reports39(7) 110834
202210.1128/mra.00987-21Park, M.-R., B. Fong, T. Tofaha, B. A. Simmons and S. SingerComplete Genome Sequences of Five Isolated Pseudomonas Strains that Catabolize Pentose Sugars and Aromatic Compounds Obtained from Lignocellulosic BiomassMicrobiology Resource Announcements11(4) e00987-21
202210.1111/gwat.13132Paradis, C. J., J. I. Miller, J.-W. Moon, S. J. Spencer, L. M. Lui, J. D. Van Nostrand, D. Ning, A. D. Steen, L. D. McKay, A. P. Arkin, J. Zhou, E. J. Alm and T. C. HazenSustained Ability of a Natural Microbial Community to Remove Nitrate from GroundwaterGroundwater60(1) 99–111
202210.1111/gcb.15986Pan, D., I. Gelfand, L. Tao, M. Abraha, K. Sun, X. Guo, J. Chen, G. P. Robertson and M. A. ZondloA new open-path eddy covariance method for nitrous oxide and other trace gases that minimizes temperature correctionsGlobal Change Biology28(4) 1446–57
202210.1515/hf-2021-0149Padmakshan, D., V. I. Timokhin, F. Lu, P. F. Schatz, R. Vanholme, W. Boerjan and J. RalphSynthesis of hydroxycinnamoyl shikimates and their role in monolignol biosynthesisHolzforschung76(2) 133–44
202210.1128/msystems.00659-22Pacheco, A. R., C. Pauvert, D. Kishore and D. SegrèToward FAIR Representations of Microbial InteractionsmSystems7(5) e00659-22
202210.3389/fpls.2021.806949Paape, T., B. Heiniger, M. Santo Domingo, M. R. Clear, M. M. Lucas and J. J. PueyoGenome-Wide Association Study Reveals Complex Genetic Architecture of Cadmium and Mercury Accumulation and Tolerance Traits in Medicago truncatulaFrontiers in Plant Science12
202210.3389/fbioe.2022.965614Otten, J. K., Y. Zou and E. T. PapoutsakisThe potential of caproate (hexanoate) production using Clostridium kluyveri syntrophic cocultures with Clostridium acetobutylicum or Clostridium saccharolyticumFrontiers in Bioengineering and Biotechnology10
202210.1186/s12934-022-01977-0Otoupal, P. B., G. M. Geiselman, A. M. Oka, C. A. Barcelos, H. Choudhary, et al.Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloidesMicrobial Cell Factories21(1) 254
202210.1021/acssuschemeng.2c03341Østby, H., A. Várnai, R. Gabriel, P. Chylenski, S. J. Horn, S. W. Singer and V. G. H. EijsinkSubstrate-Dependent Cellulose Saccharification Efficiency and LPMO Activity of Cellic CTec2 and a Cellulolytic Secretome from Thermoascus aurantiacus and the Impact of H2O2-Producing Glucose OxidaseACS Sustainable Chemistry & Engineering10(44) 14433–44
202210.1007/s43393-022-00136-1Orr, J. S., E. Zen, X. Wang and C. V. RaoEmulsion-based evolution of Escherichia coli for higher growth yield on D-xylose identifies central role of cyclic AMPSystems Microbiology and Biomanufacturing
202210.1038/s41540-022-00212-1Ohnuki, S., I. Ogawa, K. Itto-Nakama, F. Lu, A. Ranjan, et al.High-throughput platform for yeast morphological profiling predicts the targets of bioactive compoundsnpj Systems Biology and Applications8(1) 3
202210.1016/j.compchemeng.2022.107724O'Neill, E. G., R. A. Martinez-Feria, B. Basso and C. T. MaraveliasIntegrated spatially explicit landscape and cellulosic biofuel supply chain optimization under biomass yield uncertaintyComputers & Chemical Engineering160 107724
202210.1002/ecs2.3968Nugent, A. and S. D. AllisonA framework for soil microbial ecology in urban ecosystemsEcosphere13(3)
202210.1093/gigascience/giac089Novichkov, P. S., J.-M. Chandonia and A. P. ArkinCORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysisGigaScience11 giac089
202210.3389/fbioe.2022.932363Nogle, R., S. Nagaraju, S. M. Utturkar, R. J. Giannone, V. Reynoso, C. Leang, R. L. Hettich, W. P. Mitchell, S. D. Simpson, M. C. Jewett, M. Köpke and S. D. BrownClostridium autoethanogenum isopropanol production via native plasmid pCA repliconFrontiers in Bioengineering and Biotechnology10
202210.1007/s00497-021-00432-1Noble, J. A., A. Seddon, S. Uygun, A. Bright, S. E. Smith, S.-h. Shiu and R. PalaniveluThe SEEL motif and members of the MYB-related REVEILLE transcription factor family are important for the expression of LORELEI in the synergid cells of the Arabidopsis female gametophytePlant Reproduction35(1) 61–76
202210.1128/msystems.01249-21No, J. H., S. D. Nishu, J.-K. Hong, E. S. Lyou, M. S. Kim, G. N. Wee and T. K. LeeRaman-Deuterium Isotope Probing and Metagenomics Reveal the Drought Tolerance of the Soil Microbiome and Its Promotion of Plant GrowthmSystems7(1) e01249-21
202210.1073/pnas.2206744119Nethery, M. A., C. Hidalgo-Cantabrana, A. Roberts and R. BarrangouCRISPR-based engineering of phages for in situ bacterial base editingProceedings of the National Academy of Sciences119(46) e2206744119
202210.1038/s41564-022-01174-0Needham, D. M., C. Poirier, C. Bachy, E. E. George, S. Wilken, C. C. M. Yung, A. J. Limardo, M. Morando, L. Sudek, R. R. Malmstrom, P. J. Keeling, A. E. Santoro and A. Z. WordenThe microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associateNature Microbiology7(9) 1466–79
202210.3390/microorganisms10030540Naylor, D., R. McClure and J. JanssonTrends in Microbial Community Composition and Function by Soil DepthMicroorganisms10(3) 540
202210.3390/plants11040566Nayak, S., H. Bhandari, M. C. Saha, S. Ali, C. Sams and V. PantaloneIdentification of QTL Associated with Regrowth Vigor Using the Nested Association Mapping Population in SwitchgrassPlants11(4)
202210.1007/978-1-0716-1585-0_14Navid, A.Curating COBRA Models of Microbial MetabolismMicrobial Systems Biology: Methods and Protocols 321–38
202210.1007/978-1-0716-1585-0_15Navid, A.A Beginner’s Guide to the COBRA ToolboxMicrobial Systems Biology: Methods and Protocols 339–65
202210.1093/g3journal/jkac084Navarrete, T. G., C. Arias, E. Mukundi, A. P. Alonso and E. GrotewoldNatural variation and improved genome annotation of the emerging biofuel crop field pennycress (Thlaspi arvense)G3: Genes, Genomes, Genetics12(6)
202210.1073/pnas.2118879119Napier, J. D., P. P. Grabowski, J. T. Lovell, J. Bonnette, S. Mamidi, et al.A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic rangeProceedings of the National Academy of Sciences119(15) e2118879119
202210.3390/rs14061435Namoi, N., C. Jang, Z. Robins, C. H. Lin, S. H. Lim, T. Voigt and D. LeeAerial Imagery Can Detect Nitrogen Fertilizer Effects on Biomass and Stand Health of Miscanthus _ giganteusRemote Sensing14(6)
2022Namoi, N., C. Jang, Z. Robins, C.-H. Lin, S.-H. Lim, T. Voigt and D. LeeAerial Imagery Can Detect Nitrogen Fertilizer Effects on Biomass and Stand Health of Miscanthus x giganteusRemote Sensing14(6) 1435
202210.1099/ijsem.0.005469Nadal-Jimenez, P., S. Siozios, C. L. Frost, R. Court, E. Chrostek, G. C. Drew, J. D. Evans, D. J. Hawthorne, J. B. Burritt and G. D. D. HurstArsenophonus apicola sp. nov., isolated from the honeybee Apis melliferaInternational Journal of Systematic and Evolutionary Microbiology72(8)
202210.1007/978-1-0716-1720-5_12Myers, K. S., P. Behari Lal, D. R. Noguera and T. J. DonohueUsing Genome Scale Mutant Libraries to Identify Essential GenesEssential Genes and Genomes: Methods and Protocols 215–36
202210.1038/s41594-022-00774-yMurray, K. A., M. P. Hughes, C. J. Hu, M. R. Sawaya, L. Salwinski, H. Pan, S. W. French, P. M. Seidler and D. S. EisenbergIdentifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologiesNature Structural and Molecular Biology29(6) 529-536
202210.1021/acsnano.1c08043Murray, K. A., D. Evans, M. P. Hughes, M. R. Sawaya, C. J. Hu, K. N. Houk and D. EisenbergExtended _-Strands Contribute to Reversible Amyloid FormationACS Nano16(2) 2154-2163
202210.1093/plphys/kiac210Muro-Villanueva, F., H. Kim, J. Ralph and C. ChappleH-lignin can be deposited independently of CINNAMYL ALCOHOL DEHYDROGENASE C and D in ArabidopsisPlant Physiology189(4) 2015–28
202210.3389/fpls.2021.766506Munson, C. R., Y. Gao, J. C. Mortimer and D. T. MurraySolid-State Nuclear Magnetic Resonance as a Tool to Probe the Impact of Mechanical Preprocessing on the Structure and Arrangement of Plant Cell Wall PolymersFrontiers in Plant Science12
202210.1007/s00705-022-05412-yMuhle, A. A., N. A. Palmer, S. J. Edme, G. Sarath, G. Yuen, R. B. Mitchell and S. TatineniEffect of cultivar and temperature on the synergistic interaction between panicum mosaic virus and satellite panicum mosaic virus in switchgrassArchives of Virology167(5) 1247-1256
2022Muchero, W., G. Tuskan, J.-G. Chen and L. E. GunterMethods for improving callus formation and regeneration in plantsPatent, U. S.
202210.1002/yea.3699Mozzachiodi, S., F.-Y. Bai, P. Baldrian, G. Bell, K. Boundy-Mills, et al.Yeasts from temperate forestsYeast39(1–2) 4–24
202210.1186/s12934-022-01752-1Moyo, A. C., L. Dufossé, D. Giuffrida, L. J. van Zyl and M. TrindadeStructure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South AfricaMicrobial Cell Factories21(1) 43
202210.1126/sciadv.abo0902Mou, Q., X. Xue, Y. Ma, M. Banik, V. Garcia, W. Guo, J. Wang, T. Song, L.-Q. Chen and Y. LuEfficient delivery of a DNA aptamer-based biosensor into plant cells for glucose sensing through thiol-mediated uptakeScience Advances8(26) eabo0902
202210.3389/fpls.2022.938083Mottiar, Y. and S. D. MansfieldLignin p-Hydroxybenzoylation Is Negatively Correlated With Syringyl Units in PoplarFrontiers in Plant Science13
202210.1128/msphere.00231-22Morris, M. M., J. A. Kimbrel, H. Geng, M. B. Tran-Gyamfi, E. T. Yu, K. L. Sale, T. W. Lane and X. MayaliBacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salinamSphere7(4) e00231-22
202210.1016/j.rhisph.2022.100564Moran, J. J., T. J. Linley, C. N. Makarem, J. F. Kelly, E. D. Wilcox Freeburg, D. M. Cleary, M. L. Alexander and J. M. KrieselSpectroscopy-based isotopic (_13C) analysis for high spatial resolution of carbon exchange in the rhizosphereRhizosphere23 100564
202210.3389/fmicb.2022.892227Morales, D. P., A. J. Robinson, A. C. Pawlowski, C. Ark, J. M. Kelliher, P. Junier, J. H. Werner and P. S. G. ChainAdvances and Challenges in Fluorescence in situ Hybridization for Visualizing Fungal EndobacteriaFrontiers in Microbiology13
202210.1039/D2GC00488GMorais, A. R. C., J. Zhang, H. Dong, W. G. Otto, T. Mokomele, D. Hodge, V. Balan, B. E. Dale, R. M. Lukasik and L. da Costa SousaDevelopment of an ammonia pretreatment that creates synergies between biorefineries and advanced biomass logistics modelsGreen Chemistry24(11) 4443–62
202210.1111/nph.18010Moore, J. A. M., P. E. Abraham, Joshua K. Michener, W. Muchero and Melissa A. CreggerEcosystem consequences of introducing plant growth promoting rhizobacteria to managed systems and potential legacy effectsNew Phytologist234(6) 1914–8
202210.1088/1748-9326/ac661aMoore, C. E., C. D. Gibson, G. Miao, E. C. Dracup, N. Gomez-Casanovas, M. D. Masters, J. Miller, A. C von Haden, T. Meyers, E. H. DeLucia and C. J. BernacchiSubstantial carbon loss respired from a corn–soybean agroecosystem highlights the importance of careful management as we adapt to changing climateEnvironmental Research Letters17(5) 54029
202210.1016/j.tibtech.2022.08.010Moon, T. S.SynMADE: synthetic microbiota across diverse ecosystemsTrends in Biotechnology
202210.1016/j.ijfoodmicro.2022.109555Montso, P. K., C. C. Bezuidenhout, C. Mienie, Y. M. Somorin, O. A. Odeyemi, V. Mlambo and C. N. AtebaGenetic diversity and whole genome sequence analysis data of multidrug resistant atypical enteropathogenic Escherichia coli O177 strains: An assessment of food safety and public health implicationsInternational Journal of Food Microbiology365 109555
202210.1111/tpj.15501Montes, C. M., H. J. Demler, S. Li, D. G. Martin and E. A. AinsworthApproaches to investigate crop responses to ozone pollution: from O3-FACE to satellite-enabled modelingThe Plant Journal109(2) 432–46
202210.1038/s41579-021-00600-0Montaño López, J., L. Duran and J. L. AvalosPhysiological limitations and opportunities in microbial metabolic engineeringNature Reviews Microbiology20(1) 35-48
202210.1016/j.cej.2022.137117Mokomele, T., L. da Costa Sousa, A. Colbert, B. E. Dale, J. F. Görgens and V. BalanCoupling AFEX and steam-exploded sugarcane residue pellets with a room temperature CIIII-activation step lowered enzyme dosage requirements for sugar conversionChemical Engineering Journal446
202210.1016/bs.mie.2021.11.023Mok, K. C., Z. F. Hallberg and M. E. TagaPurification and detection of vitamin B12 analogsMethods in Enzymology668 61-85
202210.1021/acssuschemeng.2c03373Mohan, M., K. L. Sale, R. S. Kalb, B. A. Simmons, J. M. Gladden and S. SinghMultiscale Molecular Simulation Strategies for Understanding the Delignification Mechanism of Biomass in CyreneACS Sustainable Chemistry & Engineering10(33) 11016–29
202210.1016/j.fluid.2022.113559Mohan, M., N. Kumar, V. V. Goud, B. A. Simmons, K. L. Sale, J. M. Gladden, S. Singh and T. BanerjeeEffect of cosolvent on the solubility of glucose in ionic liquids: Experimental and molecular dynamics simulationsFluid Phase Equilibria562 113559
202210.1039/D1GC03464BMohan, M., J. D. Keasling, B. A. Simmons and S. SinghIn silico COSMO-RS predictive screening of ionic liquids for the dissolution of plasticGreen Chemistry24(10) 4140–52
202210.1039/D1GC03798FMohan, M., K. Huang, V. R. Pidatala, B. A. Simmons, S. Singh, K. L. Sale and J. M. GladdenPrediction of solubility parameters of lignin and ionic liquids using multi-resolution simulation approachesGreen Chemistry24(3) 1165–76
202210.1253/circj.CJ-22-0036Minami, T., H. Kawano, T. Yoshimuta, S. Ikeda, C. Otsubo and K. MaemuraNonbacterial thrombotic endocarditis progressed aortic stenosis of a bicuspid aortic valve in a patient with advanced cancerCirculation journal : official journal of the Japanese Circulation Society86(10) 1589
202210.1038/s41467-022-31279-3Mills, C. E., C. Waltmann, A. G. Archer, N. W. Kennedy, C. H. Abrahamson, A. D. Jackson, E. W. Roth, S. Shirman, M. C. Jewett, N. M. Mangan, M. Olvera de la Cruz and D. Tullman-ErcekVertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphologyNature Communications13(1)
202210.1093/genetics/iyac063Michel, K. J., D. C. Lima, H. Hundley, V. Singan, Y. Yoshinaga, C. Daum, K. Barry, K. W. Broman, C. Robin Buell, N. de Leon and S. M. KaepplerGenetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC populationGenetics221(2)
202210.1021/acsestengg.1c00207Michalsen, M. M., F. Kara Murdoch, F. E. Löffler, J. Wilson, P. B. Hatzinger, J. D. Istok, L. Mullins, A. Hill, R. W. Murdoch, C. Condee and K. H. KucharzykQuantitative Proteomics and Quantitative PCR as Predictors of cis-1,2-Dichlorethene and Vinyl Chloride Reductive Dechlorination Rates in Bioaugmented Aquifer MicrocosmsACS ES&T Engineering2(1) 43–53
202210.1128/msystems.00176-22Metcalf, A. J. and N. R. BoyleRhythm of the Night (and Day): Predictive Metabolic Modeling of Diurnal Growth in ChlamydomonasmSystems7(4)
202210.1038/s41597-022-01762-zMeslier, V., B. Quinquis, K. Da Silva, F. Plaza Oñate, N. Pons, H. Roume, M. Podar and M. AlmeidaBenchmarking second and third-generation sequencing platforms for microbial metagenomicsScientific Data9(1) 694
202210.1016/j.biortech.2021.126061Meng, X., C. G. Yoo, Y. Pu and A. J. RagauskasOpportunities and challenges for flow-through hydrothermal pretreatment in advanced biorefineriesBioresource Technology343 126061
202210.1016/j.agrformet.2022.109154Menefee, D., R. L. Scott, M. Abraha, J. G. Alfieri, J. Baker, et al.Unraveling the effects of management and climate on carbon fluxes of U.S. croplands using the USDA Long-Term Agroecosystem (LTAR) networkAgricultural and Forest Meteorology326 109154
202210.34133/2022/9853416Melesse Vergara, M., J. Labbé and J. TannousReflection on the Challenges, Accomplishments, and New Frontiers of Gene DrivesBioDesign Research2022 9853416
202210.1094/MPMI-10-21-0246-AMedrano, E. G. and L. K. PromGenome Sequence Data of Bacillus sp. Strain LP16S, Which Is Capable of Inhibiting the Growth of Multiple Sorghum Fungal PathogensMolecular Plant-Microbe Interactions35(3) 290-292
202210.1128/mra.00874-22McLoon, A. L., T. T. Awad, M. F. Bogardus, M. G. Buono, K. A. Devine, et al.Draft Genome Sequences for 6 Isolates of Endospore-Forming Class Bacilli Species Isolated from Soil from a Suburban, Wooded, Developed SpaceMicrobiology Resource Announcements11(11) e00874-22
202210.3389/fpls.2022.1062264McKinley, B. A., M. Thakran, S. Zemelis-Durfee, X. Huang, F. Brandizzi, W. L. Rooney, S. D. Mansfield and J. E. MulletTranscriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulationFrontiers in Plant Science13
202210.1093/g3journal/jkac295McKenzie, A. M., C. Henry, K. S. Myers, M. M. Place and J. L. KeckIdentification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coliG3 Genes|Genomes|Genetics12(12)
202210.1038/s41396-021-01139-xMcKay, L. J., H. J. Smith, E. P. Barnhart, H. D. Schweitzer, R. R. Malmstrom, D. Goudeau and M. W. FieldsActivity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methaneThe ISME Journal16(4) 915–26
202210.1038/s43705-022-00189-2McDaniel, E. A., J. J. M. van Steenbrugge, D. R. Noguera, K. D. McMahon, J. M. Raaijmakers, M. H. Medema and B. O. OysermanTbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiomeISME Communications2(1) 111
202210.1128/msystems.00372-22McClure, R., Y. Farris, R. Danczak, W. Nelson, H.-S. Song, A. Kessell, J.-Y. Lee, S. Couvillion, C. Henry, J. K. Jansson and K. S. HofmockelInteraction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil MicrobesmSystems7(5) e00372-22
202210.1128/msystems.01037-21McCausland, H. C., K. M. Wetmore, A. P. Arkin and A. KomeiliGlobal Analysis of Biomineralization Genes in Magnetospirillum magneticum AMB-1mSystems7(1) e01037-21
202210.1016/j.nbt.2021.12.003Mazzoli, R., D. G. Olson, A. M. Concu, E. K. Holwerda and L. R. LyndIn vivo evolution of lactic acid hyper-tolerant Clostridium thermocellumNew Biotechnology67 12–22
202210.1088/1748-9326/ac541bMartinez-Feria, R. A., B. Basso and S. KimBoosting climate change mitigation potential of perennial lignocellulosic crops grown on marginal landsEnvironmental Research Letters17(4) 44004
202210.1016/j.jbc.2021.101464Martinez, O. E., B. J. Mahoney, A. K. Goring, S. W. Yi, D. P. Tran, D. Cascio, M. L. Phillips, M. M. Muthana, X. Chen, M. E. Jung, J. A. Loo and R. T. ClubbInsight into the molecular basis of substrate recognition by the wall teichoic acid glycosyltransferase TagAJournal of Biological Chemistry298(2)
202210.1039/D1GC03854KMartinez, D. V., A. Rodriguez, M. A. Juarros, E. J. Martinez, T. M. Alam, B. A. Simmons, K. L. Sale, S. W. Singer and M. S. KentDepolymerization of lignin for biological conversion through sulfonation and a chelator-mediated Fenton reactionGreen Chemistry24(4) 1627–43
202210.3389/fsoil.2022.917885Martin, T. and Christine D. SprungerSensitive Measures of Soil Health Reveal Carbon Stability Across a Management Intensity and Plant Biodiversity GradientFrontiers in Soil Science2
202210.1007/978-981-16-9507-0_11Marqués-Gálvez, J. E., C. Veneault-Fourrey and A. KohlerEctomycorrhizal Symbiosis: From Genomics to Trans-Kingdom Molecular Communication and SignalingMicrobial Cross-talk in the Rhizosphere 273–96
202210.1111/tpj.15669Maqbool, S., M. A. Hassan, X. Xia, L. M. York, A. Rasheed and Z. HeRoot system architecture in cereals: progress, challenges and perspectiveThe Plant Journal110(1) 23–42
202210.1128/mra.00804-22Mandro, J. A., F. M. Nakamura, J. B. Gontijo, S. M. Tsai and A. M. VenturiniMetagenome-Assembled Genomes from Amazonian Soil Microbial ConsortiaMicrobiology Resource Announcements11(11) e00804-22
202210.1128/mra.01097-21Mamphogoro, T. P., C. N. Kamutando, M. M. Maboko, O. O. Babalola and O. A. AiyegoroWhole-Genome Sequence of Paenibacillus polymyxa Strain SRT9.1, a Promising Plant Growth-Promoting BacteriumMicrobiology Resource Announcements11(1) e01097-21
202210.1128/mra.01125-21Mamphogoro, T. P., C. N. Kamutando, M. M. Maboko, O. A. Aiyegoro and O. O. BabalolaDraft Genome Sequence of Sweet Pepper Fruit Epiphyte-Associated Bacillus cereus HRT7.7Microbiology Resource Announcements11(2) e01125-21
202210.1094/mpmi-08-21-0211-rMalvino, M. L., A. J. Bott, C. E. Green, T. Majumdar and S. R. HindInfluence of Flagellin Polymorphisms, Gene Regulation, and Responsive Memory on the Motility of Xanthomonas Species That Cause Bacterial Spot Disease of Solanaceous PlantsMolecular Plant-Microbe Interactions35(2) 157–69
202210.1111/gcbb.12927Malmstrom, C. M., A. K. Busch, E. A. Cole, P. Trebicki, P. Bernardo, A. K. Brown, D. A. Landis and B. P. WerlingEmerging wild virus of native grass bioenergy feedstock is well-established in the Midwestern USA and associated with premature stand senescenceGCB Bioenergy14(4) 463–80
202210.1021/acssuschemeng.2c05327Maitra, S., M. B. Viswanathan, K. Park, B. Kannan, S. C. Alfanar, S. M. McCoy, E. B. Cahoon, F. Altpeter, A. D. B. Leakey and V. SinghBioprocessing, Recovery, and Mass Balance of Vegetative Lipids from Metabolically Engineered “Oilcane” Demonstrates Its Potential as an Alternative Feedstock for Drop-In Fuel ProductionACS Sustainable Chemistry & Engineering10(50) 16833–44
202210.1016/j.jclepro.2022.134383Maitra, S. and V. SinghA consolidated bioprocess design to produce multiple high-value platform chemicals from lignocellulosic biomass and its technoeconomic feasibilityJournal of Cleaner Production377 134383
202210.3389/fenrg.2022.840418Maitra, S., S. P. Long and V. SinghOptimizing Chemical-Free Pretreatment for Maximizing Oil/Lipid Recovery From Transgenic Bioenergy Crops and Its Rapid Analysis Using Time Domain-NMRFrontiers in Energy Research10
202210.21926/cr.2203028Mai Pham, L. T., K. Deng, T. Northen, S. Singer, P. Adams, B. Simmons and K. SaleHeterologous Expression, Characterization, and Comparison of Laccases from the White Rot Causing Basidiomycete Cerrena UnicolorCatalysis Research2(3) 22
202210.1002/prot.26326Mahoney, B. J., A. Takayesu, A. Zhou, D. Cascio and R. T. ClubbThe structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensingProteins: Structure, Function and Bioinformatics90(7) 1457-1467
202210.1186/s12859-022-04829-1Mahmud, S., Z. Guo, F. Quadir, J. Liu and J. ChengMulti-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance mapsBMC Bioinformatics23(1)
202210.3389/fbinf.2022.866850Mageeney, C. M., G. Trubl and K. P. WilliamsImproved Mobilome Delineation in Fragmented GenomesFrontiers in Bioinformatics2
202210.1039/d1ee02540fLynd, L. R., G. T. Beckham, A. M. Guss, L. N. Jayakody, E. M. Karp, et al.Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuelsEnergy & Environmental Science15(3) 938–90
202210.3389/fmicb.2022.822541Lupini, S., J. Peña-Bahamonde, G. Bonito and D. F. RodriguesEffect of Endosymbiotic Bacteria on Fungal Resistance Toward Heavy MetalsFrontiers in Microbiology13
202210.1186/s12896-022-00753-7Luo, G., V. D. Cao, B. Kannan, H. Liu, J. Shanklin and F. AltpeterMetabolic engineering of energycane to hyperaccumulate lipids in vegetative biomassBMC Biotechnology22(1)
202210.1002/prot.26250Lubin, J. H., C. Zardecki, E. M. Dolan, C. Lu, Z. Shen, et al.Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemicProteins: Structure, Function and Bioinformatics90(5) 1054-1080
202210.1111/nph.17892Looney, B., S. Miyauchi, E. Morin, E. Drula, P. E. Courty, et al.Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom-forming fungiNew Phytologist233(5) 2294–309
202210.1016/j.scitotenv.2022.157917Lobato, A., C. O. Souza, W. M. B. S. Martins, R. R. Barata, D. S. Camargo, L. M. G. Dutra, I. C. R. S. Carneiro, C. J. S. Costa and D. M. BrasilienseGenomic characterization of BKC-1–producing Klebsiella pneumoniae strain belonging to high-risk clone sequence type 11 isolated from a river in BrazilScience of The Total Environment850 157917
202210.1021/jacs.1c10975Liu, Z., J. Huang, Y. Gu, D. S. Clark, A. Mukhopadhyay, J. D. Keasling and J. F. HartwigAssembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C_H and C_C BondsJournal of the American Chemical Society144(2) 883–90
202210.34133/2022/9863496Liu, Y., G. Yuan, M. M. Hassan, P. E. Abraham, J. C. Mitchell, et al.Biological and Molecular Components for Genetically Engineering Biosensors in PlantsBioDesign Research2022 9863496
202210.1016/j.soilbio.2021.108541Liu, Y., S. E. Evans, M. L. Friesen and L. K. TiemannRoot exudates shift how N mineralization and N fixation contribute to the plant-available N supply in low fertility soilsSoil Biology and Biochemistry165 108541
202210.1073/pnas.2208795119Liu, W. Y., C. P. Yu, C. K. Chang, H. J. Chen, M. Y. Li, Y. H. Chen, S. H. Shiu, M. S. B. Ku, S. L. Tu, M. Y. J. Lu and W. H. LiRegulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cellsProceedings of the National Academy of Sciences of the United States of America119(35)
202210.1038/s42003-022-03213-2Liu, W., M. Schoonen, T. Wang, S. McSweeney and Q. LiuCryo-EM structure of transmembrane AAA+ protease FtsH in the ADP stateCommunications Biology5(1) 257
202210.1016/B978-0-12-824469-2.00013-0Liu, R., L. Liang, M. P. Lacerda, E. F. Freed and C. A. EckertAdvances in protein engineering and its application in synthetic biologyNew Frontiers and Applications of Synthetic Biology 147–58
202210.1016/B978-0-12-824469-2.00029-4Liu, R., L. Liang, M. Habib, E. F. Freed and C. A. EckertAdvances and application of CRISPR-Cas systemsNew Frontiers and Applications of Synthetic Biology 331–48
202210.1002/prot.26186Liu, J., T. Wu, Z. Guo, J. Hou and J. ChengImproving protein tertiary structure prediction by deep learning and distance prediction in CASP14Proteins: Structure, Function and Bioinformatics90(1) 58-72
202210.1099/ijsem.0.005401Liu, J., J. Li, J. Luo, Y. Li, Z. Yang, C. Huang, F. Sun and G. WangSessilibacter corallicola gen. nov., sp. nov., a sessile bacterium isolated from coral Porites luteaInternational Journal of Systematic and Evolutionary Microbiology72(5)
202210.1016/bs.mie.2022.07.026Liu, H., P. Zhu, Q. Zhang, E. Lam and Q. LiuPlant metacaspase: A case study of microcrystal structure determination and analysisMethods in Enzymology676 103–31
202210.1038/s41598-022-11653-3Liu, H., M. A. Arbing and J. U. BowieExpanding the use of ethanol as a feedstock for cell-free synthetic biochemistry by implementing acetyl-CoA and ATP generating pathwaysScientific Reports12(1)
202210.1093/plphys/kiac588Liu, D., D. Tang, M. Xie, J. Zhang, L. Zhai, et al.Agave REVEILLE1 regulates the onset and release of seasonal dormancy in PopulusPlant Physiology191(3) 1492–504
202210.1080/07388551.2021.1924112Liu, C.-L., K. Xue, Y. Yang, X. Liu, Y. Li, T. S. Lee, Z. Bai and T. TanMetabolic engineering strategies for sesquiterpene production in microorganismCritical Reviews in Biotechnology42(1) 73–92
202210.1016/bs.abr.2022.02.002Liu, C.-J. and A. EudesLignin synthesis and bioengineering approaches toward lignin modificationAdvances in Botanical Research104 41–96
202210.1126/sciadv.adc9440Liu, A. K., J. H. Pereira, A. J. Kehl, D. J. Rosenberg, D. J. Orr, S. K. S. Chu, D. M. Banda, M. Hammel, P. D. Adams, J. B. Siegel and P. M. ShihStructural plasticity enables evolution and innovation of RuBisCO assembliesScience Advances8(34) eadc9440
202210.1002/csc2.20751Lipps, S., W. L. Rooney, S. X. Mideros and T. M. JamannIdentification of quantitative trait loci for sorghum leaf blight resistanceCrop Science62(4) 1550-1558
202210.3390/metabo12040366Linz, A. M., Y. Ma, S. Scholz, D. R. Noguera and T. J. DonohueiNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivoransMetabolites12(4) 366
202210.1186/s13068-022-02226-7Lin, H.-H., D. Mendez_Perez, J. Park, X. Wang, Y. Cheng, J. Huo, A. Mukhopadhyay, T. S. Lee and B. H. ShanksPrecursor prioritization for p-cymene production through synergistic integration of biology and chemistryBiotechnology for Biofuels and Bioproducts15(1) 126
202210.1016/j.mec.2022.e00207Lin, C.-Y., Y. Tian, K. Nelson-Vasilchik, J. Hague, R. Kakumanu, et al.Engineering sorghum for higher 4-hydroxybenzoic acid contentMetabolic Engineering Communications15 e00207
202210.1186/s13068-022-02245-4Lin, C.-Y., G. M. Geiselman, D. Liu, H. D. Magurudeniya, A. Rodriguez, et al.Evaluation of engineered low-lignin poplar for conversion into advanced bioproductsBiotechnology for Biofuels and Bioproducts15(1) 145
202210.1016/j.ymben.2022.04.004Lim, H. G., K. Rychel, A. V. Sastry, G. J. Bentley, J. Mueller, H. S. Schindel, P. E. Larsen, P. D. Laible, A. M. Guss, W. Niu, C. W. Johnson, G. T. Beckham, A. M. Feist and B. O. PalssonMachine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory networkMetabolic Engineering72 297–310
202210.1038/s41587-021-01195-wLiew, F. E., R. Nogle, T. Abdalla, B. J. Rasor, C. Canter, et al.Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scaleNature Biotechnology40(3) 335-344
202210.1038/s41598-022-07387-xLiao, P., T. Lechon, T. Romsdahl, H. Woodfield, S. Fenyk, T. Fawcett, E. Wallington, R. E. Bates, M. L. Chye, K. D. Chapman, J. L. Harwood and S. ScofieldTransgenic manipulation of triacylglycerol biosynthetic enzymes in B. napus alters lipid-associated gene expression and lipid metabolismScientific Reports12(1)
202210.1021/acssuschemeng.2c00948Liang, L., Y.-Y. Wang, S. Bhagia, V. Sethuraman, Z. Yang, et al.Chemical and Morphological Structure of Transgenic Switchgrass Organosolv Lignin Extracted by Ethanol, Tetrahydrofuran, and _-Valerolactone PretreatmentsACS Sustainable Chemistry & Engineering10(28) 9041–52
202210.1107/s2059798321011761Lian, R., B. Huang, L. Wang, Q. Liu, Y. Lin and H. LingEnd-to-end orientation estimation from 2D cryo-EM imagesActa Crystallographica Section D: Structural Biology78(Pt 2) 174–86
202210.1016/j.jmva.2021.104806Li, Y., Y. Qiu and Y. XuFrom multivariate to functional data analysis: Fundamentals, recent developments, and emerging areasJournal of Multivariate Analysis188
202210.1016/j.cub.2022.10.025Li, Y., H. Liu, J. L. Steenwyk, A. L. LaBella, M.-C. Harrison, M. Groenewald, X. Zhou, X.-X. Shen, T. Zhao, C. T. Hittinger and A. RokasContrasting modes of macro and microsynteny evolution in a eukaryotic subphylumCurrent Biology32(24) 5335–43.e4
202210.1021/acs.jafc.2c01306Li, X., S. J. Sarma, L. W. Sumner, A. D. Jones and R. L. LastSwitchgrass Metabolomics Reveals Striking Genotypic and Developmental Differences in Specialized Metabolic PhenotypesJournal of Agricultural and Food Chemistry70(26) 8010–23
202210.1111/pce.14433Li, S., C. A. Moller, N. G. Mitchell, D. G. Martin, E. J. Sacks, S. Saikia, N. R. Labonte, B. S. Baldwin, J. I. Morrison, J. N. Ferguson, A. D. B. Leakey and E. A. AinsworthThe leaf economics spectrum of triploid and tetraploid C4 grass Miscanthus x giganteusPlant, Cell & Environment45(12) 3462–75
202210.1111/gcb.16108Li, S., C. A. Moller, N. G. Mitchell, D. Lee, E. J. Sacks and E. A. AinsworthTesting unified theories for ozone response in C4 speciesGlobal Change Biology28(10) 3379–93
202210.1039/d1gc03625dLi, M., Y. Pu, X. Meng, F. Chen, R. A. Dixon and A. J. RagauskasStrikingly high amount of tricin-lignin observed from vanilla (Vanilla planifolia) aerial rootsGreen Chemistry24(1) 259–70
202210.1016/j.cj.2022.04.005Li, J., D. P. Schachtman, C. F. Creech, L. Wang, Y. Ge and Y. ShiEvaluation of UAV-derived multimodal remote sensing data for biomass prediction and drought tolerance assessment in bioenergy sorghumCrop Journal
202210.1021/acs.iecr.2c01163Li, J., C. T. Maravelias and R. C. Van LehnAdaptive Conformer Sampling for Property Prediction Using the Conductor-like Screening Model for Real SolventsIndustrial & Engineering Chemistry Research61(25) 9025–36
202210.1016/j.biotechadv.2021.107809Leynaud Kieffer Curran, L. M. C., L. T. M. Pham, K. L. Sale and B. A. SimmonsReview of advances in the development of laccases for the valorization of lignin to enable the production of lignocellulosic biofuels and bioproductsBiotechnology Advances54 107809
202210.1073/pnas.2116637119Lewin, G. R., K. S. Stocke, R. J. Lamont and M. WhiteleyA quantitative framework reveals traditional laboratory growth is a highly accurate model of human oral infectionProceedings of the National Academy of Sciences119(2) e2116637119
202210.1128/msystems.01519-21Lewin, G. R., N. M. Davis, B. R. McDonald, A. J. Book, M. G. Chevrette, S. Suh, A. Boll and C. R. CurrieLong-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goodsmSystems7(2)
202210.5194/soil-8-85-2022Levintal, E., Y. Ganot, G. Taylor, P. Freer-Smith, K. Suvocarev and H. E. DahlkeAn underground, wireless, open-source, low-cost system for monitoring oxygen, temperature, and soil moistureSOIL8(1) 85-97
202210.3389/frans.2022.1020111Lenz, R. R., H. K. Shrestha, A. A. Carrell, J. Labbé, R. L. Hettich, P. E. Abraham and J. M. LeBoldusProteomics reveals pathways linked to septoria canker resistance and susceptibility in Populus trichocarpaFrontiers in Analytical Science2
202210.1021/acs.jafc.2c04251Lee, Y.-G., C. Kim, N. Kuanyshev, N. K. Kang, Z. Fatma, Z.-Y. Wu, M.-H. Cheng, V. Singh, Y. Yoshikuni, H. Zhao and Y.-S. JinCas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic HydrolysatesJournal of Agricultural and Food Chemistry70(38) 12085–94
202210.1007/s12257-022-0217-3Lee, Y.-G., Y. Ju, L. Sun, S. Park, Y.-S. Jin and S. R. KimAcetate-rich Cellulosic Hydrolysates and Their Bioconversion Using YeastsBiotechnology and Bioprocess Engineering27(6) 890–9
202210.1007/s12275-022-1647-5Lee, S.-Y., P. S. Kim, H. Sung, D.-W. Hyun and J.-W. BaeLysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental storkJournal of Microbiology60(5) 469–77
202210.1111/gcbb.12899Lee, M. S., R. A. Boyd and D. R. OrtThe photosynthetic response of C3 and C4 bioenergy grass species to fluctuating lightGCB Bioenergy14(1) 37-53
202210.3389/fmicb.2022.849573Lee, J. A., S. Stolyar and C. J. MarxAerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by MethylobacteriaceaeFrontiers in Microbiology13
202210.1016/j.ymben.2021.12.001Lee, J.-W. and C. T. TrinhControlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer estersMetabolic Engineering69 262–74
202210.7554/eLife.76968Larue, T., H. Lindner, A. Srinivas, M. Exposito-Alonso, G. Lobet and J. R. DinnenyUncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platformeLife11
202210.1073/pnas.2101084119Lark, T. J., N. P. Hendricks, A. Smith, N. Pates, S. A. Spawn-Lee, M. Bougie, E. G. Booth, C. J. Kucharik and H. K. GibbsEnvironmental outcomes of the US Renewable Fuel StandardProceedings of the National Academy of Sciences119(9) e2101084119
202210.1128/mmbr.00041-22Lankiewicz, T. S., S. P. Lillington and M. A. O’MalleyEnzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery InnovationMicrobiology and Molecular Biology Reviews86(4) e00041-22
202210.1128/AEM.01531-21Lanahan, A., K. Zakowicz, L. Tian, D. G. Olson and L. R. LyndA Single Nucleotide Change in the polC DNA Polymerase III in Clostridium thermocellum Is Sufficient To Create a Hypermutator PhenotypeApplied and Environmental Microbiology88(1) e01531-21
202210.1111/gcb.16103Lamour, J., K. J. Davidson, K. S. Ely, G. Le Moguédec, A. D. B. Leakey, Q. Li, S. P. Serbin and A. RogersAn improved representation of the relationship between photosynthesis and stomatal conductance leads to more stable estimation of conductance parameters and improves the goodness-of-fit across diverse data setsGlobal Change Biology28(11) 3537-3556
202210.1111/gcbb.12907Lamb, A., B. Weers, B. McKinley, W. Rooney, C. Morgan, A. Marshall-Colon and J. MulletBioenergy sorghum’s deep roots: A key to sustainable biomass production on annual croplandGCB Bioenergy14(2) 132–56
202210.1016/j.tplants.2021.11.014Lam, E. and T. P. MichaelWolffia, a minimalist plant and synthetic biology chassisTrends in Plant Science27(5) 430-439
202210.1007/978-1-0716-2233-9_5Lal, P. B., F. Wells and P. J. KileyCreation of Markerless Genome Modifications in a Nonmodel Bacterium by Fluorescence-Aided RecombineeringRecombineering: Methods and Protocols 53–70
202210.1371/journal.pgen.1010270Lakey, B. D., K. S. Myers, F. Alberge, E. L. Mettert, P. J. Kiley, D. R. Noguera and T. J. DonohueThe essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesisPLoS Genetics18(6) e1010270
202210.1094/pbiomes-02-22-0007-rLagergren, J., M. Cashman, V. Melesse Vergara, P. Eller, J. G. F. M. Gazolla, H. Chhetri, J. Streich, S. Climer, P. Thornton, W. Joubert and D. JacobsonClimatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemicsPhytobiomes Journal
202210.1038/s41467-022-32829-5LaFleur, T. L., A. Hossain and H. M. SalisAutomated model-predictive design of synthetic promoters to control transcriptional profiles in bacteriaNature Communications13(1)
202210.1016/j.ygeno.2022.01.003Kumaran, S., A. C. R. Ngo, F. P. J. Schultes, V. S. Saravanan and D. TischlerIn vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.Genomics114(2) 110266
202210.1128/aem.01857-21Kuil, T., S. Hon, J. Yayo, C. Foster, G. Ravagnan, C. D. Maranas, L. R. Lynd, D. G. Olson and A. J. A. v. MarisFunctional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellumApplied and Environmental Microbiology88(4) e01857-21
202210.1186/s13068-022-02110-4Kubis, M. R., E. K. Holwerda and L. R. LyndDeclining carbohydrate solubilization with increasing solids loading during fermentation of cellulosic feedstocks by Clostridium thermocellum: documentation and diagnostic testsBiotechnology for Biofuels and Bioproducts15(1) 12
202210.1016/j.ymben.2021.12.010Kuatsjah, E., C. W. Johnson, D. Salvachúa, A. Z. Werner, M. Zahn, et al.Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarateMetabolic Engineering70 31–42
202210.1094/pbiomes-12-21-0076-rKristy, B., A. A. Carrell, E. Johnston, J. R. Cumming, D. M. Klingeman, K. Gwinn, K. C. Syring, C. Skalla, S. Emrich and M. A. CreggerChronic Drought Differentially Alters the Belowground Microbiome of Drought-Tolerant and Drought-Susceptible Genotypes of Populus trichocarpaPhytobiomes Journal6(4) 317–30
202210.1021/acs.est.2c05403Kravchenko, A. N., J. A. Richardson, J. H. Lee and A. K. GuberDistribution of Mn Oxidation States in Grassland Soils and Their Relationships with Soil PoresEnvironmental Science & Technology56(22) 16462–72
202210.1093/molbev/msac202Krause, D. J. and C. T. HittingerFunctional Divergence in a Multi-gene Family Is a Key Evolutionary Innovation for Anaerobic Growth in Saccharomyces cerevisiaeMolecular Biology and Evolution39(10) msac202
202210.1080/03772063.2020.1739571Koteswara Rao, S.Bearings-only Passive Target Tracking: Range Uncertainty Ellipse ZoneIETE Journal of Research68(4) 2968-2978
202210.17776/csj.1195087Korkmaz, E. M.The Complete Mitogenome of Redheaded Pine Sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae): Duplication of trnR Gene and Rearrangement in the ARNS1EF Gene ClusterCumhuriyet Science Journal43(4) 577–83
202210.1080/10643389.2021.2024484Kopittke, P. M., A. A. Berhe, Y. Carrillo, T. R. Cavagnaro, D. Chen, et al.Ensuring planetary survival: the centrality of organic carbon in balancing the multifunctional nature of soilsCritical Reviews in Environmental Science and Technology52(23) 4308–24
202210.1016/bs.mie.2022.07.034Koper, K., S. Hataya, A. G. Hall, T. E. Takasuka and H. A. MaedaBiochemical characterization of plant aromatic aminotransferasesMethods in Enzymology
202210.1016/j.jbc.2022.102122Koper, K., S. W. Han, D. C. Pastor, Y. Yoshikuni and H. A. MaedaEvolutionary origin and functional diversification of aminotransferasesJournal of Biological Chemistry298(8)
202210.1128/mra.00294-22Kono, M., J. N. Martinez, T. Sato and S. HarutaDraft Genome Sequence of the Thermophilic Unicellular Cyanobacterium Synechococcus sp. Strain C9Microbiology Resource Announcements11(8) e00294-22
202210.1038/s41477-022-01150-wKo, D. K. and F. BrandizziTranscriptional competition shapes proteotoxic ER stress resolutionNature Plants8(5) 481–90
202210.1038/s42003-021-02964-8Ko, D. K. and F. BrandizziAdvanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thalianaCommunications Biology5(1) 16
202210.1128/aem.02280-21Kittredge, H. A., K. M. Dougherty and S. E. EvansDead but Not Forgotten: How Extracellular DNA, Moisture, and Space Modulate the Horizontal Transfer of Extracellular Antibiotic Resistance Genes in SoilApplied and Environmental Microbiology88(7) e02280-21
202210.1007/978-1-0716-1585-0_10Kimbrel, J. A., B. M. Jeffrey and C. S. WardProkaryotic Genome AnnotationMicrobial Systems Biology: Methods and Protocols 193–214
202210.1016/j.biocontrol.2022.104920Kim, T. N., Y. V. Bukhman, M. A. Jusino, E. D. Scully, B. J. Spiesman and C. GrattonUsing high-throughput amplicon sequencing to determine diet of generalist lady beetles in agricultural landscapesBiological Control170 104920
202210.3389/fmicb.2022.940610Kim, S. R., C. A. Eckert and R. MazzoliEditorial: Microorganisms for Consolidated 2nd Generation BiorefiningFrontiers in Microbiology13 940610
202210.1016/j.soilbio.2022.108565Kim, K., J. Gil, N. E. Ostrom, H. Gandhi, M. S. Oerther, Y. Kuzyakov, A. K. Guber and A. N. KravchenkoSoil pore architecture and rhizosphere legacy define N2O production in root detritusphereSoil Biology and Biochemistry166 108565
202210.1038/s41396-021-01147-xKim, H., J. A. Kimbrel, C. A. Vaiana, J. R. Wollard, X. Mayali and C. R. BuieBacterial response to spatial gradients of algal-derived nutrients in a porous microplateThe ISME Journal16(4) 1036–45
202210.1111/mec.16717Kiefer, J. S. T., G. Schmidt, R. Krüsemer, M. Kaltenpoth and T. EnglWolbachia causes cytoplasmic incompatibility but not male-killing in a grain pest beetleMolecular Ecology31(24) 6570–87
202210.1016/j.soilbio.2022.108610Khosrozadeh, S., A. Guber, A. Kravchenko, N. Ghaderi and E. BlagodatskayaSoil oxidoreductase zymography: Visualizing spatial distributions of peroxidase and phenol oxidase activities at the root-soil interfaceSoil Biology and Biochemistry167 108610
202210.1111/1467-8489.12461Khanna, M. and R. MiaoInducing the adoption of emerging technologies for sustainable intensification of food and renewable energy production: insights from applied economicsAustralian Journal of Agricultural and Resource Economics66(1) 1–23
202210.1016/j.mib.2021.11.007Khana, D. B., M. M. Callaghan and D. Amador-NoguezNovel computational and experimental approaches for investigating the thermodynamics of metabolic networksCurrent Opinion in Microbiology66 21–31
202210.1007/s10529-021-03206-xKhan, J. A., A. M. Guss and K. C. KaoEnhancing transcription in Escherichia coli and Pseudomonas putida using bacteriophage lambda anti-terminator protein QBiotechnology Letters44(2) 253–8
202210.3389/fmicb.2022.847563Kevorkian, R. T., K. Sipes, R. Winstead, R. Paul and K. G. LloydCryptic Methane-Cycling by Methanogens During Multi-Year Incubation of Estuarine SedimentFrontiers in Microbiology13
202210.1039/D2RE00275BKenny, J. K., D. G. Brandner, S. R. Neefe, W. E. Michener, Y. Román-Leshkov, G. T. Beckham and J. W. MedlinCatalyst choice impacts aromatic monomer yields and selectivity in hydrogen-free reductive catalytic fractionationReaction Chemistry & Engineering7 2527–33
202210.3389/fevo.2022.833170Kemmerling, L. R., C. E. Rutkoski, S. E. Evans, J. A. Helms, E. S. Cordova-Ortiz, J. D. Smith, J. A. Vázquez Custodio, C. Vizza and N. M. HaddadPrairie Strips and Lower Land Use Intensity Increase Biodiversity and Ecosystem ServicesFrontiers in Ecology and Evolution10
202210.1038/s41467-022-29603-yKellogg, R. M., M. A. Moosburner, N. R. Cohen, N. J. Hawco, M. R. McIlvin, D. M. Moran, G. R. DiTullio, A. V. Subhas, A. E. Allen and M. A. SaitoAdaptive responses of marine diatoms to zinc scarcity and ecological implicationsNature Communications13(1)
202210.1186/s40168-022-01343-7Keller-Costa, T., L. Kozma, S. G. Silva, R. Toscan, J. Gonçalves, A. Lago-Lestón, N. C. Kyrpides, U. Nunes da Rocha and R. CostaMetagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiomeMicrobiome10(1) 151
202210.1021/acssynbio.1c00367Kassaw, T. K., A. J. Paton and G. PeersEpisome-Based Gene Expression Modulation Platform in the Model Diatom Phaeodactylum tricornutumACS Synthetic Biology11(1) 191-204
202210.1007/s10021-022-00758-5Kashi, N. N., E. A. Hobbie, R. K. Varner, A. S. Wymore, J. G. Ernakovich and R. GieslerNutrients Alter Methane Production and Oxidation in a Thawing Permafrost MireEcosystems
202210.1016/j.virusres.2022.198902Karaynir, A., H. Salih, B. Bozdo_an, Ö. Güçlü and D. KeskinIsolation and characterization of Brochothrix phage ADU4Virus Research321 198902
202210.1111/1462-2920.15871Karasz, D. C., A. I. Weaver, D. H. Buckley and R. C. WilhelmConditional filamentation as an adaptive trait of bacteria and its ecological significance in soilsEnvironmental Microbiology24(1) 1–17
202210.1111/gcbb.12940Kantola, I. B., M. D. Masters, E. Blanc-Betes, N. Gomez-Casanovas and E. H. DeLuciaLong-term yields in annual and perennial bioenergy crops in the Midwestern United StatesGCB Bioenergy14(6) 694–706
202210.1038/s41396-021-01062-1Kang-Yun, C. S., X. Liang, P. Dershwitz, W. Gu, A. Schepers, et al.Evidence for methanobactin “Theft” and novel chalkophore production in methanotrophs: impact on methanotrophic-mediated methylmercury degradationISME Journal16(1) 211-220
202210.1128/mra.00188-22Kang-Yun, C. S., J. Chang and J. D. SemrauUpdated Genome Sequence of the Facultative Methanotroph Methylocystis sp. Strain SB2Microbiology Resource Announcements11(6)
202210.1002/biot.202000431Kang, N. K., J. W. Lee, D. R. Ort and Y.-S. JinL-malic acid production from xylose by engineered Saccharomyces cerevisiaeBiotechnology Journal17(3) 2000431
202210.1016/j.cej.2021.133636Kang, N. K., M. Kim, K. Baek, Y. K. Chang, D. R. Ort and Y. S. JinPhotoautotrophic organic acid production: Glycolic acid production by microalgal cultivationChemical Engineering Journal433
202210.1111/nph.18281Kakouridis, A., J. A. Hagen, M. P. Kan, S. Mambelli, L. J. Feldman, D. J. Herman, P. K. Weber, J. Pett-Ridge and M. K. FirestoneRoutes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plantsNew Phytologist236(1) 210-221
202210.1111/gcbb.12914Juice, S. M., C. A. Walter, K. E. Allen, D. M. Berardi, T. W. Hudiburg, B. N. Sulman and E. R. BrzostekA new bioenergy model that simulates the impacts of plant-microbial interactions, soil carbon protection, and mechanistic tillage on soil carbon cyclingGCB Bioenergy14(3) 346–63
202210.1002/pro.4252Joyner, P. M., D. P. Tran, M. A. Zenaidee and J. A. LooCharacterization of protein–ligand binding interactions of enoyl-ACP reductase (FabI) by native MS reveals allosteric effects of coenzymes and the inhibitor triclosanProtein Science31(3) 568-579
202210.1038/s41596-021-00675-2Jones, T. S., S. M. D. Oliveira, C. J. Myers, C. A. Voigt and D. DensmoreGenetic circuit design automation with Cello 2.0Nature Protocols17(4) 1097-1113
202210.3389/fpls.2022.943585Johnston, C., L. T. García Navarrete, E. Ortiz, T. B. Romsdahl, A. Guzha, K. D. Chapman, E. Grotewold and A. P. AlonsoEffective Mechanisms for Improving Seed Oil Production in Pennycress (Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and TranscriptomicsFrontiers in Plant Science13
202210.1186/s12864-022-08797-xJohnson, A. C., T. H. Pendergast, S. Chaluvadi, J. L. Bennetzen and K. M. DevosIdentification of microRNAs responsive to arbuscular mycorrhizal fungi in Panicum virgatum (switchgrass)BMC Genomics23(1) 688
202210.1038/s41586-022-04670-9Jiang, Y. X., Q. Cao, M. R. Sawaya, R. Abskharon, P. Ge, M. DeTure, D. W. Dickson, J. Y. Fu, R. R. Ogorzalek Loo, J. A. Loo and D. S. EisenbergAmyloid fibrils in FTLD-TDP are composed of TMEM106B and not TDP-43Nature605(7909) 304-309
202210.3390/pr10040661Jia, Y., D. Kumar, J. K. Winkler-Moser, B. Dien, K. Rausch, M. E. Tumbleson and V. SinghCoprocessing Corn Germ Meal for Oil Recovery and Ethanol Production: A Process Model for Lipid-Producing Energy CropsProcesses10(4) 661
202210.1038/s41598-022-15388-zJedrzejczyk, D. J., L. D. Poulsen, M. Mohr, N. D. Damas, S. Schoffelen, A. Barghetti, R. Baumgartner, B. T. Weinert, T. Warnecke and R. T. GillCRISPR-Cas12a nucleases function with structurally engineered crRNAs: SynThetic trAcrRNAScientific Reports12(1)
202210.1016/j.coche.2022.100796Je, L., G. W. Huber, R. C. Van Lehn and V. M. ZavalaOn the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysisCurrent Opinion in Chemical Engineering36 100796
202210.1111/pce.14464Jardine, K. J., R. A. Dewhirst, S. Som, J. Lei, E. Tucker, R. P. Young, M. Portillo-Estrada, Y. Gao, L. Su, S. Fares, C. Castanha, H. V. Scheller and J. C. MortimerCell wall ester modifications and volatile emission signatures of plant response to abiotic stressPlant, Cell & Environment45(12) 3429–44
202210.1016/j.joule.2022.06.016Jang, J. H., D. G. Brandner, R. J. Dreiling, A. J. Ringsby, J. R. Bussard, L. M. Stanley, R. M. Happs, A. S. Kovvali, J. I. Cutler, T. Renders, J. R. Bielenberg, Y. Román-Leshkov and G. T. BeckhamMulti-pass flow-through reductive catalytic fractionationJoule6(8) 1859–75
202210.1128/mra.00050-22Jagtap, S. S., J.-J. Liu, H. E. Walukiewicz, J. Pangilinan, A. Lipzen, et al.Near-Complete Genome Sequence of Zygosaccharomyces rouxii NRRL Y-64007, a Yeast Capable of Growing on Lignocellulosic HydrolysatesMicrobiology Resource Announcements11(5) e00050-22
202210.1021/acsnano.1c06343Jackson, C. T., J. W. Wang, E. González-Grandío, N. S. Goh, J. Mun, S. Krishnan, F. L. Geyer, H. Keller, S. Ebert, K. Molawi, N. Kaiser and M. P. LandryPolymer-Conjugated Carbon Nanotubes for Biomolecule LoadingACS Nano16(2) 1802-1812
202210.1038/s41378-022-00357-3Iwai, K., M. Wehrs, M. Garber, J. Sustarich, L. Washburn, Z. Costello, P. W. Kim, D. Ando, W. R. Gaillard, N. J. Hillson, P. D. Adams, A. Mukhopadhyay, H. Garcia Martin and A. K. SinghScalable and automated CRISPR-based strain engineering using droplet microfluidicsMicrosystems & Nanoengineering8(1) 31
202210.1128/mra.00292-22Ingle, A. T., N. W. Fortney, K. S. Myers, K. A. Walters, M. J. Scarborough, T. J. Donohue and D. R. NogueraMetagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure HydrolysateMicrobiology Resource Announcements11(8) e00292-22
202210.1111/tpj.15903Huß, S., R. S. Judd, K. Koper, H. A. Maeda and Z. NikoloskiAn automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thalianaPlant Journal111(5) 1486-1500
202210.1002/bit.28155Hunt, K. A., F. von Netzer, D. Gorman-Lewis and D. A. StahlMicrobial maintenance energy quantified and modeled with microcalorimetryBiotechnology and Bioengineering119(9) 2413–22
202210.1111/tpj.15867Hui, C., S. Schmollinger, D. Strenkert, K. Holbrook, H. R. Montgomery, S. Chen, H. M. Nelson, P. K. Weber and S. S. MerchantSimple steps to enable reproducibility: culture conditions affecting Chlamydomonas growth and elemental compositionThe Plant Journal111(4) 995–1014
202210.1128/mra.00471-22Huang, Y., M. K. Nobu, K. Igarashi and S. KatoDraft Genome Sequence of the Alkaliphilic, Lithoautotrophic Homoacetogen Fuchsiella alkaliacetigena Z-7100TMicrobiology Resource Announcements11(8) e00471-22
202210.1038/s41477-022-01146-6Huang, X., W. Wang, T. Gong, D. Wickell, L.-Y. Kuo, et al.The flying spider-monkey tree fern genome provides insights into fern evolution and arborescenceNature Plants8(5) 500–12
202210.1038/s41929-022-00777-4Huang, X., J. Feng, J. Cui, G. Jiang, W. Harrison, X. Zang, J. Zhou, B. Wang and H. ZhaoPhotoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate additionNature Catalysis5 586–93
202210.1094/mpmi-09-21-0234-rHuang, R., H. Feng, Z. Xu, N. Zhang, Y. Liu, J. Shao, Q. Shen and R. ZhangIdentification of Adhesins in Plant Beneficial Rhizobacteria Bacillus velezensis SQR9 and Their Effect on Root ColonizationMolecular Plant-Microbe Interactions35(1) 64–72
202210.1016/j.molcel.2022.04.020Huang, C. J., B. A. Adler and J. A. DoudnaA naturally DNase-free CRISPR-Cas12c enzyme silences gene expressionMolecular Cell82(11) 2148-2160.e4
202210.1016/j.rser.2021.111822Huang, C., X. Jiang, X. Shen, J. Hu, W. Tang, X. Wu, A. Ragauskas, H. Jameel, X. Meng and Q. YongLignin-enzyme interaction: A roadblock for efficient enzymatic hydrolysis of lignocellulosicsRenewable and Sustainable Energy Reviews154 111822
202210.1093/hr/uhac043Hu, X.-L., J. Zhang, R. Kaundal, R. Kataria, J. L. Labbé, J. C. Mitchell, T. J. Tschaplinski, G. A. Tuskan, Z.-M. Cheng and X. YangDiversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosisHorticulture Research9 uhac043
202210.1111/tpj.15674Hu, S., N. Kamimura, S. Sakamoto, S. Nagano, N. Takata, et al.Rerouting of the lignin biosynthetic pathway by inhibition of cytosolic shikimate recycling in transgenic hybrid aspenThe Plant Journal110(2) 358–76
202210.1016/j.jplph.2022.153791Hu, R., J. Zhang, S. Jawdy, A. Sreedasyam, A. Lipzen, et al.Comparative genomics analysis of drought response between obligate CAM and C3 photosynthesis plantsJournal of Plant Physiology277 153791
202210.1111/biom.13624Hu, H. and Y. QiuInference for nonparanormal partial correlation via regularized rank-based nodewise regressionBiometrics
202210.3389/fbinf.2021.826370Hu, B., S. Canon, E. A. Eloe-Fadrosh, Anubhav, M. Babinski, et al.Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at ScaleFrontiers in Bioinformatics1
202210.1038/s41587-021-01146-5Hsu, C., H. Nisonoff, C. Fannjiang and J. ListgartenLearning protein fitness models from evolutionary and assay-labeled dataNature Biotechnology40(7) 1114–22
202210.1080/19390211.2022.2120146Hove, P. R., N. J. Nealon, S. H. J. Chan, S. M. Boyer, H. B. Haberecht and E. P. RyanIntegrated Profiling of Gram-Positive and Gram-Negative Probiotic Genomes, Proteomes and Metabolomes Revealed Small Molecules with Differential Growth Inhibition of Antimicrobial-Resistant PathogensJournal of Dietary Supplements1–23
202210.1111/gcb.15970Hough, M., S. McCabe, S. R. Vining, E. Pickering Pedersen, R. M. Wilson, et al.Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatlandGlobal Change Biology28(3) 950-968
202210.3389/fmicb.2022.915291Houfani, A. A., M. Basen, D. G. Olson and S. E. Blumer-SchuetteExtremophiles in Lignocellulose DegradationFrontiers in Microbiology13 915291
202210.1128/aem.01258-22Hon, S., T. Jacobson, D. M. Stevenson, M. I. Maloney, R. J. Giannone, R. L. Hettich, D. Amador-Noguez, D. G. Olson and L. R. LyndIncreasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in Clostridium thermocellumApplied and Environmental Microbiology88(22) e01258-22
202210.1029/2021GB007113Holmes, M. E., P. M. Crill, W. C. Burnett, C. K. McCalley, R. M. Wilson, S. Frolking, K. Y. Chang, W. J. Riley, R. K. Varner, S. B. Hodgkins, A. P. McNichol, S. R. Saleska, V. I. Rich and J. P. ChantonCarbon accumulation, flux, and fate in stordalen mire, a permafrost peatland in transitionGlobal Biogeochemical Cycles36(1)
202210.3791/63269Hoffman, S. M., M. A. Lalwani and J. L. AvalosLight-controlled fermentations for microbial chemical and protein productionJournal of Visualized Experiments2022(181)
202210.1126/sciadv.abo5738Hoengenaert, L., M. Wouters, H. Kim, B. De Meester, K. Morreel, S. Vandersyppe, J. Pollier, S. Desmet, G. Goeminne, J. Ralph, W. Boerjan and R. VanholmeOverexpression of the scopoletin biosynthetic pathway enhances lignocellulosic biomass processingScience Advances8(28) eabo5738
202210.1016/j.micres.2022.127109Hinenoya, A., H. Wang, E. M. Patrick, X. Zeng, L. Cao, X.-P. Li, R. L. Lindsey, B. Gillespie, Q. He, S. Yamasaki and J. LinLongitudinal surveillance and comparative characterization of Escherichia albertii in wild raccoons in the United StatesMicrobiological Research262 127109
202210.1111/nph.17825Hill, R. A., J. Wong-Bajracharya, S. Anwar, D. Coles, M. Wang, A. Lipzen, V. Ng, I. V. Grigoriev, F. Martin, I. C. Anderson, C. I. Cazzonelli, T. Jeffries, K. L. Plett and J. M. PlettAbscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpusNew Phytologist233(2) 966–82
202210.1038/s41396-022-01308-6Hestrin, R., M. Kan, M. Lafler, J. Wollard, J. A. Kimbrel, P. Ray, S. J. Blazewicz, R. Stuart, K. Craven, M. Firestone, E. E. Nuccio and J. Pett-RidgePlant-associated fungi support bacterial resilience following water limitationThe ISME Journal16(12) 2752–62
202210.1128/jb.00078-22Heryakusuma, C., D. Susanti, H. Yu, Z. Li, E. Purwantini, R. L. Hettich, V. J. Orphan and B. MukhopadhyayA Reduced F420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic ArchaeonJournal of Bacteriology204(7)
202210.3390/ijms23116070Hengge, N. N., S. J. B. Mallinson, P. Pason, V. V. Lunin, M. Alahuhta, D. Chung, M. E. Himmel, J. Westpheling and Y. J. BombleCharacterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticusInternational Journal of Molecular Sciences23(11) 6070
202210.1093/plphys/kiac485Hellinger, J., H. Kim, J. Ralph and S. D. Karlenp-Coumaroylation of lignin occurs outside of commelinid monocots in the eudicot genus Morus (mulberry)Plant Physiology191(2) 854–61
202210.3390/pr10010041He, Q. P. and J. WangSpecial issue on “big data in biology, life sciences and healthcare”Processes10(1)
202210.3390/metabo12040314He, B., C. Cai, T. McCubbin, J. C. Muriel, N. Sonnenschein, S. Hu, Z. Yuan and E. MarcellinA Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic FeasibilityMetabolites12(4) 314
202210.1128/mra.00216-22Hawkins, J. P., P. A. Ordonez and I. J. OresnikComplete Genome Sequences of Rhizobium gallicum M101 and Two Potential New Rhizobium Species Isolated from Soils in Central CanadaMicrobiology Resource Announcements11(7) e00216-22
202210.1002/biot.202100673Hassan, M. M., G. Yuan, Y. Liu, M. Alam, C. A. Eckert, G. A. Tuskan, J. F. Golz and X. YangPrecision genome editing in plants using gene targeting and prime editing: Existing and emerging strategiesBiotechnology Journal2100673
202210.1002/ecs2.4292Hartman, M. D., M. Burnham, W. J. Parton, A. Finzi, E. H. DeLucia and W. H. YangIn silico evaluation of plant nitrification suppression effects on agroecosystem nitrogen lossEcosphere13(12) e4292
202210.1021/acs.accounts.1c00719Harrison, W., X. Huang and H. ZhaoPhotobiocatalysis for Abiological TransformationsAccounts of Chemical Research55(8) 1087–96
202210.1016/j.tig.2021.08.013Harrison, M.-C., A. L. LaBella, C. T. Hittinger and A. RokasThe evolution of the GALactose utilization pathway in budding yeastsTrends in Genetics38(1) 97–106
202210.3389/fpls.2022.757810Harman-Ware, A. E., R. M. Happs, D. Macaya-Sanz, C. Doeppke, W. Muchero and S. P. DiFazioAbundance of Major Cell Wall Components in Natural Variants and Pedigrees of Populus trichocarpaFrontiers in Plant Science13
202210.1038/s41467-022-34585-yHarding, K. J., K. A. Turk-Kubo, E. W. K. Mak, P. K. Weber, X. Mayali and J. P. ZehrCell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical GyreNature Communications13(1) 6979
202210.1038/s42003-022-03157-7Hao, Z., Y. Wang, N. Ding, M. C. Saha, W. R. Scheible, K. Craven, M. Udvardi, P. S. Nico, M. K. Firestone and E. L. BrodieSpectroscopic analysis reveals that soil phosphorus availability and plant allocation strategies impact feedstock quality of nutrient-limited switchgrassCommunications Biology5(1)
202210.1016/j.mib.2022.102172Han, S. W. and Y. YoshikuniMicrobiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbesCurrent Opinion in Microbiology68
202210.1021/acssynbio.2c00386Halvorsen, T. M., D. P. Ricci, D. M. Park, Y. Jiao and M. C. YungComparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and EscapeACS Synthetic Biology11(11) 3785–96
202210.1016/j.bioflm.2022.100088Halsted, M. C., A. N. Bible, J. L. Morrell-Falvey and S. T. RettererQuantifying biofilm propagation on chemically modified surfacesBiofilm4 100088
202210.1021/acs.biochem.2c00367Hallberg, Z. F., E. C. Seth, K. Thevasundaram and M. E. TagaComparative Analysis of Corrinoid Profiles across Host-Associated and Environmental SamplesBiochemistry
202210.1038/s41598-022-12435-7Halder, U., R. Biswas, A. Kabiraj, R. Deora, M. Let, et al.Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soilScientific Reports12(1) 8439
202210.1038/s43705-022-00113-8Gushgari-Doyle, S., L. M. Lui, T. N. Nielsen, X. Wu, R. G. Malana, A. J. Hendrickson, H. Carion, F. L. Poole, M. W. W. Adams, A. P. Arkin and R. ChakrabortyGenotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditionsISME Communications2(1) 32
202210.1016/j.soilbio.2022.108633Guber, A., E. Blagodatskaya and A. KravchenkoAre enzymes transported in soils by water fluxes?Soil Biology and Biochemistry168 108633
202210.1186/s12870-022-03823-2Grzybowski, M. W., M. Zwiener, H. Jin, N. K. Wijewardane, A. Atefi, M. J. Naldrett, S. Alvarez, Y. Ge and J. C. SchnableVariation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panelBMC Plant Biology22(1)
202210.1186/s40168-022-01231-0Gregory, A. C., K. Gerhardt, Z. P. Zhong, B. Bolduc, B. Temperton, K. T. Konstantinidis and M. B. SullivanMetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populationsMicrobiome10(1)
202210.1128/msystems.00417-22Greenlon, A., E. Sieradzki, O. Zablocki, B. J. Koch, M. M. Foley, et al.Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland EcosystemsmSystems7(6) e00417-22
202210.1007/s10533-021-00851-2Graham, E. B. and K. S. HofmockelEcological stoichiometry as a foundation for omics-enabled biogeochemical models of soil organic matter decompositionBiogeochemistry157(1) 31–50
202210.1099/ijsem.0.005456Grabowski, S., E. A. Apolinario, N. O. Schneider, C. W. Marshall and K. SowersDethiosulfovibrio faecalis sp. nov., a novel proteolytic, non-sulphur-reducing bacterium isolated from a marine aquaculture solid waste bioreactorInternational Journal of Systematic and Evolutionary Microbiology72(8)
202210.1038/s41388-022-02424-5Goodsell, D. S., S. Dutta, M. Voigt, C. Zardecki and S. K. BurleyMolecular explorations of cancer biology and therapeutics at PDB-101Oncogene41(38) 4333-4335
202210.1016/j.str.2021.10.008Goodsell, D. S. and S. K. BurleyRCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogensStructure30(1) 55-68.e2
202210.3390/microorganisms10091747Gontijo, J. B., F. S. Paula, A. M. Venturini, J. A. Mandro, P. L. E. Bodelier and S. M. TsaiInsights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain SedimentsMicroorganisms10(9) 1747
202210.1111/tpj.15682Gomez-Cano, F., Y. H. Chu, M. Cruz-Gomez, H. M. Abdullah, Y. S. Lee, D. J. Schnell and E. GrotewoldExploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analysesPlant Journal110(2) 589-606
202210.1073/pnas.2110787119Goldford, J. E., A. B. George, A. I. Flamholz and D. SegrèProtein cost minimization promotes the emergence of coenzyme redundancyProceedings of the National Academy of Sciences119(14) e2110787119
202210.1088/1478-3975/ac8514Golden, A., I. Dukovski, D. Segrè and K. S. KorolevGrowth instabilities shape morphology and genetic diversity of microbial coloniesPhysical Biology19(5) 56005
202210.1111/1462-2920.16173Goff, J. L., E. G. Szink, M. P. Thorgersen, A. D. Putt, Y. Fan, et al.Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sedimentsEnvironmental Microbiology24(11) 5546–60
202210.1128/mra.00145-22Goff, J. L., L. M. Lui, T. N. Nielsen, M. P. Thorgersen, E. G. Szink, J.-M. Chandonia, F. L. Poole, J. Zhou, T. C. Hazen, A. P. Arkin and M. W. W. AdamsComplete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface EnvironmentMicrobiology Resource Announcements11(5) e00145-22
202210.1021/acs.jchemed.2c00221Goes, S. L., J. E. Nutting, N. J. Hill, S. S. Stahl and M. RafieeExploring Electrosynthesis: Bulk Electrolysis and Cyclic Voltammetry Analysis of the Shono OxidationJournal of Chemical Education99(9) 3242–8
202210.1007/s12275-022-2250-5Gim, D.-H., S.-Y. Lee, J. E. Han, J.-Y. Lee, S. M. Kang and J.-W. BaeDescription of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fishJournal of Microbiology60(11) 1061–9
202210.1021/acscatal.2c02445Gilcher, E. B., H. Chang, M. Rebarchik, G. W. Huber and J. A. DumesicEffects of Water Addition to Isopropanol for Hydrogenation of Compounds Derived from 5-Hydroxymethyl Furfural over Pd, Ru, and Cu CatalystsACS Catalysis12(16) 10186-10198
202210.1039/D1GC04650KGilcher, E. B., H. Chang, G. W. Huber and J. A. DumesicControlled hydrogenation of a biomass-derived platform chemical formed by aldol-condensation of 5-hydroxymethyl furfural (HMF) and acetone over Ru, Pd, and Cu catalystsGreen Chemistry24(5) 2146–59
202210.3390/plants11060721Gilbert, S., A. Poulev, W. Chrisler, K. Acosta, G. Orr, S. Lebeis and E. LamAuxin-Producing Bacteria from Duckweeds Have Different Colonization Patterns and Effects on Plant MorphologyPlants11(6)
202210.1016/j.cmet.2021.11.005Giera, M., O. Yanes and G. SiuzdakMetabolite discovery: Biochemistry's scientific driverCell Metabolism34(1) 21–34
202210.1111/1365-2435.14070Gibert, J. P., Z. Y. Han, D. J. Wieczynski, S. Votzke and A. YammineFeedbacks between size and density determine rapid eco-phenotypic dynamicsFunctional Ecology36(7) 1668-1680
202210.1111/1365-2435.14091Gibert, J. P., J. M. Grady and A. I. DellFood web consequences of thermal asymmetriesFunctional Ecology36(8) 1887-1899
202210.1039/D2EE00625AGeissler, C. H. and C. T. MaraveliasAnalysis of alternative bioenergy with carbon capture strategies: present and futureEnergy & Environmental Science15(7) 2679–89
202210.1111/geb.13489Gautam, S., U. Mishra, C. D. Scown, S. A. Wills, K. Adhikari and B. A. DrewniakContinental United States may lose 1.8 petagrams of soil organic carbon under climate change by 2100Global Ecology and Biogeography31(6) 1147–60
202210.1007/s00253-022-12061-3Garrido, M. M., F. E. Piccinni, M. Landoni, M. J. Peña, J. Topalian, A. Couto, S. A. Wirth, B. R. Urbanowicz and E. CamposInsights into the xylan degradation system of Cellulomonas sp. B6: biochemical characterization of rCsXyn10A and rCsAbf62AApplied Microbiology and Biotechnology106(13) 5035–49
202210.1016/j.syapm.2022.126358García-Santibañez, T., M. Rosenblueth, L. M. Bolaños, J. Martínez-Romero and E. Martínez-RomeroThe divergent genome of Scorpion Group 1 (SG1) intracellular bacterium from the venom glands of Vaejovis smithi (Scorpiones: Vaejovidae)Systematic and Applied Microbiology45(6) 126358
202210.1038/s41598-022-13525-2Garber, M. E., R. Fregoso, J. Lake, A. Kakouridis and A. MukhopadhyayPseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylationScientific Reports12(1) 10336
202210.1038/s41467-022-31343-yGao, C., L. Xu, L. Montoya, M. Madera, J. Hollingsworth, L. Chen, E. Purdom, V. Singan, J. Vogel, R. B. Hutmacher, J. A. Dahlberg, D. Coleman-Derr, P. G. Lemaux and J. W. TaylorCo-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communitiesNature Communications13(1)
202210.1111/mec.16343Gao, C., P. E. Courty, N. Varoquaux, B. Cole, L. Montoya, L. Xu, E. Purdom, J. Vogel, R. B. Hutmacher, J. A. Dahlberg, D. Coleman-Derr, P. G. Lemaux and J. W. TaylorSuccessional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expressionMolecular Ecology
202210.1073/pnas.2201160119Gan, L., K. Park, J. Chai, E. M. Updike, H. Kim, et al.Divergent evolution of extreme production of variant plant monounsaturated fatty acidsProceedings of the National Academy of Sciences119(30) e2201160119
202210.1016/j.synbio.2022.02.007Gambacorta, F. V., E. R. Wagner, T. B. Jacobson, M. Tremaine, L. K. Muehlbauer, et al.Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathwaySynthetic and Systems Biotechnology7(2) 738–49
202210.3389/fbioe.2022.1080024Gambacorta, F. V., J. J. Dietrich, J. J. Baerwald, S. J. Brown, Y. Su and B. F. PflegerCombinatorial library design for improving isobutanol production in Saccharomyces cerevisiaeFrontiers in Bioengineering and Biotechnology10
202210.3389/ffunb.2022.1063609Gabaldón, T. and C. T. HittingerEditorial: Genomic insights on fungal hybridsFrontiers in Fungal Biology3
202210.1111/pce.14270G. Viana, W., J. D. Scharwies and J. R. DinnenyDeconstructing the root system of grasses through an exploration of development, anatomy and functionPlant Cell and Environment45(3) 602-619
202210.1128/mra.00691-22Fu, H., A. Kugler, P. Huyck, R. L. Brigmon and E. A. OttesenDraft Genome Sequence of Cupriavidus basilensis SRS, a Bacterium Isolated from Stream SedimentsMicrobiology Resource Announcements11(10) e00691-22
202210.1016/j.ymben.2021.12.012Foster, C., V. S. Boorla, S. Dash, S. Gopalakrishnan, T. B. Jacobson, D. G. Olson, D. Amador-Noguez, L. R. Lynd and C. D. MaranasAssessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic modelMetabolic Engineering69 286–301
202210.1016/j.soilbio.2021.108519Fossum, C., K. Y. Estera-Molina, M. Yuan, D. J. Herman, I. Chu-Jacoby, P. S. Nico, K. D. Morrison, J. Pett-Ridge and M. K. FirestoneBelowground allocation and dynamics of recently fixed plant carbon in a California annual grasslandSoil Biology and Biochemistry165 108519
202210.1128/mra.00290-22Fortney, N. W., K. S. Myers, A. T. Ingle, K. A. Walters, M. J. Scarborough, T. J. Donohue and D. R. NogueraMetagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol BiorefineryMicrobiology Resource Announcements11(8) e00290-22
202210.1016/j.soilbio.2022.108809Fofana, A., D. Anderson, C. K. McCalley, S. Hodgkins, R. M. Wilson, D. Cronin, N. Raab, M. Torabi, R. K. Varner, P. Crill, S. R. Saleska, J. P. Chanton, M. M. Tfaily and V. I. RichMapping substrate use across a permafrost thaw gradientSoil Biology and Biochemistry175
202210.1038/s41396-021-01162-yFinley, B. K., R. L. Mau, M. Hayer, B. W. Stone, E. M. Morrissey, B. J. Koch, C. Rasmussen, P. Dijkstra, E. Schwartz and B. A. HungateSoil minerals affect taxon-specific bacterial growthThe ISME Journal16(5) 1318–26
202210.1093/jxb/erac300Ferreira, S. S., G. Goeminne, M. S. Simões, A. V. d. A. Pina, L. G. A. d. Lima, J. Pezard, A. Gutiérrez, J. Rencoret, J. C. Mortimer, J. C. del Río, W. Boerjan and I. CesarinoTranscriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghumJournal of Experimental Botany73(18) 6307–33
202210.1128/mra.00796-22Ferrari, N. A., J. V. G. Takashe, F. F. Aburjaile, V. Azevedo, M. M. d. Costa, B. Brenig, F. E. P. Rocha and U. d. P. PereiraGenome Report of Emergent Fish Pathogen Edwardsiella piscicida Recovered from Pseudoplatystoma corruscans in BrazilMicrobiology Resource Announcements11(12) e00796-22
202210.1042/BCJ20220003Fenyk, S., H. K. Woodfield, T. B. Romsdahl, E. J. Wallington, R. E. Bates, D. A. Fell, K. D. Chapman, T. Fawcett and J. L. HarwoodOverexpression of phospholipid: diacylglycerol acyltransferase in Brassica napus results in changes in lipid metabolism and oil accumulationBiochemical Journal479(6) 805-823
202210.1016/j.chom.2021.12.006Feng, J., Y. Qian, Z. Zhou, S. Ertmer, E. I. Vivas, F. Lan, J. J. Hamilton, F. E. Rey, K. Anantharaman and O. S. VenturelliPolysaccharide utilization loci in Bacteroides determine population fitness and community-level interactionsCell Host and Microbe30(2) 200-215.e12
202210.1128/jb.00563-21Felczak, M. M. and M. A. TerAvestZymomonas mobilis ZM4 Utilizes an NADP+-Dependent Acetaldehyde Dehydrogenase To Produce AcetateJournal of Bacteriology204(4) e00563-21
202210.1128/mbio.01224-22Feid, S. C., H. E. Walukiewicz, X. Wang, E. S. Nakayasu, C. V. Rao and A. J. WolfeRegulation of translation by lysine acetylation in Escherichia colimBio13(3)
202210.1038/s41588-022-01052-9Fauser, F., J. Vilarrasa-Blasi, M. Onishi, S. Ramundo, W. Patena, et al.Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtiiNature Genetics54(5) 705-714
202210.1021/acssuschemeng.2c00820Fang, Z., J. E. Jackson and E. L. HeggMild, Electroreductive Lignin Cleavage: Optimizing the Depolymerization of Authentic LigninsACS Sustainable Chemistry & Engineering10(23) 7545–52
202210.1111/tpj.15603Fan, M., J. K. Jensen, S. Zemelis-Durfee, S.-J. Kim, J.-Y. Chan, C. M. Beaudry, F. Brandizzi and C. G. WilkersonDisruption of Brachypodium lichenase alters metabolism of mixed-linkage glucan and starchThe Plant Journal109(4) 927–39
202210.1016/j.meegid.2022.105315Faleye, T. O. C., P. T. Skidmore, A. Elyaderani, A. Smith, N. Kaiser, S. Adhikari, A. Yanez, T. Perleberg, E. M. Driver, R. U. Halden, A. Varsani and M. ScotchCanine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021Infection, Genetics and Evolution103 105315
202210.1128/mra.01008-22Fadiji, A. E., A. S. Ayangbenro, A. O. Akanmu and O. O. BabalolaDraft Genome Sequence of Enterobacter mori AYS9, a Potential Plant Growth-Promoting RhizobacteriumMicrobiology Resource Announcements11(12) e01008-22
202210.1093/femsle/fnac034Estoppey, A., L. Weisskopf, E. Di Francesco, A. Vallat-Michel, S. Bindschedler, P. S. Chain and P. JunierImproved methods to assess the effect of bacteria on germination of fungal sporesFEMS Microbiology Letters369(1) fnac034
202210.1145/3500922Eslami, M., A. Adler, R. S. Caceres, J. G. Dunn, N. Kelley-Loughnane, V. A. Varaljay and H. G. MartinArtificial intelligence for synthetic biologyCommunications of the ACM65(5) 88–97
202210.1038/s41396-021-01120-8Escalas, A., F. S. Paula, F. Guilhaumon, M. Yuan, Y. Yang, L. Wu, F. Liu, J. Feng, Y. Zhang and J. ZhouMacroecological distributions of gene variants highlight the functional organization of soil microbial systemsISME Journal16(3) 726-737
202210.1111/gcb.16231Ernakovich, J. G., R. A. Barbato, V. I. Rich, C. Schädel, R. E. Hewitt, et al.Microbiome assembly in thawing permafrost and its feedbacks to climateGlobal Change Biology28(17) 5007-5026
202210.1038/s41929-022-00747-wErickson, E., A. Bleem, E. Kuatsjah, A. Z. Werner, J. L. DuBois, J. E. McGeehan, L. D. Eltis and G. T. BeckhamCritical enzyme reactions in aromatic catabolism for microbial lignin conversionNature Catalysis5(2) 86–98
202210.1111/tpj.15640Engle, K. A., R. A. Amos, J.-Y. Yang, J. Glushka, M. A. Atmodjo, L. Tan, C. Huang, K. W. Moremen and D. MohnenMultiple Arabidopsis galacturonosyltransferases synthesize polymeric homogalacturonan by oligosaccharide acceptor-dependent or de novo synthesisThe Plant Journal109(6) 1441–56
202210.1038/s41467-022-30355-yEnghiad, B., P. Xue, N. Singh, A. G. Boob, C. Shi, V. A. Petrov, R. Liu, S. S. Peri, S. T. Lane, E. D. Gaither and H. ZhaoPlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid constructionNature Communications13(1) 2697
202210.1016/j.apsoil.2021.104218Emery, S. M., L. Bell-Dereske, K. A. Stahlheber and K. L. GrossArbuscular mycorrhizal fungal community responses to drought and nitrogen fertilization in switchgrass standsApplied Soil Ecology169 104218
202210.1016/j.jfueco.2022.100072Elkins, J. G., M. Rodriguez, O. N. Cannon, R. M. Connatser, G. B. Oguntimein, M. D. Kass, B. H. West and B. H. Davisonn-Butanol or isobutanol as a value-added fuel additive to inhibit microbial degradation of stored gasolineFuel Communications12 100072
202210.1016/j.phytochem.2022.113122Elder, T., J. C. del Río, J. Ralph, J. Rencoret and H. KimDensity functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomerPhytochemistry197 113122
202210.3389/frsus.2022.910924Edwards, M. R., T. Holloway, R. B. Pierce, L. Blank, M. Broddle, et al.Satellite Data Applications for Sustainable Energy TransitionsFrontiers in Sustainability3
202210.1186/s12864-022-08918-6Edwards, B., E. D. Hornstein, N. J. Wilson and H. SederoffHigh-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomesBMC Genomics23(1)
202210.1128/AEM.01782-21Eagar, A. C., R. M. Mushinski, A. L. Horning, K. A. Smemo, R. P. Phillips and C. B. BlackwoodArbuscular Mycorrhizal Tree Communities Have Greater Soil Fungal Diversity and Relative Abundances of Saprotrophs and Pathogens than Ectomycorrhizal Tree CommunitiesApplied and Environmental Microbiology88(1)
202210.1128/aem.01648-21Dunon, V., P. N. Holmsgaard, S. Dealtry, R. Lavigne, S. J. Sørensen, K. Smalla, E. M. Top and D. SpringaelLong-Range PCR Reveals the Genetic Cargo of IncP-1 Plasmids in the Complex Microbial Community of an On-Farm Biopurification System Treating Pesticide-Contaminated WastewaterApplied and Environmental Microbiology88(3) e01648-21
202210.1042/ETLS20210267Duarte, J. M., S. Dutta, D. S. Goodsell and S. K. BurleyExploring protein symmetry at the RCSB Protein Data BankEmerging Topics in Life Sciences6(3) 231-243
202210.1038/s41396-022-01232-9Dove, N. C., N. Ta_ and S. C. HartEcological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potentialThe ISME Journal16(7) 1853–63
202210.1128/msystems.00120-22Dove, N. C., A. A. Carrell, N. L. Engle, D. M. Klingeman, M. Rodriguez, T. Wahl, T. J. Tschaplinski, W. Muchero, C. W. Schadt and M. A. CreggerRelationships between Sphaerulina musiva Infection and the Populus Microbiome and MetabolomemSystems7(4) e00120-22
202210.1016/j.mib.2022.102144Donohue, T. J.Editorial overview: Microbial activities powering societyCurrent Opinion in Microbiology67 102144
202210.3389/fchem.2021.826625Dong, H., L. D. C. Sousa, B. Ubanwa, A. D. Jones and V. BalanA new method to overcome carboxyamide formation during AFEX pretreatment of lignocellulosic biomassFrontiers in Chemistry9
202210.1016/j.ymben.2021.10.012Dinh, H. V., D. Sarkar and C. D. MaranasQuantifying the propagation of parametric uncertainty on flux balance analysisMetabolic Engineering69 26–39
202210.1111/pce.14291DiMario, R. J., R. Giuliani, N. Ubierna, A. D. Slack, A. B. Cousins and A. J. StuderLack of leaf carbonic anhydrase activity eliminates the C4 carbon-concentrating mechanism requiring direct diffusion of CO2 into bundle sheath cellsPlant Cell and Environment45(5) 1382-1397
202210.1038/s42003-022-04069-2Diao, J., R. Carr and T. S. MoonDeciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630Communications Biology5(1)
202210.1007/s12042-022-09315-9Dhungana, S. R. and D. M. BraunGenomic Analyses of SUT and TST Sugar Transporter Families in Low and High Sugar Accumulating Sugarcane Species (Saccharum spontaneum and Saccharum officinarum)Tropical Plant Biology
202210.1128/msystems.00169-22Dhakar, K., R. Zarecki, S. Medina, H. Ziadna, K. Igbaria, R. Lati, Z. Ronen, H. Eizenberg and S. FreilichModeling-Guided Amendments Lead to Enhanced Biodegradation in SoilmSystems7(4) e00169-22
202210.1093/bib/bbab476Dhakal, A., C. McKay, J. J. Tanner and J. ChengArtificial intelligence in the prediction of protein-ligand interactions: recent advances and future directionsBriefings in Bioinformatics23(1)
202210.1016/j.copbio.2022.102730Deter, H. S. and T. LuEngineering microbial consortia with rationally designed cellular interactionsCurrent Opinion in Biotechnology76 102730
202210.1128/AEM.01841-21Dershwitz, P., W. Gu, J. Roche, C. S. Kang-Yun, J. D. Semrau, T. A. Bobik, B. Fulton, H. Zischka and A. A. DiSpiritoMbnC Is Not Required for the Formation of the N-Terminal Oxazolone in the Methanobactin from Methylosinus trichosporium OB3bApplied and Environmental Microbiology88(2)
202210.1126/sciadv.abp8823Demarteau, J., A. R. Epstein, P. R. Christensen, M. Abubekerov, H. Wang, S. J. Teat, T. J. Seguin, C. W. Chan, C. D. Scown, T. P. Russell, J. D. Keasling, K. A. Persson and B. A. HelmsCircularity in mixed-plastic chemical recycling enabled by variable rates of polydiketoenamine hydrolysisScience Advances8(29) eabp8823
202210.1016/j.scitotenv.2022.155408Della Chiesa, T., G. Piñeiro, S. J. Del Grosso, W. J. Parton, P. I. Araujo and L. YahdjianHigher than expected N2O emissions from soybean crops in the Pampas Region of Argentina: Estimates from DayCent simulations and field measurementsScience of the Total Environment835
202210.1016/bs.abr.2022.02.001del Río, J. C., J. Rencoret, A. Gutiérrez, H. Kim and J. RalphUnconventional lignin monomers—Extension of the lignin paradigmAdvances in Botanical Research104 1–39
202210.1007/s00253-022-12084-wDeewan, A., J.-J. Liu, S. S. Jagtap, E. J. Yun, H. Walukiewicz, Y.-S. Jin and C. V. RaoSystem analysis of Lipomyces starkeyi during growth on various plant-based sugarsApplied Microbiology and Biotechnology106(17) 5629–42
202210.3389/fmicb.2022.855331de Raad, M., Y. V. Li, J. V. Kuehl, P. F. Andeer, S. M. Kosina, et al.A Defined Medium for Cultivation and Exometabolite Profiling of Soil BacteriaFrontiers in Microbiology13
202210.3389/fpls.2022.943349De Meester, B., P. Oyarce, R. Vanholme, R. Van Acker, Y. Tsuji, T. Vangeel, S. Van den Bosch, J. Van Doorsselaere, B. Sels, J. Ralph and W. BoerjanEngineering Curcumin Biosynthesis in Poplar Affects Lignification and Biomass YieldFrontiers in Plant Science13
202210.1111/1462-2920.15843Dang, C., J. G. V. Walkup, B. A. Hungate, R. B. Franklin, E. Schwartz and E. M. MorrisseyPhylogenetic organization in the assimilation of chemically distinct substrates by soil bacteriaEnvironmental Microbiology24(1) 357-369
202210.1016/j.algal.2021.102604Dahlin, L. R. and M. T. GuarnieriHeterologous expression of phosphite dehydrogenase in the chloroplast or nucleus enables phosphite utilization and genetic selection in Picochlorum sppAlgal Research62 102604
202210.1016/j.algal.2021.102604Dahlin, L. R. and M. T. GuarnieriHeterologous expression of phosphite dehydrogenase in the chloroplast or nucleus enables phosphite utilization and genetic selection in Picochlorum spp.Algal Research62 102604
202210.1016/j.ymben.2022.03.011Dahle, M. L., E. T. Papoutsakis and M. R. Antoniewicz13C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditionsMetabolic Engineering72 161-170
202210.1016/j.mec.2022.e00206Czajka, J. J., D. Banerjee, T. Eng, J. Menasalvas, C. Yan, N. M. Munoz, B. C. Poirier, Y.-M. Kim, S. E. Baker, Y. J. Tang and A. MukhopadhyayTuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine productionMetabolic Engineering Communications15 e00206
202210.1007/s10681-022-03005-zCuevas, H. E. and W. VermerrisLinkage map construction using limited parental genotypic informationEuphytica218(5)
202210.1002/csc2.20818Cuevas, H. E., J. E. Knoll, K. R. Harris-Shultz and S. M. PunnuriGenetic mapping of sugarcane aphid resistance in sorghum line SC112-14Crop Science
202210.1016/j.joule.2022.05.011Cruz-Morales, P., K. Yin, A. Landera, J. R. Cort, R. P. Young, et al.Biosynthesis of polycyclopropanated high energy biofuelsJoule6(7) 1590–605
202210.1128/mra.01205-21Cross, K. L., D. M. Klingeman and M. PodarComplete Genome Sequence of Human Oral Saccharibacterium “Candidatus Nanosynbacter sp. HMT352” Strain KC1Microbiology Resource Announcements11(2) e01205-21
202210.1016/j.soilbio.2022.108648Cotrufo, M. F., M. L. Haddix, M. E. Kroeger and C. E. StewartThe role of plant input physical-chemical properties, and microbial and soil chemical diversity on the formation of particulate and mineral-associated organic matterSoil Biology and Biochemistry168 108648
202210.1128/mbio.00079-22Costa, P. B. d., G. M. N. Benucci, M.-Y. Chou, J. V. Wyk, M. Chretien and G. BonitoSoil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome AssemblymBio13(2) e00079-22
202210.1021/acssuschemeng.2c04204Cortés-Peña, Y. R., C. Kurambhatti, K. Eilts, V. Singh and J. S. GuestEconomic and Environmental Sustainability of Vegetative Oil Extraction Strategies at Integrated Oilcane and Oil-Sorghum BiorefineriesACS Sustainable Chemistry & Engineering10(42) 13980–90
202210.1021/acssuschemeng.1c07442Cordon, M. J., J. Zhang, N. R. Samad, J. W. Harris, K. A. Unocic, M. Li, D. Liu and Z. LiEthanol Conversion to C4+ Olefins over Bimetallic Copper- And Lanthanum-Containing Beta Zeolite CatalystsACS Sustainable Chemistry & Engineering10(18) 5702–7
202210.1002/mas.21663Cooper, W. T., J. C. Chanton, J. D'Andrilli, S. B. Hodgkins, D. C. Podgorski, A. C. Stenson, M. M. Tfaily and R. M. WilsonA History of Molecular Level Analysis of Natural Organic Matter by FTICR Mass Spectrometry and The Paradigm Shift in Organic GeochemistryMass Spectrometry Reviews41(2) 215-239
202210.1038/s41564-022-01244-3Conway, J. M., W. G. Walton, I. Salas-González, T. F. Law, C. A. Lindberg, L. E. Crook, S. M. Kosina, C. R. Fitzpatrick, A. D. Lietzan, T. R. Northen, C. D. Jones, O. M. Finkel, M. R. Redinbo and J. L. DanglDiverse MarR bacterial regulators of auxin catabolism in the plant microbiomeNature Microbiology7(11) 1817–33
202210.1073/pnas.2107879119Contreras-López, O., E. A. Vidal, E. Riveras, J. M. Alvarez, T. C. Moyano, E. E. Sparks, J. Medina, A. Pasquino, P. N. Benfey, G. M. Coruzzi and R. A. GutiérrezSpatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrateProceedings of the National Academy of Sciences of the United States of America119(4)
202210.1242/dev.200632Conde, D., P. M. Triozzi, W. J. Pereira, H. W. Schmidt, K. M. Balmant, S. A. Knaack, A. Redondo-López, S. Roy, C. Dervinis and M. KirstSingle-nuclei transcriptome analysis of the shoot apex vascular system differentiation in PopulusDevelopment (Cambridge, England)149(21)
202210.1002/cpz1.533Colovas, J., A. F. Bintarti, M. E. Mechan Llontop, K. L. Grady and A. ShadeDo-it-Yourself Mock Community Standard for Multi-Step Assessment of Microbiome ProtocolsCurrent Protocols2(9)
202210.1128/msystems.00951-22Coker, J., K. Zhalnina, C. Marotz, D. Thiruppathy, M. Tjuanta, G. D’Elia, R. Hailu, T. Mahosky, M. Rowan, T. R. Northen and K. ZenglerA Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial EcologymSystems7(6) e00951-22
202210.3389/fpls.2022.787265Clark, T. J. and J. SchwenderElucidation of Triacylglycerol Overproduction in the C4 Bioenergy Crop Sorghum bicolor by Constraint-Based AnalysisFrontiers in Plant Science13
202210.3389/fenrg.2022.868181Choudhary, H., B. A. Simmons and J. M. GladdenComparative Study on the Pretreatment of Aspen and Maple With 1-Ethyl-3-methylimidazolium Acetate and Cholinium LysinateFrontiers in Energy Research10
202210.3390/molecules27196278Choudhary, H., V. R. Pidatala, M. Mohan, B. A. Simmons, J. M. Gladden and S. SinghRenewable Schiff-Base Ionic Liquids for Lignocellulosic Biomass PretreatmentMolecules27(19) 6278
202210.1038/s41467-022-31433-xChirania, P., E. K. Holwerda, R. J. Giannone, X. Liang, S. Poudel, J. C. Ellis, Y. J. Bomble, R. L. Hettich and L. R. LyndMetaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solidsNature Communications13(1) 3870
202210.1186/s13068-022-02213-yChipkar, S., K. Smith, E. M. Whelan, D. J. Debrauske, A. Jen, K. A. Overmyer, A. Senyk, L. Hooker-Moericke, M. Gallmeyer, J. J. Coon, A. D. Jones, T. K. Sato and R. G. OngWater-soluble saponins accumulate in drought-stressed switchgrass and may inhibit yeast growth during bioethanol productionBiotechnology for Biofuels and Bioproducts15(1) 116
202210.1021/acscatal.2c00133Chin, M., S. M. Suh, Z. Fang, E. L. Hegg and T. DiaoDepolymerization of Lignin via a Microscopic Reverse Biosynthesis PathwayACS Catalysis12(4) 2532-2539
202210.1007/s13399-022-03359-3Cheng, M.-H., S. Maitra, A. N. C. Clennon, M. Appell, B. S. Dien and V. SinghThe effects of sequential hydrothermal-mechanical refining pretreatment on cellulose structure changes and sugar recoveriesBiomass Conversion and Biorefinery
202210.1371/journal.pone.0264467Chen, Y., N. Kaplan Lease, J. W. Gin, T. L. Ogorzalek, P. D. Adams, N. J. Hillson and C. J. PetzoldModular automated bottom-up proteomic sample preparation for high-throughput applicationsPLoS ONE17(2) e0264467
202210.1038/s41467-022-31927-8Chen, Y., E. Hysolli, A. Chen, S. Casper, S. Liu, K. Yang, C. Liu and G. ChurchMultiplex base editing to convert TAG into TAA codons in the human genomeNature Communications13(1)
202210.1186/s12859-022-04683-1Chen, X. and J. ChengDISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural networkBMC Bioinformatics23
202210.1016/j.memsci.2021.120224Chen, H., Y. Tian, Z. Hu, C. Wang, P. Xie, L. Chen, F. Yang, Y. Liang, C. Mu, C. Wei, Y.-P. Ting, G. Qiu and Y. SongBis-(3_-5_)-cyclic dimeric guanosine monophosphate (c-di-GMP) mediated membrane fouling in membrane bioreactorJournal of Membrane Science646 120224
202210.1007/s11033-022-07927-8Chávez-Luzanía, R. A., A. C. Montoya-Martínez, F. I. Parra-Cota and S. de los Santos-VillalobosPangenomes-identified singletons for designing specific primers to identify bacterial strains in a plant growth-promoting consortiumMolecular Biology Reports49(11) 10489–98
202210.1128/spectrum.02346-21Chaput, G., J. Ford, L. DeDiego, A. Narayanan, W. Y. Tam, et al.Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading ConsortiumMicrobiology Spectrum10(3) e02346-21
202210.1016/j.cell.2022.08.012Chao, G., T. M. Wannier, C. Gutierrez, N. C. Borders, E. Appleton, A. Chadha, T. Lebar and G. M. ChurchhelixCAM: A platform for programmable cellular assembly in bacteria and human cellsCell185(19) 3551-3567.e39
202210.1128/aem.02346-21Chang, J., P. Peng, A. A. DiSpirito and J. D. SemrauVariable inhibition of nitrous oxide reduction in denitrifying bacteria by different forms of methanobactinApplied and Environmental Microbiology88(7)
202210.3389/fmicb.2022.791110Chai, Y. N., S. Futrell and D. P. SchachtmanAssessment of Bacterial Inoculant Delivery Methods for Cereal CropsFrontiers in Microbiology13
202210.3389/fpls.2022.866164Cesarino, I., A. Eudes, B. Urbanowicz and M. XieEditorial: Phenylpropanoid Systems Biology and BiotechnologyFrontiers in Plant Science13 866164
202210.1128/spectrum.01067-22Catlett, J. L., S. Carr, M. Cashman, M. D. Smith, M. Walter, Z. Sakkaff, C. Kelley, M. Pierobon, M. B. Cohen and N. R. BuanMetabolic Synergy between Human Symbionts Bacteroides and MethanobrevibacterMicrobiology Spectrum10(3) e01067-22
202210.1016/j.geoderma.2021.115628Cates, A. M., A. Jilling, M. M. Tfaily and R. D. JacksonTemperature and moisture alter organic matter composition across soil fractionsGeoderma409 115628
202210.1093/g3journal/jkac224Case, N. T., J. Berman, D. S. Blehert, R. A. Cramer, C. Cuomo, et al.The future of fungi: threats and opportunitiesG3 Genes|Genomes|Genetics12(11) jkac224
202210.3389/fbioe.2022.968437Carruthers, D. N. and T. S. LeeTranslating advances in microbial bioproduction to sustainable biotechnologyFrontiers in Bioengineering and Biotechnology10
202210.3389/fmicb.2022.1033631Carrell, A. A., B. B. Hicks, E. Sidelinger, E. R. Johnston, S. S. Jawdy, M. M. Clark, D. M. Klingeman and M. A. CreggerNitrogen addition alters soil fungal communities, but root fungal communities are resistant to changeFrontiers in Microbiology13 1033631
202210.3390/microorganisms10102013Carper, D. L., M. R. Appidi, S. Mudbhari, H. K. Shrestha, R. L. Hettich and P. E. AbrahamThe Promises, Challenges, and Opportunities of Omics for Studying the Plant HolobiontMicroorganisms10(10) 2013
202210.1007/s12155-021-10305-0Carlson, C. H. and L. B. SmartHeterosis for Biomass-Related Traits in Interspecific Triploid Hybrids of Willow (Salix spp.)Bioenergy Research15(2) 1042-1056
202210.1093/g3journal/jkab436Carlson, C. H., Y. Choi, A. P. Chan, C. D. Town and L. B. SmartNonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.)G3: Genes, Genomes, Genetics12(3)
202210.1016/j.ygeno.2021.12.007Cardoso, B., F. Esposito, H. Fontana, B. Fuga, Q. Moura, E. Sano, M. I. Z. Sato, C. J. Brandão, F. A. Oliveira, C. E. Levy and N. LincopanGenomic analysis of a Kpi (pilus system)-positive and CTX-M-15-producing Klebsiella pneumoniae belonging to the high-risk clone ST15 isolated from an impacted river in BrazilGenomics114(1) 378–83
202210.1093/nar/gkac459Capela, J., D. Lagoa, R. Rodrigues, E. Cunha, F. Cruz, A. Barbosa, J. Bastos, D. Lima, E. C. Ferreira, M. Rocha and O. Diasmerlin, an improved framework for the reconstruction of high-quality genome-scale metabolic modelsNucleic Acids Research50(11) 6052–66
202210.1111/pce.14208Cao, Y., X. Yan, S. Ran, J. Ralph, R. A. Smith, X. Chen, C. Qu, J. Li and L. LiuKnockout of the lignin pathway gene BnF5H decreases the S/G lignin compositional ratio and improves Sclerotinia sclerotiorum resistance in Brassica napusPlant, Cell & Environment45(1) 248–61
202210.1002/bit.28159Cao, M., V. G. Tran, J. Qin, A. Olson, S. Mishra, John C. Schultz, C. Huang, D. Xie and H. ZhaoMetabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactoneBiotechnology and Bioengineering119(9) 2529–40
202210.1371/journal.pcbi.1009828Canto-Encalada, G., D. Tec-Campos, J. D. Tibocha-Bonilla, K. Zengler, A. Zepeda and C. ZuñigaFlux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compoundsPLoS Computational Biology18(2)
202210.3389/fmicb.2021.799014Campbell, T. P., D. E. M. Ulrich, J. Toyoda, J. Thompson, B. Munsky, M. B. N. Albright, V. L. Bailey, M. M. Tfaily and J. DunbarMicrobial Communities Influence Soil Dissolved Organic Carbon Concentration by Altering Metabolite CompositionFrontiers in Microbiology12
202210.1111/nph.18392Cai, Y., Z. Zhai, J. Blanford, H. Liu, H. Shi, J. Schwender, C. Xu and J. ShanklinPurple acid phosphatase2 stimulates a futile cycle of lipid synthesis and degradation, and mitigates the negative growth effects of triacylglycerol accumulation in vegetative tissuesNew Phytologist236(3) 1128–39
202210.3390/microorganisms10050955Cai, Y., J. Yun and Z. JiaPhylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome ReconstructionMicroorganisms10(5) 955
202210.3389/fmicb.2022.864895Cabugao, K. G. M., S. Gushgari-Doyle, S. S. Chacon, X. Wu, A. Bhattacharyya, N. Bouskill and R. ChakrabortyCharacterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and ChallengesFrontiers in Microbiology13
202210.1016/j.soilbio.2022.108697Button, E. S., J. Pett-Ridge, D. V. Murphy, Y. Kuzyakov, D. R. Chadwick and D. L. JonesDeep-C storage: Biological, chemical and physical strategies to enhance carbon stocks in agricultural subsoilsSoil Biology and Biochemistry170 108697
202210.1016/j.pbi.2022.102191Busta, L., K. D. Chapman and E. B. CahoonBetter together: Protein partnerships for lineage-specific oil accumulationCurrent Opinion in Plant Biology66 102191
202210.1146/annurev-phyto-021320-010717Busby, P. E., G. Newcombe, A. S. Neat and C. AverillFacilitating Reforestation Through the Plant Microbiome: Perspectives from the PhyllosphereAnnual Review of Phytopathology60 337-356
202210.1111/gcbb.12917Burnham, M. B., S. J. Simon, D. Lee, A. D. Kent, E. H. DeLucia and W. H. YangIntra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghumGCB Bioenergy14(3) 393–410
202210.1002/pro.4213Burley, S. K., C. Bhikadiya, C. Bi, S. Bittrich, L. Chen, et al.RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3DProtein Science31(1) 187-208
202210.3390/biom12101425Burley, S. K., H. M. Berman, J. M. Duarte, Z. Feng, J. W. Flatt, et al.Protein Data Bank: A comprehensive review of 3d structure holdings and worldwide utilization by researchers, educators, and studentsBiomolecules12(10)
202210.1038/s41559-022-01892-yBuessecker, S., A. F. Sarno, M. C. Reynolds, R. Chavan, J. Park, et al.Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlandsNature Ecology & Evolution6(12) 1881–90
202210.3390/agronomy12081847Buanafina, M. M. D. O. and P. MorrisThe Impact of Cell Wall Feruloylation on Plant Growth, Responses to Environmental Stress, Plant Pathogens and Cell Wall DegradabilityAgronomy12(8)
202210.3389/fmicb.2022.825104Bryson, S. J., K. A. Hunt, D. A. Stahl and M.-K. H. WinklerMetagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor ConfigurationsFrontiers in Microbiology13
202210.1002/pro.4259Bruni, R., A. Laguerre, A. M. Kaminska, S. McSweeney, W. A. Hendrickson and Q. LiuHigh-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimeticsProtein Science31(3) 639–51
202210.1021/acs.analchem.2c01654Brown, S. L., M. A. Zenaidee, J. A. Loo, R. R. O. Loo and W. A. DonaldOn the mechanism of theta capillary nanoelectrospray ionization for the formation of highly charged protein ions directly from native solutionsAnalytical Chemistry94(38) 13010-13018
202210.1126/science.abo4326Brophy, J. A. N., K. J. Magallon, L. Duan, V. Zhong, P. Ramachandran, K. Kniazev and J. R. DinnenySynthetic genetic circuits as a means of reprogramming plant rootsScience377(6607) 747-751
202210.1111/tpj.15965Broddrick, J. T., M. A. Ware, D. Jallet, B. O. Palsson and G. PeersIntegration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolismPlant Journal
202210.1146/annurev-arplant-070721-083240Braun, D. M.Phloem loading and unloading of sucrose: What a long, strange trip from source to sinkAnnual Review of Plant Biology73 553-584
202210.1111/nph.18308Branco, S., A. Schauster, H. L. Liao and J. RuytinxMechanisms of stress tolerance and their effects on the ecology and evolution of mycorrhizal fungiNew Phytologist235(6) 2158-2175
202210.1073/pnas.2202261119Braga, L. P. P., C. Orland, E. J. S. Emilson, A. A. Fitch, H. Osterholz, T. Dittmar, N. Basiliko, N. C. S. Mykytczuk and A. J. TanentzapViruses direct carbon cycling in lake sediments under global changeProceedings of the National Academy of Sciences119(41) e2202261119
202210.1016/j.jbc.2022.102396Bowler, J. T., M. R. Sawaya, D. R. Boyer, D. Cascio, M. Bali and D. S. EisenbergMicro-electron diffraction structure of the aggregation-driving N terminus of Drosophila neuronal protein Orb2A reveals amyloid-like _-sheetsJournal of Biological Chemistry298(10)
202210.3389/fpls.2021.769194Bouché, F., D. P. Woods, J. Linden, W. Li, K. S. Mayer, R. M. Amasino and C. PérilleuxEARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyonFrontiers in Plant Science12
202210.1242/dev.200565Bossi, F., B. Jin, E. Lazarus, H. Cartwright, Y. Dorone and S. Y. RheeCHIQUITA1 maintains the temporal transition between proliferation and differentiation in Arabidopsis thalianaDevelopment (Cambridge, England)149(11)
202210.1021/acssynbio.2c00119Borchert, A. J., A. Bleem and G. T. BeckhamExperimental and Analytical Approaches for Improving the Resolution of Randomly Barcoded Transposon Insertion Sequencing (RB-TnSeq) StudiesACS Synthetic Biology11(6) 2015–21
202210.1128/mra.00909-22Boone, G., K. Griffey and J. T. CooperDraft Genome Sequence of Cold-Tolerant Pseudomonas sp. Strain NKUCC02_KPG, Isolated from Old Alexandria Reservoir in Northern Kentucky, USAMicrobiology Resource Announcements11(11) e00909-22
202210.1111/tpj.15853Boatwright, J. L., S. Sapkota, H. Jin, J. C. Schnable, Z. Brenton, R. Boyles and S. KresovichSorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversityPlant Journal111(3) 888-904
202210.1111/nph.18213Blumstein, M., A. Sala, D. J. Weston, N. M. Holbrook and R. HopkinsPlant carbohydrate storage: intra- and inter-specific trade-offs reveal a major life history traitNew Phytologist235(6) 2211–22
202210.1002/fee.2430Bloom, E. H., K. K. Graham, N. L. Haan, A. R. Heck, L. J. Gut, D. A. Landis, M. O. Milbrath, G. M. Quinlan, J. K. Wilson, Y. Zhang, Z. Szendrei and R. IsaacsResponding to the US national pollinator plan: a case study in MichiganFrontiers in Ecology and the Environment20(2) 84–92
202210.1016/j.checat.2022.04.019Bleem, A., E. Kuatsjah, G. N. Presley, D. J. Hinchen, M. Zahn, D. C. Garcia, W. E. Michener, G. König, K. Tornesakis, M. N. Allemann, R. J. Giannone, J. E. McGeehan, G. T. Beckham and J. K. MichenerDiscovery, characterization, and metabolic engineering of Rieske non-heme iron monooxygenases for guaiacol O-demethylationChem Catalysis
202210.1007/978-3-030-97185-4_3Blaby-Haas, C. E.The Mosaic Landscape of Algal Metal Transport and UsageMicrobial Metabolism of Metals and Metalloids 55–75
202210.1038/s41559-022-01721-2Blaby-Haas, C. E.Polar algae flaunt their zinc assetsNature Ecology & Evolution6(7) 851–2
202210.3389/fpls.2021.782960Biswal, A. K., T.-Y. Wu, D. Urano, R. Pelissier, J.-B. Morel, A. M. Jones and A. K. BiswalNovel Mutant Alleles Reveal a Role of the Extra-Large G Protein in Rice Grain Filling, Panicle Architecture, Plant Growth, and Disease ResistanceFrontiers in Plant Science12
202210.1186/s13068-022-02119-9Biswal, A. K., N. N. Hengge, I. M. Black, M. A. Atmodjo, S. S. Mohanty, D. Ryno, M. E. Himmel, P. Azadi, Y. J. Bomble and D. MohnenComposition and yield of non-cellulosic and cellulosic sugars in soluble and particulate fractions during consolidated bioprocessing of poplar biomass by Clostridium thermocellumBiotechnology for Biofuels and Bioproducts15(1) 23
202210.1016/j.biortech.2022.126780Bing, R. G., C. T. Straub, D. B. Sulis, J. P. Wang, M. W. W. Adams and R. M. KellyPlant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for co-production of green hydrogen and acetone: Technoeconomic analysisBioresource Technology348
202210.1021/acssynbio.2c00051Bibik, J. D., S. M. Weraduwage, A. Banerjee, K. s. Robertson, R. Espinoza-Corral, T. D. Sharkey, P. K. Lundquist and B. R. HambergerPathway Engineering, Re-targeting, and Synthetic Scaffolding Improve the Production of Squalene in PlantsACS Synthetic Biology11(6) 2121–33
202210.1002/saj2.20382Bhattacharyya, A., R. K. Kukkadapu, M. Bowden, J. Pett-Ridge and P. S. NicoFast redox switches lead to rapid transformation of goethite in humid tropical soils: A Mössbauer spectroscopy studySoil Science Society of America Journal86(2) 264–74
202210.1504/IJBET.2022.10049492Bhattacharjee, R., A. Verma, N. Sharma and S. SharmaNon-rigid registration (computed tomography - ultrasound) of liver using B-splines and free form deformationInternational Journal of Biomedical Engineering and Technology39(4) 327-346
202210.1128/msystems.00913-22Bhattacharjee, A., O. Qafoku, J. A. Richardson, L. N. Anderson, K. Schwarz, et al.A Mineral-Doped Micromodel Platform Demonstrates Fungal Bridging of Carbon Hot Spots and Hyphal Transport of Mineral-Derived NutrientsmSystems7(6) e00913-22
202210.3389/fmicb.2022.844287Bhalla, A., J. Arce, B. Ubanwa, G. Singh, R. K. Sani and V. BalanThermophilic Geobacillus WSUCF1 Secretome for Saccharification of Ammonia Fiber Expansion and Extractive Ammonia Pretreated Corn StoverFrontiers in Microbiology13
202210.1093/plphys/kiac128Bewg, W. P., S. A. Harding, N. L. Engle, B. N. Vaidya, R. Zhou, et al.Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNAPlant Physiology189(2) 516–26
202210.7554/elife.70056Berry, J. C., M. Qi, B. V. Sonawane, A. Sheflin, A. Cousins, J. Prenni, D. P. Schachtman, P. Liu and R. S. BartIncreased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal componentseLife11
202210.1099/ijsem.0.005214Bergsten, P., P. Vannier, A. Mougeolle, L. Rigaud and V. T. MarteinssonRhodothermus bifroesti sp. nov., a thermophilic bacterium isolated from the basaltic subsurface of the volcanic island SurtseyInternational Journal of Systematic and Evolutionary Microbiology72(1)
202210.1111/gcbb.13004Bendorf, J., E. Heaton, T. Hartman, G. Aslan-Sungur and A. VanLoockeAgroecosystem model simulations reveal spatial variability in relative productivity in biomass sorghum and maize in Iowa, USAGCB Bioenergy14(12) 1336–60
202210.1128/mra.00212-22Beach, N. K., K. S. Myers, T. J. Donohue and D. R. NogueraMetagenomes from 25 Low-Abundance Microbes in a Partial Nitritation Anammox MicrobiomeMicrobiology Resource Announcements11(6) e00212-22
202210.1038/s41396-021-00916-yBates, C. T., A. Escalas, J. Kuang, L. Hale, Y. Wang, et al.Conversion of marginal land into switchgrass conditionally accrues soil carbon but reduces methane consumptionISME Journal16(1) 45224
202210.1007/s12155-021-10284-2Basyal, B., C. Foster, K. L. Gross and S. M. EmeryNitrogen Fertilizer, Arbuscular Mycorrhizal Fungi, and Soil Nematodes Affect Lignin Quality and Quantity in Switchgrass (Panicum virgatum L.)BioEnergy Research15(2) 1033–41
202210.1093/lambio/ovac049Basak, C. and R. ChakrabortyA novel strain of Shigella isolated from the gut of Lepidocephalichthys guntea has in its genome a complete gene package for Type ll secretion system, and elaborate repertoire of genes responsible for multiple antibiotic-resistance and metal resistance via specific efflux channelsLetters in Applied Microbiology76(1) ovac049
202210.1111/1462-2920.16148Bartoli, C., S. Boivin, M. Marchetti, C. Gris, V. Gasciolli, M. Gaston, M.-C. Auriac, F. Debellé, L. Cottret, A. Carlier, C. Masson-Boivin, M. Lepetit and B. LefebvreRhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root developmentEnvironmental Microbiology24(11) 5509–23
202210.1093/plcell/koac171Barros, J., H. K. Shrestha, J. C. Serrani-Yarce, N. L. Engle, P. E. Abraham, T. J. Tschaplinski, R. L. Hettich and R. A. DixonProteomic and metabolic disturbances in lignin-modified Brachypodium distachyonThe Plant Cell
202210.1111/mec.16436Barge, E. G., D. R. Leopold, A. Rojas, R. Vilgalys and P. E. BusbyPhylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonismMolecular Ecology31(10) 3018–30
202210.1016/j.soilbio.2022.108761Barbour, K. M., C. Weihe, S. D. Allison and J. B. H. MartinyBacterial community response to environmental change varies with depth in the surface soilSoil Biology and Biochemistry172
202210.1016/j.rser.2022.112857Baral, N. R., S. K. Mishra, A. George, S. Gautam, U. Mishra and C. D. ScownMultifunctional landscapes for dedicated bioenergy crops lead to low-carbon market-competitive biofuelsRenewable and Sustainable Energy Reviews169 112857
202210.1016/j.jclepro.2022.133508Banerjee, S., R. Singh, K. Eilts, E. J. Sacks and V. SinghValorization of Miscanthus x giganteus for sustainable recovery of anthocyanins and enhanced production of sugarsJournal of Cleaner Production369 133508
202210.1016/j.crbiot.2021.12.002Banerjee, D., M. A. Jindra, A. J. Linot, B. F. Pfleger and C. D. MaranasEnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learningCurrent Research in Biotechnology4 1–9
202210.1038/s41467-022-28540-0Baisya, D., A. Ramesh, C. Schwartz, S. Lonardi and I. WheeldonGenome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolyticaNature Communications13(1)
202210.1073/pnas.2203708119Bai, Y., T. Cao, O. Dautermann, P. Buschbeck, M. B. Cantrell, et al.Green diatom mutants reveal an intricate biosynthetic pathway of fucoxanthinProceedings of the National Academy of Sciences of the United States of America119(38)
202210.1099/ijsem.0.005188Bae, S. S., Y.-H. Jung, Y. M. Kwon, D. Chung, G. Choi, K. Cho, W.-J. Yu and K. BaekFulvivirga lutea sp. nov., a marine bacterium isolated from seawaterInternational Journal of Systematic and Evolutionary Microbiology72(1)
202210.23919/ACC53348.2022.9867540Badr, K., Q. Peter He and J. WangUnderstanding the evolution of interspecies metabolic interactions using dynamic genome-scale metabolic modelingProceedings of the American Control Conference2022-June 450-455
202210.1016/j.mex.2022.101652Badr, K., Q. P. He and J. WangMatlab implementation of a novel semi-structured kinetic model for methanotroph-photoautotroph coculturesMethodsX9
202210.1016/j.cej.2021.133461Badr, K., Q. P. He and J. WangA novel semi-structured kinetic model of methanotroph-photoautotroph cocultures for biogas conversionChemical Engineering Journal431
202210.1146/annurev-arplant-071921-100530Bachy, C., F. Wittmers, J. Muschiol, M. Hamilton, B. Henrissat and A. Z. WordenThe Land-Sea Connection: Insights Into the Plant Lineage from a Green Algal PerspectiveAnnual Review of Plant Biology73 585-616
202210.1145/3535508.3545536Babjac, A., T. Royalty, A. D. Steen and S. J. EmrichA comparison of dimensionality reduction methods for large biological dataProceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2022
202210.1128/mra.00983-22Babalola, O. O., V. F. Agunbiade and A. E. FadijiDraft Genome Sequence of Aeromonas caviae Strain A1-2, a Potential Plant Growth-Promoting Rhizospheric BacteriumMicrobiology Resource Announcements11(12) e00983-22
202210.1128/mra.00730-22Babalola, O. O., N. A. Agbodjato, A. S. Ayangbenro, A. Adjanohoun and L. Baba-MoussaDraft Genome Sequences of Four Strains of Plant Growth-Promoting Bacteria Associated with Maize RhizosphereMicrobiology Resource Announcements11(11) e00730-22
202210.1021/acssynbio.2c00061Baas-Thomas, M. S., S. B. Oehm, N. Ostrov and G. M. ChurchCharacterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coliACS Synthetic Biology11(6) 2009-2014
202210.1016/j.syapm.2022.126326Aydin, F., I. B. Saticioglu, H. Ay, T. Kayman, E. Karakaya and S. AbayDescription of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birdsSystematic and Applied Microbiology45(4) 126326
202210.1017/qrd.2022.10Autin, L., B. A. Barbaro, A. I. Jewett, A. Ekman, S. Verma, A. J. Olson and D. S. GoodsellIntegrative structural modelling and visualisation of a cellular organelleQRB Discovery3
202210.3390/ijms23063135Aulitto, M., L. Martinez-Alvarez, G. Fiorentino, D. Limauro, X. Peng and P. ContursiA Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological ApplicationsInternational Journal of Molecular Sciences23(6) 3135
202210.1039/D1LC00705JAufrecht, J., M. Khalid, C. L. Walton, K. Tate, J. F. Cahill and S. T. RettererHotspots of root-exuded amino acids are created within a rhizosphere-on-a-chipLab on a Chip22(5) 954–63
2022Arnolds, K., G. Li, J. G. Linger and M. T. GuarnieriIMAGINE BioSecurity: Integrative Modeling and Genome-scale Engineering for Biosystems SecurityFront Range Microbiome Symposium
2022Arnolds, K., G. Li, J. G. Linger and M. T. GuarnieriIMAGINE BioSecurity: Mesocosm based methods to evaluate biocontainment strategies and impact of industrial microbes upon native ecosystemsDOE Genomic Sciences Program Annual Meeting
202210.1111/pbi.13754Aregawi, K., J. Shen, G. Pierroz, M. K. Sharma, J. Dahlberg, J. Owiti and P. G. LemauxMorphogene-assisted transformation of Sorghum bicolor allows more efficient genome editingPlant Biotechnology Journal20(4) 748-760
202210.1094/mpmi-01-22-0011-taAppidi, M., A. Webb, D. L. Carper, S. S. Jawdy, R. J. Giannone, R. L. Hettich, J. L. Morrell-Falvey and P. E. AbrahamDevelopment of an experimental approach to achieve spatially resolved plant root-associated metaproteomics using an agar-plate systemMolecular Plant-Microbe Interactions
202210.3390/app12199620Apostolakos, I., M. Tsigkrimani, S. Paramithiotis and M. MataragasWhole-Genome Sequencing and Comparative Genomic Analysis of Enterococcus spp. Isolated from Dairy Products: Genomic Diversity, Functional Characteristics, and Pathogenic PotentialApplied Sciences12(19) 9620
202210.3390/dairy3040055Apostolakos, I., S. Paramithiotis and M. MataragasFunctional and Safety Characterization of Weissella paramesenteroides Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative GenomicsDairy3(4) 799–813
202210.1016/j.jbc.2022.102111Aoki, M., J. Vinokur, K. Motoyama, R. Ishikawa, M. Collazo, D. Cascio, M. R. Sawaya, T. Ito, J. U. Bowie and H. HemmiCrystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathwaysJournal of Biological Chemistry298(7)
202210.1128/mra.00645-22Aoki, M., N. Nakahara, M. Kusube and K. SyutsuboMetagenome-Assembled Genome Sequence of Marine Rhizobiaceae sp. Strain MnEN-MB40S, Obtained from Manganese-Oxidizing Enrichment CultureMicrobiology Resource Announcements11(9) e00645-22
202210.1128/aem.00188-22Anderson, C. E., J. Zhang, L. M. Markillie, H. D. Mitchell, W. B. Chrisler, M. J. Gaffrey, G. Orr and J. S. SchillingCapturing an Early Gene Induction Event during Wood Decay by the Brown Rot Fungus Rhodonia placentaApplied and Environmental Microbiology88(8)
202210.1007/s00203-022-03298-7Amulyasai, B., R. Anusha, C. Sasikala and C. V. RamanaPhylogenomic analysis of a metagenome-assembled genome indicates a new taxon of an anoxygenic phototroph bacterium in the family Chromatiaceae and the proposal of “Candidatus Thioaporhodococcus” gen. novArchives of Microbiology204(12) 688
202210.1038/s41477-022-01270-3Amos, R. A., M. A. Atmodjo, C. Huang, Z. Gao, A. Venkat, R. Taujale, N. Kannan, K. W. Moremen and D. MohnenPolymerization of the backbone of the pectic polysaccharide rhamnogalacturonan INature Plants8(11) 1289–303
202210.1099/ijsem.0.005460Altun, S., M. Duman, H. Ay and I. B. SaticiogluShewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss)International Journal of Systematic and Evolutionary Microbiology72(7)
202210.1002/ecs2.4063Alster, C. J., S. D. Allison and K. K. TresederTrait relationships of fungal decomposers in response to drought using a dual field and laboratory approachEcosphere13(6)
202210.1093/ee/nvab121Alred, B., N. Haan, D. A. Landis and M. Sz_csDoes the Presence of the Biological Control Agent, Hypena opulenta (Lepidoptera: Erebidae) on Swallow-Worts Deter Monarch Oviposition?Environmental Entomology51(1) 77–82
202210.1007/978-1-0716-1585-0_13Allen, B. H., N. Gupta, J. N. Edirisinghe, J. P. Faria and C. S. HenryApplication of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate GenomeMicrobial Systems Biology: Methods and Protocols 291–320
202210.1177/11769343211071114Alhindi, T. and R. AlbdaiwiDraft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan ValleyEvolutionary Bioinformatics18 1–6
202210.1038/s41396-021-01088-5Albright, M. B. N., S. Louca, D. E. Winkler, K. L. Feeser, S.-J. Haig, K. L. Whiteson, J. B. Emerson and J. DunbarSolutions in microbiome engineering: prioritizing barriers to organism establishmentThe ISME Journal16(2) 331–8
202210.1038/s43705-022-00109-4Albright, M. B. N., L. V. Gallegos-Graves, K. L. Feeser, K. Montoya, J. B. Emerson, M. Shakya and J. DunbarExperimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decompositionISME Communications2(1) 24
202210.1021/jasms.1c00343Aisporna, A., H. P. Benton, A. Chen, R. J. E. Derks, J. M. Galano, M. Giera and G. SiuzdakNeutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLINJournal of the American Society for Mass Spectrometry33(3) 530–4
202210.1128/mra.00951-21Ahmed, H., K. M. DeAngelis and M. A. MorrowDraft Genome Sequence of Leifsonia poae Strain BS71, Isolated from a Drought MicrocosmMicrobiology Resource Announcements11(1) e00951-21
202210.1038/s41564-022-01258-xAdler, B. A., T. Hessler, B. F. Cress, A. Lahiri, V. K. Mutalik, R. Barrangou, J. Banfield and J. A. DoudnaBroad-spectrum CRISPR-Cas13a enables efficient phage genome editingNature Microbiology7(12) 1967–79
202210.17221/171/2021-PPSAdeleke, S. B., S. A. Ayangbenro and O. O. BabalolaEffect of endophytic bacterium, Stenotrophomonas maltophilia JVB5 on sunflowersPlant Protection Science58(3) 185–98
202210.1021/acssuschemeng.2c01211Achinivu, E. C., M. Cabrera, A. Umar, M. Yang, N. R. Baral, C. D. Scown, B. A. Simmons and J. M. GladdenIn Situ Synthesis of Protic Ionic Liquids for Biomass PretreatmentACS Sustainable Chemistry & Engineering10(37) 12090–8
202210.1073/pnas.2119952119Abskharon, R., M. R. Sawaya, Q. Cao, B. A. Nguyen, D. R. Boyer, D. Cascio and D. S. EisenbergCryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formationProceedings of the National Academy of Sciences of the United States of America119(15)
202210.1016/j.soilbio.2021.108466Abramoff, R. Z., B. Guenet, H. Zhang, K. Georgiou, X. Xu, R. A. Viscarra Rossel, W. Yuan and P. CiaisImproved global-scale predictions of soil carbon stocks with Millennial Version 2Soil Biology and Biochemistry164 108466
202210.1093/g3journal/jkac269Abeyratne, C. R., D. Macaya-Sanz, R. Zhou, K. W. Barry, C. Daum, K. Haiby, A. Lipzen, B. Stanton, Y. Yoshinaga, M. Zane, G. A. Tuskan and S. P. DiFazioHigh-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpaG3 Genes|Genomes|Genetics13(1) jkac269
202110.1016/j.copbio.2021.06.024Zuniga, C., J. D. Tibocha-Bonilla and M. J. BetenbaughKinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communitiesCurrent Opinion in Biotechnology71 91-97
202110.1111/1462-2920.15316Zinke, L. A., P. N. Evans, C. Santos-Medellín, A. L. Schroeder, D. H. Parks, R. K. Varner, V. I. Rich, G. W. Tyson and J. B. EmersonEvidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the MethanomassiliicoccalesEnvironmental Microbiology23(1) 340-357
202110.1016/j.csbj.2020.11.052Ziegler, S. J., S. J. B. Mallinson, P. C. St. John and Y. J. BombleAdvances in integrative structural biology: Towards understanding protein complexes in their cellular contextComputational and Structural Biotechnology Journal19 214–25
202110.1007/s40789-020-00394-1Zhu, T., R. Wang, N. Yi, W. Niu, L. Wang and Z. XueCorrection to: CO2 and SO2 emission characteristics of the whole process industry chain of coal processing and utilization in China (International Journal of Coal Science & Technology, (2020), 7, 1, (19-25), 10.1007/s40789-020-00297-1)International Journal of Coal Science and Technology8(1) 176
202110.1002/cssc.202101137Zhou, P., K. L. Sánchez-Rivera, G. W. Huber and R. C. Van LehnComputational Approach for Rapidly Predicting Temperature-Dependent Polymer Solubilities Using Molecular-Scale ModelsChemSusChem14(19) 4307–16
202110.3791/61707Zhou, M., S. H. Abdali, D. Dilworth, L. Liu, B. Cole, et al.Isolation of histone from sorghum leaf tissue for top down mass spectrometry profiling of potential epigenetic markersJournal of Visualized Experiments2021(169)
202110.1039/D1GC00911GZhao, Z.-M., S. Zhang, X. Meng, Y. Pu, Z.-H. Liu, W. K. Ledford, S. M. Kilbey, B.-Z. Li and A. J. RagauskasElucidating the mechanisms of enhanced lignin bioconversion by an alkali sterilization strategyGreen Chemistry23(13) 4697–709
202110.1021/acschembio.1c00267Zhao, Z., E. E. Ozcan, E. VanArsdale, J. Li, E. Kim, A. D. Sandler, D. L. Kelly, W. E. Bentley and G. F. PayneMediated Electrochemical Probing: A Systems-Level Tool for Redox BiologyACS Chemical Biology16(7) 1099–110
202110.1094/mpmi-08-20-0222-aZhao, Z., N. Bokros, S. DeBolt, P. Yang and Y. XiaGenome Sequence Resource of Bacillus sp. RRD69, a Beneficial Bacterial Endophyte Isolated from Switchgrass PlantsMolecular Plant-Microbe Interactions34(11) 1320–3
202110.3389/fpls.2021.755576Zhao, Y., X.-H. Yu and C.-J. LiuThe Inducible Accumulation of Cell Wall-Bound p-Hydroxybenzoates Is Involved in the Regulation of Gravitropic Response of PoplarFrontiers in Plant Science12
202110.1038/s41477-021-00975-1Zhao, Y., X. Yu, P.-Y. Lam, K. Zhang, Y. Tobimatsu and C.-J. LiuMonolignol acyltransferase for lignin p-hydroxybenzoylation in PopulusNature Plants7(9) 1288–300
202110.7554/eLife.69508Zhao, K., D. Kong, B. Jin, C. D. Smolke and S. Y. RheeA novel form of bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in ArabidopsiseLife10
202110.1021/acssynbio.0c00642Zhao, E. M., M. A. Lalwani, J. M. Chen, P. Orillac, J. E. Toettcher and J. L. AvalosOptogenetic Amplification Circuits for Light-Induced Metabolic ControlACS Synthetic Biology10(5) 1143-1154
202110.1088/1748-9326/abecbeZhang, X., T. J. Lark, C. M. Clark, Y. Yuan and S. D. LeDucGrassland-to-cropland conversion increased soil, nutrient, and carbon losses in the US Midwest between 2008 and 2016Environmental Research Letters16(5) 54018
202110.1158/0008-5472.CAN-21-0206Zhang, S., Y. F. Zhou, J. Cao, S. K. Burley, H. Y. Wang and X. F. S. ZhengmTORC1 Promotes ARID1A degradation and oncogenic chromatin remodeling in hepatocellular carcinomaCancer Research81(22) 5642-5665
202110.1016/j.jmva.2021.104786Zhang, L., W. Zhou and H. WangA semiparametric latent factor model for large scale temporal data with heteroscedasticityJournal of Multivariate Analysis186
202110.1093/g3journal/jkab144Zhang, L., A. MacQueen, J. Bonnette, F. B. Fritschi, D. B. Lowry and T. E. JuengerQTL _ environment interactions underlie ionome divergence in switchgrassG3 Genes|Genomes|Genetics11(7)
202110.1128/mSystems.01351-20Zhang, K., W. Zhao, D. A. Rodionov, G. M. Rubinstein, D. N. Nguyen, T. N. N. Tanwee, J. Crosby, R. G. Bing, R. M. Kelly, M. W. W. Adams and Y. ZhangGenome-scale metabolic model of caldicellulosiruptor bescii reveals optimal metabolic engineering strategies for bio-based chemical productionmSystems6(3)
202110.1039/D1GC02854EZhang, J., E. Yoo, B. H. Davison, D. Liu, J. A. Schaidle, L. Tao and Z. LiTowards cost-competitive middle distillate fuels from ethanol within a market-flexible biorefinery conceptGreen Chemistry23(23) 9534–48
202110.1016/j.cej.2021.128660Zhang, J., W. Shen, C. Collings, K. A. Vander Meulen, B. G. Fox, L. M. Vázquez Ramos, J. A. Dumesic and S.-Y. DingVisualizing plant cell wall changes proves the superiority of hydrochloric acid over sulfuric acid catalyzed _-valerolactone pretreatmentChemical Engineering Journal412 128660
202110.1007/s00374-021-01544-6Zhang, B., C. R. Penton, Z. Yu, C. Xue, Q. Chen, Z. Chen, C. Yan, Q. Zhang, M. Zhao, J. F. Quensen and J. M. TiedjeA new primer set for Clade I nosZ that recovers genes from a broader range of taxaBiology and Fertility of Soils57(4) 523–31
202110.1094/pbiomes-12-20-0090-eZhalnina, K., C. Hawkes, A. Shade, M. K. Firestone and J. Pett-RidgeManaging Plant Microbiomes for Sustainable Biofuel ProductionPhytobiomes Journal5(1) 3–13
202110.3390/plants10030513Zhai, Z., H. Liu and J. ShanklinEctopic Expression of OLEOSIN 1 and Inactivation of GBSS1 Have a Synergistic Effect on Oil Accumulation in Plant LeavesPlants10(3) 513
202110.1021/jasms.1c00113Zenaidee, M. A., B. Wei, C. Lantz, H. T. Wu, T. R. Lambeth, J. K. Diedrich, R. R. Ogorzalek Loo, R. R. Julian and J. A. LooInternal Fragments Generated from Different Top-Down Mass Spectrometry Fragmentation Methods Extend Protein Sequence CoverageJournal of the American Society for Mass Spectrometry32(7) 1752-1758
202110.1002/cbic.202000616Zegeye, E. K., N. C. Sadler, G. X. Lomas, I. K. Attah, J. K. Jansson, K. S. Hofmockel, C. R. Anderton and A. T. WrightActivity-Based Protein Profiling of Chitin CatabolismChemBioChem22(4) 717–23
202110.1007/978-1-0716-0966-8_17Zee, C. T., A. Saha, M. R. Sawaya and J. A. RodriguezAb Initio Determination of Peptide Structures by MicroEDMethods in Molecular Biology2215 329-348
202110.1016/j.copbio.2021.01.013Zaramela, L. S., O. Moyne, M. Kumar, C. Zuniga, J. D. Tibocha-Bonilla and K. ZenglerThe Sum is Greater than the Parts: Exploiting Microbial Communities to Achieve Complex FunctionsCurrent Opinion in Biotechnology67 149–57
202110.7717/peerj.11088Zablocki, O., M. Michelsen, M. Burris, N. Solonenko, J. Warwick-Dugdale, R. Ghosh, J. Pett-Ridge, M. B. Sullivan and B. TempertonVirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in naturePeerJ9 e11088
202110.1186/s43008-021-00067-xYurkov, A., A. Alves, F.-Y. Bai, K. Boundy-Mills, P. Buzzini, et al.Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changesIMA Fungus12(1) 18
202110.1021/acscatal.0c05393Yun, D., E. Z. Ayla, D. T. Bregante and D. W. FlahertyReactive Species and Reaction Pathways for the Oxidative Cleavage of 4-Octene and Oleic Acid with H2O2 over Tungsten Oxide CatalystsACS Catalysis11(5) 3137–52
202110.3389/fenrg.2021.640337Yue, F., W. Lan, L. Zhang, F. Lu, R. Sun and J. RalphEfficient Synthesis of Pinoresinol, an Important Lignin Dimeric Model CompoundFrontiers in Energy Research9
202110.1016/j.carbpol.2021.117637Yuan, Y., H. Li, W. Leite, Q. Zhang, P. V. Bonnesen, J. L. Labbé, K. L. Weiss, S. V. Pingali, K. Hong, V. S. Urban, S. Salmon and H. O’NeillBiosynthesis and characterization of deuterated chitosan in filamentous fungus and yeastCarbohydrate Polymers257 117637
202110.1128/mBio.03509-20Yuan, M. M., A. Kakouridis, E. Starr, N. Nguyen, S. Shi, J. Zhou, M. Firestone, J. Pett-Ridge and E. NuccioFungal-bacterial cooccurrence patterns differ between arbuscular mycorrhizal fungi and nonmycorrhizal fungi across soil nichesmBio12(2)
202110.1038/s41558-021-00989-9Yuan, M. M., X. Guo, L. Wu, Y. Zhang, N. Xiao, D. Ning, Z. Shi, X. Zhou, L. Wu, Y. Yang, J. M. Tiedje and J. ZhouClimate warming enhances microbial network complexity and stabilityNature Climate Change11(4) 343-348
202110.1038/s41438-021-00663-3Yuan, G., H. Lu, D. Tang, M. M. Hassan, Y. Li, J.-G. Chen, G. A. Tuskan and X. YangExpanding the application of a UV-visible reporter for transient gene expression and stable transformation in plantsHorticulture Research8
202110.1021/acssynbio.1c00455Yuan, G., M. M. Hassan, T. Yao, H. Lu, M. M. Vergara, J. L. Labbé, W. Muchero, C. Pan, J.-G. Chen, G. A. Tuskan, Y. Qi, P. E. Abraham and X. YangPlant-Based Biosensors for Detecting CRISPR-Mediated Genome EngineeringACS Synthetic Biology10(12) 3600–3
202110.1093/plphys/kiaa109Yu, X. H., Y. Cai, J. Keereetaweep, K. Wei, J. Chai, E. Deng, H. Liu and J. ShanklinBiotin Attachment Domain-Containing Proteins Mediate Hydroxy Fatty Acid-Dependent Inhibition of Acetyl CoA CarboxylasePlant Physiology185(3) 892–901
202110.1038/s41467-020-20094-3Yu, T. C., W. L. Liu, M. S. Brinck, J. E. Davis, J. Shek, G. Bower, T. Einav, K. D. Insigne, R. Phillips, S. Kosuri and G. UrtechoMultiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systemsNature Communications12(1)
202110.1111/tpj.15273Yu, L., C. Zhou, J. Fan, J. Shanklin and C. XuMechanisms and functions of membrane lipid remodeling in plantsThe Plant Journal107(1) 37–53
202110.1038/s41598-020-79975-8Yu, K. M. J., B. McKinley, W. L. Rooney and J. E. MulletHigh planting density induces the expression of GA3-oxidase in leaves and GA mediated stem elongation in bioenergy sorghumScientific Reports11(1) 46
202110.1186/s13068-021-02026-5Yu, H., C. Liu and R. A. DixonA gene-editing/complementation strategy for tissue-specific lignin reduction while preserving biomass yieldBiotechnology for Biofuels14(1) 175
202110.1038/s41592-021-01137-zYoung, J. Y., J. Berrisford and M. ChenwwPDB biocuration: on the front line of structural biologyNature Methods18(5) 431-432
202110.1093/plphys/kiaa071Young, D. Y. and Y. Shachar-HillLarge fluxes of fatty acids from membranes to triacylglycerol and back during N-deprivation and recovery in ChlamydomonasPlant Physiology185(3) 796–814
202110.1021/bk-2021-1377.ch001Yoo, C. G. and A. J. RagauskasOpportunities and Challenges of Lignin UtilizationLignin Utilization Strategies: From Processing to Applications1377 1–12
202110.3389/fmicb.2021.625752Yee, M. O., P. Kim, Y. Li, A. K. Singh, T. R. Northen and R. ChakrabortySpecialized Plant Growth Chamber Designs to Study Complex Rhizosphere InteractionsFrontiers in Microbiology12
202110.1128/AEM.03017-20Yayo, J., T. Kuil, D. G. Olson, L. R. Lynd, E. K. Holwerda and A. J. A. v. MarisLaboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and FructoseApplied and Environmental Microbiology87(9) e03017-20
202110.1093/gbe/evab198Yates, T. B., K. Feng, J. Zhang, V. Singan, S. S. Jawdy, P. Ranjan, P. E. Abraham, K. Barry, A. Lipzen, C. Pan, J. Schmutz, J.-G. Chen, G. A. Tuskan and W. MucheroThe Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpaGenome Biology and Evolution13(9)
202110.3389/fpls.2021.704697Yao, T., K. Feng, M. Xie, J. Barros, T. J. Tschaplinski, G. A. Tuskan, W. Muchero and J. G. ChenPhylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in PlantsFrontiers in Plant Science12 704697
202110.1021/acssuschemeng.0c09330Yao, A., H. Choudhary, M. Mohan, A. Rodriguez, H. Magurudeniya, J. G. Pelton, A. George, B. A. Simmons and J. M. GladdenCan Multiple Ions in an Ionic Liquid Improve the Biomass Pretreatment Efficacy?ACS Sustainable Chemistry & Engineering9(12) 4371–6
202110.1111/pbi.13550Yang, Y., J. H. Lee, M. R. Poindexter, Y. Shao, W. Liu, S. C. Lenaghan, A. H. Ahkami, E. Blumwald and C. N. StewartRational design and testing of abiotic stress-inducible synthetic promoters from poplar cis-regulatory elementsPlant Biotechnology Journal19(7) 1354-1369
2021Yang, X., G. A. Tuskan, D. Liu, R. HU, J.-G. Chen and M. XieGenes for enhancing drought and heat tolerance in plants and methods of useLLC, U. B.
202110.34133/2021/9798714Yang, X., D. Liu, H. Lu, D. J. Weston, J.-G. Chen, et al.Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide RemovalBioDesign Research2021 9798714
202110.1016/j.biombioe.2021.106275Yang, P., X. Cai, C. Leibensperger and M. KhannaAdoption of perennial energy crops in the US Midwest: Causal and heterogeneous determinantsBiomass and Bioenergy155 106275
202110.1111/gcbb.12821Yang, P., X. Cai and M. KhannaFarmers' heterogeneous perceptions of marginal land for biofuel crops in US Midwestern states considering biophysical and socioeconomic factorsGCB Bioenergy13(5) 849–61
202110.1021/acssuschemeng.1c01706Yang, M., J. Dahlberg, N. R. Baral, D. Putnam and C. D. ScownIdentifying Forage Sorghum Ideotypes for Advanced BiorefineriesACS Sustainable Chemistry & Engineering9(23) 7873–81
202110.1016/j.indcrop.2021.113587Yang, L., M. Lin, H. Zhang, C. Wang, L. Shi, W. Lan, L. Zhang, F. Yue and F. LuFerulate-sinapyl alcohol cross-coupling reaction improves the understanding of grass cell wall lignificationIndustrial Crops and Products168
202110.1093/plphys/kiab169Yang, J., E. Bertolini, M. Braud, J. Preciado, A. Chepote, H. Jiang and A. L. EvelandThe SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridisPlant Physiology187(3) 1202-1220
202110.1111/1758-2229.13012Yadav, S., M. Koenen, N. Bale, J. S. Sinninghe Damsté and L. VillanuevaThe physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological roleEnvironmental Microbiology Reports13(6) 899–910
202110.1021/acs.analchem.1c01246Xue, J., R. J. E. Derks, B. Webb, E. M. Billings, A. Aisporna, M. Giera and G. SiuzdakSingle Quadrupole Multiple Fragment Ion Monitoring Quantitative Mass SpectrometryAnalytical Chemistry93(31) 10879–89
202110.1186/s13068-020-01861-2Xu, Z., C. Pan, X. Li, N. Hao, T. Zhang, M. J. Gaffrey, Y. Pu, J. R. Cort, A. J. Ragauskas, W.-J. Qian and B. YangEnhancement of polyhydroxyalkanoate production by co-feeding lignin derivatives with glycerol in Pseudomonas putida KT2440Biotechnology for Biofuels14(1) 11
202110.3390/plants10122726Xu, Y., V. Shrestha, C. Piasecki, B. Wolfe, L. Hamilton, R. J. Millwood, M. Mazarei and C. N. StewartSustainability Trait Modeling of Field-Grown Switchgrass (Panicum virgatum) Using UAV-Based ImageryPlants10(12) 2726
202110.1038/s41467-021-23553-7Xu, L., Z. Dong, D. Chiniquy, G. Pierroz, S. Deng, et al.Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamicsNature Communications12(1)
202110.1016/j.rse.2021.112445Xie, Y. and T. J. LarkMapping annual irrigation from Landsat imagery and environmental variables across the conterminous United StatesRemote Sensing of Environment260 112445
202110.5194/essd-13-5689-2021Xie, Y., H. K. Gibbs and T. J. LarkLandsat-based Irrigation Dataset (LANID): 30 m resolution maps of irrigation distribution, frequency, and change for the US, 1997–2017Earth System Science Data13(12) 5689–710
2021Xie, M., J.-G. Chen, W. Muchero, C. Pan, D. M. Close, E. B. Gee and Q. YaoMethods of improving drought and salt resistance in a plant and genetically engineering plants with improved drought and salt resistanceLLC, U. B.
202110.1128/MRA.01410-20Xavier, R. K. M., D. Xu, P. J. McCarthy, S. Yang and G. WangGenome Sequence of Streptomyces sp. Strain HB-N217, Isolated from the Marine Sponge Forcepia sp.Microbiology Resource Announcements10(8) e01410-20
202110.1128/Spectrum.01414-21Wu, X., A. E. Kazakov, S. Gushgari-Doyle, X. Yu, V. Trotter, R. K. Stuart and R. ChakrabortyComparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in JanthinobacteriumMicrobiology Spectrum9(3) e01414-21
202110.1021/acs.est.1c00802Wu, X., A. Chauhan, A. C. Layton, M. C. Y. Lau Vetter, B. T. Stackhouse, D. E. Williams, L. Whyte, S. M. Pfiffner, T. C. Onstott and T. A. VishnivetskayaComparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High ArcticEnvironmental Science and Technology55(18) 12683-12693
202110.1038/s41598-021-92395-6Wu, T., J. Liu, Z. Guo, J. Hou and J. ChengMULTICOM2 open-source protein structure prediction system powered by deep learning and distance predictionScientific Reports11(1)
202110.1128/mBio.02595-21Wu, R., M. R. Davison, W. C. Nelson, E. B. Graham, S. J. Fansler, Y. Farris, S. L. Bell, I. Godinez, J. E. Mcdermott, K. S. Hofmockel and J. K. JanssonDNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture RegimesmBio12(6) e02595-21
202110.1038/s42003-021-02514-2Wu, R., M. R. Davison, Y. Gao, C. D. Nicora, J. E. McDermott, K. E. Burnum-Johnson, K. S. Hofmockel and J. K. JanssonMoisture modulates soil reservoirs of active DNA and RNA virusesCommunications Biology4(1) 992
202110.1093/gbe/evab148Wu, K., Z.-H. Cheng, E. Williams, N. T. Turner, D. Ran, H. Li, X. Zhou, H. Guo, W. Sung, D.-F. Liu, M. Lynch and H. LongUnexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control StrainsGenome Biology and Evolution13(8)
202110.1109/Cluster48925.2021.00053Wolf, M., J. Logan, K. Mehta, D. Jacobson, M. Cashman, A. M. Walker, G. Eisenhauer, P. Widener and A. CliffReusability First: Toward FAIR Workflows2021 IEEE International Conference on Cluster Computing (CLUSTER)444–55
202110.1128/mbio.03259-21Wilkes, R. A., J. Waldbauer and L. AristildeAnalogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic GrowthmBio12(6) e03259-21
202110.1128/mSystems.00002-21Wilken, S. E., J. M. Monk, P. A. Leggieri, C. E. Lawson, T. S. Lankiewicz, et al.Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota FungusmSystems6(1) e00002-21
202110.1128/mBio.03099-20Wilhelm, R. C., C. Pepe-Ranney, P. Weisenhorn, M. Lipton and D. H. BuckleyCompetitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural SoilmBio12(1)
202110.12688/f1000research.51494.2Werbin, Z. R., B. Hackos, J. Lopez-Nava, M. C. Dietze and J. M. BhatnagarThe National Ecological Observatory Network's soil metagenomes: assembly and basic analysisF1000Research10 299
202110.1021/jasms.0c00251Weitz, K. K., M. L. Smith, K. K. Hixson, E. A. Hill, J. K. Jansson, K. S. Hofmockel and M. S. LiptonReal-Time Mass Spectrometry Measurements of Respiration Rates in Biological SystemsJournal of the American Society for Mass Spectrometry32(3) 648–52
202110.3389/fmicb.2021.757741Wei, H., W. Wang, E. P. Knoshaug, X. Chen, S. Van Wychen, Y. J. Bomble, M. E. Himmel and M. ZhangDisruption of the Snf1 Gene Enhances Cell Growth and Reduces the Metabolic Burden in Cellulase-Expressing and Lipid-Accumulating Yarrowia lipolyticaFrontiers in Microbiology12
202110.1016/j.tibs.2021.06.007Wedow, J. M., E. A. Ainsworth and S. LiPlant biochemistry influences tropospheric ozone formation, destruction, deposition, and responseTrends in Biochemical Sciences46(12) 992–1002
202110.1016/B978-0-08-102688-5.00073-8Waugh, M. W., S. Dwaraknath and Y. LuAdvances in Metalloprotein Design and Engineering: Strategies Employed and Insights GainedComprehensive Coordination Chemistry III 900–28
202110.1038/s42003-021-02244-5Ware, I. M., M. E. Van Nuland, Z. K. Yang, C. W. Schadt, J. A. Schweitzer and J. K. BaileyClimate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenologyCommunications Biology4(1) 748
202110.1038/s43586-020-00006-xWannier, T. M., P. N. Ciaccia, A. D. Ellington, G. T. Filsinger, F. J. Isaacs, K. Javanmardi, M. A. Jones, A. M. Kunjapur, A. Nyerges, C. Pal, M. G. Schubert and G. M. ChurchRecombineering and MAGENature Reviews Methods Primers1(1)
202110.1021/acs.biomac.1c00223Wang, Y.-Y., B. Scheidemantle, C. E. Wyman, C. M. Cai and A. J. RagauskasPolyurethanes Based on Unmodified and Refined Technical Lignins: Correlation between Molecular Structure and Material PropertiesBiomacromolecules22(5) 2129–36
202110.1021/acs.chemrev.1c00260Wang, Y., P. Xue, M. Cao, T. Yu, S. T. Lane and H. ZhaoDirected Evolution: Methodologies and ApplicationsChemical Reviews121(20) 12384-12444
202110.1002/cssc.202101492Wang, Y., X. Meng, Y. Tian, K. H. Kim, L. Jia, Y. Pu, G. Leem, D. Kumar, A. Eudes, A. J. Ragauskas and C. G. YooEngineered Sorghum Bagasse Enables a Sustainable Biorefinery with p-Hydroxybenzoic Acid-Based Deep Eutectic SolventChemSusChem14(23) 5235–44
202110.1186/s12870-021-02903-zWang, Y., W. Dong, M. C. Saha, M. K. Udvardi and Y. KangImproved node culture methods for rapid vegetative propagation of switchgrass (Panicum virgatum L.)BMC Plant Biology21(1) 128
202110.1111/tpj.15365Wang, Y., K. X. Chan and S. P. LongTowards a dynamic photosynthesis model to guide yield improvement in C4 cropsThe Plant Journal107(2) 343–59
202110.1186/s12915-021-01124-yWang, Y., F. Baumdicker, P. Schweiger, S. Kuenzel and F. StaubachHorizontal gene transfer-mediated bacterial strain variation affects host fitness in DrosophilaBMC Biology19(1) 187
202110.1016/j.ymben.2021.01.004Wang, X., J. H. Pereira, S. Tsutakawa, X. Fang, P. D. Adams, A. Mukhopadhyay and T. S. LeeEfficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450Metabolic Engineering64 41–51
202110.1093/jxb/eraa432Wang, S., K. Guan, Z. Wang, E. A. Ainsworth, T. Zheng, P. A. Townsend, K. Li, C. Moller, G. Wu and C. JiangUnique contributions of chlorophyll and nitrogen to predict crop photosynthetic capacity from leaf spectroscopyJournal of Experimental Botany72(2) 341–54
202110.1111/nph.17355Wang, P., B. M. Moore, S. Uygun, M. D. Lehti-Shiu, C. S. Barry and S.-H. ShiuOptimising the use of gene expression data to predict plant metabolic pathway membershipsNew Phytologist231(1) 475–89
202110.1186/s12864-021-07397-5Wang, P., F. Meng, B. M. Moore and S.-H. ShiuImpact of short-read sequencing on the misassembly of a plant genomeBMC Genomics22(1) 99
202110.1128/MSYSTEMS.00749-20Wang, P., Y. N. Chai, R. Roston, F. E. Dayan and D. P. SchachtmanThe Sorghum bicolor root exudate sorgoleone shapes bacterial communities and delays network formationmSystems6(2)
202110.1371/journal.pcbi.1009448Wang, L., V. Upadhyay and C. D. MaranasdGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway designPLoS Computational Biology17(9) e1009448
202110.1021/acssynbio.0c00598Wang, L. and C. D. MaranasComputationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic CompoundsACS Synthetic Biology10(5) 1064–76
202110.1111/gcbb.12872Wang, J., Y. Li, C. M. Wai, G. Beuchat and L. Q. ChenIdentification and analysis of stem-specific promoters from sugarcane and energy cane for oil accumulation in their stemsGCB Bioenergy13(9) 1515-1527
202110.1016/j.csbj.2021.03.034Wang, J., D. L. Carper, L. H. Burdick, H. K. Shrestha, M. R. Appidi, P. E. Abraham, C. M. Timm, R. L. Hettich, D. A. Pelletier and M. J. DoktyczFormation, characterization and modeling of emergent synthetic microbial communitiesComputational and Structural Biotechnology Journal19 1917–27
202110.1016/j.carbpol.2021.118564Wang, H.-T., V. S. Bharadwaj, J.-Y. Yang, T. M. Curry, K. W. Moremen, Y. J. Bomble and B. R. UrbanowiczRational enzyme design for controlled functionalization of acetylated xylan for cell-free polymer biosynthesisCarbohydrate Polymers273 118564
202110.1038/s41477-021-00852-xWang, H., Y. Li, M. Chern, Y. Zhu, L.-L. Zhang, et al.Suppression of rice miR168 improves yield, flowering time and immunityNature Plants7(2) 129–36
202110.3389/fpls.2021.650109Wang, H., J.-G. Chen and Y. ChangIdentification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress ResponseFrontiers in Plant Science12
202110.1038/s41467-021-25369-xWang, B., Y. Xu, X. Wang, J. S. Yuan, C. H. Johnson, J. D. Young and J. YuA guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteriaNature Communications12(1)
202110.1002/ecs2.3562Wang, B. and S. D. AllisonDrought legacies mediated by trait trade-offs in soil microbiomesEcosphere12(6)
202110.1128/MRA.00072-21Wall, J. D., G. M. Zane, T. R. Juba, J. V. Kuehl, J. Ray, S. R. Chhabra, V. V. Trotter, M. Shatsky, K. B. D. León, K. L. Keller, K. S. Bender, G. Butland, A. P. Arkin and A. M. DeutschbauerDeletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris HildenboroughMicrobiology Resource Announcements10(11) e00072-21
202110.1128/mSystems.00443-21Walker, C., B. Dien, R. J. Giannone, P. Slininger, S. R. Thompson and C. T. TrinhExploring proteomes of robust yarrowia lipolytica isolates cultivated in biomass hydrolysate reveals key processes impacting mixed sugar utilization, lipid accumulation, and degradationmSystems6(4)
202110.1016/j.ymben.2021.01.013Wada, A., É. T. Prates, R. Hirano, A. Z. Werner, N. Kamimura, D. A. Jacobson, G. T. Beckham and E. MasaiCharacterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromaticsMetabolic Engineering64 167–79
202110.1002/agj2.20832von Haden, A. C., M. B. Burnham, W. H. Yang and E. H. DeLuciaComparative establishment and yield of bioenergy sorghum and maize following pre-emergence waterloggingAgronomy Journal113(6) 5602–11
202110.1016/j.jclepro.2021.126875Viswanathan, M. B., M.-H. Cheng, T. E. Clemente, I. Dweikat and V. SinghEconomic perspective of ethanol and biodiesel coproduction from industrial hempJournal of Cleaner Production299 126875
202110.1128/MRA.00652-21Villarreal, A. R., D. E. Campbell, S. S. Webster and R. C. HunterDraft genome sequence of scheffersomyces spartinae ARV011, a marine yeast isolateMicrobiology Resource Announcements10(45)
202110.1016/j.scitotenv.2020.144498Villa, J. A., Y. Ju, T. Yazbeck, S. Waldo, K. C. Wrighton and G. BohrerEbullition dominates methane fluxes from the water surface across different ecohydrological patches in a temperate freshwater marsh at the end of the growing seasonScience of the Total Environment767
202110.1111/1462-2920.15409Viljakainen, V. R. and L. A. HugThe phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic-degrading genesEnvironmental Microbiology23(3) 1717-1731
202110.29303/jbt.v21i2.2802Viersanova, A. and H. PurwantoDraft Genome of Lysinibacillus sphaericus Isolate 229C Pathogenic to Vector MosquitoesJurnal Biologi Tropis21(2) 576–86
202110.1021/acssynbio.1c00136Vezeau, G. E. and H. M. SalisTuning cell-free composition controls the time delay, dynamics, and productivity of TX-TL expressionACS Synthetic Biology10(10) 2508-2519
202110.1016/j.plantsci.2020.110693Verhertbruggen, Y., A. Bouder, J. Vigouroux, C. Alvarado, A. Geairon, et al.The TaCslA12 gene expressed in the wheat grain endosperm synthesizes wheat-like mannan when expressed in yeast and ArabidopsisPlant Science302 110693
202110.1111/nph.17462Veneault-Fourrey, C. and M. RepQuantitative resistance linked to late effectorsNew Phytologist231(4) 1301–3
202110.3390/jof7080609Veli_kovi_, D., M. Zhou, J. S. Schilling and J. ZhangUsing MALDI-FTICR-MS imaging to track low-molecular-weight aromatic derivatives of fungal decayed woodJournal of Fungi7(8)
202110.1371/journal.pone.0231367Vélez, J. M., R. M. Morris, R. Vilgalys, J. Labbé and C. W. SchadtPhylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representativesPLoS ONE16(1) e0231367
202110.1002/wsbm.1512Vasdekis, A. E. and A. SinghMicrobial metabolic noiseWIREs Systems Biology and Medicine13(3) e1512
202110.12688/F1000RESEARCH.27262.1Varoquaux, N. and E. PurdomA pipeline to analyse time-course gene expression data [version 1; peer review: 1 approved with reservations]F1000Research9 15342
202110.3390/rs13091763Varela, S., T. Pederson, C. J. Bernacchi and A. D. B. LeakeyUnderstanding Growth Dynamics and Yield Prediction of Sorghum Using High Temporal Resolution UAV Imagery Time Series and Machine LearningRemote Sensing13(9) 1763
202110.1128/mSystems.01194-20Vangay, P., J. Burgin, A. Johnston, K. L. Beck, D. C. Berrios, et al.Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On ActivitiesmSystems6(1)
202110.1002/ajb2.1659Valverde-Barrantes, O. J., L. Authier, H. Schimann and C. BaralotoRoot anatomy helps to reconcile observed root trait syndromes in tropical tree speciesAmerican Journal of Botany108(5) 744-755
202110.1107/S2059798321003922Vadivel, K., A. E. Schmidt, D. Cascio, K. Padmanabhan, S. Krishnaswamy, H. Brandstetter and S. P. BajajStructure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidiumActa Crystallographica Section D: Structural Biology77 809-819
202110.1094/pbiomes-12-19-0069-fiUlbrich, T. C., M. L. Friesen, S. S. Roley, L. K. Tiemann and S. E. EvansIntraspecific Variability in Root Traits and Edaphic Conditions Influence Soil Microbiomes Across 12 Switchgrass CultivarsPhytobiomes Journal5(1) 108–20
202110.7554/eLife.52770Turn_ek, J., J. K. Brunson, M. P. Martinez Viedma, T. J. Deerinck, A. Horák, M. Oborník, V. A. Bielinski and A. E. AllenProximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathwayeLife10 1-113
202110.1038/s41396-021-00919-9Turkarslan, S., N. Stopnisek, A. W. Thompson, C. E. Arens, J. J. Valenzuela, et al.Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactionsThe ISME Journal15(8) 2233–47
202110.3389/feduc.2021.711618Tully, B. J., J. Buongiorno, A. B. Cohen, J. A. Cram, A. I. Garber, et al.The Bioinformatics Virtual Coordination Network: An Open-Source and Interactive Learning EnvironmentFrontiers in Education6
202110.1201/9781003048237-19Tsai, C.-J.Genome editing of woody perennial treesGenome editing for precision crop breeding 441–57
202110.1186/s40168-021-01154-2Trubl, G., J. A. Kimbrel, J. Liquet-Gonzalez, E. E. Nuccio, P. K. Weber, J. Pett-Ridge, J. K. Jansson, M. P. Waldrop and S. J. BlazewiczActive virus-host interactions at sub-freezing temperatures in Arctic peat soilMicrobiome9(1) 208
202110.7717/peerj.12628Tross, M. C., M. Gaillard, M. Zwiener, C. Miao, R. J. Grove, B. Li, B. Benes and J. C. Schnable3D reconstruction identifies loci linked to variation in angle of individual sorghum leavesPeerJ9
202110.1525/elementa.2020.00144Treseder, K. K., C. J. Alster, L. A. Cat, M. E. Gorris, A. L. Kuhn, K. G. Lovero, F. Hagedorn, J. F. Kerekes, T. A. McHugh and E. F. SollyNutrient and stress tolerance traits linked to fungal responses to global change: Four case studiesElementa9(1)
202110.1093/jimb/kuab067Tran, V. G. and H. ZhaoEngineering robust microorganisms for organic acid productionJournal of Industrial Microbiology and Biotechnology49(2)
202110.1002/tpg2.20149Tilhou, N. W. and M. D. CaslerSubsampling and DNA pooling can increase gains through genomic selection in switchgrassThe Plant Genome14(3) e20149
202110.1186/s13068-021-02068-9Tian, Y., C.-Y. Lin, J.-H. Park, C.-Y. Wu, R. Kakumanu, et al.Overexpression of the rice BAHD acyltransferase AT10 increases xylan-bound p-coumarate and reduces lignin in Sorghum bicolorBiotechnology for Biofuels14(1) 217
202110.3389/fpls.2021.704905Tian, F., X.-L. Hu, T. Yao, X. Yang, J.-G. Chen, M.-Z. Lu and J. ZhangRecent Advances in the Roles of HSFs and HSPs in Heat Stress Response in Woody PlantsFrontiers in Plant Science12
202110.1128/AEM.01037-21Thorgersen, M. P., J. Xue, E. L. W. Majumder, V. V. Trotter, X. Ge, F. L. Poole, T. K. Owens, L. M. Lui, T. N. Nielsen, A. P. Arkin, A. M. Deutschbauer, G. Siuzdak and M. W. W. AdamsDeciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based MetabolomicsApplied and Environmental Microbiology87(21) e01037-21
202110.1128/MRA.00150-21Thompson, M. G., C. B. Eiben, A. N. Pearson and P. M. ShihDraft Genome Sequence of Mycobacterium sp. Strain JC1 DSM 3803Microbiology Resource Announcements10(19) e00150-21
202110.3389/fpls.2021.732307Tetreault, H. M., T. Gries, S. Liu, J. Toy, Z. Xin, W. Vermerris, J. Ralph, D. L. Funnell-Harris and S. E. SattlerThe Sorghum (Sorghum bicolor) Brown Midrib 30 Gene Encodes a Chalcone Isomerase Required for Cell Wall LignificationFrontiers in Plant Science12
202110.1038/s41586-021-03306-8Terrer, C., R. P. Phillips, B. A. Hungate, J. Rosende, J. Pett-Ridge, et al.A trade-off between plant and soil carbon storage under elevated CO2Nature591(7851) 599–603
202110.1186/s40168-021-01156-0ter Horst, A. M., C. Santos-Medellín, J. W. Sorensen, L. A. Zinke, R. M. Wilson, E. R. Johnston, G. Trubl, J. Pett-Ridge, S. J. Blazewicz, P. J. Hanson, J. P. Chanton, C. W. Schadt, J. E. Kostka and J. B. EmersonMinnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populationsMicrobiome9(1) 233
202110.1111/gcbb.12745Tejera, M. D., F. E. Miguez and E. A. HeatonThe older plant gets the sun: Age-related changes in Miscanthus _ giganteus phenologyGCB Bioenergy13(1) 45036
202110.1073/pnas.2100678118Teixeira, P. J. P. L., N. R. Colaianni, T. F. Law, J. M. Conway, S. Gilbert, H. Li, I. Salas-González, D. Panda, N. M. Del Risco, O. M. Finkel, G. Castrillo, P. Mieczkowski, C. D. Jones and J. L. DanglSpecific modulation of the root immune system by a community of commensal bacteriaProceedings of the National Academy of Sciences of the United States of America118(16)
202110.1016/j.copbio.2021.01.019Ta_, N., A. E. E. de Jong, Y. Li, G. Trubl, Y. Xue and N. C. DoveMetagenomic tools in microbial ecology researchCurrent Opinion in Biotechnology67 184–91
202110.1108/BEPAM-03-2020-0053Tariq, H., C. Pathirage and T. FernandoMeasuring community disaster resilience using Q-methods: a physical resilience perspectiveBuilt Environment Project and Asset Management11(4) 722-737
202110.1029/2021MS002469Tang, J., W. J. Riley, G. L. Marschmann and E. L. BrodieConceptualizing Biogeochemical Reactions With an Ohm's Law AnalogyJournal of Advances in Modeling Earth Systems13(10) e2021MS002469
202110.1107/S1600576720015526Tan, L., J. G. Elkins, B. H. Davison, E. G. Kelley and J. NickelsImplementation of a self-consistent slab model of bilayer structure in the SasView suiteJournal of Applied Crystallography54 363–70
202110.1093/pcp/pcab103Takahashi, D., I. R. Willick, J. Kasuga and D. P. Livingston IIIResponses of the Plant Cell Wall to Sub-Zero Temperatures: A Brief UpdatePlant and Cell Physiology62(12) 1858–66
202110.1002/aepp.13067Swinton, S. M., F. Dulys and S. S. H. KlammerWhy Biomass Residue Is Not as Plentiful as It Looks: Case Study on Economic Supply of Logging ResiduesApplied Economic Perspectives and Policy43(3) 1003–25
202110.3389/ffunb.2021.708358Swift, C. L., N. G. Malinov, S. J. Mondo, A. Salamov, I. V. Grigoriev and M. A. O'MalleyA Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in BioproductionFrontiers in Fungal Biology2
202110.1128/mBio.01442-21Swift, C. L., K. B. Louie, B. P. Bowen, C. A. Hooker, K. V. Solomon, V. Singan, C. Daum, C. P. Pennacchio, K. Barry, V. Shutthanandan, J. E. Evans, I. V. Grigoriev, T. R. Northen and M. A. O’malleyCocultivation of anaerobic fungi with rumen bacteria establishes an antagonistic relationshipmBio12(4)
202110.1016/j.ymben.2020.11.013Suthers, P. F., C. J. Foster, D. Sarkar, L. Wang and C. D. MaranasRecent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalismsMetabolic Engineering63 13–33
202110.1038/s41467-021-25241-ySun, L., J. W. Lee, S. Yook, S. Lane, Z. Sun, S. R. Kim and Y.-S. JinComplete and efficient conversion of plant cell wall hemicellulose into high-value bioproducts by engineered yeastNature Communications12(1) 4975
202110.1002/biot.202000142Sun, L. and Y. S. JinXylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiaeBiotechnology Journal16(4) e2000142
202110.1111/gcbb.12875Studt, J. E., M. D. McDaniel, M. D. Tejera, A. VanLoocke, A. Howe and E. A. HeatonSoil net nitrogen mineralization and leaching under Miscanthus _ giganteus and Zea maysGCB Bioenergy13(9) 1545–60
202110.1016/j.copbio.2021.07.005Streett, H., K. Charubin and E. T. PapoutsakisAnaerobic fluorescent reporters for cell identification, microbial cell biology and high-throughput screening of microbiota and genomic librariesCurrent Opinion in Biotechnology71 151-163
202110.1038/s41467-021-25691-4Stork, D. A., G. R. Squyres, E. Kuru, K. A. Gromek, J. Rittichier, A. Jog, B. M. Burton, G. M. Church, E. C. Garner and A. M. KunjapurDesigning efficient genetic code expansion in Bacillus subtilis to gain biological insightsNature Communications12(1)
202110.1038/s41467-021-23676-xStone, B. W., J. Li, B. J. Koch, S. J. Blazewicz, P. Dijkstra, M. Hayer, K. S. Hofmockel, X. J. A. Liu, R. L. Mau, E. M. Morrissey, J. Pett-Ridge, E. Schwartz and B. A. HungateNutrients cause consolidation of soil carbon flux to small proportion of bacterial communityNature Communications12(1)
202110.1071/mf20024Stoessel, D. J., A. R. van Rooyen, L. B. Beheregaray, S. M. C. Raymond, B. van Wyk, J. Haddy, J. Lieschke and A. R. WeeksPopulation genetic structure of estuary perch (Percalates colonorum Gunther) in south-eastern AustraliaMarine and Freshwater Research72(2)
202110.1007/978-1-0716-1657-4_22Stettner, S. and C. EckertCRISPR-Cas Genome Editing in the Cellulolytic Bacterium Clostridium thermocellum (C. thermocellum)CRISPR-Cas Methods: Volume 2 335–44
202110.1016/j.mec.2021.e00176Stephens, K., F. R. Zakaria, E. VanArsdale, G. F. Payne and W. E. BentleyElectronic signals are electrogenetically relayed to control cell growth and co-culture compositionMetabolic Engineering Communications13 e00176
202110.1021/acsearthspacechem.1c00087Stemple, B., K. Tinker, P. Sarkar, J. Miller, D. Gulliver and K. BibbyBiogeochemistry of the Antrim Shale Natural Gas ReservoirACS Earth and Space Chemistry5(7) 1752–61
202110.1111/1462-2920.15273Steindorff, A. S., A. Carver, S. Calhoun, K. Stillman, H. Liu, A. Lipzen, G. He, M. Yan, J. Pangilinan, K. LaButti, V. Ng, T. D. Bruns and I. V. GrigorievComparative genomics of pyrophilous fungi reveals a link between fire events and developmental genesEnvironmental Microbiology23(1) 99–109
202110.1086/716182Steidinger, B. S. and K. G. PeayOptimal allocation ratios: A square root relationship between the ratios of symbiotic costs and benefitsAmerican Naturalist198(4) 460-472
202110.1126/sciadv.abe4724Stebbing, J., G. S. Nievas, M. Falcone, S. Youhanna, P. Richardson, et al.JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortalityScience Advances7(1)
202110.1128/mSphere.00085-21Starr, E. P., S. Shi, S. J. Blazewicz, B. J. Koch, A. J. Probst, B. A. Hungate, J. Pett-Ridge, M. K. Firestone and J. F. BanfieldStable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere SoilmSphere6(5) e00085-21
202110.7554/eLife.65145Staquicini, F. I., A. Hajitou, W. H. P. Driessen, B. Proneth, M. Cardó-Vila, et al.Targeting a cell surface vitamin d receptor on tumor-associated macrophages in triple-negative breast cancereLife10
202110.1073/pnas.2105739118Staquicini, D. I., F. H. F. Tang, C. Markosian, V. J. Yao, F. I. Staquicini, et al.Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chainProceedings of the National Academy of Sciences of the United States of America118(30)
202110.1007/s00248-020-01651-1St. James, A. R., J. Lin and R. E. RichardsonRelationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USAMicrobial Ecology82(2) 429–41
202110.1038/s41396-020-00782-0St James, A. R., J. B. Yavitt, S. H. Zinder and R. E. RichardsonLinking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case studyThe ISME Journal15(1) 293–303
202110.1093/femsle/fnab153St James, A. R. and R. E. RichardsonStimulation of dissimilatory sulfate reduction in response to sulfate in microcosm incubations from two contrasting temperate peatlands near Ithaca, NY, USAFEMS Microbiology Letters368(21-24)
202110.1016/j.bioflm.2021.100052Speers, A. M. and G. RegueraCompetitive advantage of oxygen-tolerant bioanodes of Geobacter sulfurreducens in bioelectrochemical systemsBiofilm3 100052
202110.1088/1748-9326/ac2e35Spawn-Lee, S. A., T. J. Lark, H. K. Gibbs, R. A. Houghton, C. J. Kucharik, C. Malins, R. E. O. Pelton and G. P. RobertsonComment on ‘Carbon Intensity of corn ethanol in the United States: state of the science’Environmental Research Letters16(11) 118001
202110.1016/j.polymdegradstab.2021.109481Soulenthone, P., Y. Tachibana, M. Suzuki, T. Mizuno, Y. Ohta and K.-i. KasuyaCharacterization of a poly(butylene adipate-co-terephthalate) hydrolase from the mesophilic actinobacteria Rhodococcus fasciansPolymer Degradation and Stability184
202110.3389/fpls.2021.589518Soto, M. J., P. K. Prabhakar, H.-T. Wang, J. Backe, D. Chapla, M. Bartetzko, I. M. Black, P. Azadi, M. J. Peña, F. Pfrengle, K. W. Moremen, B. R. Urbanowicz and M. G. HahnAtFUT4 and AtFUT6 Are Arabinofuranose-Specific FucosyltransferasesFrontiers in Plant Science12
202110.1093/g3journal/jkab222Sorgini, C. A., L. M. Roberts, M. Sullivan, A. B. Cousins, I. Baxter and A. J. StuderThe genetic architecture of leaf stable carbon isotope composition in Zea mays and the effect of transpiration efficiency on leaf elemental accumulationG3: Genes, Genomes, Genetics11(9)
202110.1128/mSystems.00614-21Sorensen, J. W., L. A. Zinke, A. M. ter Horst, C. Santos-Medellín, A. Schroeder and J. B. EmersonDnase treatment improves viral enrichment in agricultural soil viromesmSystems6(5)
202110.1128/mSystems.00224-21Song, F., J. V. Kuehl, A. Chandran and A. P. ArkinA Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community AnalysismSystems6(5) e00224-21
202110.1111/nph.17287Sonawane, B. V., N. K. Koteyeva, D. M. Johnson and A. B. CousinsDifferences in leaf anatomy determines temperature response of leaf hydraulic and mesophyll CO2 conductance in phylogenetically related C4 and C3 grass speciesNew Phytologist230(5) 1802-1814
202110.1146/annurev-virology-010421-053015Sommers, P., A. Chatterjee, A. Varsani and G. TrublIntegrating Viral Metagenomics into an Ecological FrameworkAnnual Review of Virology8(1) 133–58
202110.1111/pbi.13606Smith, R. A., C. L. Cass, D. L. Petrik, D. Padmakshan, J. Ralph, J. C. Sedbrook and S. D. KarlenStacking AsFMT overexpression with BdPMT loss of function enhances monolignol ferulate production in Brachypodium distachyonPlant Biotechnology Journal19(9) 1878–86
202110.1126/sciadv.abk0734Smith, L. M., J. N. Agar, J. Chamot-Rooke, P. O. Danis, Y. Ge, J. A. Loo, L. Pa_a-Toliæ, Y. O. Tsybin and N. L. KelleherThe human proteoform project: Defining the human proteomeScience Advances7(46)
202110.1111/mec.15767Smith, G. R., L. C. Edy and K. G. PeayContrasting fungal responses to wildfire across different ecosystem typesMolecular Ecology30(3) 844–54
202110.1111/gcbb.12893Smercina, D. N., S. E. Evans, M. L. Friesen and L. K. TiemannTemporal dynamics of free-living nitrogen fixation in the switchgrass rhizosphereGCB Bioenergy13(11) 1814–30
202110.1094/pbiomes-09-19-0055-fiSmercina, D. N., A. W. Bowsher, S. E. Evans, M. L. Friesen, E. K. Eder, D. W. Hoyt and L. K. TiemannSwitchgrass Rhizosphere Metabolite Chemistry Driven by Nitrogen AvailabilityPhytobiomes Journal5(1) 88–96
202110.1093/femsec/fiab091Smercina, D. N., V. L. Bailey and K. S. HofmockelMicro on a macroscale: relating microbial-scale soil processes to global ecosystem functionFEMS Microbiology Ecology97(7) fiab091
202110.1128/AEM.00972-21Sipes, K., A. Almatari, A. Eddie, D. Williams, E. Spirina, E. Rivkina, R. Liang, T. C. Onstott, T. A. Vishnivetskaya and K. G. LloydEight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian PermafrostApplied and Environmental Microbiology87(19) e00972-21
202110.1002/ece3.8335Singleton, A. L., M. H. Liu, S. Votzke, A. Yammine and J. P. GibertIncreasing temperature weakens the positive effect of genetic diversity on population growthEcology and Evolution11(24) 17810-17816
202110.1089/ind.2021.0020Singh, R. and V. SinghIntegrated Biorefinery for Valorization of Engineered Bioenergy Crops—A ReviewIndustrial Biotechnology17(5) 271–82
202110.1016/j.biortech.2021.125817Singh, R., H. Liu, J. Shanklin and V. SinghHydrothermal pretreatment for valorization of genetically engineered bioenergy crop for lipid and cellulosic sugar recoveryBioresource Technology341 125817
202110.1002/bbb.2255Singh, R., B. S. Dien and V. SinghResponse surface methodology guided adsorption and recovery of free fatty acids from oil using resinBiofuels, Bioproducts and Biorefining15(5) 1485–95
202110.1016/j.biortech.2021.124772Singh, R., A. Arora and V. SinghBiodiesel from oil produced in vegetative tissues of biomass – A reviewBioresource Technology326 124772
202110.1094/pbiomes-05-20-0042-rvwSinger, E., J. P. Vogel, T. Northen, C. J. Mungall and T. E. JuengerNovel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root MicrobiomePhytobiomes Journal5(2) 122–32
202110.1093/plcell/koaa046Simpson, J. P., C. Wunderlich, X. Li, E. Svedin, B. Dilkes and C. ChappleMetabolic source isotopic pair labeling and genome-wide association are complementary tools for the identification of metabolite-gene associations in plantsPlant Cell33(3) 492-510
202110.3389/fpls.2021.714164Simpson, J. P., J. Olson, B. Dilkes and C. ChappleIdentification of the Tyrosine- and Phenylalanine-Derived Soluble Metabolomes of SorghumFrontiers in Plant Science12
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202110.1038/s41598-021-83937-zSilva, P. C., J. A. Ceja-Navarro, F. Azevedo, U. Karaoz, E. L. Brodie and B. JohanssonA novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiaeScientific Reports11(1) 4766
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202110.1111/tbed.13771Silva, J. G., W. J. Araujo, E. L. Leite, L. M. Dias, P. C. Vasconcelos, N. M. V. Silva, R. P. Oliveira, M. J. Sena, C. J. B. Oliveira and R. A. MotaFirst report of a livestock-associated methicillin-resistant Staphylococcus aureus ST126 harbouring the mecC variant in BrazilTransboundary and Emerging Diseases68(3) 1019–25
202110.1002/9783527815128.ch3Si, T., P. Xue, K. Choe, H. Zhao and J. V. SweedlerHigh-Throughput Mass Spectrometry Complements Protein EngineeringProtein Engineering: Tools and Applications 57–79
202110.1002/pmic.202100127Shrestha, H. K., M. I. V. Solis, S. S. Jawdy, G. A. Tuskan, X. Yang and P. E. AbrahamTemporal dynamics of protein and post-translational modification abundances in Populus leaf across a diurnal periodProteomics21(20) 2100127
202110.1186/s12866-021-02370-4Shrestha, H. K., M. R. Appidi, M. I. Villalobos Solis, J. Wang, D. L. Carper, L. Burdick, D. A. Pelletier, M. J. Doktycz, R. L. Hettich and P. E. AbrahamMetaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbanceBMC Microbiology21(1) 308
202110.1016/j.cub.2021.04.077Shmakova, L., S. Malavin, N. Iakovenko, T. Vishnivetskaya, D. Shain, M. Plewka and E. RivkinaA living bdelloid rotifer from 24,000-year-old Arctic permafrostCurrent Biology31(11) R712-R713
202110.3390/en14092633Shirkey, G., M. Belongeay, S. Wu, X. Ma, H. Tavakol, A. Anctil, S. Marquette-Pyatt, R. A. Stewart, P. Sinha, R. Corkish, J. Chen and I. CelikAn Environmental and Societal Analysis of the US Electrical Energy Industry Based on the Water–Energy NexusEnergies14(9) 2633
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202110.1016/j.jwpe.2021.102137Shen, X.-y., Y.-y. Zhuge, Y.-d. Liu, J. P. Shapleigh and W. LiLong-term effects of acetylene on denitrifying N2O production: Biomass performance and microbial communityJournal of Water Process Engineering42 102137
202110.1016/j.watres.2020.116571Shabtai, I. A., L. M. Lynch and Y. G. MishaelDesigning clay-polymer nanocomposite sorbents for water treatment: A review and meta-analysis of the past decadeWater Research188 116571
202110.1186/s13068-021-01905-1Serrani-Yarce, J. C., L. Escamilla-Trevino, J. Barros, L. Gallego-Giraldo, Y. Pu, A. Ragauskas and R. A. DixonTargeting hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase for lignin modification in Brachypodium distachyonBiotechnology for Biofuels14(1) 50
202110.1016/j.crmicr.2021.100055Sergio, d. l. S.-V., K. James Michael, P.-C. Fannie Isela, V.-R. Valeria, H.-K. Corina, G.-O. Luis Fernando, T. James Michael, H. Sheng Yang and P.-C. Juan JoseDraft genome sequence of Paraburkholderia sp. strain XV isolated from the rhizosphere of mango (Mangifera indica L.)Current Research in Microbial Sciences2 100055
202110.1016/j.ymben.2021.04.005Seo, H., J.-W. Lee, R. J. Giannone, N. J. Dunlap and C. T. TrinhEngineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesisMetabolic Engineering66 179–90
202110.1093/aobpla/plab056Seethepalli, A., K. Dhakal, M. Griffiths, H. Guo, G. T. Freschet and L. M. YorkRhizoVision Explorer: open-source software for root image analysis and measurement standardizationAoB PLANTS13(6) plab056
202110.1016/j.copbio.2021.01.002Scown, C. D., N. R. Baral, M. Yang, N. Vora and T. HuntingtonTechnoeconomic analysis for biofuels and bioproductsCurrent Opinion in Biotechnology67 58–64
202110.1016/j.jece.2021.105665Scott, F., L. Yañez, R. Conejeros, B. Araya and A. Vergara-FernándezTwo internal bottlenecks cause the overflow metabolism leading to poly(3-hydroxybutyrate) production in Azohydromonas lata DSM1123Journal of Environmental Chemical Engineering9(4) 105665
202110.1093/femsyr/foab066Schultz, J. C., M. Cao, A. Mejia and H. ZhaoCUT&RUN identifies centromeric DNA regions of Rhodotorula toruloides IFO0880FEMS Yeast Research21(8)
202110.1126/sciadv.abh2433Schulte, C. C. M., K. Borah, R. M. Wheatley, J. J. Terpolilli, G. Saalbach, N. Crang, D. H. de Groot, R. G. Ratcliffe, N. J. Kruger, A. Papachristodoulou and P. S. PooleMetabolic control of nitrogen fixation in rhizobium-legume symbiosesScience Advances7(31) eabh2433
202110.1073/pnas.2018181118Schubert, M. G., D. B. Goodman, T. M. Wannier, D. Kaur, F. Farzadfard, T. K. Lu, S. L. Shipman and G. M. ChurchHigh-throughput functional variant screens via in vivo production of single-stranded DNAProceedings of the National Academy of Sciences of the United States of America118(18)
202110.1093/femsec/fiab082Schreiber, L., N. Fortin, J. Tremblay, J. Wasserscheid, S. Sanschagrin, J. Mason, C. A. Wright, D. Spear, S. C. Johannessen, B. Robinson, T. King, K. Lee and C. W. GreerIn situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditionsFEMS Microbiology Ecology97(7)
202110.3389/fmicb.2021.702015Schmidt, J. M., T. M. Royalty, K. G. Lloyd and A. D. SteenPotential activities and long lifetimes of organic carbon-degrading extracellular enzymes in deep subsurface sediments of the Baltic SeaFrontiers in Microbiology12
202110.1109/TMI.2020.3024264Scheufele, K., S. Subramanian and G. BirosFully Automatic Calibration of Tumor-Growth Models Using a Single mpMRI ScanIEEE Transactions on Medical Imaging40(1) 193–204
202110.3389/fpls.2021.747225Scavuzzo-Duggan, T., N. Varoquaux, M. Madera, J. P. Vogel, J. Dahlberg, R. Hutmacher, M. Belcher, J. Ortega, D. Coleman-Derr, P. Lemaux, E. Purdom and H. V. SchellerCell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought ConditionsFrontiers in Plant Science12
2021Sawyer, C. R. and J. L. LabbéSmall RNAs at the Interface of the Plant-Fungal InteractionsFungal Genomics & Biology11(1)
202110.1007/s00203-021-02566-2Saticioglu, I. B.Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiontArchives of Microbiology203(9) 5783–92
202110.1371/journal.pcbi.1008983Sarkar, D., M. Landa, A. Bandyopadhyay, H. B. Pakrasi, J. P. Zehr and C. D. MaranasElucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modelingPLoS Computational Biology17(5) e1008983
202110.1038/s41396-021-00897-ySantos-Medellin, C., L. A. Zinke, A. M. ter Horst, D. L. Gelardi, S. J. Parikh and J. B. EmersonViromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communitiesISME Journal15(7) 1956-1970
202110.3389/fpls.2021.740534Santos, M. G., P. A. Davey, T. A. Hofmann, A. Borland, J. Hartwell and T. LawsonStomatal Responses to Light, CO2, and Mesophyll Tissue in Vicia faba and Kalanchoë fedtschenkoiFrontiers in Plant Science12
202110.1002/bit.27740Santala, S., V. Santala, N. Liu and G. StephanopoulosPartitioning metabolism between growth and product synthesis for coordinated production of wax esters in Acinetobacter baylyi ADP1Biotechnology and Bioengineering118(6) 2283-2292
202110.1016/j.tim.2020.12.010Sanford, R. A., K. G. Lloyd, K. T. Konstantinidis and F. E. LöfflerMicrobial Taxonomy Run AmokTrends in Microbiology29(5) 394-404
202110.1016/j.syapm.2021.126244Sandoval-Powers, M., S. Králová, G.-S. Nguyen, D. V. Fawwal, K. Degnes, A. S. Lewin, G. Klinkenberg, A. Wentzel and M. R. LilesStreptomyces poriferorum sp. nov., a novel marine sponge-derived Actinobacteria species expressing anti-MRSA activitySystematic and Applied Microbiology44(5) 126244
202110.1002/anie.202012213Samkian, A. E., G. R. Kiel, C. G. Jones, H. M. Bergman, J. Oktawiec, H. M. Nelson and T. D. TilleyElucidation of Diverse Solid-State Packing in a Family of Electron-Deficient Expanded Helicenes via Microcrystal Electron Diffraction (MicroED)**Angewandte Chemie - International Edition60(5) 2493-2499
202110.1093/plcell/koab042Salomé, P. A. and S. S. MerchantCo-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discoveryPlant Cell33(4) 1058-1082
202110.3389/fmicb.2021.687971Saldierna Guzmán, J. P., M. Reyes-Prieto and S. C. HartCharacterization of Erwinia gerundensis A4, an Almond-Derived Plant Growth-Promoting EndophyteFrontiers in Microbiology12
202110.3389/fpls.2021.640930Saha, P., F. Lin, S. Thibivilliers, Y. Xiong, C. Pan and L. E. BartleyPhenylpropanoid Biosynthesis Gene Expression Precedes Lignin Accumulation During Shoot Development in Lowland and Upland Switchgrass GenotypesFrontiers in Plant Science12
202110.1088/1748-9326/abd2f3Saha, D., B. Basso and G. P. RobertsonMachine learning improves predictions of agricultural nitrous oxide (N2O) emissions from intensively managed cropping systemsEnvironmental Research Letters16(2)
202110.1016/j.talanta.2021.122198Sadeghi, S., T. A. Anderson and W. A. JacksonDetermination of phosphite (HPO3_2) by a new IC/MS/MS method using an 18O-labeled HPO3_2 internal standardTalanta230
202110.1016/j.molcel.2020.12.031Saba, J., X. Cao and R. LandickBacterial Transcription Continues to Surprise: Activation by Alarmone-Mediated _-Factor TetheringMolecular Cell81(1) 8–9
202110.1016/j.ces.2021.116766Ryu, J. and C. T. MaraveliasA generalized distillation network synthesis modelChemical Engineering Science244 116766
202110.1016/j.tim.2020.06.009Ryan, M. J., M. Schloter, G. Berg, T. Kostic, L. L. Kinkel, et al.Development of Microbiome Biobanks – Challenges and OpportunitiesTrends in Microbiology29(2) 89–92
202110.3390/microorganisms9122612Ruytinx, J., S. Miyauchi, S. Hartmann-Wittulsky, M. de Freitas Pereira, F. Guinet, J.-L. Churin, C. Put, F. Le Tacon, C. Veneault-Fourrey, F. Martin and A. KohlerA Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolorMicroorganisms9(12) 2612
202110.3389/ffunb.2021.716511Rush, T. A., H. K. Shrestha, M. Gopalakrishnan Meena, M. K. Spangler, J. C. Ellis, J. L. Labbé and P. E. AbrahamBioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol ApplicationsFrontiers in Fungal Biology2
202110.3389/fbioe.2021.612893Roy, S., T. Radivojevic, M. Forrer, J. M. Marti, V. Jonnalagadda, T. Backman, W. Morrell, H. Plahar, J. Kim, N. Hillson and H. Garcia MartinMultiomics Data Collection, Visualization, and Utilization for Guiding Metabolic EngineeringFrontiers in Bioengineering and Biotechnology9
202110.1016/j.baae.2021.08.009Rowe, L., D. Gibson, D. A. Landis and R. IsaacsWild bees and natural enemies prefer similar flower species and respond to similar plant traitsBasic and Applied Ecology56 259-269
202110.1038/s41467-021-23402-7Roux, S., B. G. Paul, S. C. Bagby, S. Nayfach, M. A. Allen, et al.Ecology and molecular targets of hypermutation in the global microbiomeNature Communications12(1)
202110.1016/j.jmb.2020.11.003Rose, Y., J. M. Duarte, R. Lowe, J. Segura, C. Bi, C. Bhikadiya, L. Chen, A. S. Rose, S. Bittrich, S. K. Burley and J. D. WestbrookRCSB Protein Data Bank: Architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archiveJournal of Molecular Biology433(11)
202110.1128/MRA.00212-21Rosario, M. E., J. Camm, D. Cavanagh, D. C. Rowley and D. R. NelsonDraft Genome Sequence of Pseudoalteromonas sp. Strain JC3Microbiology Resource Announcements10(36) e00212-21
202110.1002/fes3.348Roney, H. E. and B. J. WalkerPhoton to plate: A holistic view of photosynthetic and anthropogenic energy fluxesFood and Energy Securitye348
202110.3390/metabo11030148Romsdahl, T. B., S. Kambhampati, S. Koley, U. P. Yadav, A. P. Alonso, D. K. Allen and K. D. ChapmanAnalyzing mass spectrometry imaging data of 13c-labeled phospholipids in camelina sativa and thlaspi arvense (Pennycress) embryosMetabolites11(3) 44947
202110.1094/pbiomes-11-19-0064-fiRoley, S. S., T. C. Ulbrich and G. P. RobertsonNitrogen Fixation and Resorption Efficiency Differences Among Twelve Upland and Lowland Switchgrass CultivarsPhytobiomes Journal5(1) 97–107
202110.1099/ijsem.0.004838Roldán, D. M., N. Kyrpides, T. Woyke, N. Shapiro, W. B. Whitman, S. Králová, I. Sedlá_ek, H.-J. Busse and R. J. MenesHymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, AntarcticaInternational Journal of Systematic and Evolutionary Microbiology71(6)
202110.1128/mSystems.00774-21Rodríguez-Verdugo, A.Evolving interactions and emergent functions in microbial consortiamSystems6(4)
202110.1186/s12934-021-01670-8Rodriguez, A., J. A. Meadows, N. Sun, B. A. Simmons and J. M. GladdenEvaluation of bacterial hosts for conversion of lignin-derived p-coumaric acid to 4-vinylphenolMicrobial Cell Factories20(1) 181
202110.1128/mSystems.01345-20Rodionov, D. A., I. A. Rodionova, V. A. Rodionov, A. A. Arzamasov, K. Zhang, et al.Transcriptional regulation of plant biomass degradation and carbohydrate utilization genes in the extreme thermophile Caldicellulosiruptor besciimSystems6(3)
202110.1016/J.JBC.2021.100643Robinson, K. P., A. Jochem, S. E. Johnson, T. R. Reddy, J. D. Russell, J. J. Coon and D. J. PagliariniDefining intermediates and redundancies in coenzyme Q precursor biosynthesisJournal of Biological Chemistry296
202110.7554/eLife.70564Robinson, D., M. Place, J. Hose, A. Jochem and A. P. GaschNatural variation in the consequences of gene overexpression and its implications for evolutionary trajectorieseLife10 e70564
202110.1038/s42003-021-02693-yRobinson, A. J., G. L. House, D. P. Morales, J. M. Kelliher, L. V. Gallegos-Graves, et al.Widespread bacterial diversity within the bacteriome of fungiCommunications Biology4(1) 1168
202110.1038/s41564-021-00918-8Rinke, C., M. Chuvochina, A. J. Mussig, P.-A. Chaumeil, A. A. Davín, D. W. Waite, W. B. Whitman, D. H. Parks and P. HugenholtzA standardized archaeal taxonomy for the Genome Taxonomy DatabaseNature Microbiology6(7) 946–59
202110.1186/s13068-020-01872-zRiley, L. A. and A. M. GussApproaches to genetic tool development for rapid domestication of non-model microorganismsBiotechnology for Biofuels14(1) 30
202110.1002/bmb.21578Riley, K. J., D. Vardar-Ulu, E. Pollock and S. DuttaStudents authoring molecular case studies as a partial course-based undergraduate research experience (CURE) for lab instructionBiochemistry and Molecular Biology Education49(6) 853-855
202110.1111/pbi.13510Rigoulot, S. B., T. M. Schimel, J. H. Lee, R. G. Sears, H. Brabazon, et al.Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plantsPlant Biotechnology Journal19(4) 830–43
202110.1016/J.JBC.2021.100742Richardson, J. S., D. C. Richardson and D. S. GoodsellSeeing the PDBJournal of Biological Chemistry296
202110.1016/j.cropro.2021.105576Ribeiro, V. H. V., L. S. G. Maia, N. J. Arneson, M. C. Oliveira, H. W. Read, J. M. Ané, J. B. dos Santos and R. WerleInfluence of PRE-emergence herbicides on soybean development, root nodulation and symbiotic nitrogen fixationCrop Protection144
202110.1093/plphys/kiab469Rencoret, J., M. J. Rosado, H. Kim, V. I. Timokhin, A. Gutiérrez, F. Bausch, T. Rosenau, A. Potthast, J. Ralph and J. C. del RíoFlavonoids naringenin chalcone, naringenin, dihydrotricin, and tricin are lignin monomers in papyrusPlant Physiology188(1) 208–19
202110.1093/plcell/koab055Ren, Y., M. Li, S. Guo, H. Sun, J. Zhao, et al.Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruitsThe Plant Cell33(5) 1554–73
202110.3390/metabo11100707Reese, K. L., C. L. Fisher, P. D. Lane, J. D. Jaryenneh, A. D. Jones, M. Frank and T. W. LaneAbiotic and Biotic Damage of Microalgae Generate Different Volatile Organic Compounds (VOCs) for Early Diagnosis of Algal Cultures for Biofuel ProductionMetabolites11(10) 707
202110.1029/2021JG006363Reed, D. E., J. Poe, M. Abraha, K. M. Dahlin and J. ChenModeled Surface-Atmosphere Fluxes From Paired Sites in the Upper Great Lakes Region Using Neural NetworksJGR Biogeosciences126(8) e2021JG006363
202110.1039/D0CS01297AReed, C. J., Q. N. Lam, E. N. Mirts and Y. LuMolecular understanding of heteronuclear active sites in heme–copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modellingChemical Society Reviews50(4) 2486–539
202110.1007/s10681-021-02788-xRazar, R. M., S. Makaju and A. M. MissaouiQTL mapping of biomass and forage quality traits measured using near-infrared reflectance spectroscopy (NIRS) in switchgrassEuphytica217(3) 51
202110.1111/1462-2920.15242Ray, P., Y. Guo, M. H. Chi, N. Krom, M. C. Saha and K. D. CravenSerendipita bescii promotes winter wheat growth and modulates the host root transcriptome under phosphorus and nitrogen starvationEnvironmental Microbiology23(4) 1876–88
202110.1094/mpmi-04-21-0084-rRay, P., Y. Guo, M.-H. Chi, N. Krom, C. Boschiero, B. Watson, D. Huhman, P. Zhao, V. R. Singan, E. A. Lindquist, J. Yan, C. Adam and K. D. CravenSerendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic RelationshipMolecular Plant-Microbe Interactions34(10) 1128–42
202110.1016/j.copbio.2020.12.012Rasor, B. J., B. Vögeli, G. M. Landwehr, J. W. Bogart, A. S. Karim and M. C. JewettToward sustainable, cell-free biomanufacturingCurrent Opinion in Biotechnology69 136-144
202110.3390/microorganisms9112249Ramesh, C., M. Anwesh, N. V. Vinithkumar, R. Kirubagaran and L. DufosséComplete Genome Analysis of Undecylprodigiosin Pigment Biosynthesizing Marine Streptomyces Species Displaying Potential Bioactive ApplicationsMicroorganisms9(11) 2249
202110.1016/j.electacta.2020.137326Rago, L., D. Popp, J. T. Heiker and F. HarnischElectroactive microorganisms in mouse fecesElectrochimica Acta365
202110.1080/15592324.2021.1903758R. Cope, K., T. B. Irving, S. Chakraborty and J. M. AnéPerception of lipo-chitooligosaccharides by the bioenergy crop PopulusPlant Signaling and Behavior16(6)
202110.3389/fmolb.2021.716973Quadir, F., R. S. Roy, E. Soltanikazemi and J. ChengDeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based ModellingFrontiers in Molecular Biosciences8
202110.1038/s41598-021-91827-7Quadir, F., R. S. Roy, R. Halfmann and J. ChengDNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learningScientific Reports11(1)
202110.1111/pbi.13671Qiao, Z., T. B. Yates, H. K. Shrestha, N. L. Engle, A. Flanagan, et al.Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinasePlant Biotechnology Journal19(12) 2454–68
202110.1111/pbi.13589Qiao, L., C. Lan, L. Capriotti, A. Ah-Fong, J. Nino Sanchez, R. Hamby, J. Heller, H. Zhao, N. L. Glass, H. S. Judelson, B. Mezzetti, D. Niu and H. JinSpray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptakePlant Biotechnology Journal19(9) 1756–68
202110.1016/j.mib.2021.05.003Qian, Y., F. Lan and O. S. VenturelliTowards a deeper understanding of microbial communities: integrating experimental data with dynamic modelsCurrent Opinion in Microbiology62 84-92
202110.1007/s00122-021-03798-yQi, P., T. H. Pendergast, A. Johnson, B. A. Bahri, S. Choi, A. Missaoui and K. M. DevosQuantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypesTheoretical and Applied Genetics134(7) 1957–75
202110.1371/journal.pgen.1009342Price, M. N., A. M. Deutschbauer and A. P. ArkinFour families of folate-independent methionine synthasesPLoS Genetics17(2) e1009342
202110.7717/peerj.11447Pratama, A. A., B. Bolduc, A. A. Zayed, Z. P. Zhong, J. Guo, D. R. Vik, M. C. Gazitúa, J. M. Wainaina, S. Roux and M. B. SullivanExpanding standards in viromics: In silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curationPeerJ9
202110.1186/s13068-021-01964-4Poudel, S., A. L. Cope, K. B. O’Dell, A. M. Guss, H. Seo, C. T. Trinh and R. L. HettichIdentification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targetsBiotechnology for Biofuels14(1) 116
202110.1016/j.soilbio.2021.108451Polussa, A., J. Gonzalez-Rivero, N. Fields, F. V. Jevon, S. A. Wood, W. R. Wieder and M. A. BradfordScale dependence in functional equivalence and difference in the soil microbiomeSoil Biology and Biochemistry163
202110.1016/j.ymben.2021.04.009Podolsky, I. A., S. Seppälä, H. Xu, Y.-S. Jin and M. A. O'MalleyA SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeastMetabolic Engineering66 137–47
202110.1128/MRA.00002-21Podar, P. T., K. Peyton, A. Soren, R. L. Wilpiszeski, C. C. Gilmour, D. A. Elias and M. PodarComplete Genome Sequence of Desulfobulbus oligotrophicus Prop6, an Anaerobic Deltabacterota Strain That Lacks Mercury Methylation CapabilityMicrobiology Resource Announcements10(5) e00002-21
202110.1128/MRA.00793-21Podar, N. A., D. Klingeman, F. Miranda-Sanchez, F. E. Dewhirst and M. PodarDraft Genome Sequence of Schaalia odontolytica Strain ORNL0103, a Basibiont of “Candidatus Saccharibacteria” HMT352Microbiology Resource Announcements10(44) e00793-21
202110.1021/acssynbio.1c00263Plahar, H. A., T. N. Rich, S. D. Lane, W. C. Morrell, L. Springthorpe, O. Nnadi, E. Aravina, T. Dai, M. J. Fero, N. J. Hillson and C. J. PetzoldBioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software PlatformACS Synthetic Biology10(10) 2649–60
202110.3390/d13120641Pira, H., C. Risdian, P. Kämpfer, M. Müsken, P. J. Schupp and J. WinkZooshikella harenae sp. nov., Isolated from Pacific Oyster Crassostrea gigas, and Establishment of Zooshikella ganghwensis subsp. marina subsp. nov. and Zooshikella ganghwensis subsp. ganghwensis subsp. novDiversity13(12) 641
202110.1093/plphys/kiab395Pignon, C. P., S. B. Fernandes, R. Valluru, N. Bandillo, R. Lozano, E. Buckler, M. A. Gore, S. P. Long, P. J. Brown and A. D. B. LeakeyPhenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genesPlant Physiology187(4) 254-2562
202110.1186/s13068-021-01953-7Pham, L. T. M., K. Deng, T. R. Northen, S. W. Singer, P. D. Adams, B. A. Simmons and K. L. SaleExperimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporiumBiotechnology for Biofuels14(1) 108
202110.1099/ijsem.0.004765Peta, V., R. Raths and H. BückingMassilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the OxalobacteraceaeInternational Journal of Systematic and Evolutionary Microbiology71(5)
202110.7554/eLife.65091Pessotti, R. d. C., B. L. Hansen, J. N. Reaso, J. A. Ceja-Navarro, L. El-Hifnawi, E. L. Brodie and M. F. TraxlerMultiple lineages of Streptomyces produce antimicrobials within passalid beetle galleries across eastern North AmericaeLife10 e65091
202110.1016/j.indcrop.2021.113924Pérez-Pimienta, J. A., R. M. García-López, H. O. Méndez-Acosta, V. González-Álvarez, B. A. Simmons, J. A. Méndoza-Pérez and J. Arreola-VargasIonic liquid-water mixtures enhance pretreatment and anaerobic digestion of agave bagasseIndustrial Crops and Products171 113924
202110.1128/AEM.02794-20Perez, J. M., W. S. Kontur, C. Gehl, D. M. Gille, Y. Ma, A. V. Niles, G. Umana, T. J. Donohue and D. R. NogueraRedundancy in Aromatic O-Demethylation and Ring-Opening Reactions in Novosphingobium aromaticivorans and Their Impact in the Metabolism of Plant-Derived PhenolicsApplied and Environmental Microbiology87(8) e02794-20
202110.1186/s12859-021-04472-2Pereira, W. J., F. M. Almeida, D. Conde, K. M. Balmant, P. M. Triozzi, H. W. Schmidt, C. Dervinis, G. J. Pappas and M. KirstAsc-Seurat: analytical single-cell Seurat-based web applicationBMC Bioinformatics22(1)
202110.1016/j.jrurstud.2021.04.019Pereira, C., A. Pereira, A. Budal, S. Dahal, J. Daniel-Wrabetz, J. Meshelemiah, J. Carvalho, M. J. Ramos, R. M. Carmo and R. P. Pires‘If you don't migrate, you're a nobody’: Migration recruitment networks and experiences of Nepalese farm workers in PortugalJournal of Rural Studies88 500-509
202110.1038/s41564-020-00861-0Peng, X., S. E. Wilken, T. S. Lankiewicz, S. P. Gilmore, J. L. Brown, J. K. Henske, C. L. Swift, A. Salamov, K. Barry, I. V. Grigoriev, M. K. Theodorou, D. L. Valentine and M. A. O’MalleyGenomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomesNature Microbiology6(4) 499–511
202110.1101/2021.09.28.462238Payyavula, R. S., R. Badmi, S. S. Jawdy, M. Rodriguez, L. Gunter, R. W. Sykes, K. A. Winkeler, C. M. Collins, W. H. Rottmann, J.-G. Chen, X. Yang, G. A. Tuskan and U. C. KalluriBiomass formation and sugar release efficiency of Populus modified by altered expression of a NAC transcription factorbioRxiv2021.09.28.462238
202110.3390/plants10010158Pavicic, M., K. Overmyer, A. U. Rehman, P. Jones, D. Jacobson and K. HimanenImage-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis LeavesPlants10(1)
202110.1007/978-1-0716-1032-9_5Pavan, M.Setting Up an Automated Biomanufacturing LaboratoryMethods in Molecular Biology2229 137–55
202110.1186/s13068-021-01904-2Patri, A. S., R. Mohan, Y. Pu, C. G. Yoo, A. J. Ragauskas, R. Kumar, D. Kisailus, C. M. Cai and C. E. WymanTHF co-solvent pretreatment prevents lignin redeposition from interfering with enzymes yielding prolonged cellulase activityBiotechnology for Biofuels14(1) 63
202110.1007/s12155-021-10244-wParrish, A. S., M.-S. Lee, T. B. Voigt and D. K. LeeMiscanthus _ giganteus Responses to Nitrogen Fertilization and Harvest Timing in Illinois, USABioEnergy Research14(4) 1126–35
202110.1111/gcbb.12883Park, K., S. A. Sanjaya, T. Quach and E. B. CahoonToward sustainable production of value-added bioenergy and industrial oils in oilseed and biomass feedstocksGCB Bioenergy13(10) 1610–23
202110.1007/s11627-021-10215-yParikh, A., E. J. Brant, M. C. Baloglu and F. AltpeterCRISPR/Cas-mediated genome editing in sorghum — recent progress, challenges and prospectsIn Vitro Cellular & Developmental Biology - Plant57(4) 720–30
202110.1128/mBio.03518-20Pant, S. R., S. Irigoyen, J. Liu, R. Bedre, S. A. Christensen, E. A. Schmelz, J. C. Sedbrook, K. B. G. Scholthof and K. K. MandadiBrachypodium phenylalanine ammonia lyase (PAL) promotes antiviral defenses against Panicum mosaic virus and its satellitesmBio12(1) 44943
202110.1016/j.ymben.2021.10.007Pang, B., J. Li, C. B. Eiben, E. Oksen, C. Barcelos, R. Chen, E. Englund, E. Sundstrom and J. D. KeaslingLepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuelsMetabolic Engineering68 210–9
202110.1098/rsif.2021.0348Pacheco, A. R. and D. SegrèAn evolutionary algorithm for designing microbial communities via environmental modificationJournal of The Royal Society Interface18(179) 20210348
202110.1038/s41467-021-22426-3Pacheco, A. R., M. L. Osborne and D. SegrèNon-additive microbial community responses to environmental complexityNature Communications12(1) 2365
202110.3389/fmicb.2021.720644Öztürk, Y., C. E. Blaby-Haas, N. Daum, A. Andrei, J. Rauch, F. Daldal and H.-G. KochMaturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF ProductFrontiers in Microbiology12
202110.3389/fgeed.2021.673566Oz, M. T., A. Altpeter, R. Karan, A. Merotto and F. AltpeterCRISPR/Cas9-Mediated Multi-Allelic Gene Targeting in Sugarcane Confers Herbicide ToleranceFrontiers in Genome Editing3
202110.1128/mSystems.01025-20Otwell, A. E., A. V. Carr, E. L. W. Majumder, M. K. Ruiz, R. L. Wilpiszeski, L. T. Hoang, B. Webb, S. Turkarslan, S. M. Gibbons, D. A. Elias, D. A. Stahl, G. Siuzdak and N. S. BaligaSulfur Metabolites Play Key System-Level Roles in Modulating DenitrificationmSystems6(1) e01025-20
202110.1007/s10533-020-00742-yOstrom, P. H., S. DeCamp, H. Gandhi, J. Haslun and N. E. OstromThe influence of tillage and fertilizer on the flux and source of nitrous oxide with reference to atmospheric variation using laser spectroscopyBiogeochemistry152(2–3) 143–59
202110.1111/tpj.15086Oliver, J., M. Fan, B. McKinley, S. Zemelis-Durfee, F. Brandizzi, C. Wilkerson and J. E. MulletThe AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolorThe Plant Journal105(4) 1053–71
202110.1038/s41598-021-95106-3Oliver, A., S. Podell, A. Pinowska, J. C. Traller, S. R. Smith, et al.Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatomScientific Reports11(1)
202110.1107/S2053230X21007470Ochoa, J. M., O. Mijares, A. A. Acosta, X. Escoto, N. Leon-Rivera, J. D. Marshall, M. R. Sawaya and T. O. YeatesaStructural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartmentsActa Crystallographica Section F: Structural Biology Communications77 275-285
202110.1038/s41598-021-88318-0Ocejo, M., B. Oporto, J. L. Lavín and A. HurtadoWhole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminantsScientific Reports11(1) 8998
202110.3168/jds.2021-20232Oberg, C., K. Sorensen, T. Oberg, S. Young, M. Domek, M. Culumber and D. McMahonGluconate metabolism and gas production by Paucilactobacillus wasatchensis WDC04Journal of Dairy Science104(10) 10586–93
202110.1073/pnas.2008888118Oates, N. C., A. Abood, A. M. Schirmacher, A. M. Alessi, S. M. Bird, J. P. Bennett, D. R. Leadbeater, Y. Li, A. A. Dowle, S. Liu, V. I. Tymokhin, J. Ralph, S. J. McQueen-Mason and N. C. BruceA multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1Proceedings of the National Academy of Sciences118(18) e2008888118
202110.1016/j.coche.2020.100666O’Neill, E. G. and C. T. MaraveliasTowards integrated landscape design and biofuel supply chain optimizationCurrent Opinion in Chemical Engineering31 100666
202110.1371/journal.ppat.1009138O’Brien, C. E., J. Oliveira-Pacheco, E. Ó Cinnéide, M. A. B. Haase, C. T. Hittinger, T. R. Rogers, O. Zaragoza, U. Bond and G. ButlerPopulation genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samplesPLoS Pathogens17(3) e1009138
202110.3390/biom11060898Ntana, F., W. W. Bhat, S. R. Johnson, H. J. L. Jørgensen, D. B. Collinge, B. Jensen and B. HambergerA sesquiterpene synthase from the endophytic fungus Serendipita indica catalyzes formation of viridiflorolBiomolecules11(6)
2021Ntana, F., W. W. Bhat, S. R. Johnson, H. J. L. Jørgensen, D. B. Collinge, B. Jensen and B. HambergerA Sesquiterpene Synthase from the Endophytic Fungus Serendipita indica Catalyzes Formation of ViridiflorolBiomolecules11(6) 898
202110.1016/j.ymben.2021.02.005Notonier, S., A. Z. Werner, E. Kuatsjah, L. Dumalo, P. E. Abraham, et al.Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acidMetabolic Engineering65 111–22
202110.1016/j.bej.2021.108008Norena-Caro, D. A., C. Zuniga, A. J. Pete, S. A. Saemundsson, M. R. Donaldson, A. J. Adams, K. M. Dooley, K. Zengler and M. G. BentonAnalysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576Biochemical Engineering Journal171
202110.1128/mSystems.01205-20Nicolas, A. M., A. L. Jaffe, E. E. Nuccio, M. E. Taga, M. K. Firestone and J. F. BanfieldSoil candidate phyla radiation bacteria encode components of aerobic metabolism and co-occur with nanoarchaea in the rare biosphere of rhizosphere grassland communitiesmSystems6(4)
202110.1128/MRA.00580-21Nickolson, G. P., N. M. Balasjin and C. W. MarshallDraft Genome Sequence of Staphylococcus succinus Strain GN1, Isolated from a Basement Floor in Milwaukee, WIMicrobiology Resource Announcements10(27) e00580-21
202110.1016/j.ymben.2021.02.006Ni, Z., A. E. Stine, K. E. J. Tyo and L. J. BroadbeltCurating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway designMetabolic Engineering65 79-87
202110.1016/j.watres.2020.116445Nguyen Quoc, B., S. Wei, M. Armenta, R. Bucher, P. Sukapanpotharam, D. A. Stahl, H. D. Stensel and M. H. WinklerAerobic granular sludge: Impact of size distribution on nitrification capacityWater Research188 116445
202110.1016/j.watres.2021.117119Nguyen Quoc, B., M. Armenta, J. A. Carter, R. Bucher, P. Sukapanpotharam, S. J. Bryson, D. A. Stahl, H. D. Stensel and M.-K. H. WinklerAn investigation into the optimal granular sludge size for simultaneous nitrogen and phosphate removalWater Research198 117119
202110.1021/acs.est.1c00300Neurath, R. A., J. Pett-Ridge, I. Chu-Jacoby, D. Herman, T. Whitman, P. S. Nico, A. S. Lipton, J. Kyle, M. M. Tfaily, A. Thompson and M. K. FirestoneRoot Carbon Interaction with Soil Minerals Is Dynamic, Leaving a Legacy of Microbially Derived ResiduesEnvironmental Science & Technology55(19) 13345–55
202110.1093/sysbio/syaa038Neumann, J. S., R. Desalle, A. Narechania, B. Schierwater and M. TesslerMorphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data SetsSystematic Biology70(2) 360–75
202110.1002/bit.27637Nemmaru, B., N. Ramirez, C. J. Farino, J. M. Yarbrough, N. Kravchenko and S. P. S. ChundawatReduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activityBiotechnology and Bioengineering118(3) 1141-1151
202110.1021/acs.orglett.0c03966Nelson, H. M., J. C. Siu, A. Saha, D. Cascio, S. N. MacMillan, S. B. Wu, C. Lu, J. A. Rodríguez, K. N. Houk and S. LinIsolation and X-ray Crystal Structure of an Electrogenerated TEMPO-N3Charge-Transfer ComplexOrganic Letters23(2) 454-458
202110.1080/00275514.2021.1965852Ndinga-Muniania, C., R. C. Mueller, C. R. Kuske and A. Porras-AlfaroSeasonal variation and potential roles of dark septate fungi in an arid grasslandMycologia113(6) 1181–98
202110.1099/ijsem.0.004912Nde, A. L., G. Charimba, A. Hitzeroth, L. Oosthuizen, L. Steyn, J. D. Newman and C. HugoChryseobacterium pennae sp. nov., isolated from poultry feather wasteInternational Journal of Systematic and Evolutionary Microbiology71(7)
202110.1038/s41587-020-0718-6Nayfach, S., S. Roux, R. Seshadri, D. Udwary, N. Varghese, et al.A genomic catalog of Earth’s microbiomesNature Biotechnology39(4) 499–509
202110.1038/s41597-021-00957-0Nathani, N. M., K. J. Dave, P. P. Vatsa, M. S. Mahajan, P. Sharma and C. Mootapally309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar PeninsulaScientific Data8(1) 194
202110.1073/pnas.2004846117Nasti, R. A. and D. F. VoytasAttaining the promise of plant gene editing at scaleProceedings of the National Academy of Sciences of the United States of America118(22)
202110.1038/s41467-021-27548-2Nam, H. I., Z. Shahzad, Y. Dorone, S. Clowez, K. Zhao, N. Bouain, K. S. Lay-Pruitt, H. Cho, S. Y. Rhee and H. RouachedInterdependent iron and phosphorus availability controls photosynthesis through retrograde signalingNature Communications12(1)
202110.3390/ijms22084107Nag, A., A. Gerritsen, C. Doeppke and A. E. Harman-WareMachine Learning-Based Classification of Lignocellulosic Biomass from Pyrolysis-Molecular Beam Mass Spectrometry DataInternational Journal of Molecular Sciences22(8) 4107
202110.1128/MRA.00160-21Myers, K. S., M. Place, J. Kominek, D. R. Noguera and T. J. DonohueDelila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding MotifsMicrobiology Resource Announcements10(15) e00160-21
202110.1128/mSystems.00526-21Myers, K. S., D. R. Noguera and T. J. DonohuePromoter Architecture Differences among Alphaproteobacteria and Other Bacterial TaxamSystems6(4) e00526-21
202110.1016/j.biombioe.2021.106051Murphy, E. K., Y. Mottiar, R. Y. Soolanayakanahally and S. D. MansfieldVariations in cell wall traits impact saccharification potential of Salix famelica and Salix eriocephalaBiomass and Bioenergy148 106051
202110.1093/GENETICS/IYAB087Mural, R. V., M. Grzybowski, C. Miao, A. Damke, S. Sapkota, R. E. Boyles, M. G. S. Fernandez, P. S. Schnable, B. Sigmon, S. Kresovich and J. C. SchnableMeta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghumGenetics218(3)
202110.1093/nar/gkaa983Mukherjee, S., D. Stamatis, J. Bertsch, G. Ovchinnikova, J. C. Sundaramurthi, J. Lee, M. Kandimalla, I. A. Chen, N. C. Kyrpides and T. B. K. ReddyGenomes OnLine Database (GOLD) v.8: overview and updatesNucleic Acids Research49(D1) D723–33
202110.1111/tpj.15492Muchlinski, A., M. Jia, K. Tiedge, J. S. Fell, K. A. Pelot, L. Chew, D. Davisson, Y. Chen, J. Siegel, J. T. Lovell and P. ZerbeCytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.)Plant Journal108(4) 1053-1068
202110.1016/j.apenergy.2021.117098Mousavi-Avval, S. H. and A. ShahLife cycle energy and environmental impacts of hydroprocessed renewable jet fuel production from pennycressApplied Energy297
202110.1016/j.rser.2021.111340Mousavi-Avval, S. H. and A. ShahTechno-economic analysis of hydroprocessed renewable jet fuel production from pennycress oilseedRenewable and Sustainable Energy Reviews149
202110.1016/j.copbio.2021.07.017Motabar, D., J. Li, G. F. Payne and W. E. BentleyMediated electrochemistry for redox-based biological targeting: entangling sensing and actuation for maximizing information transferCurrent Opinion in Biotechnology71 137–44
202110.3389/fsufs.2021.706142Mosier, S., S. C. Córdova and G. P. RobertsonRestoring Soil Fertility on Degraded Lands to Meet Food, Fuel, and Climate Security Needs via PerennializationFrontiers in Sustainable Food Systems5
202110.3390/cells10092217Moseley, R. C., F. Motta, G. A. Tuskan, S. B. Haase and X. YangInference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoiCells10(9) 2217
202110.1093/sysbio/syaa066Morales-Briones, D. F., G. Kadereit, D. T. Tefarikis, M. J. Moore, S. A. Smith, S. F. Brockington, A. Timoneda, W. C. Yim, J. C. Cushman and Y. YangDisentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.lSystematic Biology70(2) 219-235
202110.1016/j.cub.2021.03.067Moore, W. M., C. Chan, T. Ishikawa, E. A. Rennie, H. M. L. Wipf, V. Benites, M. Kawai-Yamada, J. C. Mortimer and H. V. SchellerReprogramming sphingolipid glycosylation is required for endosymbiont persistence in Medicago truncatulaCurrent Biology31(11) 2374–85.e4
202110.1111/gcbb.12788Moore, C. E., A. C. von Haden, M. B. Burnham, I. B. Kantola, C. D. Gibson, B. J. Blakely, E. C. Dracup, M. D. Masters, W. H. Yang, E. H. DeLucia and C. J. BernacchiEcosystem-scale biogeochemical fluxes from three bioenergy crop candidates: How energy sorghum compares to maize and miscanthusGCB Bioenergy13(3) 445–58
202110.1093/jxb/erab090Moore, C. E., K. Meacham-Hensold, P. Lemonnier, R. A. Slattery, C. Benjamin, C. J. Bernacchi, T. Lawson and A. P. CavanaghThe effect of increasing temperature on crop photosynthesis: from enzymes to ecosystemsJournal of Experimental Botany72(8) 2822–44
202110.1093/plcell/koab287Moore, B. M., Y. S. Lee, P. Wang, C. Azodi, E. Grotewold and S.-H. ShiuModeling temporal and hormonal regulation of plant transcriptional response to woundingThe Plant Cell34(2) 867–88
202110.1111/mmi.14717Monge, E. C. and J. G. GardnerEfficient chito-oligosaccharide utilization requires two TonB-dependent transporters and one hexosaminidase in Cellvibrio japonicusMolecular Microbiology116(2) 366-380
202110.1128/MRA.00531-21Mok, S., P. R. Flanagan, E. Roycroft, T. R. Rogers and M. M. FitzgibbonDraft Genome Sequences of Clinical Respiratory Isolates of Mycobacterium goodii Recovered in IrelandMicrobiology Resource Announcements10(31) e00531-21
202110.1039/D1GC01622AMohan, M., H. Choudhary, A. George, B. A. Simmons, K. Sale and J. M. GladdenTowards understanding of delignification of grassy and woody biomass in cholinium-based ionic liquidsGreen Chemistry23(16) 6020–35
202110.1016/j.cub.2021.03.089Mohammadi, S., L. Yang, A. Harpak, S. Herrera-Álvarez, M. del Pilar Rodríguez-Ordoñez, J. Peng, K. Zhang, J. F. Storz, S. Dobler, A. J. Crawford and P. AndolfattoConcerted evolution reveals co-adapted amino acid substitutions in Na+K+-ATPase of frogs that prey on toxic toadsCurrent Biology31(12) 2530-2538.e10
202110.1021/acs.est.0c06452Mishra, S. K., S. Gautam, U. Mishra and C. D. ScownPerformance-Based Payments for Soil Carbon Sequestration Can Enable a Low-Carbon BioeconomyEnvironmental Science & Technology55(8) 5180–8
202110.1101/gr.266429.120Michael, T. P., E. Ernst, N. Hartwick, P. Chu, D. Bryant, et al.Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth controlGenome Research31(2) 225–38
202110.1002/ppj2.20022Miao, C., A. Guo, A. M. Thompson, J. Yang, Y. Ge and J. C. SchnableAutomation of leaf counting in maize and sorghum using deep learningPlant Phenome Journal4(1)
202110.3390/life11060551Meyer, C., Y. Nakamura, B. J. Rasor, A. S. Karim, M. C. Jewett and C. TanAnalysis of the innovation trend in cell-free synthetic biologyLife11(6)
202110.1038/s41396-020-00757-1Metcalfe, K. S., R. Murali, S. W. Mullin, S. A. Connon and V. J. OrphanExperimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophyThe ISME Journal15(2) 377–96
202110.1021/bk-2021-1377.ch011Meng, X., M. Poonia, C. G. Yoo and A. J. RagauskasRecent Advances in Synthesis and Application of Lignin NanoparticlesLignin Utilization Strategies: From Processing to Applications1377 273–93
202110.1073/pnas.2026330118Meng, X., Z. Liang, X. Dai, Y. Zhang, S. Mahboub, D. W. Ngu, R. L. Roston and J. C. SchnablePredicting transcriptional responses to cold stress across plant speciesProceedings of the National Academy of Sciences of the United States of America118(10)
202110.1007/s10482-021-01656-xMenes, R. J., E. V. Machin, D. M. Roldán, N. Kyrpides, T. Woyke, W. B. Whitman and H.-J. BusseFrigoriflavimonas asaccharolytica gen. nov., sp. nov., a novel psychrophilic esterase and protease producing bacterium isolated from AntarcticaAntonie van Leeuwenhoek114(12) 1991–2002
202110.1371/journal.pone.0255083Mendes, I. V., M. B. Garcia, A. C. A. Bitencourt, R. H. Santana, P. d. C. Lins, R. Silveira, B. A. Simmons, J. M. Gladden, R. H. Kruger and B. F. QuirinoBacterial diversity dynamics in microbial consortia selected for lignin utilizationPLoS ONE16(9) e0255083
202110.1038/s41467-021-22765-1McGivern, B. B., M. M. Tfaily, M. A. Borton, S. M. Kosina, R. A. Daly, C. D. Nicora, S. O. Purvine, A. R. Wong, M. S. Lipton, D. W. Hoyt, T. R. Northen, A. E. Hagerman and K. C. WrightonDecrypting bacterial polyphenol metabolism in an anoxic wetland soilNature Communications12(1)
202110.1128/MRA.00628-21McDermith, E. J., A. R. Sterling, M. J. Bertin and B. D. JenkinsDraft Genome Sequence of Salegentibacter sp. Strain BDJ18, a Plankton-Associated Bacterium in the Northeast Atlantic OceanMicrobiology Resource Announcements10(36) e00628-21
202110.1128/MRA.00244-21McDaniel, E. A., R. Wever, B. O. Oyserman, D. R. Noguera and K. D. McMahonGenome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient RemovalMicrobiology Resource Announcements10(18) e00244-21
202110.1128/mSystems.00474-21McDaniel, E. A., F. Moya-Flores, N. K. Beach, P. Y. Camejo, B. O. Oyserman, M. Kizaric, E. H. Khor, D. R. Noguera and K. D. McMahonMetabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved MetatranscriptomicsmSystems6(4) e00474-21
202110.1039/D1GC00243KMcClelland, D. J., B.-X. Wang, W. T. Cordell, Y. R. Cortes-Peña, E. B. Gilcher, L. Zhang, J. S. Guest, B. F. Pfleger, G. W. Huber and J. A. DumesicRenewable linear alpha-olefins by base-catalyzed dehydration of biologically-derived fatty alcoholsGreen Chemistry23(12) 4338–54
202110.1071/FP20332Mayer, J. A., B. W. M. Wone, D. C. Alexander, L. Guo, J. A. Ryals and J. C. CushmanMetabolic profiling of epidermal and mesophyll tissues under water-deficit stress in Opuntia ficus-indica reveals stress-adaptive metabolic responsesFunctional Plant Biology48(7) 717-731
202110.1007/978-3-030-63512-1_13Mayali, X.Microscale Carbon Cycling Between Bacteria and Algae Under the SunMicrobes: The Foundation Stone of the Biosphere 205–10
202110.3389/fmicb.2021.651282Mavrodi, O. V., J. R. McWilliams, J. O. Peter, A. Berim, K. A. Hassan, L. D. H. Elbourne, M. K. LeTourneau, D. R. Gang, I. T. Paulsen, D. M. Weller, L. S. Thomashow, A. S. Flynt and D. V. MavrodiRoot Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere PseudomonasFrontiers in Microbiology12
202110.1128/MRA.00664-21Martinez, J. N., A. Nishihara and S. HarutaMetagenome-Assembled Genome Sequences Recovered from Epilithic River Biofilm in the Tama River, JapanMicrobiology Resource Announcements10(38) e00664-21
202110.1128/MRA.01380-20Martin, R. M., M. Kausch, K. Yap, J. D. Wehr, G. L. Boyer and S. W. WilhelmMetagenome-Assembled Genome Sequences of Raphidiopsis raciborskii and Planktothrix agardhii from a Cyanobacterial Bloom in Kissena Lake, New York, USAMicrobiology Resource Announcements10(2) e01380-20
202110.1128/mSystems.00987-21Martien, J. I., E. A. Trujillo, T. B. Jacobson, M. Tatli, A. S. Hebert, D. M. Stevenson, J. J. Coon and D. Amador-NoguezMetabolic Remodeling during Nitrogen Fixation in Zymomonas mobilismSystems6(6) e00987-21
202110.1093/nar/gkaa721Marchand, J. A., M. D. Pierson Smela, T. H. H. Jordan, K. Narasimhan and G. M. ChurchTBDB: A database of structurally annotated T-box riboswitch:tRNA pairsNucleic Acids Research49(D1) D229-D235
202110.1016/j.jbc.2021.100602Mamode Cassim, A., Y. Navon, Y. Gao, M. Decossas, L. Fouillen, et al.Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulationJournal of Biological Chemistry296 100602
202110.1038/s41596-020-00455-4Majumder, E. L. W., E. M. Billings, H. P. Benton, R. L. Martin, A. Palermo, C. Guijas, M. M. Rinschen, X. Domingo-Almenara, J. R. Montenegro-Burke, B. A. Tagtow, R. S. Plumb and G. SiuzdakCognitive analysis of metabolomics data for systems biologyNature Protocols16(3) 1376–418
202110.1016/j.biortech.2020.124424Maitra, S. and V. SinghBalancing sugar recovery and inhibitor generation during energycane processing: Coupling cryogenic grinding with hydrothermal pretreatment at low temperaturesBioresource Technology321 124424
202110.1111/gcbb.12841Maitra, S., B. Dien, S. P. Long and V. SinghDevelopment and validation of time-domain 1H-NMR relaxometry correlation for high-throughput phenotyping method for lipid contents of lignocellulosic feedstocksGCB Bioenergy13(7) 1179-1190
202110.1093/plphys/kiab499Mahon, E. L., L. de Vries, S.-K. Jang, S. Middar, H. Kim, F. Unda, J. Ralph and S. D. MansfieldExogenous chalcone synthase expression in developing poplar xylem incorporates naringenin into ligninsPlant Physiology188(2) 984–96
202110.7150/jgen.53019Maguvu, T. E., A. O. Oladipo and C. C. BezuidenhoutAnalysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven HeterogeneityJournal of Genomics9 26–37
202110.3390/microorganisms9091928Maguvu, T. E. and C. C. BezuidenhoutWhole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South AfricaMicroorganisms9(9) 1928
202110.1039/D0GC03260CMagurudeniya, H. D., N. R. Baral, A. Rodriguez, C. D. Scown, J. Dahlberg, D. Putnam, A. George, B. A. Simmons and J. M. GladdenUse of ensiled biomass sorghum increases ionic liquid pretreatment efficiency and reduces biofuel production cost and carbon footprintGreen Chemistry23(8) 3127–40
202110.1007/s11119-021-09810-1Maestrini, B. and B. BassoSubfield crop yields and temporal stability in thousands of US Midwest fieldsPrecision Agriculture22(6) 1749–67
202110.1146/annurev-arplant-080620-031054Maeda, H. A. and A. R. FernieEvolutionary History of Plant MetabolismAnnual Review of Plant Biology72 185-216
202110.1007/s10532-021-09932-3Ma, Y., T. J. Donohue and D. R. NogueraKinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustrisBiodegradation32(2) 179–92
202110.1093/plcell/koab025Ma, F., P. A. Salomé, S. S. Merchant and M. PellegriniSingle-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phasePlant Cell33(4) 1042-1057
202110.1097/MOH.0000000000000651Ma, F., G. E. Hernandez, M. Romay and M. L. Iruela-ArispeSingle-cell RNA sequencing to study vascular diversity and functionCurrent Opinion in Hematology28(3) 221-229
202110.1021/jacs.1c03129Lyu, M., L. Kong, Z. Yang, Y. Wu, C. E. McGhee and Y. LuPNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence FidelityJournal of the American Chemical Society143(26) 9724–8
202110.1038/s41467-021-25976-8Luo, Y., G. Jiang, T. Yu, Y. Liu, L. Vo, H. Ding, Y. Su, W. W. Qian, H. Zhao and J. PengECNet is an evolutionary context-integrated deep learning framework for protein engineeringNature Communications12(1) 5743
202110.1073/pnas.2019462118Luo, S., B. G. Coutinho, P. Dadhwal, Y. Oda, J. Ren, A. L. Schaefer, E. P. Greenberg, C. S. Harwood and L. TongStructural basis for a bacterial Pip system plant effector recognition proteinProceedings of the National Academy of Sciences118(10) e2019462118
202110.1021/jacs.1c08635Luo, H., E. P. Weeda, M. Alherech, C. W. Anson, S. D. Karlen, Y. Cui, C. E. Foster and S. S. StahlOxidative Catalytic Fractionation of Lignocellulosic Biomass under Non-alkaline ConditionsJournal of the American Chemical Society143(37) 15462–70
202110.1371/journal.pcbi.1008972Lui, L. M., T. N. Nielsen and A. P. ArkinA method for achieving complete microbial genomes and improving bins from metagenomics dataPLoS Computational Biology17(5) e1008972
202110.3389/fmicb.2021.642422Lui, L. M., E. L.-W. Majumder, H. J. Smith, H. K. Carlson, F. von Netzer, M. W. Fields, D. A. Stahl, J. Zhou, T. C. Hazen, N. S. Baliga, P. D. Adams and A. P. ArkinMechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial EcologyFrontiers in Microbiology12
202110.1039/D1GC01507ALu, F., C. Wang, M. Chen, F. Yue and J. RalphA facile spectroscopic method for measuring lignin content in lignocellulosic biomassGreen Chemistry23(14) 5106–12
202110.1038/s41586-020-03127-1Lovell, J. T., A. H. MacQueen, S. Mamidi, J. Bonnette, J. Jenkins, et al.Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrassNature590(7846) 438–44
202110.1021/acssynbio.0c00372Lovelett, R. J., E. M. Zhao, M. A. Lalwani, J. E. Toettcher, I. G. Kevrekidis and J. L. AvalosDynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering ApplicationsACS Synthetic Biology10(2) 219-227
202110.1007/s00253-021-11399-4Lopez, C., M. Cao, Z. Yao and Z. ShaoRevisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineeringApplied Microbiology and Biotechnology105(14) 5959–72
202110.3390/microorganisms9061329Lopes, L. D., Y. N. Chai, E. L. Marsh, J. F. Rajewski, I. Dweikat and D. P. SchachtmanSweet sorghum genotypes tolerant and sensitive to nitrogen stress select distinct root endosphere and rhizosphere bacterial communitiesMicroorganisms9(6)
202110.1039/9781839161056-00102Loo, J. A., A. K. Goring, C. Lantz, B. Wei and M. A. ZenaideeInvestigating 3D Structures of Native Proteins and Complexes through Electron-based DissociationNew Developments in Mass Spectrometry2021-January 102-133
202110.1111/1758-2229.12892Lloyd, K. G.Time as a microbial resourceEnvironmental Microbiology Reports13(1) 18–21
202110.1016/j.cell.2021.01.052Liu, Y., P. Cruz-Morales, A. Zargar, M. S. Belcher, B. Pang, E. Englund, Q. Dan, K. Yin and J. D. KeaslingBiofuels for a sustainable futureCell184(6) 1636–47
202110.1111/tpj.15108Liu, X., R. Van Acker, W. Voorend, A. Pallidis, G. Goeminne, J. Pollier, K. Morreel, H. Kim, H. Muylle, M. Bosio, J. Ralph, R. Vanholme and W. BoerjanRewired phenolic metabolism and improved saccharification efficiency of a Zea mays cinnamyl alcohol dehydrogenase 2 (zmcad2) mutantThe Plant Journal105(5) 1240–57
202110.1016/B978-0-12-821477-0.00001-5Liu, R., L. Liang, S. Stettner, E. F. Freed and C. A. EckertCRISPR-based tools for microbial cell factoriesMicrobial Cell Factories Engineering for Production of Biomolecules 95–113
202110.1016/j.tibtech.2020.07.005Liu, R., L. Liang, E. F. Freed and R. T. GillDirected Evolution of CRISPR/Cas Systems for Precise Gene EditingTrends in Biotechnology39(3) 262–73
202110.1007/s00253-021-11394-9Liu, J.-J., W. Woodruff, A. Deewan, S. S. Jagtap, E. J. Yun, H. E. Walukiewicz, Y.-S. Jin and C. V. RaoInvestigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approachApplied Microbiology and Biotechnology105(12) 5103–12
202110.1128/mSystems.00201-21Liu, J., P. Villanueva, J. Choi, S. Gunturu, Y. Ouyang, L. K. Tiemann, J. R. Cole, K. R. Glanville, S. J. Hall, M. D. McDaniel, J. Lee and A. HoweMetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target GenesmSystems6(5) e00201-21
202110.1038/s41598-020-79733-wLiu, J., A. Cheng, M. Wang, M. Liu, D. Zhu, et al.Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2Scientific Reports11(1) 616
202110.1016/j.celrep.2021.108789Liu, H., A. L. Shiver, M. N. Price, H. K. Carlson, V. V. Trotter, Y. Chen, V. Escalante, J. Ray, K. E. Hern, C. J. Petzold, P. J. Turnbaugh, K. C. Huang, A. P. Arkin and A. M. DeutschbauerFunctional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environmentsCell Reports34(9) 108789
202110.1038/s41598-021-88899-wLiu, H. and J. U. BowieCell-free synthetic biochemistry upgrading of ethanol to 1,3 butanediolScientific Reports11(1)
202110.1016/j.copbio.2020.09.011Liu, D., M. Liberton, J. I. Hendry, J. Aminian-Dehkordi, C. D. Maranas and H. B. PakrasiEngineering biology approaches for food and nutrient production by cyanobacteriaCurrent Opinion in Biotechnology67 1–6
202110.3390/cells10030582Liu, D., R. Hu, J. Zhang, H. B. Guo, H. Cheng, L. Li, A. M. Borland, H. Qin, J. G. Chen, W. Muchero, G. A. Tuskan and X. YangOverexpression of an Agave Phosphoenolpyruvate Carboxylase Improves Plant Growth and Stress ToleranceCells10(3)
202110.1128/AEM.01742-21Linz, A. M., Y. Ma, J. M. Perez, K. S. Myers, W. S. Kontur, D. R. Noguera and T. J. DonohueAromatic Dimer Dehydrogenases from Novosphingobium aromaticivorans Reduce Monoaromatic DiketonesApplied and Environmental Microbiology87(24) e01742-21
202110.1371/journal.pone.0233249Linardi_, M. and S. A. BraybrookIdentification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stressesPLoS ONE16(44290)
202110.1007/s10533-021-00790-yLin, Y., A. N. Campbell, A. Bhattacharyya, N. DiDonato, A. M. Thompson, M. M. Tfaily, P. S. Nico, W. L. Silver and J. Pett-RidgeDifferential effects of redox conditions on the decomposition of litter and soil organic matterBiogeochemistry154(1) 1–15
202110.1016/j.mec.2021.e00164Lin, P. C., F. Zhang and H. B. PakrasiEnhanced limonene production in a fast-growing cyanobacterium through combinatorial metabolic engineeringMetabolic Engineering Communications12
202110.1021/acsomega.1c04750Lin, H.-H., Y. Cheng, J. Huo and B. H. ShanksSelective Ammonolysis of Bioderived Esters for Biobased Amide SynthesisACS Omega6(44) 30040–9
202110.1038/s41467-021-23202-zLin, H., H. J. Lee, N. Tague, J. B. Lugagne, C. Zong, F. Deng, J. Shin, L. Tian, W. Wong, M. J. Dunlop and J. X. ChengMicrosecond fingerprint stimulated Raman spectroscopic imaging by ultrafast tuning and spatial-spectral learningNature Communications12(1)
202110.1016/j.ymben.2021.04.011Lin, C.-Y., K. M. Vuu, B. Amer, P. M. Shih, E. E. K. Baidoo, H. V. Scheller and A. EudesIn-planta production of the biodegradable polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC): Stacking reduced biomass recalcitrance with value-added co-productMetabolic Engineering66 148–56
202110.1186/s13068-021-01891-4Lin, C.-Y., B. S. Donohoe, Y. J. Bomble, H. Yang, M. Yunes, N. S. Sarai, T. Shollenberger, S. R. Decker, X. Chen, M. C. McCann, M. P. Tucker, H. Wei and M. E. HimmelIron incorporation both intra- and extra-cellularly improves the yield and saccharification of switchgrass (Panicum virgatum L.) biomassBiotechnology for Biofuels14(1) 55
202110.1021/acssuschemeng.1c03765Lim, H. G., T. Eng, D. Banerjee, G. Alarcon, A. K. Lau, M.-R. Park, B. A. Simmons, B. O. Palsson, S. W. Singer, A. Mukhopadhyay and A. M. FeistGeneration of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory EvolutionACS Sustainable Chemistry & Engineering9(34) 11512–23
202110.1016/j.jbc.2021.100385Liberato, M. V., E. Teixeira Prates, T. A. Gonçalves, A. Bernardes, N. Vilela, J. Fattori, G. C. Ematsu, M. Chinaglia, E. R. Machi Gomes, A. C. Migliorini Figueira, A. Damasio, I. Polikarpov, M. S. Skaf and F. M. SquinaInsights into the dual cleavage activity of the GH16 laminarinase enzyme class on _-1,3 and _-1,4 glycosidic bondsJournal of Biological Chemistry296 100385
202110.1093/bioinformatics/btab347Liber, J. A., G. Bonito and G. M. N. BenucciCONSTAX2: improved taxonomic classification of environmental DNA markersBioinformatics37(21) 3941–3
202110.3389/fmicb.2021.680267Liao, H.-L., G. Bonito, K. Hameed, S. H. Wu, K.-H. Chen, J. Labbé, C. W. Schadt, G. A. Tuskan, F. Martin, A. Kuo, K. Barry, I. V. Grigoriev and R. VilgalysHeterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root FungiFrontiers in Microbiology12
202110.1016/j.scitotenv.2021.147589Liang, X., Y. Wang, Y. Zhang, B. Li and M. RadosevichBacteriophage-host depth distribution patterns in soil are maintained after nutrient stimulation in vitroScience of The Total Environment787 147589
202110.1186/s40168-021-01057-2Liang, R., Z. Li, M. C. Y. Lau Vetter, T. A. Vishnivetskaya, O. G. Zanina, K. G. Lloyd, S. M. Pfiffner, E. M. Rivkina, W. Wang, J. Wiggins, J. Miller, R. L. Hettich and T. C. OnstottGenomic reconstruction of fossil and living microorganisms in ancient Siberian permafrostMicrobiome9(1)
202110.1021/acssynbio.0c00253Liang, L., R. Liu, E. F. Freed, C. A. Eckert and R. T. GillTranscriptional regulatory networks involved in C3-C4 alcohol stress response and tolerance in yeastACS Synthetic Biology10(1) 19-28
202110.1029/2021JG006392Liang, J., G. Wang, S. Singh, S. Jagadamma, L. Gu, C. W. Schadt, J. D. Wood, P. J. Hanson and M. A. MayesIntensified Soil Moisture Extremes Decrease Soil Organic Carbon Decomposition: A Mechanistic Modeling AnalysisJournal of Geophysical Research: Biogeosciences126(8)
202110.1111/gcb.15833Liang, D. and G. P. RobertsonNitrification is a minor source of nitrous oxide (N2O) in an agricultural landscape and declines with increasing management intensityGlobal Change Biology27(21) 5599–613
202110.1111/tpj.15042Li, Z., P. Zhou, R. Della Coletta, T. Zhang, A. B. Brohammer, et al.Single-parent expression drives dynamic gene expression complementation in maize hybridsPlant Journal105(1) 93-107
202110.1016/j.cub.2021.01.074Li, Y., J. L. Steenwyk, Y. Chang, Y. Wang, T. Y. James, J. E. Stajich, J. W. Spatafora, M. Groenewald, C. W. Dunn, C. T. Hittinger, X. X. Shen and A. RokasA genome-scale phylogeny of the kingdom FungiCurrent Biology31(8) 1653–65.e5
202110.1021/acssuschemeng.0c08055Li, Y., S. S. Bhagwat, Y. R. Cortés-Peña, D. Ki, C. V. Rao, Y.-S. Jin and J. S. GuestSustainable Lactic Acid Production from Lignocellulosic BiomassACS Sustainable Chemistry & Engineering9(3) 1341–51
202110.1016/j.watres.2021.117505Li, W., J. Gao, J.-l. Zhuang, G.-j. Yao, X. Zhang, Y.-d. Liu, Q.-k. Liu, J. P. Shapleigh and L. MaMetagenomics and metatranscriptomics uncover the microbial community associated with high S0 production in a denitrifying desulfurization granular sludge reactorWater Research203 117505
202110.1111/pce.13962Li, S., C. A. Moller, N. G. Mitchell, D. Lee and E. A. AinsworthBioenergy sorghum maintains photosynthetic capacity in elevated ozone concentrationsPlant, Cell & Environment44(3) 729–46
202110.1016/j.nbt.2020.10.005Li, M., Y. Pu, F. Chen and A. J. RagauskasSynthesis and Characterization of Lignin-grafted-poly(_-caprolactone) from Different Biomass SourcesNew Biotechnology60 189–99
202110.1186/s13068-020-01852-3Li, M., X. Lang, M. Moran Cabrera, S. De Keyser, X. Sun, N. Da Silva and I. WheeldonCRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianusBiotechnology for Biofuels14(1)
202110.1002/adma.202007758Li, J., S. P. Wang, G. Zong, E. Kim, C.-Y. Tsao, E. VanArsdale, L.-X. Wang, W. E. Bentley and G. F. PayneInteractive Materials for Bidirectional Redox-Based CommunicationAdvanced Materials33(18) 2007758
202110.1021/accountsmr.1c00075Li, J., C. Chen, J. Y. Zhu, A. J. Ragauskas and L. HuIn Situ Wood Delignification toward Sustainable ApplicationsAccounts of Materials Research2(8) 606–20
202110.1146/annurev-ento-040920-061140Li, H., S. E. Young, M. Poulsen and C. R. CurrieSymbiont-Mediated Digestion of Plant Biomass in Fungus-Farming InsectsAnnual Review of Entomology66 297–316
202110.1111/pbi.13581Li, G., S. Sretenovic, E. Eisenstein, G. Coleman and Y. QiHighly efficient C-to-T and A-to-G base editing in a Populus hybridPlant Biotechnology Journal19(6) 1086-1088
202110.1016/j.algal.2021.102492Li, C. T., K. Trigani, C. Zuñiga, R. Eng, E. Chen, K. Zengler and M. J. BetenbaughExamining the impact of carbon dioxide levels and modulation of resulting hydrogen peroxide in Chlorella vulgarisAlgal Research60
202110.1016/j.soilbio.2021.108349Li, B.-B., S. S. Roley, D. S. Duncan, J. Guo, J. F. Quensen, H.-Q. Yu and J. M. TiedjeLong-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analysesSoil Biology and Biochemistry160 108349
202110.1094/phyto-02-21-0053-rLenz, R. R., K. B. Louie, K. L. Søndreli, S. S. Galanie, J.-G. Chen, W. Muchero, B. P. Bowen, T. R. Northen and J. M. LeBoldusMetabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours PostinoculationPhytopathology111(11) 2052–66
202110.1002/prot.26222Lensink, M. F., G. Brysbaert, T. Mauri, N. Nadzirin, S. Velankar, et al.Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experimentProteins: Structure, Function and Bioinformatics89(12) 1800-1823
202110.3389/fmicb.2021.725756Leichty, S. I., C. P. Kasanke, S. L. Bell and K. S. HofmockelSite and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial CommunitiesFrontiers in Microbiology12
202110.1016/j.rser.2020.110613Leibensperger, C., P. Yang, Q. K. Zhao, S. R. Wei and X. M. CaiThe synergy between stakeholders for cellulosic biofuel development: Perspectives, opportunities, and barriersRenewable and Sustainable Energy Reviews137
202110.1093/jpe/rtab018Lei, C., M. Abraha, J. Chen and Y.-J. SuLong-term variability of root production in bioenergy crops from ingrowth core measurementsJournal of Plant Ecology14(5) 757–70
202110.1038/s41561-021-00852-8Lehmann, J., A. Cowie, C. A. Masiello, C. Kammann, D. Woolf, J. E. Amonette, M. L. Cayuela, M. Camps-Arbestain and T. WhitmanBiochar in climate change mitigationNature Geoscience14(12) 883-892
202110.1146/annurev-bioeng-082120-022836Leggieri, P. A., Y. Liu, M. Hayes, B. Connors, S. Seppälä, M. A. O'Malley and O. S. VenturelliIntegrating Systems and Synthetic Biology to Understand and Engineer MicrobiomesAnnual Review of Biomedical Engineering23(1) 169–201
202110.1186/s12934-021-01684-2Leggieri, P. A., C. Kerdman-Andrade, T. S. Lankiewicz, M. T. Valentine and M. A. O’MalleyNon-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-cultureMicrobial Cell Factories20(1) 199
202110.1093/nar/gkab781Lee, Y.-J., N. Dai, S. I. Müller, C. Guan, M. J. Parker, et al.Pathways of thymidine hypermodificationNucleic Acids Research50(6) 3001–17
202110.1007/s12275-021-1323-1Lee, S.-Y., H. Sung, P. S. Kim, H. S. Kim, J.-Y. Lee, J.-Y. Lee, Y.-S. Jeong, E. J. Tak, J. E. Han, D.-W. Hyun and J.-W. BaeDescription of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birdsJournal of Microbiology59(11) 978–87
202110.1016/j.ymben.2021.09.008Lee, S.-B., M. Tremaine, M. Place, L. Liu, A. Pier, D. J. Krause, D. Xie, Y. Zhang, R. Landick, A. P. Gasch, C. T. Hittinger and T. K. SatoCrabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiaeMetabolic Engineering68 119–30
202110.1073/pnas.2105124118Lee, S., E. T. Sieradzki, A. M. Nicolas, R. L. Walker, M. K. Firestone, C. Hazard and G. W. NicolMethane-derived carbon flows into host-virus networks at different trophic levels in soilProceedings of the National Academy of Sciences of the United States of America118(32)
202110.1002/ppp3.10181Lee, M. R. and C. V. HawkesWidespread co-occurrence of Sebacinales and arbuscular mycorrhizal fungi in switchgrass roots and soils has limited dependence on soil carbon or nutrientsPlants, People, Planet3(5) 614–26
202110.1094/pbiomes-07-20-0056-fiLee, M. R. and C. V. HawkesPlant and Soil Drivers of Whole-Plant Microbiomes: Variation in Switchgrass Fungi from Coastal to Mountain SitesPhytobiomes Journal5(1) 69–79
202110.1016/j.copbio.2020.10.012Lee, J. W., S. Yook, H. Koh, C. V. Rao and Y. S. JinEngineering xylose metabolism in yeasts to produce biofuels and chemicalsCurrent Opinion in Biotechnology67 15–25
202110.1007/s00253-021-11436-2Lee, J. W., Y.-G. Lee, Y.-S. Jin and C. V. RaoMetabolic engineering of non-pathogenic microorganisms for 2,3-butanediol productionApplied Microbiology and Biotechnology105(14) 5751–67
202110.3390/microorganisms9020321Lee, J. A., A. C. Baugh, N. J. Shevalier, B. Strand, S. Stolyar and C. J. MarxCross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial CommunityMicroorganisms9(2)
202110.1002/bit.27926Lee, J.-W., H. Seo, C. Young and C. T. TrinhProbing specificities of alcohol acyltransferases for designer ester biosynthesis with a high-throughput microbial screening platformBiotechnology and Bioengineering118(12) 4655–67
202110.1038/s41396-020-00805-wLawson, C. E., G. H. L. Nuijten, R. M. de Graaf, T. B. Jacobson, M. Pabst, D. M. Stevenson, M. S. M. Jetten, D. R. Noguera, K. D. McMahon, D. Amador-Noguez and S. LückerAutotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mappingISME Journal15(3) 673-687
202110.1128/mSystems.00173-21Lawson, C. E., A. B. Mundinger, H. Koch, T. B. Jacobson, C. A. Weathersby, M. S. M. Jetten, M. Pabst, D. Amador-Noguez, D. R. Noguera, K. McMahon, S. Lücker, S. J. Hallam and B. L. MellbyeInvestigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13C-Tracer AnalysismSystems6(4) e00173-21
202110.3390/rs13050968Lark, T. J., I. H. Schelly and H. K. GibbsAccuracy, Bias, and Improvements in Mapping Crops and Cropland across the United States Using the USDA Cropland Data LayerRemote Sensing13(5) 968
202110.1021/acs.jproteome.0c00952Lantz, C., M. A. Zenaidee, B. Wei, Z. Hemminger, R. R. Ogorzalek Loo and J. A. LooClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass SpectrometryJournal of Proteome Research20(4) 1928-1935
202110.1038/s41545-021-00134-1Landreau, M., H. J. You, D. A. Stahl and M. K. H. WinklerImmobilization of active ammonia-oxidizing archaea in hydrogel beadsnpj Clean Water4(1)
202110.1111/omi.12323Lamont, E. I., A. Gadkari, K. A. Kerns, T. T. To, D. Daubert, G. Kotsakis, B. Bor, X. He and J. S. McLeanModified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitroMolecular Oral Microbiology36(1) 37–49
202110.1021/acssynbio.1c00229Lalwani, M. A., E. M. Zhao, S. A. Wegner and J. L. AvalosThe Neurospora crassa Inducible Q System Enables Simultaneous Optogenetic Amplification and Inversion in Saccharomyces cerevisiae for Bidirectional Control of Gene ExpressionACS Synthetic Biology10(8) 2060-2075
202110.1021/acssynbio.1c00182Lalwani, M. A., H. Kawabe, R. L. Mays, S. M. Hoffman and J. L. AvalosOptogenetic control of microbial consortia populations for chemical productionACS Synthetic Biology10(8) 2015-2029
202110.1038/s41589-020-0639-1Lalwani, M. A., S. S. Ip, C. Carrasco-López, C. Day, E. M. Zhao, H. Kawabe and J. L. AvalosOptogenetic control of the lac operon for bacterial chemical and protein productionNature Chemical Biology17(1) 71-79
202110.3389/fevo.2021.715381Lalejini, A., A. J. Ferguson, N. A. Grant and C. OfriaAdaptive Phenotypic Plasticity Stabilizes Evolution in Fluctuating EnvironmentsFrontiers in Ecology and Evolution9
202110.1128/AEM.00808-21Lal, P. B., F. Wells, K. S. Myers, R. Banerjee, A. M. Guss and P. J. KileyImproving Mobilization of Foreign DNA into Zymomonas mobilis Strain ZM4 by Removal of Multiple Restriction SystemsApplied and Environmental Microbiology87(19) e00808-21
202110.1109/BIBM52615.2021.9669503Labhishetty, S., I. Lourentzou, M. J. Volk, S. Mishra, H. Zhao and C. ZhaiTriGORank: A Gene Ontology Enriched Learning-to-Rank Framework for Trigenic Fitness Prediction2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)1841–8
202110.1371/journal.pbio.3001185LaBella, A. L., D. A. Opulente, J. L. Steenwyk, C. T. Hittinger and A. RokasSignatures of optimal codon usage in metabolic genes inform budding yeast ecologyPLoS Biology19(4) e3001185
202110.1002/bbb.2212Kurambhatti, C., D. Kumar and V. SinghTechnical and economic feasibility of an integrated ethanol and anthocyanin coproduction process using purple corn stoverBiofuels, Bioproducts and Biorefining15(3) 719–35
202110.1016/j.cpb.2021.100229Kumari, S., V. Kumar, K. Beilsmith, S. M. D. Seaver, S. Canon, et al.A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in SorghumCurrent Plant Biology28 100229
202110.1016/j.ymben.2021.06.009Kumar, P., P. A. Adamczyk, X. Zhang, R. B. Andrade, P. A. Romero, P. Ramanathan and J. L. ReedActive and machine learning-based approaches to rapidly enhance microbial chemical productionMetabolic Engineering67 216-226
202110.1002/vzj2.20124Kuhl, A. S., A. D. Kendall, R. L. van Dam, S. K. Hamilton and D. W. HyndmanRoot water uptake of biofuel crops revealed by coupled electrical resistivity and soil water content measurementsVadose Zone Journal20(4) e20124
202110.1016/j.jbc.2021.100758Kuatsjah, E., A. C. K. Chan, R. Katahira, S. J. Haugen, G. T. Beckham, M. E. P. Murphy and L. D. EltisStructural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6Journal of Biological Chemistry296 100758
202110.1002/bit.27576Kuanyshev, N., C. V. Rao, B. Dien and Y. S. JinDomesticating a food spoilage yeast into an organic acid-tolerant metabolic engineering host: Lactic acid production by engineered Zygosaccharomyces bailiiBiotechnology and Bioengineering118(1) 372–82
202110.1002/biot.202100238Kuanyshev, N., A. Deewan, S. S. Jagtap, J. Liu, B. Selvam, L.-Q. Chen, D. Shukla, C. V. Rao and Y.-S. JinIdentification and analysis of sugar transporters capable of co-transporting glucose and xylose simultaneouslyBiotechnology Journal16(11) 2100238
202110.1002/prot.26231Kryshtafovych, A., J. Moult, W. M. Billings, D. Della Corte, K. Fidelis, et al.Modeling SARS-CoV-2 proteins in the CASP-commons experimentProteins: Structure, Function and Bioinformatics89(12) 1987-1996
202110.1111/1462-2920.15705Kroeger, M. E., M. Rae DeVan, J. Thompson, R. Johansen, L. V. Gallegos-Graves, D. Lopez, A. Runde, T. Yoshida, B. Munsky, S. Sevanto, M. B. N. Albright and J. DunbarMicrobial community composition controls carbon flux across litter types in early phase of litter decompositionEnvironmental Microbiology23(11) 6676–93
202110.1016/j.soilbio.2021.108297Kravchenko, A. N., H. Zheng, Y. Kuzyakov, G. P. Robertson and A. K. GuberBelowground interplant carbon transfer promotes soil carbon gains in diverse plant communitiesSoil Biology and Biochemistry159 108297
202110.1128/mSystems.00537-21Kothari, A., S. Roux, H. Zhang, A. Prieto, D. Soneja, et al.Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental TolerancemSystems6(3) e00537-21
202110.3389/fmicb.2021.757856Kosina, S. M., P. Rademacher, K. M. Wetmore, M. de Raad, M. Zemla, G. M. Zane, J. J. Zulovich, R. Chakraborty, B. P. Bowen, J. D. Wall, M. Auer, A. P. Arkin, A. M. Deutschbauer and T. R. NorthenBiofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture BiofilmsFrontiers in Microbiology12
202110.1111/tpj.15044Ko, D. K. and F. BrandizziA temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPRThe Plant Journal105(1) 254–70
202110.1111/nph.17373Kivlin, S. N., C. V. Hawkes, M. Pape_, K. K. Treseder and C. AverillThe future of microbial ecological niche theory and modelingNew Phytologist231(2) 508–11
202110.1201/9781003243090Kim, Y. J., J. Y. Jung and U. MishraManaging Soil Organic Carbon for Climate Change Mitigation and Food SecuritySoil Organic Carbon and Feeding the Future 25–46
202110.1128/AEM.00524-21Kim, S.-K., J. Russell, M. Cha, M. E. Himmel, Y. J. Bomble and J. WestphelingCoexpression of a _-d-Xylosidase from Thermotoga maritima and a Family 10 Xylanase from Acidothermus cellulolyticus Significantly Improves the Xylan Degradation Activity of the Caldicellulosiruptor bescii ExoproteomeApplied and Environmental Microbiology87(14) e0052421
202110.1093/pcp/pcab106Kim, S.-J. and F. BrandizziAdvances in Cell Wall Matrix Research with a Focus on Mixed-Linkage GlucanPlant and Cell Physiology62(12) 1839–46
202110.1038/s41589-021-00834-2Kim, L. J., M. Ohashi, Z. Zhang, D. Tan, M. Asay, D. Cascio, J. A. Rodriguez, Y. Tang and H. M. NelsonProspecting for natural products by genome mining and microcrystal electron diffractionNature Chemical Biology17(8) 872-877
202110.1007/s11104-021-04871-7Kim, K., T. Kutlu, A. Kravchenko and A. GuberDynamics of N2O in vicinity of plant residues: a microsensor approachPlant and Soil462(1) 331–47
2021Kim, K.Change of Soil Micro-Environments During Plant Decomposition and Its Effect on Carbon and Nitrogen DynamicsDissertation(28866173) 164
202110.3389/fbioe.2020.612832Kim, J., S. T. Coradetti, Y.-M. Kim, Y. Gao, J. Yaegashi, J. D. Zucker, N. Munoz, E. M. Zink, K. E. Burnum-Johnson, S. E. Baker, B. A. Simmons, J. M. Skerker, J. M. Gladden and J. K. MagnusonMulti-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloidesFrontiers in Bioengineering and Biotechnology8
202110.1016/j.ymben.2021.02.002Kim, J., E. E. K. Baidoo, B. Amer, A. Mukhopadhyay, P. D. Adams, B. A. Simmons and T. S. LeeEngineering Saccharomyces cerevisiae for isoprenol productionMetabolic Engineering64 154–66
202110.1038/s42003-021-02057-6Kiefer, J. S. T., S. Batsukh, E. Bauer, B. Hirota, B. Weiss, J. C. Wierz, T. Fukatsu, M. Kaltenpoth and T. EnglInhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensisCommunications Biology4(1) 554
202110.1002/wsbm.1500Kichuk, T. C., C. Carrasco-López and J. L. AvalosLights up on organelles: Optogenetic tools to control subcellular structure and organizationWIREs Mechanisms of Disease13(1)
202110.1038/s42003-021-02464-9Khlystov, N. A., Y. Yoshikuni, S. Deutsch and E. S. SattelyA plant host, Nicotiana benthamiana, enables the production and study of fungal lignin-degrading enzymesCommunications Biology4(1)
202110.1086/713026Khanna, M., D. Rajagopal and D. ZilbermanLessons Learned from US Experience with Biofuels: Comparing the Hype with the EvidenceReview of Environmental Economics and Policy15(1) 67–86
202110.1111/ajae.12189Khanna, M., X. Chen, W. Wang and A. OliverRepeal of the Clean Power Plan: Social Cost and Distributional ImplicationsAmerican Journal of Agricultural Economics104(1) 33–51
202110.1111/gcbb.12877Khanna, M., L. Chen, B. Basso, X. Cai, J. L. Field, K. Guan, C. Jiang, T. J. Lark, T. L. Richard, S. A. Spawn-Lee, P. Yang and K. Y. ZippRedefining marginal land for bioenergy crop productionGCB Bioenergy13(10) 1590–609
202110.1093/plphys/kiab197Khakhar, A., C. Wang, R. Swanson, S. Stokke, F. Rizvi, S. Sarup, J. Hobbs and D. F. VoytasVipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotypePlant Physiology186(4) 2222-2238
202110.1128/mSystems.01307-20Khadempour, L., J. E. Kyle, B.-J. M. Webb-Robertson, C. D. Nicora, F. B. Smith, R. D. Smith, M. S. Lipton, C. R. Currie, E. S. Baker and K. E. Burnum-JohnsonFrom Plants to Ants: Fungal Modification of Leaf Lipids for Nutrition and Communication in the Leaf-Cutter Ant Fungal Garden EcosystemmSystems6(2) e01307-20
202110.1016/j.mib.2021.05.010Kennedy, N. W., C. E. Mills, T. M. Nichols, C. H. Abrahamson and D. Tullman-ErcekBacterial microcompartments: tiny organelles with big potentialCurrent Opinion in Microbiology63 36-42
202110.1016/j.jmb.2020.11.020Kennedy, N. W., S. P. Ikonomova, M. Slininger Lee, H. W. Raeder and D. Tullman-ErcekSelf-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment AssemblyJournal of Molecular Biology433(2) 166721
202110.1111/gcbb.12826Kemmerling, L. R., S. R. Griffin and N. M. HaddadOptimizing pollinator conservation and crop yield among perennial bioenergy cropsGCB Bioenergy13(7) 1030–42
202110.1038/s41579-021-00577-wKeasling, J., H. Garcia Martin, T. S. Lee, A. Mukhopadhyay, S. W. Singer and E. SundstromMicrobial production of advanced biofuelsNature Reviews Microbiology19(11) 701–15
202110.1016/j.tibtech.2020.07.008Ke, J., B. Wang and Y. YoshikuniMicrobiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable AgricultureTrends in Biotechnology39(3) 244–61
202110.3389/fpls.2021.669064Kates, H. R., J. R. Doby, C. M. Siniscalchi, R. LaFrance, D. E. Soltis, P. S. Soltis, R. P. Guralnick and R. A. FolkThe Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing SuccessFrontiers in Plant Science12
2021Katari, M. S., S. Tyagi and D. ShashaStatistics is easy case studies on real scientific datasetsSynthesis Lectures on Mathematics and Statistics13 26665
202110.1128/AEM.00546-21Karthikeyan, S., L. H. Orellana, E. R. Johnston, J. K. Hatt, F. E. Löffler, H. L. Ayala-del-Río, G. González and K. T. KonstantinidisMetagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen CyclingApplied and Environmental Microbiology87(12)
202110.1038/s41598-021-01533-7Juyal, A., A. Guber, M. Oerther, M. Quigley and A. KravchenkoPore architecture and particulate organic matter in soils under monoculture switchgrass and restored prairie in contrasting topographyScientific Reports11(1) 21998
202110.1093/femsec/fiab003Junier, P., G. Cailleau, I. Palmieri, C. Vallotton, O. C. Trautschold, et al.Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungiFEMS Microbiology Ecology97(2) fiab003
202110.1007/s11242-021-01654-7Jung, H. and C. MeilePore-scale numerical investigation of evolving porosity and permeability driven by biofilm growthTransport in Porous Media139(2) 203-221
202110.1128/MRA.00412-21Joshi, S., P. T. Podar, F. E. Dewhirst and M. PodarComplete Genome Sequence of Human Oral Actinomyces sp. HMT175 Strain ORNL0102, a Host of the Saccharibacterium (TM7) HMT957Microbiology Resource Announcements10(23) e00412-21
202110.1021/acsomega.1c00997Joshi, R. P., A. McNaughton, D. G. Thomas, C. S. Henry, S. R. Canon, L. A. McCue and N. KumarQuantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical ReactionsACS Omega6(14) 9948–59
202110.1111/nph.17583Joo, Y., H. Kim, M. Kang, G. Lee, S. Choung, H. Kaur, S. Oh, J. W. Choi, J. Ralph, I. T. Baldwin and S.-G. KimPith-specific lignification in Nicotiana attenuata as a defense against a stem-boring herbivoreNew Phytologist232(1) 332–44
202110.1016/j.envsoft.2021.105111Jones, C. D., A. D. Reddy, J. Jeong, J. R. Williams, S. K. Hamilton, M. Z. Hussain, V. Bandaru and R. C. IzaurraldeImproved hydrological modeling with APEX and EPIC: Model description, testing, and assessment of bioenergy producing landscape scenariosEnvironmental Modelling & Software143 105111
202110.1016/bs.mie.2021.01.046Johnson, Z. J., D. D. Krutkin, P. Bohutskyi and M. G. KalyuzhnayaMetals and methylotrophy: Via global gene expression studiesMethods in Enzymology650 185-213
202110.1021/acs.jproteome.0c00813Johnson, A., M. Stadlmeier and M. WührTMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 LevelJournal of Proteome Research20(6) 3043–52
202110.1002/pld3.309Jing, B., T. Ishikawa, N. Soltis, N. Inada, Y. Liang, et al.The Arabidopsis thaliana nucleotide sugar transporter GONST2 is a functional homolog of GONST1Plant Direct5(3) e00309
202110.1093/jxb/eraa609Jiang, S.-C., N. L. Engle, Z. Z. Banday, N. M. Cecchini, H. W. Jung, T. J. Tschaplinski and J. T. GreenbergALD1 accumulation in Arabidopsis epidermal plastids confers local and non-autonomous disease resistanceJournal of Experimental Botany72(7) 2710–26
202110.1039/D0GC03664AJiang, H. J., S. Miao, S. Imberti, B. A. Simmons, R. Atkin and G. G. WarrLiquid nanostructure of choline lysinate with water and a model lignin residueGreen Chemistry23(2) 856–66
202110.5194/essd-13-281-2021Jiang, C., K. Guan, G. Wu, B. Peng and S. WangA daily, 250M and real-time gross primary productivity product (2000–present) covering the contiguous United StatesEarth System Science Data13(2) 281–98
202110.1021/acs.est.1c02236Jiang, C., K. Guan, M. Khanna, L. Chen and J. PengAssessing Marginal Land Availability Based on Land Use Change Information in the Contiguous United StatesEnvironmental Science & Technology55(15) 10794–804
202110.1111/gcb.15795Jian, J., B. Bond-Lamberty, D. Hao, B. N. Sulman, K. F. Patel, J. Zheng, K. Dorheim, S. C. Pennington, M. D. Hartman, D. Warner and W. R. WiederLeveraging observed soil heterotrophic respiration fluxes as a novel constraint on global-scale modelsGlobal Change Biology27(20) 5392-5403
202110.1214/20-AOAS1431Jernigan, R., K. Jia, Z. Ren and W. ZhouLarge-scale multiple inference of collective dependence with applications to protein functionAnnals of Applied Statistics15(2) 902-924
202110.1021/jacs.1c01885Jellen, M. J., I. Liepuoniute, M. Jin, C. G. Jones, S. Yang, X. Jiang, H. M. Nelson, K. N. Houk and M. A. Garcia-GaribayEnhanced Gearing Fidelity Achieved through Macrocyclization of a Solvated Molecular Spur GearJournal of the American Chemical Society143(20) 7740-7747
202110.1007/s00253-021-11213-1Jayakody, L. N. and Y.-S. JinIn-depth understanding of molecular mechanisms of aldehyde toxicity to engineer robust Saccharomyces cerevisiaeApplied Microbiology and Biotechnology105(7) 2675–92
202110.3389/fpls.2021.652319Jarvis, B. A., T. B. Romsdahl, M. G. McGinn, T. J. Nazarenus, E. B. Cahoon, K. D. Chapman and J. C. SedbrookCRISPR/Cas9-Induced fad2 and rod1 Mutations Stacked With fae1 Confer High Oleic Acid Seed Oil in Pennycress (Thlaspi arvense L.)Frontiers in Plant Science12
202110.1099/ijsem.0.005100Jansson, M. K., S. Hering and M. E. J. BuhlParvimonas parva sp. nov., derived from a human genito-urinary lesionInternational Journal of Systematic and Evolutionary Microbiology71(12)
202110.1093/jxb/erab176Jaikumar, N. S., S. S. Stutz, S. B. Fernandes, A. D. B. Leakey, C. J. Bernacchi, P. J. Brown and S. P. LongCan improved canopy light transmission ameliorate loss of photosynthetic efficiency in the shade? An investigation of natural variation in Sorghum bicolorJournal of Experimental Botany72(13) 4965–80
202110.1007/s00253-021-11549-8Jagtap, S. S., A. Deewan, J.-J. Liu, H. E. Walukiewicz, E. J. Yun, Y.-S. Jin and C. V. RaoIntegrating transcriptomic and metabolomic analysis of the oleaginous yeast Rhodosporidium toruloides IFO0880 during growth under different carbon sourcesApplied Microbiology and Biotechnology105(19) 7411–25
202110.1186/s13068-021-02039-0Jagtap, S. S., A. A. Bedekar, V. Singh, Y.-S. Jin and C. V. RaoMetabolic engineering of the oleaginous yeast Yarrowia lipolytica PO1f for production of erythritol from glycerolBiotechnology for Biofuels14(1) 188
202110.1146/annurev-micro-060621-043448Jacobson, T. B., M. M. Callaghan and D. Amador-NoguezHostile Takeover: How Viruses Reprogram Prokaryotic MetabolismAnnual Review of Microbiology75(1) 515–39
202110.3390/ijms22157880Jabusch, L. K., P. W. Kim, D. Chiniquy, Z. Zhao, B. Wang, B. Bowen, A. J. Kang, Y. Yoshikuni, A. M. Deutschbauer, A. K. Singh and T. R. NorthenMicrofabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant–Microbe InteractionsInternational Journal of Molecular Sciences22(15) 7880
202110.1111/nph.17062Jabre, I., S. Chaudhary, W. Guo, M. Kalyna, A. S. N. Reddy, W. Chen, R. Zhang, C. Wilson and N. H. SyedDifferential nucleosome occupancy modulates alternative splicing in Arabidopsis thalianaNew Phytologist229(4) 1937-1945
202110.1111/nph.17713Irving, T. B., B. Alptekin, B. Kleven and J. M. AnéA critical review of 25 years of glomalin research: a better mechanical understanding and robust quantification techniques are requiredNew Phytologist232(4) 1572-1581
202110.3389/fbioe.2021.724304Ingle, A. T., N. W. Fortney, K. A. Walters, T. J. Donohue and D. R. NogueraMixed Acid Fermentation of Carbohydrate-Rich Dairy Manure HydrolysateFrontiers in Bioengineering and Biotechnology9
202110.1038/s41598-021-91181-8Ing, N., K. Deng, Y. Chen, M. Aulitto, J. W. Gin, T. L. M. Pham, C. J. Petzold, S. W. Singer, B. Bowen, K. L. Sale, B. A. Simmons, A. K. Singh, P. D. Adams and T. R. NorthenA multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activitiesScientific Reports11(1) 11803
202110.3390/plants10122611Im, J. H., S. Son, J.-H. Ko, K.-H. Kim, C. S. An and K.-H. HanNuclear Translocation of Soybean MPK6, GmMPK6, Is Mediated by Hydrogen Peroxide in Salt StressPlants10(12) 2611
202110.1371/journal.pgen.1009510Im, J. H., J.-H. Ko, W.-C. Kim, B. Crain, D. Keathley and K.-H. HanMitogen-activated protein kinase 6 negatively regulates secondary wall biosynthesis by modulating MYB46 protein stability in Arabidopsis thalianaPLoS Genetics17(4) e1009510
202110.1515/hf-2021-0015Ikeda, T., N. Takata, S. Sakamoto, S. Hu, Nuoendagula, S. Hishiyama, N. Mitsuda, W. Boerjan, J. Ralph and S. KajitaImproved chemical pulping and saccharification of a natural mulberry mutant deficient in cinnamyl alcohol dehydrogenaseHolzforschung75(10) 968–77
202110.1016/j.micres.2020.126640Igiehon, N. O., O. O. Babalola, X. Cheseto and B. TortoEffects of rhizobia and arbuscular mycorrhizal fungi on yield, size distribution and fatty acid of soybean seeds grown under drought stressMicrobiological Research242 126640
202110.1038/s41438-021-00606-yHyden, B., C. H. Carlson, F. E. Gouker, J. Schmutz, K. Barry, A. Lipzen, A. Sharma, L. Sandor, G. A. Tuskan, G. Feng, M. S. Olson, S. P. DiFazio and L. B. SmartIntegrative genomics reveals paths to sex dimorphism in Salix purpurea LHorticulture Research8
202110.1007/s00248-020-01638-yHutchinson, M. I., T. A. S. Bell, L. V. Gallegos-Graves, J. Dunbar and M. AlbrightMerging Fungal and Bacterial Community Profiles via an Internal ControlMicrobial Ecology82(2) 484–97
202110.1038/s41598-021-99877-7Hussain, M. Z., S. K. Hamilton, G. P. Robertson and B. BassoPhosphorus availability and leaching losses in annual and perennial cropping systems in an upper US Midwest landscapeScientific Reports11(1) 20367
202110.7554/eLife.63775Huss, P., A. Meger, M. Leander, K. Nishikawa and S. RamanMapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanningeLife10 e63775
202110.1016/j.mimet.2021.106294Hunt, K. A., J. Forbes, F. Taub, N. Elliott, J. Hardwicke, R. Petersen, N. Stopnisek, D. A. C. Beck and D. A. StahlAn automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substratesJournal of Microbiological Methods188 106294
202110.1128/mBio.00466-21Hungate, B. A., J. C. Marks, M. E. Power, E. Schwartz, K. J. v. Groenigen, et al.The Functional Significance of Bacterial PredatorsmBio12(2) e00466-21
202110.1021/acssuschemeng.1c04836Huang, K., X. Peng, L. Kong, W. Wu, Y. Chen and C. T. MaraveliasGreenhouse Gas Emission Mitigation Potential of Chemicals Produced from BiomassACS Sustainable Chemistry & Engineering9(43) 14480–7
202110.1039/D1GC01727FHuang, K., M. Mohan, A. George, B. A. Simmons, Y. Xu and J. M. GladdenIntegration of acetic acid catalysis with one-pot protic ionic liquid configuration to achieve high-efficient biorefinery of poplar biomassGreen Chemistry23(16) 6036–49
202110.1038/s41557-021-00801-3Huang, J., Z. Liu, B. J. Bloomer, D. S. Clark, A. Mukhopadhyay, J. D. Keasling and J. F. HartwigUnnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzymeNature Chemistry13(12) 1186–91
202110.3390/cells10061526Hu, Z., Z. Nie, C. Yan, H. Huang, X. Ma, Y. Wang, N. Ye, G. A. Tuskan, X. Yang and H. YinTranscriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnierianaCells10(6) 1526
202110.1038/s41438-021-00570-7Hu, X.-L., H. Lu, M. M. Hassan, J. Zhang, G. Yuan, P. E. Abraham, H. K. Shrestha, M. I. Villalobos Solis, J.-G. Chen, T. J. Tschaplinski, M. J. Doktycz, G. A. Tuskan, Z.-M. Cheng and X. YangAdvances and perspectives in discovery and functional analysis of small secreted proteins in plantsHorticulture Research8(1) 130
202110.1002/pei3.10056Hsieh, J.-F., S. T. Krause, D. Kainer, J. Degenhardt, W. J. Foley and C. KülheimCharacterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infectionPlant-Environment Interactions2(4) 177–93
202110.1038/s41477-021-00877-2Horton, P., S. P. Long, P. Smith, S. A. Banwart and D. J. BeerlingTechnologies to deliver food and climate security through agricultureNature Plants7(3) 250–5
202110.1186/s13068-021-02008-7Hoffman, S. M., M. Alvarez, G. Alfassi, D. M. Rein, S. Garcia-Echauri, Y. Cohen and J. L. AvalosCellulosic biofuel production using emulsified simultaneous saccharification and fermentation (eSSF) with conventional and thermotolerant yeastsBiotechnology for Biofuels14(1)
202110.1007/s11103-021-01136-wHodgson-Kratky, K., V. Perlo, A. Furtado, H. Choudhary, J. M. Gladden, B. A. Simmons, F. Botha and R. J. HenryAssociation of gene expression with syringyl to guaiacyl ratio in sugarcane ligninPlant Molecular Biology106(1) 173–92
202110.1002/btpr.3172Hillman, E. T., M. Li, C. A. Hooker, J. A. Englaender, I. Wheeldon and K. V. SolomonHydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianusBiotechnology Progress37(5)
202110.3390/microorganisms9091986Hillman, E. T., E. M. Frazier, E. K. Shank, A. N. Ortiz-Velez, J. A. Englaender and K. V. SolomonAnaerobic fungal mevalonate pathway genomic biases lead to heterologous toxicity underpredicted by codon adaptation indicesMicroorganisms9(9)
202110.1111/nph.17527Hestrin, R., P. K. Weber, J. Pett-Ridge and J. LehmannPlants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transportNew Phytologist231(5) 1746–57
202110.1094/pbiomes-04-20-0029-fiHestrin, R., M. R. Lee, B. K. Whitaker and J. Pett-RidgeThe Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic DistributionPhytobiomes Journal5(1) 14–28
202110.3390/microorganisms9050985Hervé, V., A. Simon, F. Randevoson, G. Cailleau, G. Rajoelison, H. Razakamanarivo, S. Bindschedler, E. Verrecchia and P. JunierFunctional Diversity of the Litter-Associated Fungi from an Oxalate-Carbonate Pathway Ecosystem in MadagascarMicroorganisms9(5) 985
202110.1099/ijsem.0.004977Hering, S., M. K. Jansson and M. E. J. BuhlEikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic speciesInternational Journal of Systematic and Evolutionary Microbiology71(9)
202110.3390/metabo11030168Hendry, J. I., H. V. Dinh, D. Sarkar, L. Wang, A. Bandyopadhyay, H. B. Pakrasi and C. D. MaranasA genome-scale metabolic model of anabaena 33047 to guide genetic modifications to overproduce nylon monomersMetabolites11(3)
202110.1111/1365-2656.13407Helms, J. A., IV, K. A. Roeder, S. E. Ijelu, I. Ratcliff and N. M. HaddadBioenergy landscapes drive trophic shifts in generalist antsJournal of Animal Ecology90(3) 738–50
202110.3389/fmicb.2021.695517Hebdon, S. D., A. T. Gerritsen, Y. P. Chen, J. G. Marcano and K. J. ChouGenome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellumFrontiers in Microbiology12 695517
202110.1038/s42003-021-02009-0Healey, A. L., M. Shepherd, G. J. King, J. B. Butler, J. S. Freeman, et al.Pests, diseases, and aridity have shaped the genome of Corymbia citriodoraCommunications Biology4(1) 537
202110.1128/mBio.03620-20He, X., G. L. Chadwick, C. P. Kempes, V. J. Orphan and C. MeileControls on interspecies electron transport and size limitation of anaerobically methane-oxidizing microbial consortiamBio12(3)
202110.1002/celc.202100425He, X., G. Chadwick, F. Jiménez Otero, V. Orphan and C. MeileSpatially resolved electron transport through anode-respiring Geobacter sulfurreducens biofilms: Controls and constraintsChemElectroChem8(10) 1697
202110.1111/jipb.13163Hawkins, C., D. Ginzburg, K. Zhao, W. Dwyer, B. Xue, A. Xu, S. Rice, B. Cole, S. Paley, P. Karp and S. Y. RheePlant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algaeJournal of Integrative Plant Biology63(11) 1888-1905
202110.1016/j.tplants.2021.06.015Hassan, M. M., Y. Zhang, G. Yuan, K. De, J.-G. Chen, W. Muchero, G. A. Tuskan, Y. Qi and X. YangConstruct design for CRISPR/Cas-based genome editing in plantsTrends in Plant Science26(11) 1133–52
202110.1002/9783527815128.ch8Harnden, K. A., Y. Wang, L. Vo, H. Zhao and Y. LuEngineering Artificial MetalloenzymesProtein Engineering: Tools and Applications 177–205
202110.1186/s13068-021-01908-yHarman-Ware, A. E., D. Macaya-Sanz, C. R. Abeyratne, C. Doeppke, K. Haiby, G. A. Tuskan, B. Stanton, S. P. DiFazio and M. F. DavisAccurate determination of genotypic variance of cell wall characteristics of a Populus trichocarpa pedigree using high-throughput pyrolysis-molecular beam mass spectrometryBiotechnology for Biofuels14(1) 59
202110.1039/D1GC02744AHaridevan, H., D. A. C. Evans, A. J. Ragauskas, D. J. Martin and P. K. AnnamalaiValorisation of technical lignin in rigid polyurethane foam: a critical evaluation on trends, guidelines and future perspectivesGreen Chemistry23(22) 8725–53
202110.1002/bbb.2185Happs, R. M., A. W. Bartling, C. Doeppke, A. E. Harman-Ware, R. Clark, E. G. Webb, M. J. Biddy, J.-G. Chen, G. A. Tuskan, M. F. Davis, W. Muchero and B. H. DavisonCover Image, Volume 15, Issue 1Biofuels, Bioproducts and Biorefining15(1) i-i
202110.1002/bbb.2148Happs, R. M., A. W. Bartling, C. Doeppke, A. E. Harman-Ware, R. Clark, E. G. Webb, M. J. Biddy, J.-G. Chen, G. A. Tuskan, M. F. Davis, W. Muchero and B. H. DavisonEconomic impact of yield and composition variation in bioenergy crops: Populus trichocarpaBiofuels, Bioproducts and Biorefining15(1) 176–88
202110.1186/s13068-021-01897-yHapps, R. M., B. Addison, C. Doeppke, B. S. Donohoe, M. F. Davis and A. E. Harman-WareComparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomassBiotechnology for Biofuels14(1) 58
202110.1186/s12870-021-02842-9Hao, Z., S. Yogiswara, T. Wei, V. T. Benites, A. Sinha, G. Wang, E. E. K. Baidoo, P. C. Ronald, H. V. Scheller, D. Loqué and A. EudesExpression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.)BMC Plant Biology21(1) 56
202110.1073/pnas.2023348118Hanson, A. D., D. R. McCarty, C. S. Henry, X. Xian, J. Joshi, J. A. Patterson, J. D. García-García, S. D. Fleischmann, N. D. Tivendale and A. H. MillarThe number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineeringProceedings of the National Academy of Sciences118(13) e2023348118
202110.1128/msystems.00765-21Handakumbura, P. P., A. R. Ubach and A. K. BattuVisualizing the Hidden Half: Plant-Microbe Interactions in the RhizospheremSystems6(5)
202110.1111/1462-2920.15423Hage, H., S. Miyauchi, M. Virágh, E. Drula, B. Min, et al.Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decayEnvironmental Microbiology23(10) 5716-5732
202110.1093/genetics/iyaa012Haase, M. A. B., J. Kominek, D. A. Opulente, X.-X. Shen, A. L. LaBella, X. Zhou, J. DeVirgilio, A. B. Hulfachor, C. P. Kurtzman, A. Rokas and C. T. HittingerRepeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible lossGenetics217(2)
202110.1016/bs.aecr.2021.01.003Haan, N. L., B. G. Iuliano, C. Gratton and D. A. LandisDesigning agricultural landscapes for arthropod-based ecosystem services in North AmericaAdvances in Ecological Research64 191–250
202110.1039/D1CB00112DHa, N. S., M. de Raad, L. Z. Han, A. Golini, C. J. Petzold and T. R. NorthenFaster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnologyRSC Chemical Biology2(5) 1331–51
202110.1111/nph.17383Ha, C. M., X. Rao, G. Saxena and R. A. DixonGrowth–defense trade-offs and yield loss in plants with engineered cell wallsNew Phytologist231(1) 60–74
202110.3390/genes12020288Guo, Z., M. Xu, H. Nagano, L. V. Clark, E. J. Sacks and T. YamadaCharacterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensisGenes12(2) 288
202110.1093/bioinformatics/btab355Guo, Z., T. Wu, J. Liu, J. Hou and J. ChengImproving deep learning-based protein distance prediction in CASP14Bioinformatics37(19) 3190-3196
202110.34133/2021/9805489Guo, X., Y. Qiu, D. Nettleton, C. T. Yeh, Z. Zheng, S. Hey and P. S. SchnableKAT4IA: K-means assisted training for image analysis of field-grown plant phenotypesPlant Phenomics2021
202110.3390/ijms22095020Guo, Q., L. Liu, W. C. Yim, J. C. Cushman and B. J. BarklaMembrane profiling by free flow electrophoresis and swath-ms to characterize subcellular compartment proteomes in Mesembryanthemum crystallinumInternational Journal of Molecular Sciences22(9)
202110.1186/s40168-020-00990-yGuo, J., B. Bolduc, A. A. Zayed, A. Varsani, G. Dominguez-Huerta, T. O. Delmont, A. A. Pratama, M. C. Gazitúa, D. Vik, M. B. Sullivan and S. RouxVirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA virusesMicrobiome9(1)
202110.1111/ejss.13005Guber, A., T. Kutlu, M. Rivers and A. KravchenkoMass-balance approach to quantify water distribution in soils based on X-ray computed tomography imagesEuropean Journal of Soil Science72(2) 578–92
202110.1016/j.soilbio.2021.108225Guber, A., E. Blagodatskaya, A. Juyal, B. S. Razavi, Y. Kuzyakov and A. KravchenkoTime-lapse approach to correct deficiencies of 2D soil zymographySoil Biology and Biochemistry157 108225
202110.1016/j.xplc.2021.100209Grzybowski, M., N. K. Wijewardane, A. Atefi, Y. Ge and J. C. SchnableHyperspectral reflectance-based phenotyping for quantitative genetics in crops: Progress and challengesPlant Communications2(4)
202110.1093/jxb/erab437Griffiths, M., X. Wang, K. Dhakal, H. Guo, A. Seethepalli, Y. Kang and L. M. YorkInteractions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.)Journal of Experimental Botany73(3) 967–79
202110.1002/saj2.20273Grace, P. and G. P. RobertsonSoil carbon sequestration potential and the identification of hotspots in the eastern Corn Belt of the United StatesSoil Science Society of America Journal85(5) 1410–24
202110.1016/j.watres.2021.117426Gottshall, E. Y., S. J. Bryson, K. I. Cogert, M. Landreau, C. J. Sedlacek, D. A. Stahl, H. Daims and M. WinklerSustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteriaWater Research202
202110.1186/s12859-021-04232-2Goren, E., C. Wang, Z. He, A. M. Sheflin, D. Chiniquy, J. E. Prenni, S. Tringe, D. P. Schachtman and P. LiuFeature selection and causal analysis for microbiome studies in the presence of confounding using standardizationBMC Bioinformatics22(1)
202110.1186/s12951-021-01178-8González-Grandío, E., G. S. Demirer, C. T. Jackson, D. Yang, S. Ebert, K. Molawi, H. Keller and M. P. LandryCarbon nanotube biocompatibility in plants is determined by their surface chemistryJournal of Nanobiotechnology19(1)
202110.1039/D0GC03855EGong, C., N. Bryant, X. Meng, S. Bhagia, Y. Pu, D. Xin, C. Bender Koch, C. Felby, L. G. Thygesen, A. Ragauskas and S. T. ThomsenDouble bonus: surfactant-assisted biomass pelleting benefits both the pelleting process and subsequent enzymatic saccharification of the pretreated pelletsGreen Chemistry23(2) 1050–61
202110.1038/s41598-021-85992-yGonçalves, D. R. P., U. Mishra, S. Wills and S. GautamRegional environmental controllers influence continental scale soil carbon stocks and future carbon dynamicsScientific Reports11(1) 6474
202110.1515/hf-2020-0130Goacher, R. E., Y. Mottiar and S. D. MansfieldToF-SIMS imaging reveals that p-hydroxybenzoate groups specifically decorate the lignin of fibres in the xylem of poplar and willowHolzforschung75(5) 452–62
202110.1007/s00425-021-03774-2Gleadow, R. M., B. A. McKinley, C. K. Blomstedt, A. C. Lamb, B. L. Møller and J. E. MulletRegulation of dhurrin pathway gene expression during Sorghum bicolor developmentPlanta254(6) 119
202110.1016/j.copbio.2020.12.020Glasgow, E., K. Vander Meulen, N. Kuch and B. G. FoxMultifunctional cellulases are potent, versatile tools for a renewable bioeconomyCurrent Opinion in Biotechnology67 141–8
202110.1128/mSystems.00933-20Glanville, D. G., C. Mullineaux-Sanders, C. J. Corcoran, B. T. Burger, S. Imam, T. J. Donohue and A. T. UlijaszA High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosamSystems6(1) e00933-20
202110.1038/s42003-021-01767-1Gimeno, A., C. E. Stanley, Z. Ngamenie, M.-H. Hsung, F. Walder, S. S. Schmieder, S. Bindschedler, P. Junier, B. Keller and S. VogelgsangA versatile microfluidic platform measures hyphal interactions between Fusarium graminearum and Clonostachys rosea in real-timeCommunications Biology4(1) 262
202110.1016/j.enpol.2021.112159Giarola, S., A. Molar-Cruz, K. Vaillancourt, O. Bahn, L. Sarmiento, A. Hawkes and M. BrownThe role of energy storage in the uptake of renewable energy: A model comparison approachEnergy Policy151
202110.1016/j.apenergy.2021.117539Geissler, C. H. and C. T. MaraveliasEconomic, energetic, and environmental analysis of lignocellulosic biorefineries with carbon captureApplied Energy302 117539
202110.1111/1751-7915.13832Gauttam, R., A. Mukhopadhyay, B. A. Simmons and S. W. SingerDevelopment of dual-inducible duet-expression vectors for tunable gene expression control and CRISPR interference-based gene repression in Pseudomonas_ putida KT2440Microbial Biotechnology14(6) 2659–78
202110.1073/pnas.2022838118Garruss, A. S., K. M. Collins and G. M. ChurchDeep representation learning improves prediction of LacI-mediated transcriptional repressionProceedings of the National Academy of Sciences of the United States of America118(27)
202110.1007/s00253-021-11614-2Gardner, J. G. and H. J. SchreierUnifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systemsApplied Microbiology and Biotechnology105(21-22) 8109-8127
202110.1016/j.ymben.2021.07.009Garcia, S. and C. T. TrinhComputational design and analysis of modular cells for large libraries of exchangeable product synthesis modulesMetabolic Engineering67 453–63
202110.1016/j.mec.2021.e00162Garcia, D. C., J. L. N. Dinglasan, H. Shrestha, P. E. Abraham, R. L. Hettich and M. J. DoktyczA lysate proteome engineering strategy for enhancing cell-free metabolite productionMetabolic Engineering Communications12 e00162
202110.1007/s00253-021-11322-xGarcia, C. A. and J. G. GardnerBacterial _-diglucoside metabolism: perspectives and potential for biotechnology and biomedicineApplied Microbiology and Biotechnology105(10) 4033-4052
202110.1016/j.mimet.2021.106337Garcia, C. A. and J. G. GardnerDevelopment and evaluation of an agar capture system (ACS) for high-throughput screening of insoluble particulate substrates with bacterial growth and enzyme activity assaysJournal of Microbiological Methods190
202110.1016/j.csbj.2021.10.029Garcia, B. J., R. Simha, M. Garvin, A. Furches, P. Jones, J. G. F. M. Gazolla, P. D. Hyatt, C. W. Schadt, D. Pelletier and D. JacobsonA k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomesComputational and Structural Biotechnology Journal19 5911–9
202110.1109/MLHPC54614.2021.00010Gao, M., P. Lund-Andersen, A. Morehead, S. Mahmud, C. Chen, et al.High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and FunctionProceedings of MLHPC 2021: Workshop on Machine Learning in High Performance Computing Environments, Held in conjunction with SC 2021: The International Conference for High Performance Computing, Networking, Storage and Analysis46-57
202110.3390/biology10040309Ganie, S. A. and A. S. N. ReddyStress-induced changes in alternative splicing landscape in rice: Functional significance of splice isoforms in stress toleranceBiology10(4)
202110.1073/pnas.2017714118Gallaher, S. D., R. J. Craig, I. Ganesan, S. O. Purvine, S. R. McCorkle, et al.Widespread polycistronic gene expression in green algaeProceedings of the National Academy of Sciences of the United States of America118(7)
202110.1021/acssuschemeng.0c07020Galebach, P. H., M. Beussman, J. Johnson, T. Fredriksen, C. Wang, M. P. Lanci and G. W. HuberCatalytic Conversion of Pyrolysis Oil to Alcohols and Alkanes in Supercritical Methanol over the CuMgAlOx CatalystACS Sustainable Chemistry and Engineering9(5) 2067-2079
202110.1073/pnas.2025689118Gabriel, R., N. Thieme, Q. Liu, F. Li, L. T. Meyer, et al.The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungiProceedings of the National Academy of Sciences118(26) e2025689118
202110.1186/s13068-021-02018-5Gabriel, R., R. Mueller, L. Floerl, C. Hopson, S. Harth, T. Schuerg, A. Fleissner and S. W. SingerCAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugarsBiotechnology for Biofuels14(1) 169
202110.1038/s41561-021-00725-0Fullerton, K. M., M. O. Schrenk, M. Yücel, E. Manini, M. Basili, et al.Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent marginNature Geoscience14(5) 301-306
202110.1111/nph.17572Freschet, G. T., L. Pagès, C. M. Iversen, L. H. Comas, B. Rewald, et al.A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurementsNew Phytologist232(3) 973–1122
202110.1128/AEM.02541-20Fracchia, F., L. Mangeot-Peter, L. Jacquot, F. Martin, C. Veneault-Fourrey and A. DeveauColonization of Naive Roots from Populus tremula x alba Involves Successive Waves of Fungi and Bacteria with Different Trophic AbilitiesApplied and Environmental Microbiology87(6) e02541-20
202110.1016/j.copbio.2020.11.010Foster, C. J., L. Wang, H. V. Dinh, P. F. Suthers and C. D. MaranasBuilding kinetic models for metabolic engineeringCurrent Opinion in Biotechnology67 35–41
202110.1128/MSYSTEMS.01325-20Foster, C., K. Charubin, E. T. Papoutsakis and C. D. MaranasaModeling growth kinetics, interspecies cell fusion, and metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii syntrophic coculturemSystems6(1)
202110.3389/fbioe.2021.695306Fortney, N. W., N. J. Hanson, P. R. F. Rosa, T. J. Donohue and D. R. NogueraDiverse Profile of Fermentation Byproducts From Thin StillageFrontiers in Bioengineering and Biotechnology9
202110.1002/aps3.11410Folk, R. A., H. R. Kates, R. LaFrance, D. E. Soltis, P. S. Soltis and R. P. GuralnickHigh-throughput methods for efficiently building massive phylogenies from natural history collectionsApplications in Plant Sciences9(2)
202110.1093/molbev/msaa221Foflonker, F. and C. E. Blaby-HaasColocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function DiscoveryMolecular Biology and Evolution38(2) 650–62
202110.1038/s41396-021-00992-0Flieder, M., J. Buongiorno, C. W. Herbold, B. Hausmann, T. Rattei, K. G. Lloyd, A. Loy and K. WasmundNovel taxa of Acidobacteriota implicated in seafloor sulfur cyclingThe ISME Journal15(11) 3159–80
202110.3389/fmicb.2021.729289Fischer, M. S., F. G. Stark, T. D. Berry, N. Zeba, T. Whitman and M. F. TraxlerPyrolyzed substrates induce aromatic compound metabolism in the post-fire fungus, Pyronema domesticumFrontiers in Microbiology12
202110.1111/mec.15823Fischer, E. K., Y. Song, K. A. Hughes, W. Zhou and K. L. HokeNonparallel transcriptional divergence during parallel adaptationMolecular Ecology30(6) 1516-1530
202110.1525/elementa.2021.00124Finks, S. S., C. Weihe, S. Kimball, S. D. Allison, A. C. Martiny, K. K. Treseder and J. B. H. MartinyMicrobial community response to a decade of simulated global changes depends on the plant communityElementa9(1)
202110.1038/s41589-020-00710-5Filsinger, G. T., T. M. Wannier, F. B. Pedersen, I. D. Lutz, J. Zhang, et al.Characterizing the portability of phage-encoded homologous recombination proteinsNature Chemical Biology17(4) 394-402
202110.3389/fclim.2021.603239Field, J. L.Revisiting “Additional Carbon”: Tracking Atmosphere–Ecosystem Carbon Exchange to Establish Mitigation and Negative Emissions From Bio-Based SystemsFrontiers in Climate3
202110.1128/JVI.01868-20Ferrero, S., M. D. Flores, C. Short, C. A. Vazquez, L. E. Clark, et al.Antibody-based inhibition of pathogenic new world hemorrhagic fever mammarenaviruses by steric occlusion of the human transferrin receptor 1 apical domainJournal of Virology95(17)
202110.3389/fevo.2021.639852Ferreira, L. S. d. S., A. C. d. A. Butarelli, R. d. C. Sousa, M. A. d. Oliveira, P. H. G. Moraes, et al.High-Quality Draft Genome Sequence of Pantanalinema sp. GBBB05, a Cyanobacterium From Cerrado BiomeFrontiers in Ecology and Evolution9
202110.3390/toxins13120892Ferrara, M., A. Gallo, C. Cervini, L. Gambacorta, M. Solfrizzo, S. E. Baker and G. PerroneEvidence of the Involvement of a Cyclase Gene in the Biosynthesis of Ochratoxin A in Aspergillus carbonariusToxins13(12) 892
202110.1021/acs.est.0c04358Ferin, K. M., L. Chen, J. Zhong, S. Acquah, E. A. Heaton, M. Khanna and A. VanLoockeWater Quality Effects of Economically Viable Land Use Change in the Mississippi River Basin under the Renewable Fuel StandardEnvironmental Science & Technology55(3) 1566–75
202110.3389/fmicb.2021.628308Fenton, C. A., Q. Tang, D. G. Olson, M. I. Maloney, J. L. Bose, L. R. Lynd and A. W. FentonInhibition of Pyruvate Kinase From Thermoanaerobacterium saccharolyticum by IMP Is Independent of the Extra-C DomainFrontiers in Microbiology12
202110.1016/j.copbio.2020.09.010Fenster, J. A. and C. A. EckertHigh-Throughput Functional Genomics for Energy ProductionCurrent Opinion in Biotechnology67 7–14
202110.1016/j.str.2021.02.004Feng, Z., J. D. Westbrook, R. Sala, O. S. Smart, G. Bricogne, M. Matsubara, I. Yamada, S. Tsuchiya, K. F. Aoki-Kinoshita, J. C. Hoch, G. Kurisu, S. Velankar, S. K. Burley and J. Y. YoungEnhanced validation of small-molecule ligands and carbohydrates in the Protein Data BankStructure29(4) 393-400.e1
202110.1186/s13068-021-01958-2Felczak, M. M., R. M. Bowers, T. Woyke and M. A. TerAvestZymomonas diversity and potential for biofuel productionBiotechnology for Biofuels14(1) 112
202110.1007/s10482-021-01633-4Fasusi, O. A., A. E. Amoo and O. O. BabalolaCharacterization of plant growth-promoting rhizobacterial isolates associated with food plants in South AfricaAntonie van Leeuwenhoek114(10) 1683–708
202110.1016/j.molp.2021.01.001Farmer, A., S. Thibivilliers, K. H. Ryu, J. Schiefelbein and M. LibaultSingle-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell levelMolecular Plant14(3) 372-383
202110.1039/d0gc03597aFang, Z., M. G. Flynn, J. E. Jackson and E. L. HeggThio-assisted reductive electrolytic cleavage of lignin _-O-4 models and authentic ligninGreen Chemistry23(1) 412–21
202110.3389/fpls.2021.626168Fanelli, A., D. M. Rancour, M. Sullivan, S. D. Karlen, J. Ralph, D. M. Riaño-Pachón, R. Vicentini, T. d. F. Silva, A. Ferraz, R. D. Hatfield and E. RomanelOverexpression of a Sugarcane BAHD Acyltransferase Alters Hydroxycinnamate Content in Maize Cell WallFrontiers in Plant Science12
202110.3390/v13010074Faleye, T. O. C., E. Driver, D. Bowes, S. Adhikari, D. Adams, A. Varsani, R. U. Halden and M. ScotchPan-Enterovirus Amplicon-Based High-Throughput Sequencing Detects the Complete Capsid of a EVA71 Genotype C1 Variant via Wastewater-Based Epidemiology in ArizonaViruses13(1) 74
202110.1186/s12879-021-06526-5Faleye, T. O. C., D. Adams, S. Adhikari, H. Sandrolini, R. U. Halden, A. Varsani and M. ScotchUse of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university settingBMC Infectious Diseases21(1) 810
202110.1073/pnas.2020024118Ewens, S. D., A. F. S. Gomberg, T. P. Barnum, M. A. Borton, H. K. Carlson, K. C. Wrighton and J. D. CoatesThe diversity and evolution of microbial dissimilatory phosphite oxidationProceedings of the National Academy of Sciences of the United States of America118(11)
202110.1073/pnas.2101177118Eshel, G., V. Araus, S. Undurraga, D. C. Soto, C. Moraga, et al.Plant ecological genomics at the limits of life in the Atacama DesertProceedings of the National Academy of Sciences of the United States of America118(46)
202110.1073/pnas.2022241118Epihov, D. Z., K. Saltonstall, S. A. Batterman, L. O. Hedin, J. S. Hall, M. van Breugel, J. R. Leake and D. J. BeerlingLegume–microbiome interactions unlock mineral nutrients in regrowing tropical forestsProceedings of the National Academy of Sciences118(11) e2022241118
202110.1016/j.ymben.2021.04.015Eng, T., D. Banerjee, A. K. Lau, E. Bowden, R. A. Herbert, J. Trinh, J.-P. Prahl, A. Deutschbauer, D. Tanjore and A. MukhopadhyayEngineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactorMetabolic Engineering66 229–38
202110.1038/s41396-021-00920-2Emmett, B. D., V. Lévesque-Tremblay and M. J. HarrisonConserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungiISME Journal15(8) 2276-2288
202110.1038/s41467-021-25983-9Emerson, J. B., R. K. Varner, M. Wik, D. H. Parks, R. B. Neumann, et al.Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakesNature Communications12(1)
202110.1093/nar/gkab990Eloe-Fadrosh, E. A., F. Ahmed, Anubhav, M. Babinski, J. Baumes, et al.The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resourceNucleic Acids Research50(D1) D828–36
202110.21769/BioProtoc.4156Ellis-Guardiola, K., J. Soule and R. T. ClubbMethods for the extraction of heme prosthetic groups from hemoproteinsBio-protocol11(18)
202110.3389/fmicb.2020.607679Ellis-Guardiola, K., B. J. Mahoney and R. T. ClubbNEAr Transporter (NEAT) Domains: Unique Surface Displayed Heme Chaperones That Enable Gram-Positive Bacteria to Capture Heme-Iron From HemoglobinFrontiers in Microbiology11
202110.1021/jacsau.0c00103Ellis, E. S., D. J. Hinchen, A. Bleem, L. Bu, S. J. B. Mallinson, et al.Engineering a Cytochrome P450 for Demethylation of Lignin-Derived Aromatic AldehydesJACS Au1(3) 252–61
202110.3389/fpls.2021.642848Elder, T., J. Rencoret, J. C. del Río, H. Kim and J. RalphRadical Coupling Reactions of Hydroxystilbene Glucosides and Coniferyl Alcohol: A Density Functional Theory StudyFrontiers in Plant Science12
202110.3389/fgeed.2021.654996Eid, A., C. Mohan, S. Sanchez, D. Wang and F. AltpeterMultiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid SugarcaneFrontiers in Genome Editing3
202110.1111/gcbb.12870Edmonds, P., K. J. Franz, E. A. Heaton, A. L. Kaleita, M. L. Soupir and A. VanLoockePlanting miscanthus instead of row crops may increase the productivity and economic performance of farmed potholesGCB Bioenergy13(9) 1481–97
202110.1002/csc2.20392Edmé, S. J., G. Sarath, N. Palmer, G. Y. Yuen, A. A. Muhle, R. Mitchell, S. Tatineni and C. TobiasGenetic (co)variation and accuracy of selection for resistance to viral mosaic disease and production traits in an inter-ecotypic switchgrass breeding populationCrop Science61(3) 1652-1665
202110.1016/j.jinorgbio.2021.111496Eckert, P., A. Johs, J. D. Semrau, A. A. DiSpirito, J. Richardson, R. Sarangi, E. Herndon, B. Gu and E. M. PierceSpectroscopic and computational investigations of organometallic complexation of group 12 transition metals by methanobactins from Methylocystis sp. SB2Journal of Inorganic Biochemistry223
202110.1093/g3journal/jkab074Ecale Zhou, C. L., J. Kimbrel, R. Edwards, K. McNair, B. A. Souza and S. MalfattiMultiPhATE2: code for functional annotation and comparison of phage genomesG3 Genes|Genomes|Genetics11(5)
202110.1038/s41596-021-00593-3Dukovski, I., D. Baji_, J. M. Chacón, M. Quintin, J. C. C. Vila, S. Sulheim, A. R. Pacheco, D. B. Bernstein, W. J. Riehl, K. S. Korolev, A. Sanchez, W. R. Harcombe and D. SegrèA metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)Nature Protocols16(11) 5030–82
202110.1073/pnas.2021683118Drott, M. T., T. A. Rush, T. R. Satterlee, R. J. Giannone, P. E. Abraham, C. Greco, N. Venkatesh, J. M. Skerker, N. L. Glass, J. L. Labbé, M. G. Milgroom and N. P. KellerMicroevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungiProceedings of the National Academy of Sciences118(21) e2021683118
202110.1016/j.hal.2021.102037Dreher, T. W., E. W. Davis, R. S. Mueller and T. G. OttenComparative genomics of the ADA clade within the NostocalesHarmful Algae104 102037
202110.1093/oso/9780197534755.001.0001Drahos, P.Survival governance: Energy and climate in the Chinese century
202110.1128/MRA.00864-20Doyle, D. A., K. E. Duncan and R. S. TannerGenome Sequence of Clostridium sp. Strain P21, a CO-Fermenting Acetogen Isolated from Old HayMicrobiology Resource Announcements10(11)
202110.3389/feduc.2021.711535Dow, E. G., E. M. Wood-Charlson, S. J. Biller, T. Paustian, A. Schirmer, C. S. Sheik, J. M. Whitham, R. Krebs, C. C. Goller, B. Allen, Z. Crockett and A. P. ArkinBioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source PlatformFrontiers in Education6
202110.1128/mSphere.01316-20Dove, N. C., A. M. Veach, W. Muchero, T. Wahl, J. C. Stegen, C. W. Schadt and M. A. CreggerAssembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic FactorsmSphere6(3) e01316-20
202110.1038/s41467-021-22408-5Dove, N. C., M. S. Torn, S. C. Hart and N. Ta_Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profileNature Communications12(1) 2089
202110.1111/nph.17248Dove, N. C., D. M. Klingeman, A. A. Carrell, M. A. Cregger and C. W. SchadtFire alters plant microbiome assembly patterns: integrating the plant and soil microbial response to disturbanceNew Phytologist230(6) 2433–46
202110.1016/j.xpro.2021.101025Dorone, Y., S. Boeynaems and S. Y. RheeLive imaging Arabidopsis thaliana embryos under different hydration conditionsSTAR Protocols2(4)
202110.1016/j.cell.2021.06.009Dorone, Y., S. Boeynaems, E. Flores, B. Jin, S. Hateley, et al.A prion-like protein regulator of seed germination undergoes hydration-dependent phase separationCell184(16) 4284-4298.e27
202110.1073/pnas.2004834117Dong, O. X. and P. C. RonaldTargeted DNA insertion in plantsProceedings of the National Academy of Sciences118(22) e2004834117
202110.1371/journal.pone.0240390Dong, H., L. V. Clark, X. Jin, K. Anzoua, L. Bagmet, et al.Managing flowering time in Miscanthus and sugarcane to facilitate intra- and intergeneric crossesPLoS One16(1) e0240390
202110.1002/bit.27896Dong, C., Z. Shi, L. Huang, H. Zhao, Z. Xu and J. LianCloning and characterization of a panel of mitochondrial targeting sequences for compartmentalization engineering in Saccharomyces cerevisiaeBiotechnology and Bioengineering118(11) 4269–77
202110.1016/j.ymben.2021.03.005Dong, C., J. C. Schultz, W. Liu, J. Lian, L. Huang, Z. Xu and H. ZhaoIdentification of novel metabolic engineering targets for S-adenosyl-L-methionine production in Saccharomyces cerevisiae via genome-scale engineeringMetabolic Engineering66 319-327
202110.1093/femsyr/foab002Domenzain, I., F. Li, E. J. Kerkhoven and V. SiewersEvaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts speciesFEMS Yeast Research21(1)
202110.1038/s41589-020-00729-8Dolberg, T. B., A. T. Meger, J. D. Boucher, W. K. Corcoran, E. E. Schauer, A. N. Prybutok, S. Raman and J. N. LeonardComputation-guided optimization of split protein systemsNature Chemical Biology17(5) 531–9
202110.1039/d0an02022bDo, H., S. R. Kwon, S. Baek, C. S. Madukoma, M. K. Smiley, L. E. Dietrich, J. D. Shrout and P. W. BohnRedox cycling-based detection of phenazine metabolites secreted from Pseudomonas aeruginosa in nanopore electrode arraysAnalyst146(4) 1346–54
202110.3791/62852Dinglasan, J. L. N., D. T. Reeves, R. L. Hettich and M. J. DoktyczLiquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free SystemsJoVE(175) e62852
202110.1016/j.copbio.2021.05.010Ding, Y., T. R. Northen, A. Khalil, A. Huffaker and E. A. SchmelzGetting back to the grass roots: harnessing specialized metabolites for improved crop stress resilienceCurrent Opinion in Biotechnology70 174–86
202110.1111/pce.13872Ding, N., R. Huertas, I. Torres-Jerez, W. Liu, B. Watson, W. R. Scheible and M. UdvardiTranscriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitationPlant, Cell & Environment44(1) 186–202
202110.1093/nar/gkab765Dibaeinia, P. and S. SinhaDeciphering enhancer sequence using thermodynamics-based models and convolutional neural networksNucleic Acids Research49(18) 10309–27
202110.3390/ijms222413199Di Costanzo, F., V. Di Dato, L. J. van Zyl, A. Cutignano, F. Esposito, M. Trindade and G. RomanoThree Novel Bacteria Associated with Two Centric Diatom Species from the Mediterranean Sea, Thalassiosira rotula and Skeletonema marinoiInternational Journal of Molecular Sciences22(24) 13199
202110.1016/j.jplph.2021.153541Dhungana, S. R. and D. M. BraunSugar transporters in grasses: Function and modulation in source and storage tissuesJournal of Plant Physiology266
202110.3390/plants10020411Dewhirst, R. A., J. Lei, C. A. Afseth, C. Castanha, C. M. Wistrom, J. C. Mortimer and K. J. JardineAre Methanol-Derived Foliar Methyl Acetate Emissions a Tracer of Acetate-Mediated Drought Survival in Plants?Plants10(2) 411
202110.1021/acsearthspacechem.0c00299Dewhirst, R. A., P. Handakumbura, C. S. Clendinen, E. Arm, K. Tate, W. Wang, N. M. Washton, R. P. Young, J. C. Mortimer, N. G. McDowell and K. J. JardineHigh Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpaACS Earth and Space Chemistry5(8) 1813–28
202110.3390/ijms22168843Devireddy, A. R., T. J. Tschaplinski, G. A. Tuskan, W. Muchero and J.-G. ChenRole of Reactive Oxygen Species and Hormones in Plant Responses to Temperature ChangesInternational Journal of Molecular Sciences22(16) 8843
202110.1016/j.csbj.2021.01.004Desmet, S., Y. Saeys, K. Verstaen, R. Dauwe, H. Kim, C. Niculaes, A. Fukushima, G. Goeminne, R. Vanholme, J. Ralph, W. Boerjan and K. MorreelMaize specialized metabolome networks reveal organ-preferential mixed glycosidesComputational and Structural Biotechnology Journal19 1127–44
202110.1128/AEM.00286-21Dershwitz, P., N. L. Bandow, J. Yang, J. D. Semrau, M. T. McEllistrem, et al.Oxygen generation via water splitting by a novel biogenic metal ion-binding compoundApplied and Environmental Microbiology87(14) 44940
202110.1038/s41565-021-00854-yDemirer, G. S., T. N. Silva, C. T. Jackson, J. B. Thomas, D. W. Ehrhardt, S. Y. Rhee, J. C. Mortimer and M. P. LandryNanotechnology to advance CRISPR–Cas genetic engineering of plantsNature Nanotechnology16(3) 243–50
202110.1016/j.jcat.2021.03.013Demir, B., T. Kropp, E. B. Gilcher, M. Mavrikakis and J. A. DumesicEffects of water on the kinetics of acetone hydrogenation over Pt and Ru catalystsJournal of Catalysis403 215–27
202110.1021/acssynbio.0c00591Delorenzo, D. M., J. Diao, R. Carr, Y. Hu and T. S. MoonAn Improved CRISPR Interference Tool to Engineer Rhodococcus opacusACS Synthetic Biology10(4) 786-798
202110.1128/MRA.00060-21Dell’Anno, F., L. J. v. Zyl, M. Trindade, C. Brunet, A. Dell’Anno, A. Ianora and C. SansoneGenome Sequence of an Alkaliphilus Species Isolated from Historically Contaminated Sediments of the Gulf of Naples (Mediterranean Sea)Microbiology Resource Announcements10(11) e00060-21
202110.1093/g3journal/jkab210Dell’Anno, F., L. J. van Zyl, M. Trindade, C. Brunet, A. Dell’Anno, A. Ianora and C. SansoneMetagenome-assembled genome (MAG) of Oceancaulis alexandrii NP7 isolated from Mediterranean Sea polluted marine sediments and its bioremediation potentialG3 Genes|Genomes|Genetics11(9)
202110.1002/9781119545958.ch7del Río, J. C., J. Rencoret, A. Gutiérrez, W. Lan, H. Kim and J. RalphLignin Monomers Derived from the Flavonoid and Hydroxystilbene Biosynthetic PathwaysRecent Advances in Polyphenol Research 177–206
202110.1093/plphys/kiab546de Vries, L., H. A. MacKay, R. A. Smith, Y. Mottiar, S. D. Karlen, F. Unda, E. Muirragui, C. Bingman, K. Vander Meulen, E. T. Beebe, B. G. Fox, J. Ralph and S. D. MansfieldpHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplarPlant Physiology188(2) 1014–27
202110.1186/s13068-021-02010-zde Vries, L., S. Guevara-Rozo, M. Cho, L.-Y. Liu, S. Renneckar and S. D. MansfieldTailoring renewable materials via plant biotechnologyBiotechnology for Biofuels14(1) 167
202110.1111/pbi.13651de Vries, L., M. Brouckaert, A. Chanoca, H. Kim, M. R. Regner, et al.CRISPR-Cas9 editing of CAFFEOYL SHIKIMATE ESTERASE 1 and 2 shows their importance and partial redundancy in lignification in Populus tremula _ P. albaPlant Biotechnology Journal19(11) 2221–34
202110.1016/j.agee.2020.107150De Antoni Migliorati, M., W. J. Parton, M. J. Bell, W. Wang and P. R. GraceSoybean fallow and nitrification inhibitors: Strategies to reduce N2O emission intensities and N losses in Australian sugarcane cropping systemsAgriculture, Ecosystems & Environment306
202110.1021/acssuschemeng.0c07925Das, L., E. C. Achinivu, C. A. Barcelos, E. Sundstrom, B. Amer, E. E. K. Baidoo, B. A. Simmons, N. Sun and J. M. GladdenDeconstruction of Woody Biomass via Protic and Aprotic Ionic Liquid Pretreatment for Ethanol ProductionACS Sustainable Chemistry & Engineering9(12) 4422–32
202110.3389/fpls.2021.687652Dale, R., S. Oswald, A. Jalihal, M.-F. LaPorte, D. M. Fletcher, A. Hubbard, S.-H. Shiu, A. D. L. Nelson and A. BuckschOvercoming the Challenges to Enhancing Experimental Plant Biology With Computational ModelingFrontiers in Plant Science12
202110.1007/s11120-020-00806-yDahlgren, K. K., C. Gates, T. Lee and J. C. CameronProximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002Photosynthesis Research147(2) 177–95
202110.1093/molbev/msab111Cusack, S. A., P. Wang, S. G. Lotreck, B. M. Moore, F. Meng, J. K. Conner, P. J. Krysan, M. D. Lehti-Shiu and S.-H. ShiuPredictive Models of Genetic Redundancy in Arabidopsis thalianaMolecular Biology and Evolution38(8) 3397–414
202110.1016/bs.adioch.2021.02.003Cui, Y., S. L. Goes and S. S. StahlSequential oxidation-depolymerization strategies for lignin conversion to low molecular weight aromatic chemicalsAdvances in Inorganic Chemistry77 99–136
202110.3390/plants10081536Cui, Y., D. Chen, Y. Jiang, D. Xu, P. Balint-Kurti and G. StaceyVariation in gene expression between two sorghum bicolor lines differing in innate immunity responsePlants10(8)
202110.1038/s41598-021-99994-3Cuevas, H. E., C. M. Cruet-Burgos, L. K. Prom, J. E. Knoll, L. R. Stutts and W. VermerrisThe inheritance of anthracnose (Colletotrichum sublineola) resistance in sorghum differential lines QL3 and IS18760Scientific Reports11(1)
202110.3389/fpls.2021.737690Crowe, J. D., P. Hao, S. Pattathil, H. Pan, S.-Y. Ding, D. B. Hodge and J. K. JensenXylan Is Critical for Proper Bundling and Alignment of Cellulose Microfibrils in Plant Secondary Cell WallsFrontiers in Plant Science12
202110.1128/MRA.00040-21Cross, K. L., F. Dewhirst and M. PodarComplete Genome Sequence of Human Oral Actinomyces sp. HMT897 Strain ORNL0104, a Host of the Saccharibacterium (TM7) HMT351Microbiology Resource Announcements10(14) e00040-21
202110.1094/pbiomes-01-20-0009-fiCregger, M. A., D. L. Carper, S. Christel, M. J. Doktycz, J. Labbé, et al.Plant–Microbe Interactions: From Genes to Ecosystems Using Populus as a Model SystemPhytobiomes Journal5(1) 29–38
202110.3389/fpls.2021.639769Coleman, H. D., A. M. Brunner and C.-J. TsaiSynergies and Entanglement in Secondary Cell Wall Development and Abiotic Stress Response in TreesFrontiers in Plant Science12
202110.1038/s42003-021-02477-4Cole, B., D. Bergmann, C. E. Blaby-Haas, I. K. Blaby, K. E. Bouchard, et al.Plant single-cell solutions for energy and the environmentCommunications Biology4(1) 962
202110.1080/19490976.2020.1869502Coker, J. K., O. Moyne, D. A. Rodionov and K. ZenglerCarbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human healthGut Microbes13(1) 44944
202110.1038/s41592-021-01146-yCohen, A. E.A new era of synchrotron-enabled macromolecular crystallographyNature Methods18(5) 433-434
202110.1016/j.jbc.2021.100431Chundawat, S. P. S., B. Nemmaru, M. Hackl, S. K. Brady, M. A. Hilton, M. M. Johnson, S. Chang, M. J. Lang, H. Huh, S.-H. Lee, J. M. Yarbrough, C. A. López and S. GnanakaranMolecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose IIIJournal of Biological Chemistry296 100431
202110.1093/femsmc/xtab020Chuckran, P. F., B. A. Hungate, E. Schwartz and P. DijkstraVariation in genomic traits of microbial communities among ecosystemsFEMS Microbes2 xtab020
202110.1128/mSystems.00161-21Chuckran, P. F., V. Fofanov, B. A. Hungate, E. M. Morrissey, E. Schwartz, J. Walkup and P. DijkstraRapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial CommunitymSystems6(3) e00161-21
202110.1111/jpy.13132Chorazyczewski, A. M., I.-S. Huang, H. Abdulla, X. Mayali and P. V. ZimbaThe Influence of Bacteria on the Growth, Lipid Production, and Extracellular Metabolite Accumulation by Phaeodactylum tricornutum (Bacillariophyceae)Journal of Phycology57(3) 931–40
202110.1021/jasms.1c00013Choe, K., P. Xue, H. Zhao and J. V. SweedlermacroMS: Image-Guided Analysis of Random Objects by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass SpectrometryJournal of the American Society for Mass Spectrometry32(5) 1180–8
202110.1186/s13068-021-02029-2Cho, J.-S., M.-H. Kim, E.-K. Bae, Y.-I. Choi, H.-W. Jeon, K.-H. Han and J.-H. KoField evaluation of transgenic hybrid poplars with desirable wood properties and enhanced growth for biofuel production by bicistronic expression of PdGA20ox1 and PtrMYB3 in wood-forming tissueBiotechnology for Biofuels14(1) 177
202110.3389/fmicb.2021.598180Chiniquy, D., E. M. Barnes, J. Zhou, K. Hartman, X. Li, A. Sheflin, A. Pella, E. Marsh, J. Prenni, A. M. Deutschbauer, D. P. Schachtman and S. G. TringeMicrobial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related PhylotypesFrontiers in Microbiology12
202110.1016/j.mib.2021.08.006Chiappino-Pepe, A., V. Pandey and O. BillkerGenome reconstructions of metabolism of Plasmodium RBC and liver stagesCurrent Opinion in Microbiology63 259-266
202110.1021/acssuschemeng.1c01629Cheng, M.-H., B. S. Dien, Y.-S. Jin, S. Thompson, J. Shin, P. J. Watson Slininger, N. Qureshi and V. SinghConversion of High-Solids Hydrothermally Pretreated Bioenergy Sorghum to Lipids and Ethanol Using Yeast CulturesACS Sustainable Chemistry & Engineering9(25) 8515–25
202110.1111/mec.15773Cheng, J., Y. Yang, M. M. Yuan, Q. Gao, L. Wu, Z. Qin, Z. J. Shi, E. A. G. Schuur, J. R. Cole, J. M. Tiedje and J. ZhouWinter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stabilityMolecular Ecology30(4) 926-937
202110.1038/s41598-021-90303-6Chen, X., J. Liu, Z. Guo, T. Wu, J. Hou and J. ChengProtein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14Scientific Reports11(1)
202110.1016/j.xplc.2021.100215Chen, T.-C., M. Chern, M. Steinwand, D. Ruan, Y. Wang, A. Isharani and P. RonaldPaladin, a tyrosine phosphatase-like protein, is required for XA21-mediated immunity in ricePlant Communications2(4) 100215
202110.1099/ijsem.0.004801Chen, S., S. Zheng, D. Zhang, B. Hetharua, J. Gui, X. An and H. XuIsolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sedimentInternational Journal of Systematic and Evolutionary Microbiology71(5)
202110.1029/2020MS002284Chen, P., Y. Yuan, W. Li, S. D. LeDuc, T. J. Lark, X. Zhang and C. ClarkAssessing the Impacts of Recent Crop Expansion on Water Quality in the Missouri River Basin Using the Soil and Water Assessment ToolJournal of Advances in Modeling Earth Systems13(6) e2020MS002284
202110.1021/acs.nanolett.0c05038Chen, P., Y. Li, Y. Nishiyama, S. V. Pingali, H. M. O’Neill, Q. Zhang and L. A. BerglundSmall Angle Neutron Scattering Shows Nanoscale PMMA Distribution in Transparent Wood BiocompositesNano Letters21(7) 2883–90
202110.1038/s41592-021-01303-3Chen, L., W. Lu, L. Wang, X. Xing, Z. Chen, et al.Metabolite discovery through global annotation of untargeted metabolomics dataNature Methods18(11) 1377–85
202110.1088/1748-9326/abd7afChen, L., D. Debnath, J. Zhong, K. Ferin, A. VanLoocke and M. KhannaThe economic and environmental costs and benefits of the renewable fuel standardEnvironmental Research Letters16(3) 34021
202110.1021/acs.est.0c06133Chen, L., E. Blanc-Betes, T. W. Hudiburg, D. Hellerstein, S. Wallander, E. H. DeLucia and M. KhannaAssessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program LandEnvironmental Science & Technology55(2) 1301–9
202110.3868/11-00559-001Chen, J.Biophysical Models and Applications in Ecosystem AnalysisMichigan State University Press
202110.1093/nar/gkaa939Chen, I. A., K. Chu, K. Palaniappan, A. Ratner, J. Huang, et al.The IMG/M data management and analysis system v.6.0: new tools and advanced capabilitiesNucleic Acids Research49(D1) D751–63
202110.1186/s13068-020-01865-yChen, F., C. Zhuo, X. Xiao, T. H. Pendergast and K. M. DevosA rapid thioacidolysis method for biomass lignin composition and tricin analysisBiotechnology for Biofuels14(1) 18
202110.1002/prot.26052Chen, C., T. Wu, Z. Guo and J. ChengCombination of deep neural network with attention mechanism enhances the explainability of protein contact predictionProteins: Structure, Function and Bioinformatics89(6) 697-707
202110.1137/19m129961xChen, C., S. Reiz, C. D. Yu, H. J. Bungartz and G. BirosFast Approximation of the Gauss--Newton Hessian Matrix for the Multilayer PerceptronSIAM Journal on Matrix Analysis and Applications42(1) 165–84
202110.1186/s12859-020-03952-1Chen, C., J. Hou, X. Shi, H. Yang, J. A. Birchler and J. ChengDeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networksBMC Bioinformatics22(1)
202110.1093/bioinformatics/btaa902Chen, C., J. Hou, X. Shi, H. Yang, J. A. Birchler and J. ChengGNET2: an R package for constructing gene regulatory networks from transcriptomic dataBioinformatics37(14) 2068–9
202110.1073/pnas.2106480118Chen, C., V. S. Boorla, D. Banerjee, R. Chowdhury, V. S. Cavener, R. H. Nissly, A. Gontu, N. R. Boyle, K. Vandegrift, M. S. Nair, S. V. Kuchipudi and C. D. MaranasComputational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2Proceedings of the National Academy of Sciences118(42) e2106480118
202110.1007/978-981-16-3595-3_6Chellappan, M. and M. T. RanjithMetagenomic Approaches for Insect SymbiontsMicrobial Approaches for Insect Pest Management 271–313
202110.1073/pnas.2101254118Chase, A. B., C. Weihe and J. B. H. MartinyAdaptive differentiation and rapid evolution of a soil bacterium along a climate gradientProceedings of the National Academy of Sciences of the United States of America118(18)
202110.1128/AEM.02301-20Chang, J., D. D. Kim, J. D. Semrau, J. Y. Lee, H. Heo, W. Gu and S. YoonEnhancement of Nitrous Oxide Emissions in Soil Microbial Consortia via Copper Competition between Proteobacterial Methanotrophs and DenitrifiersApplied and Environmental Microbiology87(5) 44941
202110.1039/d1gc02865kChang, H., M. S. Kim, G. W. Huber and J. A. DumesicDesign of closed-loop recycling production of a Diels-Alder polymer from a biomass-derived difuran as a functional additive for polyurethanesGreen Chemistry23(23) 9479-9488
202110.1039/D1GC00311AChang, H., I. Bajaj, A. H. Motagamwala, A. Somasundaram, G. W. Huber, C. T. Maravelias and J. A. DumesicSustainable production of 5-hydroxymethyl furfural from glucose for process integration with high fructose corn syrup infrastructureGreen Chemistry23(9) 3277–88
202110.1186/s13068-021-02033-6Chandrasekar, M., L. Joshi, K. Krieg, S. Chipkar, E. Burke, D. J. Debrauske, K. D. Thelen, T. K. Sato and R. G. OngA high solids field-to-fuel research pipeline to identify interactions between feedstocks and biofuel productionBiotechnology for Biofuels14(1) 179
202110.3390/cryst11101227Chai, L., P. Zhu, J. Chai, C. Pang, B. Andi, S. McSweeney, J. Shanklin and Q. LiuAlphaFold Protein Structure Database for Sequence-Independent Molecular ReplacementCrystals11(10) 1227
202110.1111/1462-2920.15785Cha, G., K. A. Meinhardt, L. H. Orellana, J. K. Hatt, M. W. Pannu, D. A. Stahl and K. T. KonstantinidisThe influence of alfalfa-switchgrass intercropping on microbial community structure and functionEnvironmental Microbiology23(11) 6828-6843
202110.1021/acssynbio.0c00471Cetnar, D. P. and H. M. SalisSystematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operonsACS Synthetic Biology10(2) 318-332
202110.1186/s40168-021-01042-9Ceja-Navarro, J. A., Y. Wang, D. Ning, A. Arellano, L. Ramanculova, M. M. Yuan, A. Byer, K. D. Craven, M. C. Saha, E. L. Brodie, J. Pett-Ridge and M. K. FirestoneProtist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants developMicrobiome9(1)
202110.1002/ecs2.3638Cates, A. M., B. D. Wills, T. N. Kim, D. A. Landis, C. Gratton, H. W. Read and R. D. JacksonNo evidence of top-down effects by ants on litter decomposition in a temperate grasslandEcosphere12(7) e03638
202110.1002/ppj2.20014Casto, A. L., H. Schuhl, J. C. Tovar, Q. Wang, R. S. Bart, N. Fahlgren and M. A. GehanPicturing the future of foodPlant Phenome Journal4(1)
202110.1002/csc2.20609Casto, A. L., K. M. Murphy and M. A. GehanCoping with cold: Sorghum cold stress from germination to maturityCrop Science61(6) 3894-3907
202110.1128/MRA.00759-21Castillo, D. J., M. W. V. Goethem and T. P. MakhalanyaneThree Draft Single-Cell Genome Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern OceanMicrobiology Resource Announcements10(39) e00759-21
202110.1007/s12010-021-03594-wCastaño, J. D., M. Zhou and J. SchillingTowards an Understanding of Oxidative Damage in an _-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics ApproachApplied Biochemistry and Biotechnology193(10) 3287-3300
202110.1128/mBio.02040-21Castaño, J., J. Zhang, M. Zhou, C. F. Tsai, J. Y. Lee, C. Nicora and J. SchillingA fungal secretome adapted for stress enabled a radical wood decay mechanismmBio12(4)
202110.1007/s10664-021-09940-0Cashman, M., J. Firestone, M. B. Cohen, T. Thianniwet and W. NiuAn empirical investigation of organic software product linesEmpirical Software Engineering26(3) 44
202110.3389/fmicb.2021.791089Carruthers, D. N. and T. S. LeeDiversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model MicroorganismsFrontiers in Microbiology12
202110.1128/mSystems.01306-20Carper, D. L., D. J. Weston, A. Barde, C. M. Timm, T.-Y. Lu, et al.Cultivating the Bacterial Microbiota of Populus RootsmSystems6(3) e01306-20
202110.1038/s41396-021-00921-1Carim, S., A. L. Azadeh, A. E. Kazakov, M. N. Price, P. J. Walian, L. M. Lui, T. N. Nielsen, R. Chakraborty, A. M. Deutschbauer, V. K. Mutalik and A. P. ArkinSystematic discovery of pseudomonad genetic factors involved in sensitivity to tailocinsThe ISME Journal15(8) 2289–305
202110.1038/s41594-021-00646-xCao, Q., D. R. Boyer, M. R. Sawaya, R. Abskharon, L. Saelices, B. A. Nguyen, J. Lu, K. A. Murray, F. Kandeel and D. S. EisenbergCryo-EM structures of hIAPP fibrils seeded by patient-extracted fibrils reveal new polymorphs and conserved fibril coresNature Structural and Molecular Biology28(9) 724-730
202110.1016/j.copbio.2021.01.005Candry, P. and R. GaniguéChain elongators, friends, and foesCurrent Opinion in Biotechnology67 99-110
202110.3389/fmicb.2021.679894_ade_, N., N. Bellora, R. Ulloa, M. Tome, H. Petkovi_, M. Groenewald, C. T. Hittinger and D. LibkindHanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative EnvironmentsFrontiers in Microbiology12
202110.1073/pnas.2022982118Busta, L., E. Schmitz, D. K. Kosma, J. C. Schnable and E. B. CahoonA co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistryProceedings of the National Academy of Sciences of the United States of America118(12)
202110.1093/nar/gkaa1038Burley, S. K., C. Bhikadiya, C. Bi, S. Bittrich, L. Chen, et al.RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciencesNucleic Acids Research49(1) D437-D451
202110.1016/j.str.2021.04.010Burley, S. K. and H. M. BermanOpen-access data: A cornerstone for artificial intelligence approaches to protein structure predictionStructure29(6) 515-520
202110.1016/j.jbc.2021.100559Burley, S. K.Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and developmentJournal of Biological Chemistry296
202110.3390/ijms22062845Burjoski, V. and A. S. N. ReddyThe landscape of rna-protein interactions in plants: Approaches and current statusInternational Journal of Molecular Sciences22(6) 44952
202110.1021/acssuschemeng.0c08829Brunner, M., S. Imberti, B. A. Simmons, G. G. Warr and R. AtkinLiquid Nanostructure of Cholinium Argininate Biomass SolventsACS Sustainable Chemistry & Engineering9(7) 2880–90
202110.1016/j.jpdc.2020.11.006Brunn, M., N. Himthani, G. Biros, M. Mehl and A. MangFast GPU 3D diffeomorphic image registrationJournal of Parallel and Distributed Computing149 149–62
202110.1186/s13068-021-02083-wBrown, J. L., C. L. Swift, S. J. Mondo, S. Seppala, A. Salamov, et al.Co_cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substratesBiotechnology for Biofuels14(1)
202110.1128/mSystems.00835-21Brisson, V., X. Mayali, B. Bowen, A. Golini, M. Thelen, R. K. Stuart and T. R. NorthenIdentification of Effector Metabolites Using Exometabolite Profiling of Diverse MicroalgaemSystems6(6) e00835-21
202110.1128/MRA.01427-20Bridges, C. M., M. C. Nelson, J. Graf and D. J. GageDraft Genome Sequences of Dysgonomonas sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower TermiteMicrobiology Resource Announcements10(4) e01427-20
202110.1128/MRA.00079-21Bridges, C. M. and D. J. GageDraft Genome Sequences of Dysgonomonas sp. Strains GY75 and GY617, Isolated from the Hindgut of Reticulitermes flavipesMicrobiology Resource Announcements10(12) e00079-21
202110.1097/ebp.0000000000001228Brewington, J., J. Cloud, C. Johansson, D. Olson and J. SmileyIn patients with Clostridium difficile infection, is fecal microbiota transplant better than vancomycin for resolving diarrhea?Evidence-Based Practice24(10) 39–40
202110.1002/biot.202100237Brant, E. J., M. C. Baloglu, A. Parikh and F. AltpeterCRISPR/Cas9 mediated targeted mutagenesis of LIGULELESS-1 in sorghum provides a rapidly scorable phenotype by altering leaf inclination angleBiotechnology Journal16(11) 2100237
202110.1039/D1GC01591EBrandner, D. G., J. S. Kruger, N. E. Thornburg, G. G. Facas, J. K. Kenny, et al.Flow-through solvolysis enables production of native-like lignin from biomassGreen Chemistry23(15) 5437–41
202110.1186/s12864-021-07957-9Braga, L. P. P., R. V. Pereira, L. F. Martins, L. M. S. Moura, F. B. Sanchez, J. S. L. Patané, A. M. da Silva and J. C. SetubalGenome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactionsBMC Genomics22(1) 652
202110.1007/s10533-021-00789-5Bradford, M. A., S. A. Wood, E. T. Addicott, E. P. Fenichel, N. Fields, J. González-Rivero, F. V. Jevon, D. S. Maynard, E. E. Oldfield, A. Polussa, E. B. Ward and W. R. WiederQuantifying microbial control of soil organic matter dynamics at macrosystem scalesBiogeochemistry156(1) 19-40
202110.1094/pbiomes-07-20-0051-rBowsher, A. W., G. M. N. Benucci, G. Bonito and A. ShadeSeasonal Dynamics of Core Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf BacteriaPhytobiomes Journal5(1) 60–8
202110.3389/fmars.2021.611937Bourbonnais, A., C. Frey, X. Sun, L. A. Bristow, A. Jayakumar, N. E. Ostrom, K. L. Casciotti and B. B. WardProtocols for Assessing Transformation Rates of Nitrous Oxide in the Water ColumnFrontiers in Marine Science8
202110.1128/MRA.01485-20Borre, I. and E. C. SonnenscheinDraft Genome Sequences of Nine Environmental Bacterial Isolates Colonizing PlasticMicrobiology Resource Announcements10(11) e01485-20
202110.1002/tpg2.20114Bornowski, N., K. J. Michel, J. P. Hamilton, S. Ou, A. S. Seetharam, et al.Genomic variation within the maize stiff-stalk heterotic germplasm poolPlant Genome14(3)
202110.3389/fenrg.2021.781552Bomble, Y. J. and M. C. JewettEditorial: Cell Free Biocatalysis for the Production of BioproductsFrontiers in Energy Research9
202110.1038/s43705-021-00083-3Bolduc, B., O. Zablocki, J. Guo, A. A. Zayed, D. Vik, P. Dehal, E. M. Wood-Charlson, A. Arkin, N. Merchant, J. Pett-Ridge, S. Roux, M. Vaughn and M. B. SullivaniVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecologyISME Communications1(1) 77
202110.1002/cbic.202000452Bogart, J. W., M. D. Cabezas, B. Vögeli, D. A. Wong, A. S. Karim and M. C. JewettCell-Free Exploration of the Natural Product Chemical SpaceChemBioChem22(1) 84-91
202110.1186/s40168-020-00983-xBlaustein, R. A., L. M. Michelitsch, A. J. Glawe, H. Lee, S. Huttelmaier, N. Hellgeth, S. Ben Maamar and E. M. HartmannToothbrush microbiomes feature a meeting ground for human oral and environmental microbiotaMicrobiome9(1) 32
202110.1073/pnas.2100281118Blaby-Haas, C. E.Cyanobacteria provide a new paradigm in the regulation of cofactor dependenceProceedings of the National Academy of Sciences118(7) e2100281118
202110.1038/s41592-021-01100-yBiswas, S., G. Khimulya, E. C. Alley, K. M. Esvelt and G. M. ChurchLow-N protein engineering with data-efficient deep learningNature Methods18(4) 389-396
202110.1111/1758-2229.12943Bing, R. G., D. B. Sulis, J. P. Wang, M. W. W. Adams and R. M. KellyThermophilic microbial deconstruction and conversion of natural and transgenic lignocelluloseEnvironmental Microbiology Reports13(3) 272-293
202110.1371/journal.pone.0248607Bible, A. N., M. Chang and J. L. Morrell-FalveyIdentification of a diguanylate cyclase expressed in the presence of plants and its application for discovering candidate gene products involved in plant colonization by Pantoea sp. YR343PLoS ONE16(7) e0248607
202110.1128/MRA.00884-20Bhattacharjee, A., L. N. Anderson, T. Alfaro, A. Porras-Alfaro, A. Jumpponen, K. S. Hofmockel, J. K. Jansson, C. R. Anderton and W. C. NelsonDraft Genome Sequence of Fusarium sp. Strain DS 682, a Novel Fungal Isolate from the Grass RhizosphereMicrobiology Resource Announcements10(1) e00884-20
202110.1016/j.scitotenv.2020.144429Bhatia, S. K., S. S. Jagtap, A. A. Bedekar, R. K. Bhatia, K. Rajendran, A. Pugazhendhi, C. V. Rao, A. E. Atabani, G. Kumar and Y. H. YangRenewable biohydrogen production from lignocellulosic biomass using fermentation and integration of systems with other energy generation technologiesScience of the Total Environment765 144429
202110.1021/acssuschemeng.1c05441Bhagwat, S. S., Y. Li, Y. R. Cortés-Peña, E. C. Brace, T. A. Martin, H. Zhao and J. S. GuestSustainable Production of Acrylic Acid via 3-Hydroxypropionic Acid from Lignocellulosic BiomassACS Sustainable Chemistry & Engineering9(49) 16659–69
202110.1021/acssuschemeng.0c04240Berstis, L., T. Elder, R. Dixon, M. Crowley and G. T. BeckhamCoupling of Flavonoid Initiation Sites with Monolignols Studied by Density Functional TheoryACS Sustainable Chemistry & Engineering9(4) 1518–28
202110.1016/j.ohx.2021.e00208Berry, T. D., C. Creelman, N. Nickerson, A. Enders and T. WhitmanAn open-source, automated, gas sampling peripheral for laboratory incubation experiments using cavity ring-down spectroscopyHardwareX10
202110.1186/s13059-021-02289-zBernstein, D. B., S. Sulheim, E. Almaas and D. SegrèAddressing uncertainty in genome-scale metabolic model reconstruction and analysisGenome Biology22(1) 64
202110.1186/s13068-020-01867-wBeri, D., C. D. Herring, S. Blahova, S. Poudel, R. J. Giannone, R. L. Hettich and L. R. LyndCoculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadingsBiotechnology for Biofuels14(1) 24
202110.1038/s41598-021-91394-xBenedict, A. B., P. Ghosh, S. M. Scott and J. S. GriffittsA conserved rhizobial peptidase that interacts with host-derived symbiotic peptidesScientific Reports11(1) 11779
202110.1002/agg2.20214Bendorf, J., S. Hubbard, C. J. Kucharik and A. VanLoockeRapid changes in agricultural land use and hydrology in the Driftless RegionAgrosystems, Geosciences & Environment4(4) e20214
202110.1098/rspb.2021.0621Bell-Dereske, L. P. and S. E. EvansContributions of environmental and maternal transmission to the assembly of leaf fungal endophyte communitiesProceedings of the Royal Society B: Biological Sciences288(1956) 20210621
202110.5194/soil-7-47-2021Belanger, M. A., C. Vizza, G. P. Robertson and S. S. RoleyQuantifying and correcting for pre-assay CO2 loss in short-term carbon mineralization assaysSOIL7(1) 47–52
202110.1128/mSystems.00906-21Beach, N. K., K. S. Myers, B. R. Owen, M. Seib, T. J. Donohue and D. R. NogueraExploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox MicrobiomemSystems6(5) e00906-21
202110.1021/acs.biochem.1c00613Bathe, U., B. J. Leong, D. R. McCarty, C. S. Henry, P. E. Abraham, M. A. Wilson and A. D. HansonThe Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its RepairBiochemistry60(47) 3555–65
202110.1093/plcell/koaa016Bastiaanse, H., I. M. Henry, H. Tsai, M. Lieberman, C. Canning, L. Comai and A. GrooverA systems genetics approach to deciphering the effect of dosage variation on leaf morphology in PopulusPlant Cell33(4) 940-960
202110.1038/s41467-021-21763-7Basso, B., R. A. Martinez-Feria, L. Rill and J. T. RitchieContrasting long-term temperature trends reveal minor changes in projected potential evapotranspiration in the US MidwestNature Communications12(1) 1476
202110.1016/j.agsy.2021.103244Basso, B., J. W. Jones, J. Antle, R. A. Martinez-Feria and B. VermaEnabling circularity in grain production systems with novel technologies and policyAgricultural Systems193 103244
202110.1038/s43016-021-00283-zBasso, B.Precision conservation for a changing climateNature Food2(5) 322–3
202110.1039/D1EE01642CBartling, A. W., M. L. Stone, R. J. Hanes, A. Bhatt, Y. Zhang, et al.Techno-economic analysis and life cycle assessment of a biorefinery utilizing reductive catalytic fractionationEnergy & Environmental Science14(8) 4147–68
202110.1089/crispr.2021.29126.rbaBarrangou, R.The CRISPR Chronicles and the Power of StorytellingThe CRISPR Journal4(2) 158–9
202110.1073/pnas.2115292118Barnett, S. E., N. D. Youngblut, C. N. Koechli and D. H. BuckleyMultisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cyclingProceedings of the National Academy of Sciences of the United States of America118(47)
202110.1021/acssuschemeng.0c07920Barcelos, C. A., A. M. Oka, J. Yan, L. Das, E. C. Achinivu, et al.High-Efficiency Conversion of Ionic Liquid-Pretreated Woody Biomass to Ethanol at the Pilot ScaleACS Sustainable Chemistry & Engineering9(11) 4042–53
202110.1111/1365-2656.13541Barbour, M. A. and J. P. GibertGenetic and plastic rewiring of food webs under climate changeJournal of Animal Ecology90(8) 1814-1830
202110.1021/acssuschemeng.1c03772Baral, N. R., M. Yang, B. G. Harvey, B. A. Simmons, A. Mukhopadhyay, T. S. Lee and C. D. ScownProduction Cost and Carbon Footprint of Biomass-Derived Dimethylcyclooctane as a High-Performance Jet Fuel BlendstockACS Sustainable Chemistry & Engineering9(35) 11872–82
202110.1016/j.jclepro.2020.123593Baral, N. R., Z. D. Asher, D. Trinko, E. Sproul, C. Quiroz-Arita, J. C. Quinn and T. H. BradleyBiomass feedstock transport using fuel cell and battery electric trucks improves lifecycle metrics of biofuel sustainability and economyJournal of Cleaner Production279 123593
202110.3389/fbioe.2021.766674Banerjee, D., T. Eng, Y. Sasaki, A. Srinivasan, A. Oka, R. A. Herbert, J. Trinh, V. R. Singan, N. Sun, D. Putnam, C. D. Scown, B. Simmons and A. MukhopadhyayGenomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid StressFrontiers in Bioengineering and Biotechnology9
202110.1128/mbio.03408-21Bandyopadhyay, A., Z. Ye, Z. Benedikty, M. Trtilek and H. B. PakrasiAntenna Modification Leads to Enhanced Nitrogenase Activity in a High Light-Tolerant CyanobacteriummBio12(6)
202110.1002/cpz1.153Balasubramanian, V. K., S. O. Purvine, Y. Liang, R. T. Kelly, L. Pasa-Tolic, W. B. Chrisler, E. Blumwald, C. N. Stewart, Y. Zhu and A. H. AhkamiCell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing PlatformCurrent Protocols1(5)
202110.1094/pbiomes-09-19-0050-fiBahulikar, R. A., S. R. Chaluvadi, I. Torres-Jerez, J. Mosali, J. L. Bennetzen and M. UdvardiNitrogen Fertilization Reduces Nitrogen Fixation Activity of Diverse Diazotrophs in Switchgrass RootsPhytobiomes Journal5(1) 80–7
202110.1093/plcell/koaa021Baetsen-Young, A., H. Chen, S. H. Shiu and B. DayContrasting transcriptional responses to Fusarium virguliforme colonization in symptomatic and asymptomatic hostsThe Plant Cell33(2) 224–47
202110.1002/bit.27603Badr, K., W. Whelan, Q. P. He and J. WangFast and easy quantitative characterization of methanotroph–photoautotroph coculturesBiotechnology and Bioengineering118(2) 703-714
202110.1007/s00425-021-03718-wBabst, B. A., A. Karve, A. Sementilli, I. Dweikat and D. M. BraunPhysiology and whole-plant carbon partitioning during stem sugar accumulation in sweet dwarf sorghumPlanta254(4)
202110.1128/MRA.00954-20Babalola, O. O., R. R. Molefe and A. E. AmooMetagenome Assembly and Metagenome-Assembled Genome Sequences from the Rhizosphere of Maize Plants in Mafikeng, South AfricaMicrobiology Resource Announcements10(8) e00954-20
202110.1128/MRA.00029-21Babalola, O. O., O. A. Fasusi, A. E. Amoo and A. S. AyangbenroDraft Genomic Analysis of Pseudomonas sp. Strain OA3, a Potential Plant Growth-Promoting Rhizospheric BacteriumMicrobiology Resource Announcements10(11) e00029-21
202110.1016/j.rhisph.2021.100342Babalola, O. O., O. A. Fasusi, A. E. Amoo and A. S. AyangbenroGenomic analysis of a Pseudomonas strain with multiple plant growth promoting propertiesRhizosphere18 100342
202110.1128/MRA.00482-21Babalola, O. O., B. S. Adeleke and A. S. AyangbenroDraft Genome Sequencing of Stenotrophomonas indicatrix BOVIS40 and Stenotrophomonas maltophilia JVB5, Two Strains with Identifiable Genes Involved in Plant Growth PromotionMicrobiology Resource Announcements10(28) e00482-21
202110.1038/s41467-021-21449-0Azeez, A., Y. C. Zhao, R. K. Singh, Y. S. Yordanov, M. Dash, P. Miskolczi, K. Stojkovi_, S. H. Strauss, R. P. Bhalerao and V. B. BusovEARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancyNature Communications12(1)
202110.1128/MRA.01411-20Ateba, T. P., K. A. Alayande and M. MwanzaMetagenomes and Assembled Genomes from Diarrhea-Affected Cattle (Bos taurus)Microbiology Resource Announcements10(7) e01411-20
202110.1016/j.isci.2021.103405Ataeian, M., A. Vadlamani, M. Haines, D. Mosier, X. Dong, M. Kleiner, M. Strous and A. K. HawleyProteome and strain analysis of cyanobacterium Candidatus “Phormidium alkaliphilum” reveals traits for success in biotechnologyiScience24(12)
202110.1016/j.copbio.2021.05.004Arnolds, K. L., L. R. Dahlin, L. Ding, C. Wu, J. Yu, W. Xiong, C. Zuniga, Y. Suzuki, K. Zengler, J. G. Linger and M. T. GuarnieriBiotechnology for secure biocontainment designs in an emerging bioeconomyCurrent Opinion in Biotechnology71 25-31
202110.1016/j.copbio.2021.05.004Arnolds, K. L., L. R. Dahlin, L. Ding, C. Wu, J. Yu, W. Xiong, C. Zuniga, Y. Suzuki, K. Zengler, J. G. Linger and M. T. GuarnieriBiotechnology for secure biocontainment designs in an emerging bioeconomyCurrent Opinion in Biotechnology71 25–31
202110.1089/ast.2020.2313Angelos, E., D. K. Ko, S. Zemelis-Durfee and F. BrandizziRelevance of the Unfolded Protein Response to Spaceflight-Induced Transcriptional Reprogramming in ArabidopsisAstrobiology21(3) 367–80
202110.1039/D1GC03022AAndo, D., F. Lu, H. Kim, A. Eugene, Y. Tobimatsu, R. Vanholme, T. J. Elder, W. Boerjan and J. RalphIncorporation of catechyl monomers into lignins: lignification from the non-phenolic end via Diels–Alder cycloaddition?Green Chemistry23(22) 8995–9013
202110.3389/fpls.2021.708902Anaokar, S., H. Liu, J. Keereetaweep, Z. Zhai and J. ShanklinMobilizing Vacuolar Sugar Increases Vegetative Triacylglycerol AccumulationFrontiers in Plant Science12
202110.3389/fbioe.2021.613307Amer, B. and E. E. K. BaidooOmics-Driven Biotechnology for Industrial ApplicationsFrontiers in Bioengineering and Biotechnology9
202110.3389/fmicb.2021.655987Alster, C. J., S. D. Allison, S. I. Glassman, A. C. Martiny and K. K. TresederExploring Trait Trade-Offs for Fungal Decomposers in a Southern California GrasslandFrontiers in Microbiology12
202110.1007/s12571-021-01156-wAllee, A., L. R. Lynd and V. VazeCross-national analysis of food security drivers: comparing results based on the Food Insecurity Experience Scale and Global Food Security IndexFood Security13(5) 1245–61
202110.1021/acscentsci.1c00729Alherech, M., S. Omolabake, C. M. Holland, G. E. Klinger, E. L. Hegg and S. S. StahlFrom Lignin to Valuable Aromatic Chemicals: Lignin Depolymerization and Monomer Separation via Centrifugal Partition ChromatographyACS Central Science7(11) 1831–7
202110.1002/prot.26247Alexander, L. T., R. Lepore, A. Kryshtafovych, A. Adamopoulos, M. Alahuhta, et al.Target highlights in CASP14: Analysis of models by structure providersProteins: Structure, Function, and Bioinformatics89(12) 1647–72
202110.3389/fpls.2021.762067Ahlawat, Y. K., A. Nookaraju, A. E. Harman-Ware, C. Doeppke, A. K. Biswal and C. P. JoshiGenetic Modification of KNAT7 Transcription Factor Expression Enhances Saccharification and Reduces Recalcitrance of Woody Biomass in PoplarsFrontiers in Plant Science12 762067
202110.1099/mic.0.001126Adler, B. A., A. E. Kazakov, C. Zhong, H. Liu, E. Kutter, L. M. Lui, T. N. Nielsen, H. Carion, A. M. Deutschbauer, V. K. Mutalik and A. P. ArkinThe genetic basis of phage susceptibility, cross-resistance and host-range in SalmonellaMicrobiology167(12)
202110.3389/fpls.2021.675208Adhikari, P., S. X. Mideros and T. M. JamannDifferential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicumFrontiers in Plant Science12
202110.1094/mpmi-10-20-0272-scAdeniji, A. A., A. S. Ayangbenro and O. O. BabalolaGenomic Exploration of Bacillus thuringiensis MORWBS1.1, Candidate Biocontrol Agent, Predicts Genes for Biosynthesis of Zwittermicin, 4,5-DOPA Dioxygenase Extradiol, and Quercetin 2,3-DioxygenaseMolecular Plant-Microbe Interactions34(6) 602–5
202110.3390/plants10091776Adeleke, B. S., A. S. Ayangbenro and O. O. BabalolaGenomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting TraitsPlants10(9) 1776
202110.1039/D1GC01186CAchinivu, E. C., M. Mohan, H. Choudhary, L. Das, K. Huang, H. D. Magurudeniya, V. R. Pidatala, A. George, B. A. Simmons and J. M. GladdenA predictive toolset for the identification of effective lignocellulosic pretreatment solvents: a case study of solvents tailored for lignin extractionGreen Chemistry23(18) 7269–89
202110.1039/D1GC02667DAchinivu, E. C., S. Frank, N. R. Baral, L. Das, M. Mohan, P. Otoupal, E. Shabir, S. Utan, C. D. Scown, B. A. Simmons and J. GladdenAlkanolamines as Dual Functional Solvents for Biomass Deconstruction and Bioenergy ProductionGreen Chemistry23(21) 8611–31
202110.1039/D0EE02870CAbu-Omar, M. M., K. Barta, G. T. Beckham, J. S. Luterbacher, J. Ralph, R. Rinaldi, Y. Román-Leshkov, J. S. M. Samec, B. F. Sels and F. WangGuidelines for performing lignin-first biorefiningEnergy & Environmental Science14(1) 262–92
202110.1093/femsec/fiaa260Abramov, A., T. Vishnivetskaya and E. RivkinaAre permafrost microorganisms as old as permafrost?FEMS Microbiology Ecology97(2)
202110.1088/1748-9326/ac1815Abraha, M., J. Chen, S. K. Hamilton, P. Sciusco, C. Lei, G. Shirkey, J. Yuan and G. P. RobertsonAlbedo-induced global warming impact of Conservation Reserve Program grasslands converted to annual and perennial bioenergy cropsEnvironmental Research Letters16(8) 84059
202110.1016/j.bbrc.2021.02.046Abdelhamid, A. G. and N. K. El-DougdougComparative genomics of the gut commensal Bifidobacterium bifidum reveals adaptation to carbohydrate utilizationBiochemical and Biophysical Research Communications547 155–61
202010.1038/s41467-020-17612-8Zuñiga, C., T. Li, M. T. Guarnieri, J. P. Jenkins, C. T. Li, K. Bingol, Y. M. Kim, M. J. Betenbaugh and K. ZenglerSynthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growthNature Communications11(1)
202010.1104/pp.19.00854Zienkiewicz, A., K. Zienkiewicz, E. Poliner, J. A. Pulman, Z. Y. Du, G. Stefano, C. H. Tsai, P. Horn, I. Feussner, E. M. Farre, K. L. Childs, F. Brandizzi and C. BenningThe Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen AvailabilityPlant Physiology182(2) 819–39
202010.1111/gcb.15319Zhu, X., R. D. Jackson, E. H. DeLucia, J. M. Tiedje and C. LiangThe soil microbial carbon pump: From conceptual insights to empirical assessmentsGlobal Change Biology26(11) 6032–9
202010.1038/s41467-020-15830-8Zhu, P., X. H. Yu, C. Wang, Q. Zhang, W. Liu, S. McSweeney, J. Shanklin, E. Lam and Q. LiuStructural basis for Ca2+-dependent activation of a plant metacaspaseNature Communications11(1) 2249
202010.1021/jacs.0c00199Zhou, Y., G. E. Klinger, E. L. Hegg, C. M. Saffron and J. E. JacksonMultiple Mechanisms Mapped in Aryl Alkyl Ether Cleavage via Aqueous Electrocatalytic Hydrogenation over Skeletal NickelJournal of the American Chemical Society142(8) 4037–50
202010.3390/genes11080843Zhou, R., D. Macaya-Sanz, J. Schmutz, J. W. Jenkins, G. A. Tuskan and S. P. DiFazioSequencing and Analysis of the Sex Determination Region of Populus trichocarpaGenes11(8)
202010.1186/s13059-020-1952-4Zhou, R., D. Macaya-Sanz, C. H. Carlson, J. Schmutz, J. W. Jenkins, et al.A willow sex chromosome reveals convergent evolution of complex palindromic repeatsGenome Biology21(1) 38
202010.1016/j.ymeth.2019.10.007Zhou, M., N. Malhan, A. H. Ahkami, K. Engbrecht, G. Myers, J. Dahlberg, J. Hollingsworth, J. A. Sievert, R. Hutmacher, M. Madera, P. G. Lemaux, K. K. Hixson, C. Jansson and L. Pa_a-Toli_Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimationMethods184 29-39
202010.1039/d0sc04392cZhou, M., C. Lantz, K. A. Brown, Y. Ge, L. Pa_a-Toli_, J. A. Loo and F. LermyteHigher-order structural characterisation of native proteins and complexes by top-down mass spectrometryChemical Science11(48) 12918-12936
202010.3390/molecules25092108Zheng, Y., A. Pierce, W. L. Wagner, H. V. Scheller, D. Mohnen, M. Ackermann and S. J. MentzerWater-Dependent Blending of Pectin Films: The Mechanics of Conjoined BiopolymersMolecules25(9)
202010.1021/acs.est.0c01028Zheng, H., K. Kim, A. Kravchenko, M. Rivers and A. GuberTesting Os Staining Approach for Visualizing Soil Organic Matter Patterns in Intact Samples via X-ray Dual-Energy Tomography ScanningEnvironmental Science & Technology54(14) 8980–9
202010.1002/cssc.202001401Zhao, Z. M., Z. H. Liu, Y. Pu, X. Meng, J. Xu, J. S. Yuan and A. J. RagauskasEmerging Strategies for Modifying Lignin Chemistry to Enhance Biological Lignin ValorizationChemSusChem13(20) 5423–32
202010.1016/j.rser.2020.110265Zhao, Q., X. Cai, W. Mischo and L. MaHow do the research and public communities view biofuel development?Renewable and Sustainable Energy Reviews133
202010.1061/(ASCE)WR.1943-5452.0001197Zhao, Q., X. Cai and Y. LiAlgorithm Design Based on Derived Operation Rules for a System of Reservoirs in ParallelJournal of Water Resources Planning and Management146(5)
202010.3390/microorganisms8040608Zhao, J., X. Zhao, J. Wang, Q. Gong, X. Zhang and G. ZhangIsolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in AgricultureMicroorganisms8(4)
202010.1021/acssynbio.0c00305Zhao, E. M., M. A. Lalwani, R. J. Lovelett, S. A. Garciá-Echauri, S. M. Hoffman, C. L. Gonzalez, J. E. Toettcher, I. G. Kevrekidis and J. L. AvalosDesign and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic EngineeringACS Synthetic Biology9(12) 3254-3266
202010.1128/AEM.01036-20Zhang, Y. Z., W. X. Zhang and X. L. ChenMechanisms for induction of microbial extracellular proteases in response to exterior proteinsApplied and Environmental Microbiology86(19)
202010.1016/j.agee.2020.107085Zhang, Y. J., N. L. Haan and D. A. LandisLandscape composition and configuration have scale-dependent effects on agricultural pest suppressionAgriculture, Ecosystems & Environment302
202010.1016/j.biteb.2020.100517Zhang, Y., J. Serate, D. Xie, S. Gajbhiye, P. Kulzer, G. Sanford, J. D. Russell, M. McGee, C. Foster, J. J. Coon, R. Landick and T. K. SatoProduction of hydrolysates from unmilled AFEX-pretreated switchgrass and comparative fermentation with Zymomonas mobilisBioresource Technology Reports11
202010.1186/s12870-020-2275-zZhang, X., S. B. Fernandes, C. Kaiser, P. Adhikari, P. J. Brown, S. X. Mideros and T. M. JamannConserved defense responses between maize and sorghum to Exserohilum turcicumBMC Plant Biology20(1) 67
202010.1111/pbi.13254Zhang, J., M. Xie, M. Li, J. Ding, Y. Pu, et al.Overexpression of a Prefoldin _ subunit gene reduces biomass recalcitrance in the bioenergy crop PopulusPlant Biotechnology Journal18(3) 859–71
202010.3389/fpls.2020.00652Zhang, J., G. A. Tuskan, T. J. Tschaplinski, W. Muchero and J. G. ChenTranscriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in PopulusFrontiers in Plant Science11 652
202010.1093/gigascience/giaa018Zhang, J., R. Hu, A. Sreedasyam, T. M. Garcia, A. Lipzen, et al.Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolismGigaScience9(3)
202010.1111/gcb.14994Zhang, H., D. S. Goll, Y. P. Wang, P. Ciais, W. R. Wieder, R. Abramoff, Y. Huang, B. Guenet, A. K. Prescher, R. A. Viscarra Rossel, P. Barré, C. Chenu, G. Zhou and X. TangMicrobial dynamics and soil physicochemical properties explain large-scale variations in soil organic carbonGlobal Change Biology26(4) 2668-2685
202010.1111/gcbb.12728Zeri, M., W. H. Yang, G. Cunha-Zeri, C. D. Gibson and C. J. BernacchiNitrous oxide fluxes over establishing biofuel crops: Characterization of temporal variability using the cross-wavelet analysisGCB Bioenergy12(9) 756–70
202010.1021/jasms.0c00160Zenaidee, M. A., C. Lantz, T. Perkins, W. Jung, R. R. O. Loo and J. A. LooInternal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass SpectrometryJournal of the American Society for Mass Spectrometry31(9) 1896-1902
202010.1128/MMBR.00030-17Zamora, M., C. A. Ziegler, P. L. Freddolino and A. J. WolfeA thermosensitive, phase-variable epigenetic switch: Pap revisitedMicrobiology and Molecular Biology Reviews84(3)
202010.34133/2020/3686791Yuan, G., M. Hassan, D. Liu, S. D. Lim, W. C. Yim, J. C. Cushman, K. Markel, P. M. Shih, H. Lu, D. J. Weston, J. G. Chen, T. J. Tschaplinski, G. A. Tuskan and X. YangBiosystems Design to Accelerate C3-to-CAM ProgressionBioDesign Research2020
202010.1074/jbc.H120.014701Yu, X.-H. and J. ShanklinSolving a furan fatty acid biosynthesis puzzleJournal of Biological Chemistry295(29) 9802–3
202010.1002/rcm.8858Yu, L., E. Harris, D. Lewicka-Szczebak, M. Barthel, M. R. A. Blomberg, et al.What can we learn from N2O isotope data? – Analytics, processes and modellingRapid Communications in Mass Spectrometry34(20)
202010.1038/s41586-020-2468-5Yu, H. and J. R. LeadbetterBacterial chemolithoautotrophy via manganese oxidationNature583(7816) 453–8
202010.1007/s00138-020-01088-zYu, G. H., A. Zare, H. D. Y. Sheng, R. Matamala, J. Reyes-Cabrera, F. B. Fritschi and T. E. JuengerRoot identification in minirhizotron imagery with multiple instance learningMachine Vision and Applications31(6)
202010.1007/978-3-030-65414-6_30Yu, G., A. Zare, W. Xu, R. Matamala, J. Reyes-Cabrera, F. B. Fritschi and T. E. JuengerWeakly supervised minirhizotron image segmentation with MIL-CAMLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)12540 LNCS 433-449
202010.1016/j.jpdc.2019.07.008Young, M. T., J. D. Hinkle, R. Kannan and A. RamanathanDistributed Bayesian optimization of deep reinforcement learning algorithmsJournal of Parallel and Distributed Computing139 43–52
202010.1016/j.biortech.2020.122784Yoo, C. G., X. Meng, Y. Pu and A. J. RagauskasThe critical role of lignin in lignocellulosic biomass conversion and recent pretreatment strategies: A comprehensive reviewBioresource Technology301 122784
202010.1016/j.bpj.2020.04.009Yin, S., M. Tien and H. YangPrior-Apprised Unsupervised Learning of Subpixel Curvilinear Features in Low Signal/Noise ImagesVaccine118(10) 2458–69
202010.3389/fpls.2020.572137Yao, T., J. Zhang, M. Xie, G. Yuan, T. J. Tschaplinski, W. Muchero and J. G. ChenTranscriptional Regulation of Drought Response in Arabidopsis and Woody PlantsFrontiers in Plant Science11 572137
202010.34133/2020/8051764Yang, X., J. I. Medford, K. Markel, P. M. Shih, H. C. De Paoli, et al.Plant Biosystems Design Research Roadmap 1.0BioDesign Research2020 8051764
202010.1002/tpg2.20006Yang, X., Z. Luo, J. Todd, S. Sood and J. WangGenome-wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)Plant Genome13(1)
202010.3389/fpls.2020.00394Yang, X., J. C. Cushman, A. M. Borland and Q. LiuEditorial: Systems Biology and Synthetic Biology in Relation to Drought Tolerance or Avoidance in PlantsFrontiers in Plant Science11
202010.1088/1748-9326/ab865fYang, P., Q. K. Zhao and X. M. CaiMachine learning based estimation of land productivity in the contiguous US using biophysical predictorsEnvironmental Research Letters15(7)
202010.1073/pnas.2000053117Yang, M., N. R. Baral, B. A. Simmons, J. C. Mortimer, P. M. Shih and C. D. ScownAccumulation of high-value bioproducts in planta can improve the economics of advanced biofuelsProceedings of the National Academy of Sciences of the United States of America117(15) 8639–48
202010.1016/j.biortech.2019.122240Yang, H., C. G. Yoo, X. Meng, Y. Pu, W. Muchero, G. A. Tuskan, T. J. Tschaplinski, A. J. Ragauskas and L. YaoStructural changes of lignins in natural Populus variants during different pretreatmentsBioresource Technology295 122240
202010.1016/j.ymben.2020.05.008Yan, Q., T. R. Simmons, W. T. Cordell, N. J. Hernández Lozada, C. J. Breckner, X. Chen, M. A. Jindra and B. F. PflegerMetabolic engineering of _-oxidation to leverage thioesterases for production of 2-heptanone, 2-nonanone and 2-undecanoneMetabolic Engineering61 335-343
202010.1016/j.ymben.2019.04.009Yan, Q. and B. F. PflegerRevisiting metabolic engineering strategies for microbial synthesis of oleochemicalsMetabolic Engineering58 35–46
202010.1104/pp.19.01467Yamamoto, M., H. Tomiyama, A. Koyama, H. Okuizumi, S. Liu, et al.A Century-Old Mystery Unveiled: Sekizaisou is a Natural Lignin MutantPlant Physiology182(4) 1821–8
202010.1016/bs.mie.2020.04.054Xue, P., T. Si and H. ZhaoOptically guided mass spectrometry to screen microbial colonies for directed enzyme evolutionMethods in Enzymology644 255–73
202010.1002/bit.27343Xue, P., T. Si, S. Mishra, L. Zhang, K. Choe, J. V. Sweedler and H. ZhaoA mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acidsBiotechnology and Bioengineering117(7) 2131–8
202010.1016/j.compag.2020.105466Xu, W. H., G. H. Yu, A. Zare, B. Zurweller, D. Rowland, J. Reyes-Cabrera, F. B. Fritschi, R. Matamala and T. E. JuengerOvercoming small minirhizotron datasets using transfer learningComputers and Electronics in Agriculture175
202010.1093/nar/gkaa131Xu, P., C. Modavi, B. Demaree, F. Twigg, B. Liang, C. Sun, W. Zhang and A. R. AbateMicrofluidic automated plasmid library enrichment for biosynthetic gene cluster discoveryNucleic Acids Research48(8) e48
202010.1021/acschembio.0c00019Xu, J. H., J. Eberhardt, B. Hill-Payne, G. E. González-Paéz, J. O. Castellón, B. F. Cravatt, S. Forli, D. W. Wolan and K. M. BackusIntegrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and SelectivityACS Chemical Biology15(2) 575-586
202010.1016/j.soilbio.2020.107986Xu, J., S. S. Roley, M. M. Tfaily, R. K. Chu and J. M. TiedjeOrganic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scalesSoil Biology and Biochemistry150
202010.1016/j.plipres.2020.101069Xu, C., J. Fan and J. ShanklinMetabolic and functional connections between cytoplasmic and chloroplast triacylglycerol storageProgress in Lipid Research80 101069
202010.1002/pld3.178Xie, M., J. Zhang, V. R. Singan, M. J. McGranahan, P. R. LaFayette, et al.Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effectPlant Direct4(1) e00178
202010.1016/j.biombioe.2020.105473Xiao, Y., C. Poovaiah, F. Unda, L. Ritchie, M. Dombrov, C. Phalen, A. Argyros and H. ColemanExpression of the Trichoderma reesei expansin-like protein, swollenin, in poplar results in biomass with improved sugar release by enzymatic hydrolysisBiomass and Bioenergy134
202010.1016/j.cbpa.2020.05.003Wu, Y., Z. Yang and Y. LuPhotocaged functional nucleic acids for spatiotemporal imaging in biologyCurrent Opinion in Chemical Biology57 95–104
202010.1002/bbb.2083Wu, X. Y., J. H. Jiang, C. M. Wang, J. Liu, Y. Q. Pu, A. Ragauskas, S. M. Li and B. YangLignin-derived electrochemical energy materials and systemsBiofuels, Bioproducts and Biorefining14(3) 650–72
202010.1038/s41396-020-0635-1Wu, R., B. Chai, J. R. Cole, S. K. Gunturu, X. Guo, R. Tian, J. D. Gu, J. Zhou and J. M. TiedjeTargeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warmingISME Journal14(7) 1651-1662
202010.1021/acssuschemeng.9b07226Wu, J., R. P. Chandra, K. H. Kim, C. S. Kim, Y. Q. Pu, A. J. Ragauskas and J. N. SaddlerEnhancing Enzyme-Mediated Hydrolysis of Mechanical Pulps by Deacetylation and DelignificationACS Sustainable Chemistry & Engineering8(15) 5847–55
202010.1038/s41396-020-00753-5Wu, B., F. Liu, A. Zhou, J. Li, L. Shu, et al.Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgarisThe ISME Journal14(11) 2862–76
202010.1016/j.soilbio.2019.107678Woolet, J. and T. WhitmanPyrogenic organic matter effects on soil bacterial community compositionSoil Biology and Biochemistry141
202010.1111/nph.16546Woods, D. P., Y. Dong, F. Bouché, K. Mayer, L. Varner, T. S. Ream, N. Thrower, C. Wilkerson, A. Cartwright, R. Sibout, D. Laudencia-Chingcuanco, J. Vogel and R. M. AmasinoMutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyonNew Phytologist227(6) 1725-1735
202010.1371/journal.pone.0232437Wilpiszeski, R. L., C. M. Gionfriddo, A. M. Wymore, J. W. Moon, K. A. Lowe, et al.In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbationsPLoS One15(9) e0232437
202010.1016/j.mec.2019.e00107Wilken, S. E., S. Seppälä, T. S. Lankiewicz, M. Saxena, J. K. Henske, A. A. Salamov, I. V. Grigoriev and M. A. O'MalleyGenomic and proteomic biases inform metabolic engineering strategies for anaerobic fungiMetabolic Engineering Communications10
202010.1111/jpy.12920Wilken, S., C. J. Choi and A. Z. WordenContrasting Mixotrophic Lifestyles Reveal Different Ecological Niches in Two Closely Related Marine ProtistsJournal of Phycology56(1) 52–67
202010.1099/ijsem.0.004029Wilhelm, R. C., S. J. L. Murphy, N. M. Feriancek, D. C. Karasz, C. M. DeRito, J. D. Newman and D. H. BuckleyParaburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soilInternational Journal of Systematic and Evolutionary Microbiology70(3) 2137–46
202010.1099/ijsem.0.004387Wilhelm, R. C., K. T. Cyle, C. E. Martinez, D. C. Karasz, J. D. Newman and D. H. BuckleyParaburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madsenianaInternational Journal of Systematic and Evolutionary Microbiology70(9) 5093–105
202010.1029/2019JG005601Wik, M., B. F. Thornton, R. K. Varner, C. McCalley and P. M. CrillStable Methane Isotopologues From Northern Lakes Suggest That Ebullition Is Dominated by Sub-Lake Scale ProcessesJournal of Geophysical Research: Biogeosciences125(10)
202010.1002/bit.27364Whitehead, T. A., S. Banta, W. E. Bentley, M. J. Betenbaugh, C. Chan, et al.The importance and future of biochemical engineeringBiotechnology and Bioengineering117(8) 2305–18
202010.1016/j.drudis.2020.02.002Westbrook, J. D., R. Soskind, B. P. Hudson and S. K. BurleyImpact of the Protein Data Bank on antineoplastic approvalsDrug Discovery Today25(5) 837–50
202010.1111/tpj.14949Weiss, T., C. Wang, X. Kang, H. Zhao, M. Elena Gamo, C. G. Starker, P. A. Crisp, P. Zhou, N. M. Springer, D. F. Voytas and F. ZhangOptimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridisThe Plant Journal104(3) 828–38
202010.1111/gcb.15365Waring, B. G., B. N. Sulman, S. Reed, A. P. Smith, C. Averill, et al.From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing worldGlobal Change Biology26(12) 6631–43
202010.1073/pnas.2001588117Wannier, T. M., A. Nyerges, H. M. Kuchwara, M. Czikkely, D. Balogh, G. T. Filsinger, N. C. Borders, C. J. Gregg, M. J. Lajoie, X. Rios, C. Pál and G. M. ChurchImproved bacterial recombineering by parallelized protein discoveryProceedings of the National Academy of Sciences of the United States of America117(24) 13689-13698
202010.3389/fenrg.2020.00149Wang, Y. Y., P. Sengupta, B. Scheidemantle, Y. Q. Pu, C. E. Wyman, C. M. Cai and A. J. RagauskasEffects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane PropertiesFrontiers in Energy Research8
202010.1021/acscatal.0c02489Wang, Y. J., X. Q. Huang, J. S. Hui, L. T. Vo and H. M. ZhaoStereoconvergent Reduction of Activated Alkenes by a Nicotinamide Free Synergistic Photobiocatalytic SystemACS Catalysis10(16) 9431–7
202010.1016/j.jhydrol.2020.124777Wang, G. S., W. J. Huang, G. Y. Zhou, M. A. Mayes and J. Z. ZhouModeling the processes of soil moisture in regulating microbial and carbon-nitrogen cyclingJournal of Hydrology585
202010.1021/acs.accounts.9b00544Wang, F. and S. S. StahlElectrochemical Oxidation of Organic Molecules at Lower Overpotential: Accessing Broader Functional Group Compatibility with Electron-Proton Transfer MediatorsAccounts of Chemical Research53(3) 561–74
202010.1016/j.synbio.2020.01.002Wang, B. and H. ZhaoUnleashing the power of energy storage: Engineering _-oxidation pathways for polyketide productionSynthetic and Systems Biotechnology5(1) 21–2
202010.1021/acssuschemeng.0c01538Walker, T. W., N. Kuch, K. A. Vander Meulen, C. F. M. Clewett, G. W. Huber, B. G. Fox and J. A. DumesicSolid-state NMR studies of solvent-mediated, acid-catalyzed woody biomass pre-treatment for enzymatic conversion of residual celluloseACS Sustainable Chemistry & Engineering8(16) 6551–63
202010.1126/sciadv.aba7599Walker, T. W., N. Frelka, Z. Shen, A. K. Chew, J. Banick, S. Grey, M. S. Kim, J. A. Dumesic, R. C. Van Lehn and G. W. HuberRecycling of multilayer plastic packaging materials by solvent-targeted recovery and precipitationScience Advances6(47)
202010.1007/s11244-020-01260-9Walker, T. W., A. K. Chew, R. C. Van Lehn, J. A. Dumesic and G. W. HuberRational Design of Mixed Solvent Systems for Acid-Catalyzed Biomass Conversion Processes Using a Combined Experimental, Molecular Dynamics and Machine Learning ApproachTopics in Catalysis63(45115) 649–63
202010.1128/MRA.01356-19Walker, C., S. Ryu, S. Haridas, H. Na, M. Zane, K. LaButti, K. Barry, I. V. Grigoriev and C. T. TrinhDraft Genome Assemblies of Ionic Liquid-Resistant Yarrowia lipolytica PO1f and Its Superior Evolved Strain, YlCW001Microbiology Resource Announcements9(9)
202010.1128/AEM.02299-19Walker, C., S. Ryu, R. J. Giannone, S. Garcia and C. T. TrinhUnderstanding and Eliminating the Detrimental Effect of Thiamine Deficiency on the Oleaginous Yeast Yarrowia lipolyticaApplied and Environmental Microbiology86(3)
202010.1111/gcb.15124von Haden, A. C., W. H. Yang and E. H. DeLuciaSoils' dirty little secret: Depth-based comparisons can be inadequate for quantifying changes in soil organic carbon and other mineral soil propertiesGlobal Change Biology26(7) 3759–70
202010.1021/acssynbio.0c00129Volk, M. J., I. Lourentzou, S. Mishra, L. T. Vo, C. Zhai and H. ZhaoBiosystems Design by Machine LearningACS Synthetic Biology9(7) 1514–33
202010.1016/j.indcrop.2020.112906Viswanathan, M. B., K. Park, M. H. Cheng, E. B. Cahoon, I. Dweikat, T. Clemente and V. SinghVariability in structural carbohydrates, lipid composition, and cellulosic sugar production from industrial hemp varietiesIndustrial Crops and Products157
202010.1093/femsec/fiaa229Vishnivetskaya, T. A., A. L. Almatari, E. V. Spirina, X. Wu, D. E. Williams, S. M. Pfiffner and E. M. RivkinaInsights into community of photosynthetic microorganisms from permafrostFEMS Microbiology Ecology96(12)
202010.1094/MPMI-04-20-0082-TAVillalobos Solis, M. I., S. Poudel, C. Bonnot, H. K. Shrestha, R. L. Hettich, C. Veneault-Fourrey, F. Martin and P. E. AbrahamA Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe InteractionsMolecular Plant-Microbe Interactions33(10) 1177–88
202010.1002/lno.11467Villa, J. A., Y. Ju, T. Stephen, C. Rey-Sanchez, K. C. Wrighton and G. BohrerPlant-mediated methane transport in emergent and floating-leaved species of a temperate freshwater mineral-soil wetlandLimnology and Oceanography65(7) 1635-1650
202010.1038/s41598-020-71672-wVijaya Kumar, S., P. E. Abraham, G. B. Hurst, K. Chourey, A. N. Bible, R. L. Hettich, M. J. Doktycz and J. L. Morrell-FalveyA carotenoid-deficient mutant of the plant-associated microbe Pantoea sp. YR343 displays an altered membrane proteomeScientific Reports10(1) 14985
202010.1128/mSystems.00250-20Vera, J. M., I. N. Ghosh, Y. Zhang, A. S. Hebert, J. J. Coon and R. LandickGenome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and PromotersmSystems5(4)
202010.1128/mSystems.00092-20Veach, A. M., H. Chen, Z. K. Yang, A. D. Labbe, N. L. Engle, T. J. Tschaplinski, C. W. Schadt and M. A. CreggerPlant Hosts Modify Belowground Microbial Community Response to Extreme DroughtmSystems5(3)
202010.1111/nph.16555VanWallendael, A., J. Bonnette, T. E. Juenger, F. B. Fritschi, P. A. Fay, R. B. Mitchell, J. Lloyd-Reilley, F. M. Rouquette, Jr., G. C. Bergstrom and D. B. LowryGeographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)New Phytologist227(6) 1696–708
202010.1038/s41467-020-14724-zVanBuren, R., C. Man Wai, X. Wang, J. Pardo, A. E. Yocca, et al.Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teffNature Communications11(1) 884
202010.1111/nph.16729Valverde-Barrantes, O. J., H. Maherali, C. Baraloto and C. B. BlackwoodIndependent evolutionary changes in fine-root traits among main clades during the diversification of seed plantsNew Phytologist228(2) 541-553
202010.1038/s41589-020-0631-9Valliere, M. A., T. P. Korman, M. A. Arbing and J. U. BowieA bio-inspired cell-free system for cannabinoid production from inexpensive inputsNature Chemical Biology16(12) 1427-1433
202010.1007/978-1-0716-0195-2_8Utturkar, S., A. Dassanayake, S. Nagaraju and S. D. BrownBacterial Differential Expression Analysis MethodsMethods in Molecular Biology2096 89–112
202010.1128/mSphere.00898-20Urtecho, G., D. E. Campbell, D. M. Hershey, F. A. Hussain, R. J. Whitaker and G. A. O'TooleDiscovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18mSphere5(6) 44939
202010.1094/MPMI-06-19-0154-RTuleski, T. R., J. Kimball, F. P. do Amaral, T. P. Pereira, M. Z. Tadra-Sfeir, F. de Oliveira Pedrosa, E. Maltempi de Souza, P. Balint-Kurti, R. A. Monteiro and G. StaceyHerbaspirillum rubrisubalbicans as a Phytopathogenic Model to Study the Immune System of Sorghum bicolorMolecular Plant-Microbe Interactions33(2) 235–46
202010.1093/jxb/eraa060Tsogtbaatar, E., J. C. Cocuron and A. P. AlonsoNon-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesisJournal of Experimental Botany71(10) 3037–51
202010.54203/scil.2020.wvj57Tshipamba, M. E., N. Lubanza and M. MwanzaGenome Analysis of Antimicrobial Resistance Genes and Virulence Factors in Multidrug-Resistant Campylobacter fetus Subspecies Isolated from Sheath WashWorld's Veterinary Journal10(4) 465–80
202010.1128/MRA.00852-20Tshipamba, M. E., K. A. Alayande, N. Lubanza and M. MwanzaWhole-Genome Sequencing of Multidrug-Resistant Campylobacter fetus subsp. fetus NWU_ED24, Isolated from a Bovine Sheath Wash SampleMicrobiology Resource Announcements9(40)
202010.1128/MRA.00854-20Tshipamba, M. E., S. A. Akinola, L. Ngoma and M. MwanzaGenome Sequence of Campylobacter fetus subsp. venerealis NW_ED23, Isolated from Bovine Sheath WashMicrobiology Resource Announcements9(40)
202010.1104/pp.19.01550Tsai, C. J., P. Xu, L. J. Xue, H. Hu, B. Nyamdari, et al.Compensatory Guaiacyl Lignin Biosynthesis at the Expense of Syringyl Lignin in 4CL1-Knockout PoplarPlant Physiology183(1) 123–36
202010.1038/s41598-020-61081-4Toubiana, D., N. Sade, L. Liu, M. M. Rubio Wilhelmi, Y. Brotman, U. Luzarowska, J. P. Vogel and E. BlumwaldCorrelation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing toleranceScientific Reports10(1)
202010.1073/pnas.2020204117Todor, H., H. Osadnik, E. A. Campbell, K. S. Myers, H. Li, T. J. Donohue and C. A. GrossRewiring the specificity of extracytoplasmic function sigma factorsProceedings of the National Academy of Sciences of the United States of America117(52) 33496–506
202010.1021/acssuschemeng.0c05651Timokhin, V. I., M. Regner, A. H. Motagamwala, C. Sener, S. D. Karlen, J. A. Dumesic and J. RalphProduction of p-Coumaric Acid from Corn GVL-LigninACS Sustainable Chemistry & Engineering8(47) 17427–38
202010.1558/wap.20355Tigchelaar, M.‘I do the peer review by myself’: A Chinese international student’s approach to process writingWriting and Pedagogy12(44960) 395-422
202010.1093/synbio/ysaa005Tiedge, K., A. Muchlinski and P. ZerbeGenomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challengesSynthetic Biology5(1) ysaa005
202010.1186/s40168-020-00825-wTian, R., D. Ning, Z. He, P. Zhang, S. J. Spencer, et al.Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicityMicrobiome8(1) 51
202010.1038/s41589-019-0452-xThorwall, S., C. Schwartz, J. W. Chartron and I. WheeldonStress-tolerant non-conventional microbes enable next-generation chemical biosynthesisNature Chemical Biology16(2) 113–21
202010.1021/acssynbio.9b00292Thompson, M. G., A. N. Pearson, J. F. Barajas, P. Cruz-Morales, N. Sedaghatian, Z. Costello, M. E. Garber, M. R. Incha, L. E. Valencia, E. E. K. Baidoo, H. G. Martin, A. Mukhopadhyay and J. D. KeaslingIdentification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putidaACS Synthetic Biology9(1) 53–62
202010.1002/saj2.20010Thies, S., D. R. Joshi, S. A. Bruggeman, S. A. Clay, U. Mishra, J. Morile-Miller and D. E. ClayFertilizer timing affects nitrous oxide, carbon dioxide, and ammonia emissions from soilSoil Science Society of America Journal84(1) 115–30
202010.1038/s41598-020-73446-wTessler, M., J. P. Gaffney, A. G. Oliveira, A. Guarnaccia, K. C. Dobi, N. A. Gujarati, M. Galbraith, J. D. Mirza, J. S. Sparks, V. A. Pieribone, R. J. Wood and D. F. GruberA putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phylaScientific Reports10(1) 17724
202010.1002/csc2.20083Taylor, M., X. W. Zhao, M. D. Casler and Y. W. JiangTranscriptome profiling reveals differentially expressed genes associated with flowering time in contrasting switchgrass genotypesCrop Science60(3) 1472–87
202010.1186/s40168-020-00838-5Tao, X., J. Feng, Y. Yang, G. Wang, R. Tian, et al.Winter warming in Alaska accelerates lignin decomposition contributed by ProteobacteriaMicrobiome8(1)
202010.1016/j.ijepes.2020.106279Tang, Z., J. Liu, Y. Liu and L. XuStochastic reserve scheduling of energy storage system in energy and reserve marketsInternational Journal of Electrical Power and Energy Systems123
202010.3390/biology9070155Tan, M. H., S. R. Smith, K. K. Hixson, J. Tan, J. K. McCarthy, A. B. Kustka and A. E. AllenThe importance of protein phosphorylation for signaling and metabolism in response to diel light cycling and nutrient availability in a marine diatomBiology9(7) 44951
202010.1105/tpc.19.00628Takeuchi, T., B. B. Sears, C. Lindeboom, Y. T. Lin, N. Fekaris, K. Zienkiewicz, A. Zienkiewicz, E. Poliner and C. BenningChlamydomonas CHT7 Is Required for an Effective Quiescent State by Regulating Nutrient-Responsive Cell Cycle Gene ExpressionThe Plant Cell32(4) 1240–69
202010.1104/pp.20.00864Takeuchi, T., Y. T. Lin, N. Fekaris, J. Umen, B. B. Sears and C. BenningModulation of CHT7 Complexes during Light/Dark- and Nitrogen-Mediated Life Cycle Transitions of ChlamydomonasPlant Physiology184(4) 1762–74
202010.1016/j.compchemeng.2020.107126Taifan, G. S. P. and C. T. MaraveliasIntegration of graphical approaches into optimization-based design of multistage liquid extractionComputers & Chemical Engineering143
202010.1002/aic.16235Suthers, P. F. and C. D. MaranasChallenges of cultivated meat production and applications of genome-scale metabolic modelingVaccine66(6)
202010.1016/j.mec.2020.e00148Suthers, P. F., H. V. Dinh, Z. Fatma, Y. Shen, S. H. J. Chan, J. D. Rabinowitz, H. Zhao and C. D. MaranasGenome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids productionMetabolic Engineering Communications11 e00148
202010.3389/fpls.2020.596301Sun, Y., Z. Qiao, W. Muchero and J. G. ChenLectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell SurfaceFrontiers in Plant Science11 596301
202010.1038/s41467-020-17116-5Sun, M., R. A. Folk, M. A. Gitzendanner, P. S. Soltis, Z. Chen, D. E. Soltis and R. P. GuralnickRecent accelerated diversification in rosids occurred outside the tropicsNature Communications11(1) 3333
202010.1002/ajb2.1479Sun, M., R. A. Folk, M. A. Gitzendanner, P. S. Soltis, Z. Chen, D. E. Soltis and R. P. GuralnickEstimating rates and patterns of diversification with incomplete sampling: a case study in the rosidsAmerican Journal of Botany107(6) 895–909
202010.1002/bit.27508Sun, L., C. A. Atkinson, Y. G. Lee and Y. S. JinHigh-level _-carotene production from xylose by engineered Saccharomyces cerevisiae without overexpression of a truncated HMG1 (tHMG1)Biotechnology and Bioengineering117(11) 3522–32
202010.1128/MRA.00326-20Sun, E. W. H., S. Hajirezaie, M. Dooner, T. A. Vishnivetskaya, A. Layton, A. Chauhan, S. M. Pfiffner, L. G. Whyte, T. C. Onstott and M. C. Y. LaueThaumarchaea genome sequences from a high Arctic active layerMicrobiology Resource Announcements9(21)
202010.1021/acs.bioconjchem.0c00163Sue, C. K., S. A. McConnell, K. Ellis-Guardiola, J. M. Muroski, R. A. McAllister, J. Yu, A. I. Alvarez, C. Chang, R. R. Ogorzalek Loo, J. A. Loo, H. Ton-That and R. T. ClubbKinetics and Optimization of the Lysine-Isopeptide Bond Forming Sortase Enzyme from Corynebacterium diphtheriaeBioconjugate Chemistry31(6) 1624-1634
202010.1088/1361-6420/ab649cSubramanian, S., K. Scheufele, M. Mehl and G. BirosWhere Did the Tumor Start? An Inverse Solver with Sparse Localization for Tumor Growth ModelsInverse Problems36(4)
202010.1038/s41598-020-76730-xSubedi, N. R., P. S. Jung, E. L. Bredeweg, S. Nemati, S. E. Baker, D. N. Christodoulides and A. E. VasdekisIntegrative quantitative-phase and airy light-sheet imagingInverse Problems10(1) 20150
202010.1094/PHYTO-04-20-0132-RVWStutts, L. R. and W. VermerrisElucidating anthracnose resistance mechanisms in sorghum-a reviewPhytopathology110(12) 1863-1876
202010.1038/s41396-020-00738-4Stuart, R. K., E. R. A. Pederson, P. D. Weyman, P. K. Weber, U. Rassmussen and C. L. DupontBidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualismThe ISME Journal14(12) 3068–78
202010.1007/s00216-020-02544-5Strobbia, P., R. A. Odion, M. Maiwald, B. Sumpf and T. Vo-DinhDirect SERDS sensing of molecular biomarkers in plants under field conditionsAnalytical and Bioanalytical Chemistry412(14) 3457–66
202010.1016/j.copbio.2020.01.010Streich, J., J. Romero, J. Gazolla, D. Kainer, A. Cliff, E. T. Prates, J. B. Brown, S. Khoury, G. A. Tuskan, M. Garvin, D. Jacobson and A. L. HarfoucheCan exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?Current Opinion in Biotechnology61 217–25
202010.1186/s13068-020-01675-2Straub, C. T., R. G. Bing, J. P. Wang, V. L. Chiang, M. W. W. Adams and R. M. KellyUse of the lignocellulose-degrading bacterium Caldicellulosiruptor bescii to assess recalcitrance and conversion of wild-type and transgenic poplarBiotechnology for Biofuels13 43
202010.1002/bit.27529Straub, C. T., R. G. Bing, J. K. Otten, L. M. Keller, B. M. Zeldes, M. W. W. Adams and R. M. KellyMetabolically engineered Caldicellulosiruptor bescii as a platform for producing acetone and hydrogen from lignocelluloseBiotechnology and Bioengineering117(12) 3799–808
202010.1534/g3.120.401498Stoneman, H. R., R. L. Wrobel, M. Place, M. Graham, D. J. Krause, M. De Chiara, G. Liti, J. Schacherer, R. Landick, A. P. Gasch, T. K. Sato and C. T. HittingerCRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse PopulationsG3 Genes|Genomes|Genetics10(11) 4287–94
202010.1016/j.bej.2020.107707Stone, K., M. Hilliard, K. Badr, A. Bradford, Q. P. He and J. WangComparative study of oxygen-limited and methane-limited growth phenotypes of Methylomicrobium buryatense 5GB1Biochemical Engineering Journal161
202010.3389/fmars.2020.00718Steen, A. D., S. Kusch, H. A. Abdulla, N. Caki_, S. Coffinet, et al.Analytical and Computational Advances, Opportunities, and Challenges in Marine Organic Biogeochemistry in an Era of “Omics”Frontiers in Marine Science7
202010.1002/cbic.201900611Stadlmeier, M., L. S. Runtsch, F. Streshnev, M. Wuhr and T. CarellA Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass SpectrometryChemBioChem21(1–2) 103–7
202010.1016/j.jbiotec.2019.12.002Srivastava, P. A., E. L. Hegg, B. G. Fox and R. M. YennamalliPreDSLpmo: A neural network-based prediction tool for functional annotation of lytic polysaccharide monooxygenasesJournal of Biotechnology308 148–55
202010.1016/j.micpath.2019.103856Srivastava, N., S. Tiwari, K. Bhandari, A. K. Biswal and A. K. S. RawatNovel derivatives of plant monomeric phenolics: act as inhibitors of bacterial cell-to-cell communicationMicrobial Pathogenesis141 103856
202010.1002/ael2.20030Sprunger, C. D., T. Martin and M. MannSystems with greater perenniality and crop diversity enhance soil biological healthAgricultural & Environmental Letters5(1)
202010.3390/land9120479Spiesman, B., B. Iuliano and C. GrattonTemporal resource continuity increases predator abundance in a metapopulation model: Insights for conservation and biocontrolLand9(12) 44942
202010.1093/nar/gkaa264Song, Q., J. Lee, S. Akter, M. Rogers, R. Grene and S. LiPrediction of condition-specific regulatory genes using machine learningNucleic Acids Research48(11) e62
202010.3389/fpls.2020.00479Song, B., S. Zhao, W. Shen, C. Collings and S. Y. DingDirect Measurement of Plant Cellulose Microfibril and Bundles in Native Cell WallsFrontiers in Plant Science11 479
202010.1111/tpj.14849Sonawane, B. V. and A. B. CousinsMesophyll CO2 conductance and leakiness are not responsive to short- and long-term soil water limitations in the C4 plant Sorghum bicolorThe Plant Journal103(4) 1590–602
202010.1021/acssuschemeng.0c03622Smith, P. J., M. E. Ortiz-Soto, C. Roth, W. J. Barnes, J. Seibel, B. R. Urbanowicz and F. PfrengleEnzymatic Synthesis of Artificial PolysaccharidesACS Sustainable Chemistry & Engineering8(32) 11853–71
202010.1016/j.chemphyslip.2020.104980Smith, M. D. and J. C. SmithEffects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulationChemistry and Physics of Lipids233 104980
202010.1111/nph.16432Smith, G. R. and K. G. PeayStepping forward from relevance in mycorrhizal ecologyNew Phytologist226(2) 292–4
202010.1093/femsec/fiaa208Smercina, D. N., S. E. Evans, M. L. Friesen and L. K. TiemannImpacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and functionFEMS Microbiology Ecology96(12)
202010.1111/gcbb.12729Slessarev, E. W., E. E. Nuccio, K. J. McFarlane, C. E. Ramon, M. Saha, M. K. Firestone and J. Pett_RidgeQuantifying the effects of switchgrass Panicum virgatum on deep organic C stocks using natural abundance 14C in three marginal soilsGCB Bioenergy12(10) 834–47
202010.1007/s12010-020-03293-ySitepu, I., L. Enriquez, V. Nguyen, R. Fry, B. Simmons, S. Singer, C. Simmons and K. L. Boundy-MillsIonic Liquid Tolerance of Yeasts in Family Dipodascaceae and Genus WickerhamomycesApplied Biochemistry and Biotechnology191(4) 1580–93
202010.1002/ece3.6266Simon, S. J., T. J. Tschaplinski, J. M. LeBoldus, K. Keefover-Ring, M. Azeem, J. G. Chen, D. Macaya-Sanz, W. L. MacDonald, W. Muchero and S. P. DiFazioHost plant genetic control of associated fungal and insect species in a Populus hybrid crossEcology and Evolution10(11) 5119–34
202010.3389/fpls.2020.00599Simmons, T., A. B. Styer, G. Pierroz, A. P. Gonçalves, R. Pasricha, A. B. Hazra, P. Bubner and D. Coleman-DerrDrought Drives Spatial Variation in the Millet Root MicrobiomeFrontiers in Plant Science11
202010.1038/s41576-019-0186-3Silverman, A. D., A. S. Karim and M. C. JewettCell-free gene expression: an expanded repertoire of applicationsNature Reviews Genetics21(3) 151-170
202010.1128/mSystems.00151-20Sieradzki, E. T., B. J. Koch, A. Greenlon, R. Sachdeva, R. R. Malmstrom, R. L. Mau, S. J. Blazewicz, M. K. Firestone, K. S. Hofmockel, E. Schwartz, B. A. Hungate and J. Pett-RidgeMeasurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental DesignmSystems5(4)
202010.1093/nar/gkaa600Sidore, A. M., C. Plesa, J. A. Samson, N. B. Lubock and S. KosuriDropSynth 2.0: High-fidelity multiplexed gene synthesis in emulsionsNucleic Acids Research48(16) E95
202010.1038/s41598-020-64921-5Sickle, J. J., C. Ni, D. Shen, Z. Wang, M. Jin and T. LuIntegrative Circuit-Host Modeling of a Genetic Switch in Varying EnvironmentsScientific Reports10(1) 8383
202010.1038/s41564-020-0720-2Sichert, A., C. H. Corzett, M. S. Schechter, F. Unfried, S. Markert, D. Becher, A. Fernandez-Guerra, M. Liebeke, T. Schweder, M. F. Polz and J. H. HehemannVerrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidanNature Microbiology5(8) 1026-1039
202010.1117/12.2567752Shuhui, Y., M. J. Amin, T. E. Nyssa and Y. HawThree-dimensional super line-localization in low signal-to-noise microscope images via prior-apprised unsupervised learning (PAUL)Proceedings of the SPIE
202010.1021/acssuschemeng.0c05998Shi, R. and J. S. GuestBioSTEAM-LCA: An Integrated Modeling Framework for Agile Life Cycle Assessment of Biorefineries under UncertaintyACS Sustainable Chemistry & Engineering8(51) 18903–14
202010.1038/s41467-020-18124-1Sherkhanov, S., T. P. Korman, S. Chan, S. Faham, H. Liu, M. R. Sawaya, W. T. Hsu, E. Vikram, T. Cheng and J. U. BowieIsobutanol production freed from biological limits using synthetic biochemistryNature Communications11(1)
202010.1016/j.soilbio.2020.107742Sher, Y., N. R. Baker, D. Herman, C. Fossum, L. Hale, X. Zhang, E. Nuccio, M. Saha, J. Zhou, J. Pett-Ridge and M. FirestoneMicrobial extracellular polysaccharide production and aggregate stability controlled by switchgrass (Panicum virgatum) root biomass and soil water potentialSoil Biology and Biochemistry143
202010.1021/acs.iecr.9b06086Shen, Z. Z. and R. C. Van LehnSolvent Selection for the Separation of Lignin-Derived Monomers Using the Conductor-like Screening Model for Real SolventsIndustrial & Engineering Chemistry Research59(16) 7755–64
202010.1126/sciadv.abd0079Shen, X. X., J. L. Steenwyk, A. L. LaBella, D. A. Opulente, X. Zhou, J. Kominek, Y. Li, M. Groenewald, C. T. Hittinger and A. RokasGenome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum AscomycotaScience Advances6(45)
202010.1038/s41467-020-20005-6Shen, X. X., Y. Li, C. T. Hittinger, X. X. Chen and A. RokasAn investigation of irreproducibility in maximum likelihood phylogenetic inferenceNature Communications11(1) 6096
202010.1111/nph.16089Sheehan, H., T. Feng, N. Walker-Hale, S. Lopez-Nieves, B. Pucker, et al.Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in CaryophyllalesNew Phytologist227(3) 914–29
202010.1186/s13104-020-04968-9Sharma, R., Y. Liang, M. Y. Lee, V. R. Pidatala, J. C. Mortimer and H. V. SchellerAgrobacterium-mediated transient transformation of sorghum leaves for accelerating functional genomics and genome editing studiesBMC Research Notes13(1)
202010.7554/eLife.56275Sharma, K., M. Palatinszky, G. Nikolov, D. Berry and E. A. ShankTransparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganismseLife9
202010.1042/BCJ20200480Sharkey, T. D., A. L. Preiser, S. M. Weraduwage and L. GogSource of 12C in Calvin-Benson cycle intermediates and isoprene emitted from plant leaves fed with 13CO2Biochemical Journal477(17) 3237-3252
202010.1016/j.biortech.2020.122896Sharara, M. A., K. Sahoo, A. D. Reddy, S. Kim, X. S. Zhang, B. Dale, C. D. Jones, R. C. Izaurralde and T. M. RungeSustainable feedstock for bioethanol production: Impact of spatial resolution on the design of a sustainable biomass supply-chainBioresource Technology302
202010.1093/nar/gkaa621Shaffer, M., M. A. Borton, B. B. McGivern, A. A. Zayed, S. L. La Rosa, et al.DRAM for distilling microbial metabolism to automate the curation of microbiome functionNucleic Acids Research48(16) 8883-8900
202010.3389/fcell.2020.566702Sertbas, M. and K. O. UlgenGenome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat PathogensFrontiers in Cell and Developmental Biology8
202010.1134/S1021443720020144Seong, E. S., M. R. Jeon, J. H. Choi, J. H. Yoo, J. G. Lee, J. K. Na, N. Y. Kim and C. Y. YuOverexpression of S-Adenosylmethionine Synthetase Enhances Tolerance to Cold Stress in TobaccoRussian Journal of Plant Physiology67(2) 242–9
202010.1002/bit.27360Seo, H., P. N. Nicely and C. T. TrinhEndogenous carbohydrate esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from celluloseBiotechnology and Bioengineering117(7) 2223–36
202010.3390/metabo10060250Sengupta, A., P. Pritam, D. Jaiswal, A. Bandyopadhyay, H. B. Pakrasi and P. P. WangikarPhotosynthetic Co-Production of Succinate and Ethylene in A Fast-Growing Cyanobacterium, Synechococcus elongatus PCC 11801Metabolites10(6)
202010.1093/femsle/fnaa045Semrau, J. D., A. A. DiSpirito, P. K. Obulisamy and C. S. Kang-YunMethanobactin from methanotrophs: genetics, structure, function and potential applicationsFEMS Microbiology Letters367(5)
202010.1007/s10980-020-01022-8Sciusco, P., J. Q. Chen, M. Abraha, C. Lei, G. P. Robertson, R. Lafortezza, G. Shirkey, Z. T. Ouyang, R. Zhang and R. JohnSpatiotemporal variations of albedo in managed agricultural landscapes: inferences to global warming impacts (GWI)Landscape Ecology35(6) 1385–402
202010.1104/pp.19.00760Schwarz, B., C. B. Azodi, S. H. Shiu and P. BauerPutative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis RootsPlant Physiology182(3) 1420–39
202010.1128/mSystems.00755-20Scarborough, M. J., J. J. Hamilton, E. A. Erb, T. J. Donohue and D. R. NogueraDiagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic ModelsmSystems5(5)
202010.1002/pld3.207Sasse, J., S. M. Kosina, M. de Raad, J. S. Jordan, K. Whiting, K. Zhalnina and T. R. NorthenRoot morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyonPlant Direct4(7) e00207
202010.1111/tpj.14746Sarkar, D. and C. D. MaranasSNPeffect: identifying functional roles of SNPs using metabolic networksThe Plant Journal103(2) 512–31
202010.1186/s13068-020-01690-3Sander, K. B., D. Chung, D. M. Klingeman, R. J. Giannone, M. Rodriguez, Jr., J. Whitham, R. L. Hettich, B. H. Davison, J. Westpheling and S. D. BrownGene targets for engineering osmotolerance in Caldicellulosiruptor besciiBiotechnology for Biofuels13 50
202010.1038/s41598-020-77684-wSamira, R., J. A. Kimball, L. F. Samayoa, J. B. Holland, T. M. Jamann, P. J. Brown, G. Stacey and P. J. Balint-KurtiGenome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghumScientific Reports10(1) 20817
202010.1016/j.cub.2020.05.043Salem, H., R. Kirsch, Y. Pauchet, A. Berasategui, K. Fukumori, M. Moriyama, M. Cripps, D. Windsor, T. Fukatsu and N. M. GerardoSymbiont Digestive Range Reflects Host Plant Breadth in Herbivorous BeetlesCurrent Biology30(15) 2875–86.e4
202010.3390/microorganisms8081137Saint-Vincent, P. M., M. Ridout, N. L. Engle, T. J. Lawrence, M. L. Yeary, T. J. Tschaplinski, G. Newcombe and D. A. PelletierIsolation, Characterization, and Pathogenicity of Two Pseudomonas syringae Pathovars from Populus trichocarpa SeedsMicroorganisms8(8)
202010.1099/ijsem.0.004465Saini, M. K., W. ChihChe, N. Soulier, A. Sebastian, I. Albert, V. Thiel, D. A. Bryant, S. Hanada and M. TankCaldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, JapanInternational Journal of Systematic and Evolutionary Microbiology70(11) 5701–10
202010.3390/plants9101383Sade, N., F. Weng, H. Tajima, Y. Zeron, L. Zhang, M. M. R. Wilhelmi, G. Day, Z. Peleg and E. BlumwaldA cytoplasmic receptor-like kinase contributes to salinity tolerancePlants9(10) 44938
202010.1016/j.compchemeng.2020.107072Ryu, J. and C. T. MaraveliasComputationally efficient optimization models for preliminary distillation column design and separation energy targetingComputers & Chemical Engineering143
202010.1002/aic.16994Ryu, J. and C. T. MaraveliasEfficient generalized shortcut distillation model with improved accuracy for superstructure-based process synthesisAIChE Journal66(11)
202010.1016/j.compchemeng.2019.106653Ryu, J., L. X. Kong, A. E. P. de Lima and C. T. MaraveliasA generalized superstructure-based framework for process synthesisComputers & Chemical Engineering133
202010.1128/AEM.00909-20Russell, J. F., M. L. Russo, X. Wang, N. Hengge, D. Chung, L. Wells, Y. J. Bomble and J. WestphelingDeletion of a Peptidylprolyl Isomerase Gene Results in the Inability of Caldicellulosiruptor bescii To Grow on Crystalline Cellulose without Affecting Protein Glycosylation or Growth on Soluble SubstratesApplied and Environmental Microbiology86(20)
202010.3390/f11020213Russell, A. E. and W. J. PartonModeling the Effects of Global Change on Ecosystem Processes in a Tropical RainforestForests11(2)
202010.1002/anie.202003105Ruprecht, C., M. P. Bartetzko, D. Senf, A. Lakhina, P. J. Smith, et al.A Glycan Array-Based Assay for the Identification and Characterization of Plant GlycosyltransferasesAngewandte Chemie International Edition59(30) 12493–8
202010.1007/s10295-020-02299-zRubinstein, G. M., G. L. Lipscomb, A. M. Williams-Rhaesa, G. J. Schut, R. M. Kelly and M. W. W. AdamsEngineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy sourceJournal of Industrial Microbiology and Biotechnology47(8) 585–97
202010.1002/saj2.20082Ruan, L. L. and G. P. RobertsonNo-till establishment improves the climate benefit of bioenergy crops on marginal grasslandsSoil Science Society of America Journal84(4) 1280–95
202010.1002/cbic.201900560Rodrigues, A. V., D. J. Tantillo, A. Mukhopadhyay, J. D. Keasling and H. R. BellerInsight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical EnzymeChemBioChem21(5) 663–71
202010.1534/g3.120.401489Robinson, A. J., D. O. Natvig and P. S. G. ChainGenomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial AssociateG3 Genes|Genomes|Genetics10(8) 2573–83
202010.3389/fenrg.2020.563352Roberts, N., M. Hilliard, Q. P. He and J. WangA Microalgae-Methanotroph Coculture is a Promising Platform for Fuels and Chemical Production From WastewaterFrontiers in Energy Research8
202010.1021/acssuschemeng.9b04451Rigual, V., G. Papa, A. Rodriguez, M. Wehrs, K. H. Kim, M. Oliet, M. V. Alonso, J. M. Gladden, A. Mukhopadhyay, B. A. Simmons and S. SinghEvaluating Protic Ionic Liquid for Woody Biomass One-Pot Pretreatment + Saccharification, Followed by Rhodosporidium toruloides CultivationACS Sustainable Chemistry & Engineering8(2) 782–91
202010.1107/S2059798320008049Richards, L. S., C. Millan, J. Miao, M. W. Martynowycz, M. R. Sawaya, T. Gonen, R. J. Borges, I. Usonb and J. A. RodriguezFragment-based determination of a proteinase K structure from MicroED data using ARCiMBOLDO_SHREDDERActa Crystallographica Section D: Structural Biology76 703-712
202010.1073/pnas.1912434117Ribeiro, C. L., D. Conde, K. M. Balmant, C. Dervinis, M. G. Johnson, et al.The uncharacterized gene EVE contributes to vessel element dimensions in PopulusProceedings of the National Academy of Sciences of the United States of America117(9) 5059–66
202010.1128/MRA.00770-20Reyes, S. M., E. Bolettieri, D. Allen and A. G. HayGenome Sequences of Four Strains of Acinetobacter bereziniae Isolated from Human Milk Pumped with a Personal Breast Pump and Hand-Washed Milk Collection SuppliesMicrobiology Resource Announcements9(44)
202010.7554/eLife.62669Renganaath, K., R. Cheung, L. Day, S. Kosuri, L. Kruglyak and F. W. AlbertSystematic identification of cis-regulatory variants that cause gene expression differences in a yeast crosseLife9 12785
202010.1016/j.isci.2019.100795Ren, H., C. Shi and H. ZhaoComputational Tools for Discovering and Engineering Natural Product Biosynthetic PathwaysiScience23(1) 100795
202010.1038/s41467-020-16687-7Reis, F., R. Kirsch, Y. Pauchet, E. Bauer, L. C. Bilz, K. Fukumori, T. Fukatsu, G. Kölsch and M. KaltenpothBacterial symbionts support larval sap feeding and adult folivory in (semi-)aquatic reed beetlesNature Communications11(1) 2964
202010.1021/acssynbio.0c00394Reis, A. C. and H. M. SalisAn Automated Model Test System for Systematic Development and Improvement of Gene Expression ModelsACS Synthetic Biology9(11) 3145–56
202010.1007/s10021-019-00407-4Reed, D. E., J. Chen, M. Abraha, G. P. Robertson and K. M. DahlinThe Shifting Role of mRUE for Regulating Ecosystem ProductionEcosystems23(2) 359–69
202010.1042/BST20190492Reddy, A. S. N., J. Huang, N. H. Syed, A. Ben-Hur, S. Dong and L. GuDecoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologiesBiochemical Society Transactions48(6) 2399-2414
202010.1111/pbi.13309Rauschendorfer, J., Y. Yordanov, P. Dobrev, R. Vankova, R. Sykes, C. Külheim and V. BusovOverexpression of a developing xylem cDNA library in transgenic poplar generates high mutation rate specific to wood formationPlant Biotechnology Journal18(6) 1434-1443
202010.1016/j.copbio.2020.10.001Rapp, K. M., J. P. Jenkins and M. J. BetenbaughPartners for life: building microbial consortia for the futureCurrent Opinion in Biotechnology66 292–300
202010.1073/pnas.2014294117Ramundo, S., Y. Asakura, P. A. Salomé, D. Strenkert, M. Boone, et al.Coexpressed subunits of dual genetic origin define a conserved supercomplex mediating essential protein import into chloroplastsProceedings of the National Academy of Sciences of the United States of America117(51) 32739-32749
202010.1111/nph.16827Ralph, J.Tricin and tricin-lignins in Medicago versus in monocotsNew Phytologist228(1) 11–4
202010.1111/1758-2229.12838Rajeev, L., M. E. Garber and A. MukhopadhyayTools to map target genes of bacterial two-component system response regulatorsEnvironmental Microbiology Reports12(3) 267–76
202010.1021/acssuschemeng.0c04433Ragauskas, A. and X. Z. MengACS Sustainable Chemistry & Engineering Virtual Special Issue on Recent Advances in Biomass Characterization and ModelingACS Sustainable Chemistry & Engineering8(28) 10321–2
202010.1186/s12870-020-02714-8R, M. R. and A. MissaouiQTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x uplandBMC Plant Biology20(1) 537
202010.1002/saj2.20159Purcell, A. M., P. Dijkstra, B. Finley, M. Hayer, B. J. Koch, R. L. Mau, E. Morrissey, K. Papp, E. Schwartz, B. W. Stone and B. A. HungateQuantitative stable isotope probing with H2O to measure taxon-specific microbial growthSoil Science Society of America Journal84(5) 1503–18
202010.1128/mSystems.00291-20Price, M. N., A. M. Deutschbauer and A. P. ArkinGapMind: Automated Annotation of Amino Acid BiosynthesismSystems5(3)
202010.3389/fmicb.2020.01646Presley, G. N., J. Zhang, S. O. Purvine and J. S. SchillingFunctional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay MechanismsFrontiers in Microbiology11
202010.1016/j.algal.2020.101953Polle, J. E. W., R. Roth, A. Ben-Amotz and U. GoodenoughUltrastructure of the green alga Dunaliella salina strain CCAP19/18 (Chlorophyta) as investigated by quick-freeze deep-etch electron microscopyAlgal Research49
202010.3389/ffgc.2020.00097Policelli, N., T. R. Horton, A. T. Hudon, T. R. Patterson and J. M. BhatnagarBack to Roots: The Role of Ectomycorrhizal Fungi in Boreal and Temperate Forest RestorationFrontiers in Forests and Global Change3
202010.1128/mBio.02293-19Pold, G., L. A. Domeignoz-Horta, E. W. Morrison, S. D. Frey, S. A. Sistla and K. M. DeAngelisCarbon Use Efficiency and Its Temperature Sensitivity Covary in Soil BacteriamBio11(1)
202010.1525/elementa.069Pold, G., L. A. Domeignoz-Horta and K. M. DeAngelisHeavy and wet: The consequences of violating assumptions of measuring soil microbial growth efficiency using the 18O water methodElementa8(1)
202010.1016/j.agrformet.2020.108188Poe, J., D. E. Reed, M. Abraha, J. Q. Chen, K. M. Dahlin and A. R. DesaiGeospatial coherence of surface-atmosphere fluxes in the upper Great Lakes regionAgricultural and Forest Meteorology295
202010.1128/MRA.00644-20Podar, M., J. Turner, L. H. Burdick and D. A. PelletierComplete Genome Sequence of Starkeya sp. Strain ORNL1, a Soil Alphaproteobacterium Isolated from the Rhizosphere of Populus deltoidesMicrobiology Resource Announcements9(27)
202010.1128/MRA.00617-20Podar, M., J. Turner, L. H. Burdick and D. A. PelletierComplete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides RhizosphereMicrobiology Resource Announcements9(27)
202010.1111/nph.16759Plett, J. M., K. L. Plett, J. Wong-Bajracharya, M. de Freitas Pereira, M. D. Costa, A. Kohler, F. Martin and I. C. AndersonMycorrhizal effector PaMiSSP10b alters polyamine biosynthesis in Eucalyptus root cells and promotes root colonizationNew Phytologist228(2) 712–27
202010.1002/jbm.a.36811Pierce, A., Y. Zheng, W. L. Wagner, H. V. Scheller, D. Mohnen, A. Tsuda, M. Ackermann and S. J. MentzerPectin biopolymer mechanics and microstructure associated with polysaccharide phase transitionsJournal of Biomedical Materials Research Part A108(2) 246–53
202010.1086/706198Petipas, R. H., A. W. Bowsher, C. S. Bekkering, C. N. Jack, E. E. McLachlan, R. A. White, B. S. Younginger, L. K. Tiemann, S. E. Evans and M. L. FriesenInteractive Effects of Microbes and Nitrogen on Panicum virgatum Root Functional Traits and Patterns of Phenotypic SelectionInternational Journal of Plant Sciences181(1) 20–32
202010.1029/2019JG005526Perryman, C. R., C. K. Mccalley, A. Malhotra, M. F. Fahnestock, N. N. Kashi, J. G. Bryce, R. Giesler and R. K. VarnerThaw Transitions and Redox Conditions Drive Methane Oxidation in a Permafrost PeatlandJournal of Geophysical Research: Biogeosciences125(3)
202010.1038/s41467-020-15559-4Peris, D., W. G. Alexander, K. J. Fisher, R. V. Moriarty, M. G. Basuino, E. J. Ubbelohde, R. L. Wrobel and C. T. HittingerSynthetic hybrids of six yeast speciesNature Communications11(1) 2085
202010.1128/MRA.00159-20Pelletier, D. A., L. H. Burdick, M. Podar, C. W. Schadt and U. C. KalluriDraft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides RootsMicrobiology Resource Announcements9(12)
202010.1017/s143192762002190xParrell, D., K. Lemmer, T. Donohue and E. WrightDeletion of the ntrYX Two Component System in Rhodobacter sphaeroides Causes the Generation of Diverse Extracellular Membrane StructuresMicroscopy and Microanalysis26(S2) 2522–3
202010.1007/s10822-020-00289-yParks, C. D., Z. Gaieb, M. Chiu, H. Yang, C. Shao, et al.D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energiesJournal of Computer-Aided Molecular Design34(2) 99-119
202010.15252/msb.20209584Park, Y., A. Espah Borujeni, T. E. Gorochowski, J. Shin and C. A. VoigtPrecision design of stable genetic circuits carried in highly-insulated E. coli genomic landing padsMolecular Systems Biology16(8)
202010.1111/tpj.14870Park, S. and S. Y. DingThe N-terminal zinc finger of CELLULOSE SYNTHASE6 is critical in defining its functional properties by determining the level of homodimerization in ArabidopsisThe Plant Journal103(5) 1826–38
202010.1002/cssc.202000268Park, M. R., Y. Chen, M. Thompson, V. T. Benites, B. Fong, C. J. Petzold, E. E. K. Baidoo, J. M. Gladden, P. D. Adams, J. D. Keasling, B. A. Simmons and S. W. SingerResponse of Pseudomonas putida to Complex, Aromatic-Rich Fractions from BiomassChemSusChem13(17) 4455–67
202010.1111/gcbb.12684Parajuli, S., B. Kannan, R. Karan, G. Sanahuja, H. Liu, E. Garcia-Ruiz, D. Kumar, V. Singh, H. M. Zhao, S. Long, J. Shanklin and F. AltpeterTowards oilcane: Engineering hyperaccumulation of triacylglycerol into sugarcane stemsGCB Bioenergy12(7) 476–90
202010.1002/ecy.2887Papp, K., B. A. Hungate and E. SchwartzGlucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIPEcology101(1) e02887
202010.1007/978-981-10-6739-6_49-1Papa, G., B. A. Simmons and N. SunScale-Up of the Ionic Liquid-Based Biomass Conversion ProcessesEncyclopedia of Ionic Liquids 1–8
202010.1186/s12864-020-6554-8Panchy, N. L., J. P. Lloyd and S. H. ShiuImproved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics dataBMC Genomics21(1) 159
202010.1016/j.coisb.2020.09.007Ostrov, N., A. Nyerges, A. Chiappino-Pepe, A. Rudolph, M. Baas-Thomas and G. M. ChurchSynthetic genomes with altered genetic codesCurrent Opinion in Systems Biology24 32–40
202010.1128/AEM.01888-19Oshlag, J. Z., Y. Ma, K. Morse, B. T. Burger, R. A. Lemke, S. D. Karlen, K. S. Myers, T. J. Donohue and D. R. NogueraAnaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustrisApplied and Environmental Microbiology86(3)
202010.1094/Pbiomes-05-20-0044-ROnufrak, A. J., G. M. Williams, W. E. Klingeman, M. A. Cregger, D. M. Klingeman, J. M. DeBruyn, M. D. Ginzel and D. HadziabdicRegional Differences in the Structure of Juglans nigra Phytobiome Reflect Geographical Differences in Thousand Cankers Disease SeverityPhytobiomes Journal4(4) 388–404
202010.1371/journal.pcbi.1008137Ong, W. K., D. K. Courtney, S. Pan, R. B. Andrade, P. J. Kiley, B. F. Pfleger and J. L. ReedModel-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4PLoS Computational Biology16(8) e1008137
202010.1080/15321819.2020.1804933Olayinka, A., I. M. Ifeorah, O. Omotosho, T. O. C. Faleye, O. Odukaye, O. Bolaji, I. Ibitoye, O. Ope-Ewe, M. O. Adewumi and J. A. AdenijiA possible risk of environmental exposure to HEV in Ibadan, Oyo State, NigeriaJournal of Immunoassay and Immunochemistry41(5) 875–84
202010.1534/g3.120.401402Olatoye, M. O., L. V. Clark, N. R. Labonte, H. Dong, M. S. Dwiyanti, et al.Training Population Optimization for Genomic Selection in MiscanthusG3 Genes|Genomes|Genetics10(7) 2465–76
202010.1021/acssynbio.0c00159Oh, E. J., R. Liu, L. Liang, E. F. Freed, C. A. Eckert and R. T. GillMultiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display PlatformACS Synthetic Biology9(8) 2197–202
202010.1093/femsyr/foz089Oh, E. J. and Y. S. JinEngineering of Saccharomyces cerevisiae for efficient fermentation of celluloseFEMS Yeast Research20(1)
202010.3390/ijms21249706Ogden, A. J., S. Abdali, K. M. Engbrecht, M. Zhou and P. P. HandakumburaDistinct Preflowering Drought Tolerance Strategies of Sorghum bicolor Genotype RTx430 Revealed by Subcellular Protein ProfilingInternational Journal of Molecular Sciences21(24)
202010.1038/s41396-019-0582-xNuccio, E. E., E. Starr, U. Karaoz, E. L. Brodie, J. Zhou, S. G. Tringe, R. R. Malmstrom, T. Woyke, J. F. Banfield, M. K. Firestone and J. Pett-RidgeNiche differentiation is spatially and temporally regulated in the rhizosphereThe ISME Journal14(4) 999–1014
202010.1002/agj2.20184Novak, J. M., D. W. Watts, P. J. Bauer, D. L. Karlen, P. G. Hunt and U. MishraLoamy sand soil approaches organic carbon saturation after 37 years of conservation tillageAgronomy Journal112(4) 3152–62
202010.1111/mmi.14459North, J. A., J. A. Wildenthal, T. J. Erb, B. S. Evans, K. M. Byerly, J. A. Gerlt and F. R. TabitaA bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coliMolecular Microbiology113(5) 923–37
202010.1126/science.abb6310North, J. A., A. B. Narrowe, W. Xiong, K. M. Byerly, G. Zhao, S. J. Young, S. Murali, J. A. Wildenthal, W. R. Cannon, K. C. Wrighton, R. L. Hettich and F. R. TabitaA nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesisScience369(6507) 1094–8
202010.1016/j.soilbio.2020.107952Norman, J. S., D. N. Smercina, J. T. Hileman, L. K. Tiemann and M. L. FriesenSoil aminopeptidase induction is unaffected by inorganic nitrogen availabilitySoil Biology and Biochemistry149
202010.1038/s41467-020-18560-zNing, D., M. Yuan, L. Wu, Y. Zhang, X. Guo, X. Zhou, Y. Yang, A. P. Arkin, M. K. Firestone and J. ZhouA quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warmingNature Communications11(1) 4717
202010.1021/acssuschemeng.0c00779Nill, J. D. and T. JeohThe Role of Evolving Interfacial Substrate Properties on Heterogeneous Cellulose Hydrolysis KineticsACS Sustainable Chemistry & Engineering8(17) 6722–33
202010.3390/genes11060625Nikolaou, E., A. T. M. Hubbard, J. Botelho, T. A. M. Marschall, D. M. Ferreira and A. P. RobertsAntibiotic Resistance Is Associated with Integrative and Conjugative Elements and Genomic Islands in Naturally Circulating Streptococcus pneumoniae Isolates from Adults in Liverpool, UKGenes11(6)
202010.1016/j.bej.2020.107496Nichols, T. M., N. W. Kennedy and D. Tullman-ErcekA genomic integration platform for heterologous cargo encapsulation in 1,2-propanediol utilization bacterial microcompartmentsBiochemical Engineering Journal156
202010.1038/s41467-020-19983-4Neupert, J., S. D. Gallaher, Y. Lu, D. Strenkert, N. Segal, R. Barahimipour, S. T. Fitz-Gibbon, M. Schroda, S. S. Merchant and R. BockAn epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga ChlamydomonasNature Communications11(1)
202010.1128/MRA.00718-20Nelson, W. C., L. N. Anderson, R. Wu, J. E. McDermott, S. L. Bell, A. Jumpponen, S. J. Fansler, K. J. Tyrrell, Y. Farris, K. S. Hofmockel and J. K. JanssonTerabase Metagenome Sequencing of Grassland Soil MicrobiomesMicrobiology Resource Announcements9(32)
202010.1146/annurev-environ-012320-082720Naylor, D., N. Sadler, A. Bhattacharjee, E. B. Graham, C. R. Anderton, R. McClure, M. Lipton, K. S. Hofmockel and J. K. JanssonSoil Microbiomes Under Climate Change and Implications for Carbon CyclingAnnual Review of Environment and Resources45 29–59
202010.1128/mBio.01349-20Naylor, D., S. Fansler, C. Brislawn, W. C. Nelson, K. S. Hofmockel, J. K. Jansson and R. McClureDeconstructing the Soil Microbiome into Reduced-Complexity Functional ModulesmBio11(4)
202010.1007/s11104-020-04616-yNash, J., R. Laushman and C. SchadtEctomycorrhizal fungal diversity interacts with soil nutrients to predict plant growth despite weak plant-soil feedbacksPlant and Soil453(44928) 445–58
202010.1021/acssuschemeng.9b06556Nandiwale, K. Y., A. M. Danby, A. Ramanathan, R. V. Chaudhari, A. H. Motagamwala, J. A. Dumesic and B. SubramaniamEnhanced Acid-Catalyzed Lignin Depolymerization in a Continuous Reactor with Stable ActivityACS Sustainable Chemistry & Engineering8(10) 4096–106
202010.1038/s41598-020-73253-3Nanda, P., P. Patra, M. Das and A. GhoshReconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveriScientific Reports10(1) 16314
202010.1128/MRA.00880-20Myers, K. S., J. M. Vera, K. C. Lemmer, A. M. Linz, R. Landick, D. R. Noguera and T. J. DonohueGenome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria, Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444Microbiology Resource Announcements9(36)
202010.1128/MRA.00587-20Myers, K. S., M. Place, D. R. Noguera and T. J. DonohueCOnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus DatabaseMicrobiology Resource Announcements9(25)
202010.1007/s10841-020-00248-wMyers, A. T., N. L. Haan and D. A. LandisVideo surveillance reveals a community of largely nocturnal Danaus plexippus (L.) egg predatorsJournal of Insect Conservation24(4) 731–7
202010.1371/journal.pbio.3000877Mutalik, V. K., B. A. Adler, H. S. Rishi, D. Piya, C. Zhong, B. Koskella, E. M. Kutter, R. Calendar, P. S. Novichkov, M. N. Price, A. M. Deutschbauer and A. P. ArkinHigh-throughput mapping of the phage resistance landscape in E. coliPLoS Biology18(10) e3000877
202010.1111/mpp.12999Murphree, C., S. B. Kim, S. Karre, R. Samira and P. Balint-KurtiUse of virus-induced gene silencing to characterize genes involved in modulating hypersensitive cell death in maizeMolecular Plant Pathology21(12) 1662-1676
202010.1099/ijsem.0.004360Muramatsu, S., M. Kanamuro, Y. Sato-Takabe, S. Hirose, Y. Muramatsu, S. Takaichi and S. HanadaRoseobacter cerasinus sp. nov., isolated from a fish farmInternational Journal of Systematic and Evolutionary Microbiology70(9) 4920–6
202010.1002/pro.3974Mulligan, V. K., C. S. Kang, M. R. Sawaya, S. Rettie, X. Li, I. Antselovich, T. W. Craven, A. M. Watkins, J. W. Labonte, F. DiMaio, T. O. Yeates and D. BakerComputational design of mixed chirality peptide macrocycles with internal symmetryProtein Science29(12) 2433-2445
202010.1104/pp.20.00997Müller, L. M., L. Campos-Soriano, V. Levesque-Tremblay, A. Bravo, D. A. Daniels, S. Pathak, H. J. Park and M. J. HarrisonConstitutive overexpression of RAM1 leads to an increase in arbuscule density in brachypodium distachyonPlant Physiology184(3) 1263-1272
202010.1016/j.rser.2020.109764Mousavi-Avval, S. H. and A. ShahTechno-economic analysis of pennycress production, harvest and post-harvest logistics for renewable jet fuelRenewable and Sustainable Energy Reviews123
202010.1128/MRA.00956-20Morrow, M. A., G. Pold and K. M. DeAngelisDraft Genome Sequence of a Terrestrial Planctomycete, Singulisphaera sp. Strain GP187, Isolated from Forest SoilMicrobiology Resource Announcements9(50)
202010.1038/s41893-019-0456-2Moreira, M. M. R., J. E. A. Seabra, L. R. Lynd, S. M. Arantes, M. P. Cunha and J. J. M. GuilhotoSocio-environmental and land-use impacts of double-cropped maize ethanol in BrazilNature Sustainability3(3) 209–16
202010.3389/fmicb.2020.00005Moosburner, M. A., P. Gholami, J. K. McCarthy, M. Tan, V. A. Bielinski and A. E. AllenMultiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9Frontiers in Microbiology11 5
202010.1111/gcbb.12743Moore, C. E., D. M. Berardi, E. Blanc-Betes, E. C. Dracup, S. Egenriether, et al.The carbon and nitrogen cycle impacts of reverting perennial bioenergy switchgrass to an annual maize crop rotationGCB Bioenergy12(11) 941–54
202010.1093/insilicoplants/diaa005Moore, B. M., P. Wang, P. Fan, A. Lee, B. Leong, Y. R. Lou, C. A. Schenck, K. Sugimoto, R. Last, M. D. Lehti-Shiu, C. S. Barry and S. H. ShiuWithin- and cross-species predictions of plant specialized metabolism genes using transfer learningIn Silico Plants2(1) diaa005
202010.1016/j.chemosphere.2020.126951Moon, J. W., C. J. Paradis, D. C. Joyner, F. von Netzer, E. L. Majumder, et al.Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquiferChemosphere255 126951
202010.1111/gcb.14925Monteiro, L. A., A. M. Allee, E. E. Campbell, L. R. Lynd, J. R. Soares, et al.Assessment of yield gaps on global grazed-only permanent pasture using climate binningGlobal Change Biology26(3) 1820–32
202010.1007/s00253-020-10469-3Monge, E. C., M. Levi, J. N. Forbin, M. D. Legesse, B. A. Udo, T. N. deCarvalho and J. G. GardnerHigh-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substratesApplied Microbiology and Biotechnology104(8) 3379–89
202010.1038/s41467-020-18923-6Mitros, T., A. M. Session, B. T. James, G. A. Wu, M. B. Belaffif, et al.Genome biology of the paleotetraploid perennial biomass crop MiscanthusNature Communications11(1) 5442
202010.1111/tpj.14957Miller, G. P., W. W. Bhat, E. R. Lanier, S. R. Johnson, D. T. Mathieu and B. HambergerThe biosynthesis of the anti-microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all-cis prenyl intermediateThe Plant Journal104(3) 693–705
202010.1016/j.algal.2020.101967Metcalf, A. J., A. Nagygyor and N. R. BoyleRapid Annotation of Photosynthetic Systems (RAPS): automated algorithm to generate genome-scale metabolic networks from algal genomesAlgal Research50
202010.1039/d0gc00661kMeng, X. Z., Y. Q. Pu, M. Li and A. J. RagauskasA biomass pretreatment using cellulose-derived solvent CyreneGreen Chemistry22(9) 2862–72
202010.1021/acssynbio.9b00407McConnell, S. A., K. A. Cannon, C. Morgan, R. McAllister, B. R. Amer, R. T. Clubb and T. O. YeatesDesigned Protein Cages as Scaffolds for Building Multienzyme MaterialsACS Synthetic Biology9(2) 381–91
202010.1038/s41598-020-67878-7McClure, R. S., J. Y. Lee, T. R. Chowdhury, E. M. Bottos, R. A. White, 3rd, Y. M. Kim, C. D. Nicora, T. O. Metz, K. S. Hofmockel, J. K. Jansson and H. S. SongIntegrated network modeling approach defines key metabolic responses of soil microbiomes to perturbationsScientific Reports10(1) 10882
202010.3389/fmicb.2020.01987McClure, R., D. Naylor, Y. Farris, M. Davison, S. J. Fansler, K. S. Hofmockel and J. K. JanssonDevelopment and Analysis of a Stable, Reduced Complexity Model Soil MicrobiomeFrontiers in Microbiology11 1987
202010.1038/s41540-019-0122-3Mazharul Islam, M., V. C. Thomas, M. Van Beek, J. S. Ahn, A. A. Alqarzaee, C. Zhou, P. D. Fey, K. W. Bayles and R. SahaAn integrated computational and experimental study to investigate Staphylococcus aureus metabolismnpj Systems Biology and Applications6(1) 3
202010.3389/fpls.2020.00843Mazarei, M., H. L. Baxter, A. Srivastava, G. Li, H. Xie, et al.Silencing Folylpolyglutamate Synthetase1 (FPGS1) in Switchgrass (Panicum virgatum L.) Improves Lignocellulosic Biofuel ProductionFrontiers in Plant Science11 843
202010.1146/annurev-marine-010419-010714Mayali, X.NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale ImpactsAnnual Review of Marine Science12 449–67
202010.1021/acs.analchem.9b05718May, J. C., R. Knochenmuss, J. C. Fjeldsted and J. A. McLeanResolution of Isomeric Mixtures in Ion Mobility Using a Combined Demultiplexing and Peak Deconvolution TechniqueAnalytical Chemistry92(14) 9482–92
202010.1038/s41598-020-59494-2Martinez-Feria, R. A. and B. BassoUnstable crop yields reveal opportunities for site-specific adaptations to climate variabilityScientific Reports10(1) 2885
202010.1111/gcbb.12726Martinez-Feria, R. and B. BassoPredicting soil carbon changes in switchgrass grown on marginal lands under climate change and adaptation strategiesGCB Bioenergy12(9) 742-755
202010.3389/fevo.2020.00092Martinez, N. D.Allometric Trophic Networks From Individuals to Socio-Ecosystems: Consumer–Resource Theory of the Ecological Elephant in the RoomFrontiers in Ecology and Evolution8
202010.1016/j.copbio.2019.11.014Markel, K., M. S. Belcher and P. M. ShihDefining and engineering bioenergy plant feedstock ideotypesCurrent Opinion in Biotechnology62 196–201
202010.1101/2020.06.17.157016Marchand, J. A., M. D. Pierson Smela, T. H. H. Jordan, K. Narasimhan and G. M. ChurchTBDB – A database of structurally annotated T-box riboswitch:tRNA pairsAIChE Annual Meeting, Conference Proceedings2020-November
202010.1146/annurev-bioeng-062117-121105Mang, A., S. Bakas, S. Subramanian, C. Davatzikos and G. BirosIntegrated Biophysical Modeling and Image Analysis: Application to Neuro-OncologyAnnual Review of Biomedical Engineering22 309–41
202010.1038/s41587-020-0681-2Mamidi, S., A. Healey, P. Huang, J. Grimwood, J. Jenkins, et al.A genome resource for green millet Setaria viridis enables discovery of agronomically valuable lociNature Biotechnology38(10) 1203-1210
202010.1038/s41396-020-0683-6Malik, A. A., T. Swenson, C. Weihe, E. W. Morrison, J. B. H. Martiny, E. L. Brodie, T. R. Northen and S. D. AllisonDrought and plant litter chemistry alter microbial gene expression and metabolite productionISME Journal14(9) 2236-2247
202010.1038/s41396-019-0510-0Malik, A. A., J. B. H. Martiny, E. L. Brodie, A. C. Martiny, K. K. Treseder and S. D. AllisonDefining trait-based microbial strategies with consequences for soil carbon cycling under climate changeThe ISME Journal14(1) 1–9
202010.3390/plants9010097Mahmud, K., S. Makaju, R. Ibrahim and A. MissaouiCurrent Progress in Nitrogen Fixing Plants and Microbiome ResearchPlants9(1)
202010.1111/nph.16507MacKinnon, K. J. M., B. J. Cole, C. Yu, J. H. Coomey, N. T. Hartwick, M. S. Remigereau, T. Duffy, T. P. Michael, S. A. Kay and S. P. HazenChanges in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulationNew Phytologist227(6) 1709-1724
202010.1021/acs.jproteome.0c00253MacGilvray, M. E., E. Shishkova, M. Place, E. R. Wagner, J. J. Coon and A. P. GaschPhosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress ResponsesJournal of Proteome Research19(8) 3405–17
202010.1093/bioinformatics/btz592Ma, F. and M. PellegriniACTINN: automated identification of cell types in single cell RNA sequencingBioinformatics36(2) 533–8
202010.1016/j.ymben.2020.07.010Luo, Z., N. Liu, Z. Lazar, A. Chatzivasileiou, V. Ward, J. Chen, J. Zhou and G. StephanopoulosEnhancing isoprenoid synthesis in Yarrowia lipolytica by expressing the isopentenol utilization pathway and modulating intracellular hydrophobicityMetabolic Engineering61 344–51
202010.1002/anie.201914703Luo, X., Y. Li, N. K. Gupta, B. Sels, J. Ralph and L. ShuaiProtection Strategies Enable Selective Conversion of BiomassAngewandte Chemie International Edition59(29) 11704–16
202010.1371/journal.pcbi.1007673Lugagne, J. B., H. Lin and M. J. DunlopDeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learningPLoS Computational Biology16(4) e1007673
202010.1021/acs.analchem.0c00985Lu, W., X. Xing, L. Wang, L. Chen, S. Zhang, M. R. McReynolds and J. D. RabinowitzImproved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and IntensityAnalytical Chemistry92(17) 11573–81
202010.34133/2020/9078303Lu, H., G. Yuan, S. H. Strauss, T. J. Tschaplinski, G. A. Tuskan, J.-G. Chen and X. YangReconfiguring Plant Metabolism for Biodegradable Plastic ProductionBioDesign Research2020
202010.1038/s41598-020-63372-2Lu, H., M. I. Gordon, V. Amarasinghe and S. H. StraussExtensive transcriptome changes during seasonal leaf senescence in field-grown black cottonwood (Populus trichocarpa Nisqually-1)Scientific Reports10(1) 6581
202010.1128/mSystems.00651-19Liu, Y. F., J. Chen, L. S. Zaramela, L. Y. Wang, S. M. Mbadinga, Z. W. Hou, X. L. Wu, J. D. Gu, K. Zengler and B. Z. MuGenomic and Transcriptomic Evidence Supports Methane Metabolism in ArchaeoglobimSystems5(2)
202010.1016/j.ymben.2020.06.005Liu, Y., I. N. Ghosh, J. Martien, Y. Zhang, D. Amador-Noguez and R. LandickRegulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilisMetabolic Engineering61 261–74
202010.1021/acs.analchem.0c02124Liu, X., R. Zhu, T. Chen, P. Song, F. Lu, F. Xu, J. Ralph and X. ZhangMild Acetylation and Solubilization of Ground Whole Plant Cell Walls in EmimAc: A Method for Solution-State NMR in DMSO-d6Analytical Chemistry92(19) 13101–9
202010.1073/pnas.2004091117Liu, W. Y., H. H. Lin, C. P. Yu, C. K. Chang, H. J. Chen, J. J. Lin, M. Y. J. Lu, S. L. Tu, S. H. Shiu, S. H. Wu, M. S. B. Ku and W. H. LiMaize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growthProceedings of the National Academy of Sciences of the United States of America117(35) 21747-21756
202010.1073/pnas.2012245117Liu, W. Y., H. H. Lin, C. P. Yu, C. K. Chang, H. J. Chen, J. J. Lin, M. J. Lu, S. L. Tu, S. H. Shiu, S. H. Wu, M. S. B. Ku and W. H. LiMaize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growthProceedings of the National Academy of Sciences of the United States of America117(35) 21747–56
202010.1002/bit.27541Liu, W. Q., C. Wu, M. C. Jewett and J. LiCell-free protein synthesis enables one-pot cascade biotransformation in an aqueous-organic biphasic systemBiotechnology and Bioengineering117(12) 4001–8
202010.1007/s00299-019-02488-wLiu, W., M. R. Rudis, M. H. Cheplick, R. J. Millwood, J. P. Yang, C. A. Ondzighi-Assoume, G. A. Montgomery, K. P. Burris, M. Mazarei, J. D. Chesnut and C. N. Stewart, Jr.Lipofection-mediated genome editing using DNA-free delivery of the Cas9/gRNA ribonucleoprotein into plant cellsPlant Cell Reports39(2) 245–57
202010.1146/annurev-bioeng-060418-052203Liu, S., H. Huh, S. H. Lee and F. HuangThree-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue SpecimensAnnual Review of Biomedical Engineering22 155–84
202010.1038/s41467-020-17721-4Liu, R., L. Liang, E. F. Freed, A. Choudhury, C. A. Eckert and R. T. GillEngineering regulatory networks for complex phenotypes in E. coliNature Communications11(1) 4050
202010.1016/j.copbio.2019.07.003Liu, N., S. Santala and G. StephanopoulosMixed carbon substrates: a necessary nuisance or a missed opportunity?Current Opinion in Biotechnology62 15–21
202010.1038/s41467-019-13986-6Liu, F., J. Mao, W. Kong, Q. Hua, Y. Feng, R. Bashir and T. LuInteraction variability shapes succession of synthetic microbial ecosystemsNature Communications11(1) 309
202010.1038/s41598-019-57319-5Lin, P. C., F. Zhang and H. B. PakrasiEnhanced production of sucrose in the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973Scientific Reports10(1)
202010.1534/g3.120.401122Lin, F., E. Z. Lazarus and S. Y. RheeQTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in PlantsG3 Genes|Genomes|Genetics10(7) 2411–21
202010.1186/s13068-020-01707-xLin, C. Y. and A. EudesStrategies for the production of biochemicals in bioenergy cropsBiotechnology for Biofuels13 71
202010.1111/tpj.14783Lim, S. D., J. A. Mayer, W. C. Yim and J. C. CushmanPlant tissue succulence engineering improves water-use efficiency, water-deficit stress attenuation and salinity tolerance in ArabidopsisPlant Journal103(3) 1049-1072
202010.1093/femsyr/foaa008Libkind, D., D. Peris, F. A. Cubillos, J. L. Steenwyk, D. A. Opulente, Q. K. Langdon, A. Rokas and C. T. HittingerInto the wild: new yeast genomes from natural environments and new tools for their analysisFEMS Yeast Research20(2)
202010.3389/fbioe.2020.00710Liang, L., R. Liu, E. F. Freed and C. A. EckertSynthetic Biology and Metabolic Engineering Employing Escherichia coli for C2–C6 Bioalcohol ProductionFrontiers in Bioengineering and Biotechnology8
202010.1016/j.ymben.2019.09.007Liang, L., R. Liu, K. E. O. Foster, AlakshChoudhury, S. Cook, J. C. Cameron, W. V. Srubar and R. T. GillGenome engineering of E. coli for improved styrene productionMetabolic Engineering57 74-84
202010.3389/fmicb.2020.568588Liang, D., Y. Ouyang, L. Tiemann and G. P. RobertsonNiche Differentiation of Bacterial Versus Archaeal Soil Nitrifiers Induced by Ammonium Inhibition Along a Management GradientFrontiers in Microbiology11 568588
202010.1021/jacs.0c07657Li, Y. L., C. T. Zee, J. B. Lin, V. M. Basile, M. Muni, M. D. Flores, J. Munárriz, R. B. Kaner, A. N. Alexandrova, K. N. Houk, S. H. Tolbert and Y. RubinFjord-Edge Graphene Nanoribbons with Site-Specific Nitrogen SubstitutionJournal of the American Chemical Society142(42) 18093-18102
202010.1002/cssc.202000753Li, Y., S. D. Karlen, B. Demir, H. Kim, J. Luterbacher, J. A. Dumesic, S. S. Stahl and J. RalphMechanistic Study of Diaryl Ether Bond Cleavage during Palladium-Catalyzed Lignin HydrogenolysisChemSusChem13(17) 4487–94
202010.1021/acssuschemeng.0c03423Li, W. Q., N. Wanninayake, X. Gao, M. Li, Y. Q. Pu, D. Y. Kim, A. J. Ragauskas and J. ShiMechanistic Insight into Lignin Slow Pyrolysis by Linking Pyrolysis Chemistry and Carbon Material PropertiesACS Sustainable Chemistry & Engineering8(42) 15843–54
202010.1016/j.algal.2019.101755Li, T. T., L. Q. Jiang, Y. F. Hu, J. T. Paul, C. Zuniga, K. Zengler and M. J. BetenbaughCreating a synthetic lichen: Mutualistic co-culture of fungi and extracellular polysaccharide-secreting cyanobacterium Nostoc PCC 7413Algal Research45
202010.1105/tpc.19.00300Li, H. M., D. Schnell and S. M. ThegProtein Import Motors in Chloroplasts: On the Role of ChaperonesThe Plant Cell32(3) 536–42
202010.1038/s41467-020-19566-3Li, H., C. Y. Sun, Y. Fang, C. M. Carlson, H. Xu, A. Je_ovnik, J. Sosa-Calvo, R. Zarnowski, H. A. Bechtel, J. H. Fournelle, D. R. Andes, T. R. Schultz, P. U. P. A. Gilbert and C. R. CurrieBiomineral armor in leaf-cutter antsNature Communications11(1)
202010.1128/mBio.01325-20Leu, A. O., S. J. McIlroy, J. Ye, D. H. Parks, V. J. Orphan and G. W. TysonLateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family MethanoperedenaceaemBio11(3)
202010.1038/s41396-020-0590-xLeu, A. O., C. Cai, S. J. McIlroy, G. Southam, V. J. Orphan, Z. Yuan, S. Hu and G. W. TysonAnaerobic methane oxidation coupled to manganese reduction by members of the MethanoperedenaceaeThe ISME Journal14(4) 1030–41
202010.1016/j.cub.2020.06.011Leopold, D. R. and P. E. BusbyHost Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and FunctionCurrent Biology30(16) 3260–6.e5
202010.1128/mBio.00957-20Lemmer, K. C., F. Alberge, K. S. Myers, A. C. Dohnalkova, R. E. Schaub, J. D. Lenz, S. Imam, J. P. Dillard, D. R. Noguera and T. J. DonohueThe NtrYX Two-Component System Regulates the Bacterial Cell EnvelopemBio11(3)
202010.1074/jbc.RA120.013697Lemke, R. A. S., S. M. Olson, K. Morse, S. D. Karlen, A. Higbee, E. T. Beebe, J. Ralph, J. J. Coon, B. G. Fox and T. J. DonohueA bacterial biosynthetic pathway for methylated furan fatty acidsJournal of Biological Chemistry295(29) 9786–801
202010.1038/s41561-020-0612-3Lehmann, J., C. M. Hansel, C. Kaiser, M. Kleber, K. Maher, S. Manzoni, N. Nunan, M. Reichstein, J. P. Schimel, M. S. Torn, W. R. Wieder and I. Kögel-KnabnerPersistence of soil organic carbon caused by functional complexityNature Geoscience13(8) 529-534
202010.1007/s00792-019-01116-5Lee, L. L., J. R. Crosby, G. M. Rubinstein, T. Laemthong, R. G. Bing, C. T. Straub, M. W. W. Adams and R. M. KellyThe biology and biotechnology of the genus Caldicellulosiruptor: recent developments in ‘Caldi World’Extremophiles24(1)
202010.1016/j.csbj.2020.05.023Lee, J. Y., N. C. Sadler, R. G. Egbert, C. R. Anderton, K. S. Hofmockel, J. K. Jansson and H. S. SongDeep learning predicts microbial interactions from self-organized spatiotemporal patternsComputational and Structural Biotechnology Journal18 1259–69
202010.1016/j.copbio.2019.12.017Lee, J. W. and C. T. TrinhTowards renewable flavors, fragrances, and beyondCurrent Opinion in Biotechnology61 168–80
202010.1016/j.ymben.2020.10.003Lee, J. W., S. Kwak, J. J. Liu, S. Yu, E. J. Yun, D. H. Kim, C. Liu, K. H. Kim and Y. S. JinEnhanced 2'-Fucosyllactose production by engineered Saccharomyces cerevisiae using xylose as a co-substrateMetabolic Engineering62 322–9
202010.1016/j.ifacol.2020.12.542Lee, J., J. Wang, J. Flores-Cerrillo and Q. P. HeImproving featured-based soft sensing through feature selectionIFAC-PapersOnLine53 11338-11343
202010.1021/acs.iecr.9b06049Lee, J., J. Flores-Cerrillo, J. Wang and Q. P. HeConsistency-Enhanced Evolution for Variable Selection Can Identify Key Chemical Information from Spectroscopic DataIndustrial & Engineering Chemistry Research59(8) 3446–57
202010.1038/s41467-020-18045-zLark, T. J., S. A. Spawn, M. Bougie and H. K. GibbsCropland expansion in the United States produces marginal yields at high costs to wildlifeNature Communications11(1) 4295
202010.1016/j.landusepol.2020.104727Lark, T. J.Protecting our prairies: Research and policy actions for conserving America's grasslandsLand Use Policy97
202010.1364/AO.384674Larimer, C. J., E. H. Denis, J. D. Suter and J. J. MoranOptical coherence tomography imaging of plant root growth in soilApplied Optics59(8) 2474–81
202010.15389/agrobiology.2020.4.816engLaptev, G. Y.Genomic and Phenotypical Potential of Antimicrobial Activity of a Bacillus Strain Bacillus megaterium _-4801Sel'skokhozyaistvennaya Biologiya [Agricultural Biology]55(4) 816–29
202010.1371/journal.pgen.1008680Langdon, Q. K., D. Peris, J. I. Eizaguirre, D. A. Opulente, K. V. Buh, K. Sylvester, M. Jarzyna, M. E. Rodríguez, C. A. Lopes, D. Libkind and C. Todd HittingerPostglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybridsPLoS Genetics16(4)
202010.1016/j.mec.2020.e00145Lang, X., P. B. Besada-Lombana, M. Li, N. A. Da Silva and I. WheeldonDeveloping a broad-range promoter set for metabolic engineering in the thermotolerant yeast Kluyveromyces marxianusMetabolic Engineering Communications11 e00145
202010.1002/bit.27202Lane, S., Y. Zhang, E. J. Yun, L. Ziolkowski, G. Zhang, Y. S. Jin and J. L. AvalosXylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiaeBiotechnology and Bioengineering117(2) 372–81
202010.1021/acs.energyfuels.0c03131Landucci, L., R. A. Smith, S. Liu, S. D. Karlen and J. RalphEudicot Nutshells: Cell-Wall Composition and Biofuel Feedstock PotentialEnergy & Fuels34(12) 16274–83
202010.3390/life10110299Lacerda, M. P., E. J. Oh and C. EckertThe Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of BiofuelsLife10(11)
202010.5194/gmd-13-4413-2020Kyker-Snowman, E., W. R. Wieder, S. D. Frey and A. S. GrandyStoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1.0)Geoscientific Model Development13(9) 4413–34
202010.1002/biot.201900173Kwak, S., E. J. Yun, S. Lane, E. J. Oh, K. H. Kim and Y. S. JinRedirection of the Glycolytic Flux Enhances Isoprenoid Production in Saccharomyces cerevisiaeBiotechnology Journal15(2) e1900173
202010.1371/journal.pone.0226235Kurumbang, N. P., J. M. Vera, A. S. Hebert, J. J. Coon and R. LandickHeterologous expression of a glycosyl hydrolase and cellular reprogramming enable Zymomonas mobilis growth on cellobiosePLoS One15(8) e0226235
202010.1021/acschembio.0c00055Kuru, E., R. M. Määttälä, K. Noguera, D. A. Stork, K. Narasimhan, J. Rittichier, D. Wiegand and G. M. ChurchRelease factor inhibiting antimicrobial peptides improve nonstandard amino acid incorporation in wild-type bacterial cellsACS Chemical Biology15(7) 1852-1861
202010.3390/microorganisms8071002Kulyashov, M., S. E. Peltek and I. R. AkberdinA Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianusMicroorganisms8(7)
202010.1016/j.ymben.2020.06.004Krüger, A., A. P. Mueller, G. A. Rybnicky, N. L. Engle, Z. K. Yang, T. J. Tschaplinski, S. D. Simpson, M. Köpke and M. C. JewettDevelopment of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathwaysMetabolic Engineering62 95-105
202010.1111/ejss.13001Kravchenko, A., A. Guber, A. Gunina, M. Dippold and Y. KuzyakovPore_scale view of microbial turnover: Combining 14 C imaging, _CT and zymography after adding soluble carbon to soil pores of specific sizesEuropean Journal of Soil Science72(2) 593–607
202010.1016/j.copbio.2020.02.017Köpke, M. and S. D. SimpsonPollution to products: recycling of ‘above ground’ carbon by gas fermentationCurrent Opinion in Biotechnology65 180-189
202010.1104/pp.20.00547Kong, Q., S. K. Singh, J. J. Mantyla, S. Pattanaik, L. Guo, L. Yuan, C. Benning and W. MaTeosinte branched1/cycloidea/ proliferating cell factor4 interacts with wrinkled1 to mediate seed oil biosynthesisPlant Physiology184(2) 658-665
202010.1016/j.compchemeng.2019.106650Kong, L. and C. T. MaraveliasExpanding the scope of distillation network synthesis using superstructure-based methodsComputers and Chemical Engineering133
202010.1074/jbc.RA119.011239Koendjbiharie, J. G., S. Hon, M. Pabst, R. Hooftman, D. M. Stevenson, J. Cui, D. Amador-Noguez, L. R. Lynd, D. G. Olson and R. van KranenburgThe pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolaseJournal of Biological Chemistry295(7) 1867–78
202010.1111/tpj.14940Ko, D. K. and F. BrandizziNetwork-based approaches for understanding gene regulation and function in plantsThe Plant Journal104(2) 302–17
202010.1002/cssc.202001238Klinger, G. E., Y. Zhou, J. A. Foote, A. M. Wester, Y. Cui, M. Alherech, S. S. Stahl, J. E. Jackson and E. L. HeggNucleophilic Thiols Reductively Cleave Ether Linkages in Lignin Model Polymers and LigninChemSusChem13(17) 4394–9
202010.1111/tpj.14897Kim, S. Y., D. J. Stessman, D. A. Wright, M. H. Spalding, S. C. Huber and D. R. OrtArabidopsis plants expressing only the redox-regulated Rca-_ isoform have constrained photosynthesis and plant growthThe Plant Journal103(6) 2250–62
202010.1111/gcbb.12768Kim, S. Y., R. A. Slattery and D. R. OrtA role for differential Rubisco activase isoform expression in C4 bioenergy grasses at high temperatureGCB Bioenergy13(1) 211–23
202010.1073/pnas.2007245117Kim, S. J., B. Chandrasekar, A. C. Rea, L. Danhof, S. Zemelis-Durfee, N. Thrower, Z. S. Shepard, M. Pauly, F. Brandizzi and K. KeegstraThe synthesis of xyloglucan, an abundant plant cell wall polysaccharide, requires CSLC functionProceedings of the National Academy of Sciences of the United States of America117(33) 20316–24
202010.1021/acs.est.0c01097Kim, S., X. Zhang, A. D. Reddy, B. E. Dale, K. D. Thelen, C. D. Jones, R. C. Izaurralde, T. Runge and C. MaraveliasCarbon-Negative Biofuel ProductionEnvironmental Science & Technology54(17) 10797–807
202010.1016/j.geoderma.2020.114506Kim, K., A. Guber, M. Rivers and A. KravchenkoContribution of decomposing plant roots to N2O emissions by water absorptionGeoderma375
202010.1021/acssuschemeng.9b06389Kim, H., Q. Z. Li, S. D. Karlen, R. A. Smith, R. Shi, J. Liu, C. M. Yang, S. Tunlaya-Anukit, J. P. Wang, H. M. Chang, R. R. Sederoff, J. Ralph and V. L. ChiangMonolignol Benzoates Incorporate into the Lignin of Transgenic Populus trichocarpa Depleted in C3H and C4HACS Sustainable Chemistry & Engineering8(9) 3644–54
202010.1007/s12155-020-10149-0Khanna, M., W. W. Wang and M. C. WangAssessing the Additional Carbon Savings with BiofuelBioEnergy Research13(4) 1082–94
202010.1002/was.000400041Khalid, M., M. J. Doktycz and S. T. RettererNano-enabled chemical imagingWiley Imaging and Microscopy Journal
202010.7554/eLife.52786Khakhar, A., C. G. Starker, J. C. Chamness, N. Lee, S. Stokke, C. Wang, R. Swanson, F. Rizvi, T. Imaizumi and D. F. VoytasBuilding customizable auto-luminescent luciferase-based reporters in plantseLife9
202010.3389/fmicb.2020.570770Khadempour, L., H. Fan, K. Keefover-Ring, C. Carlos-Shanley, N. S. Nagamoto, M. A. Dam, M. T. Pupo and C. R. CurrieMetagenomics Reveals Diet-Specific Specialization of Bacterial Communities in Fungus Gardens of Grass- and Dicot-Cutter AntsFrontiers in Microbiology11
202010.1080/07060661.2019.1626910Kerio, S., H. A. Daniels, M. Gomez-Gallego, J. F. Tabima, R. R. Lenz, K. L. Sondreli, N. J. Grunwald, N. Williams, R. Mcdougal and J. M. LeBoldusFrom genomes to forest management - tackling invasive Phytophthora species in the era of genomicsCanadian Journal of Plant Pathology42(1) 1–29
202010.1021/acs.est.0c01676Kent, J., M. D. Hartman, D. K. Lee and T. HudiburgSimulated Biomass Sorghum GHG Reduction Potential is Similar to MaizeEnvironmental Science & Technology54(19) 12456–66
202010.1128/mBio.00569-20Kempher, M. L., X. Tao, R. Song, B. Wu, D. A. Stahl, J. D. Wall, A. P. Arkin, A. Zhou and J. ZhouEffects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated TemperaturemBio11(4)
202010.1002/pld3.235Kebrom, T. H., B. A. McKinley and J. E. MulletShade signals alter the expression of circadian clock genes in newly-formed bioenergy sorghum internodesPlant Direct4(6)
202010.1016/j.mec.2019.e00114Kay, J. E. and M. C. JewettA cell-free system for production of 2,3-butanediol is robust to growth-toxic compoundsMetabolic Engineering Communications10 e00114
202010.1111/gcbb.12777Kasanke, C. P., Q. Zhao, S. Bell, A. M. Thompson and K. S. HofmockelCan switchgrass increase carbon accrual in marginal soils? The importance of site selectionGCB Bioenergy13(2) 320–35
202010.1002/cssc.201903345Karlen, S. D., P. Fasahati, M. Mazaheri, J. Serate, R. A. Smith, et al.Assessing the Viability of Recovery of Hydroxycinnamic Acids from Lignocellulosic Biorefinery Alkaline Pretreatment Waste StreamsChemSusChem13(8) 2012–24
202010.1093/SYNBIO/YSAA019Karim, A. S., F. Liew, S. Garg, B. Vögeli, B. J. Rasor, A. Gonnot, M. Pavan, A. Juminaga, S. D. Simpson, M. Köpke and M. C. JewettModular cell-free expression plasmids to accelerate biological design in cellsSynthetic Biology5(1)
202010.1038/s41589-020-0559-0Karim, A. S., Q. M. Dudley, A. Juminaga, Y. Yuan, S. A. Crowe, et al.In vitro prototyping and rapid optimization of biosynthetic enzymes for cell designNature Chemical Biology16(8) 912-919
202010.1007/s12155-019-10066-xKar, S., T. Y. Weng, T. Nakashima, A. Villanueva-Morales, J. R. Stewart, E. J. Sacks, Y. Terajima and T. YamadaField Performance of Saccharum x Miscanthus Intergeneric Hybrids (Miscanes) Under Cool Climatic Conditions of Northern JapanBioEnergy Research13(1) 132–46
202010.1111/pce.13721Kankanala, P., P. Jones, R. S. Nandety, D. A. Jacobson and K. S. MysorePlasticity of Phymatotrichopsis omnivora infection strategies is dependent on host and nonhost plant responsesPlant, Cell & Environment43(4) 1084–101
202010.1111/1462-2920.14959Kang, H., X. Chen, M. Kemppainen, A. G. Pardo, C. Veneault-Fourrey, A. Kohler and F. M. MartinThe small secreted effector protein MiSSP7.6 of Laccaria bicolor is required for the establishment of ectomycorrhizal symbiosisEnvironmental Microbiology22(4) 1435–46
202010.34133/2020/7914051Kalluri, U. C., X. Yang and S. D. WullschlegerPlant Biosystems Design for a Carbon-Neutral BioeconomyBioDesign Research2020
202010.7717/peerj.9942Jung, H. and C. D. MeileNumerical investigation of microbial quorum sensing under various flow conditionsPeerJ8 e9942
202010.3390/en13215805Juneja, A., D. Kumar, V. K. Singh, Yadvika and V. SinghChemical Free Two-Step Hydrothermal Pretreatment to Improve Sugar Yields from Energy CaneEnergies13(21)
202010.1039/c9cp05339eJu, Z., W. Xiao, X. Yao, X. Tan, B. A. Simmons, K. L. Sale and N. SunTheoretical study on the microscopic mechanism of lignin solubilization in Keggin-type polyoxometalate ionic liquidsPhysical Chemistry Chemical Physics22(5) 2878–86
202010.1007/978-1-0716-0195-2_15Jones, P., D. Weighill, M. Shah, S. Climer, J. Schmutz, A. Sreedasyam, G. Tuskan and D. JacobsonNetwork Modeling of Complex Data SetsMetabolic Pathway Engineering2096 197–215
202010.1016/j.rser.2019.109513Johansson, R., S. Meyer, J. Whistance, W. Thompson and D. DebnathGreenhouse gas emission reduction and cost from the United States biofuels mandateRenewable and Sustainable Energy Reviews119
202010.1007/s00253-020-10663-3Jiang, L., T. Li, J. Jenkins, Y. Hu, C. L. Brueck, H. Pei and M. J. BetenbaughEvidence for a mutualistic relationship between the cyanobacteria Nostoc and fungi Aspergilli in different environmentsApplied Microbiology and Biotechnology104(14) 6413–26
202010.5194/hess-24-1251-2020Jiang, C., K. Guan, M. Pan, Y. Ryu, B. Peng and S. WangBESS-STAIR: a framework to estimate daily, 30_m, and all-weather crop evapotranspiration using multi-source satellite data for the US Corn BeltHydrology and Earth System Sciences24(3) 1251–73
202010.1038/s41467-020-19428-yJian, S., J. Li, G. Wang, L. A. Kluber, C. W. Schadt, J. Liang and M. A. MayesMulti-year incubation experiments boost confidence in model projections of long-term soil carbon dynamicsNature Communications11(1) 5864
202010.3390/en13226022Jia, Y. Y., D. Kumar, J. K. Winkler-Moser, B. Dien and V. SinghRecoveries of Oil and Hydrolyzed Sugars from Corn Germ Meal by Hydrothermal Pretreatment: A Model Feedstock for Lipid-Producing Energy CropsEnergies13(22)
202010.1007/s00248-019-01406-7Jha, P. N., A. B. Gomaa, Y. G. Yanni, A. Y. El-Saadany, T. M. Stedtfeld, R. D. Stedtfeld, S. Gantner, B. Chai, J. Cole, S. A. Hashsham and F. B. DazzoAlterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium BiofertilizerMicrobial Ecology79(2) 367–82
202010.1128/MRA.00229-20Jennings, E. C., M. W. Korthauer and J. B. BenoitGenome Sequence of a Blattabacterium Strain Isolated from the Viviparous Cockroach, Diploptera punctataMicrobiology Resource Announcements9(35)
202010.1038/s41579-019-0265-7Jansson, J. K. and K. S. HofmockelSoil microbiomes and climate changeNature Reviews Microbiology18(1) 35–46
202010.1146/annurev-micro-022020-051835James, T. Y., J. E. Stajich, C. T. Hittinger and A. RokasToward a Fully Resolved Fungal Tree of LifeAnnual Review of Microbiology74 291–313
202010.1111/nph.16744Jallet, D., D. Xing, A. Hughes, M. Moosburner, M. P. Simmons, A. E. Allen and G. PeersMitochondrial fatty acid _-oxidation is required for storage-lipid catabolism in a marine diatomNew Phytologist228(3) 946–58
202010.1016/j.synbio.2020.01.004Jakociunas, T., A. K. Klitgaard, E. E. Kontou, J. B. Nielsen, E. Thomsen, et al.Programmable polyketide biosynthesis platform for production of aromatic compounds in yeastSynthetic and Systems Biotechnology5(1) 11–8
202010.1038/s41598-020-66916-8Jakes, J. E., S. L. Zelinka, C. G. Hunt, P. Ciesielski, C. R. Frihart, D. Yelle, L. Passarini, S. C. Gleber, D. Vine and S. VogtMeasurement of moisture-dependent ion diffusion constants in wood cell wall layers using time-lapse micro X-ray fluorescence microscopyScientific Reports10(1)
202010.1021/bk-2020-1374.ch013Jagtap, S. S., A. A. Bedekar and C. V. RaoQuorum sensing in yeastQuorum Sensing: Microbial Rules of LifeChapter 13 235–50
202010.1128/mSystems.00736-19Jacobson, T. B., T. K. Korosh, D. M. Stevenson, C. Foster, C. Maranas, D. G. Olson, L. R. Lynd and D. Amador-NoguezIn Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H TracersmSystems5(2)
202010.1002/eap.2047Jach-Smith, L. C. and R. D. JacksonInorganic N addition replaces N supplied to switchgrass (Panicum virgatum) by arbuscular mycorrhizal fungiEcological Applications30(2) e02047
202010.1007/978-3-030-30659-5_4Ispas, C.Decision-making training of teachers for inclusive schoolStudies in Systems, Decision and Control247 79-89
202010.1098/rstb.2019.0242Isobe, K., N. J. Bouskill, E. L. Brodie, E. A. Sudderth and J. B. H. MartinyPhylogenetic conservation of soil bacterial responses to simulated global changesPhilosophical Transactions of the Royal Society B: Biological Sciences375(1798)
202010.1016/j.semcdb.2020.02.014Ischebeck, T., H. E. Krawczyk, R. T. Mullen, J. M. Dyer and K. D. ChapmanLipid droplets in plants and algae: Distribution, formation, turnover and functionSeminars in Cell & Developmental Biology108 82–93
202010.1016/j.mec.2019.e00119Incha, M. R., M. G. Thompson, J. M. Blake-Hedges, Y. Liu, A. N. Pearson, M. Schmidt, J. W. Gin, C. J. Petzold, A. M. Deutschbauer and J. D. KeaslingLeveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putidaMetabolic Engineering Communications10 e00119
202010.1002/bit.27544Hwang, J., A. Hari, R. Cheng, J. G. Gardner and D. LoboKinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of _-glucosidase function in xCellvibrio japonicusBiotechnology and Bioengineering117(12) 3876–90
202010.1016/j.scitotenv.2020.139379Hussain, M. Z., G. P. Robertson, B. Basso and S. K. HamiltonLeaching losses of dissolved organic carbon and nitrogen from agricultural soils in the upper US MidwestScience of the Total Environment734 139379
202010.1002/bbb.2087Huntington, T., X. G. Cui, U. Mishra and C. D. ScownMachine learning to predict biomass sorghum yields under future climate scenariosBiofuels, Bioproducts and Biorefining14(3) 566–77
202010.1038/s41586-020-2406-6Huang, X., B. Wang, Y. Wang, G. Jiang, J. Feng and H. ZhaoPhotoenzymatic enantioselective intermolecular radical hydroalkylationNature584(7819) 69–74
202010.1016/j.cbpa.2020.02.004Huang, X., M. Cao and H. ZhaoIntegrating biocatalysis with chemocatalysis for selective transformationsCurrent Opinion in Chemical Biology55 161–70
202010.1007/s11104-020-04568-3Huang, W. J., S. Gilbert, A. Poulev, K. Acosta, S. Lebeis, C. L. Long and E. LamHost-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystemsPlant and Soil452(44928) 379–95
202010.1016/j.isci.2019.100751Huang, K., P. Fasahati and C. T. MaraveliasSystem-Level Analysis of Lignin Valorization in Lignocellulosic BiorefineriesiScience23(1) 100751
202010.1128/MRA.00676-20Hovorukha, V., A. Bhattacharyya, O. Iungin, H. Tashyreva, V. Romanovska, et al.Draft Genome Sequences of Six Strains Isolated from the Rhizosphere of Wheat Grown in Cadmium-Contaminated SoilMicrobiology Resource Announcements9(34)
202010.3389/fmicb.2020.00796Hough, M., A. McClure, B. Bolduc, E. Dorrepaal, S. Saleska, V. Klepac-Ceraj and V. RichBiotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw GradientFrontiers in Microbiology11 796
202010.1021/acs.iecr.9b05873Hossain, A., M. S. Rahaman, D. Lee, T. K. Phung, C. G. Canlas, B. A. Simmons, S. Renneckar, W. Reynolds, A. George, S. Tulaphol and N. SathitsuksanohEnhanced Softwood Cellulose Accessibility by H3PO4 Pretreatment: High Sugar Yield without Compromising Lignin IntegrityIndustrial & Engineering Chemistry Research59(2) 1010–24
202010.1038/s41587-020-0584-2Hossain, A., E. Lopez, S. M. Halper, D. P. Cetnar, A. C. Reis, D. Strickland, E. Klavins and H. M. SalisAutomated design of thousands of nonrepetitive parts for engineering stable genetic systemsNature Biotechnology38(12) 1466–75
202010.7554/eLife.52063Hose, J., L. E. Escalante, K. J. Clowers, H. A. Dutcher, D. Robinson, V. Bouriakov, J. J. Coon, E. Shishkova and A. P. GaschThe genetic basis of aneuploidy tolerance in wild yeasteLife9
202010.1038/s41598-020-73715-8Horák, A., A. E. Allen and M. OborníkCommon origin of ornithine–urea cycle in opisthokonts and stramenopilesScientific Reports10(1)
202010.1007/978-1-0716-0195-2_3Hon, S., L. Tian, T. Zheng, J. Cui, L. R. Lynd and D. G. OlsonMethods for Metabolic Engineering of Thermoanaerobacterium saccharolyticumMetabolic Pathway Engineering2096 21–43
202010.1128/AEM.01795-20Holwerda, E. K., J. Zhou, S. Hon, D. M. Stevenson, D. Amador-Noguez, L. R. Lynd and J. P. van DijkenMetabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticumApplied and Environmental Microbiology86(23)
202010.1186/s13068-020-01680-5Holwerda, E. K., D. G. Olson, N. M. Ruppertsberger, D. M. Stevenson, S. J. L. Murphy, M. I. Maloney, A. A. Lanahan, D. Amador-Noguez and L. R. LyndMetabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol productionBiotechnology for Biofuels13 40
202010.1099/ijsem.0.003798Hirose, S., M. Tank, E. Hara, H. Tamaki, K. Mori, S. Takaichi, S. Haruta and S. HanadaAquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class BetaproteobacteriaInternational Journal of Systematic and Evolutionary Microbiology70(1) 596–603
202010.1099/mgen.0.000399Hillman, E. T., A. J. Kozik, C. A. Hooker, J. L. Burnett, Y. Heo, V. A. Kiesel, C. J. Nevins, J. Oshiro, M. M. Robins, R. D. Thakkar, S. T. Wu and S. R. LindemannComparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among speciesMicrobial Genomics6(7)
202010.1126/sciadv.aba1269Hill, N. C., J. W. Tay, S. Altus, D. M. Bortz and J. C. CameronLife cycle of a cyanobacterial carboxysomeScience Advances6(19) eaba1269
202010.1042/BST20190119Hidalgo-Cantabrana, C. and R. BarrangouCharacterization and applications of Type I CRISPR-Cas systemsBiochemical Society Transactions48(1) 15–23
202010.1073/pnas.2010087117Henry, K. K., W. Ross, K. S. Myers, K. C. Lemmer, J. M. Vera, R. Landick, T. J. Donohue and R. L. GourseA majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activationProceedings of the National Academy of Sciences of the United States of America117(47) 29658–68
202010.1146/annurev-arplant-081519-040100Hennacy, J. H. and M. C. JonikasProspects for Engineering Biophysical CO2 Concentrating Mechanisms into Land Plants to Enhance YieldsAnnual Review of Plant Biology71 461–85
202010.1016/j.coche.2020.05.008Hendry, J. I., H. V. Dinh, C. Foster, S. Gopalakrishnan, L. Wang and C. D. MaranasMetabolic flux analysis reaching genome wide coverage: lessons learned and future perspectivesCurrent Opinion in Chemical Engineering30 17–25
202010.1016/j.agee.2019.106780Helms, J. A., S. E. Ijelu, B. D. Wills, D. A. Landis and N. M. HaddadAnt biodiversity and ecosystem services in bioenergy landscapesAgriculture, Ecosystems & Environment290
202010.1016/j.envint.2020.106068He, Z., Y. Deng, M. Xu, J. Li, J. Liang, et al.Microbial functional genes commonly respond to elevated carbon dioxideEnvironment International144
202010.3390/pr8080951He, Q. P. and J. WangApplication of Systems Engineering Principles and Techniques in Biological Big Data Analytics: A ReviewProcesses8(8)
202010.34133/2020/9350905Hassan, M. M., G. Yuan, J.-G. Chen, G. A. Tuskan and X. YangPrime Editing Technology and Its Prospects for Future Applications in Plant Biology ResearchBioDesign Research2020
202010.1002/ecs2.3280Hartman, M. D., W. J. Parton, J. D. Derner, D. K. Schulte, W. K. Smith, D. E. Peck, K. A. Day, S. J. Del Grosso, S. Lutz, B. A. Fuchs, M. Chen and W. GaoSeasonal grassland productivity forecast for the U.S. Great Plains using Grass_CastEcosphere11(11)
202010.21203/rs.3.rs-23478/v1Harman-Ware, A. E., D. Macaya-Sans, C. R. Abeyratne, C. Doeppke, K. Haiby, G. A. Tuskan, B. Stanton, S. P. DiFazio and M. F. DavisAccurate Determination of Genotypic Variance of Cell Wall Characteristics of a Populus trichocarpa Pedigree Using High-Throughput Pyrolysis-Molecular Beam Mass SpectrometryBiotechnology for Biofuels
202010.1002/pld3.268Harding, S. A., C. J. Frost and C. J. TsaiDefoliation-induced compensatory transpiration is compromised in SUT4-RNAi PopulusPlant Direct4(9) e00268
202010.1073/pnas.1821684116Hannon, J. R., L. R. Lynd, O. Andrade, P. T. Benavides, G. T. Beckham, et al.Technoeconomic and life-cycle analysis of single-step catalytic conversion of wet ethanol into fungible fuel blendstocksProceedings of the National Academy of Sciences of the United States of America117(23) 12576–83
202010.1021/acscatal.0c01498Han, X. T., H. Y. Sheng, C. Yu, T. W. Walker, G. W. Huber, J. S. Qiu and S. JinElectrocatalytic Oxidation of Glycerol to Formic Acid by CuCo2O4 Spinel Oxide Nanostructure CatalystsACS Catalysis10(12) 6741–52
202010.1021/acssynbio.9b00420Hammer, S. K., Y. Zhang and J. L. AvalosMitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in Saccharomyces cerevisiaeACS Synthetic Biology9(3) 546–55
202010.1093/gigascience/giaa093Hamilton, J. P., G. T. Godden, E. Lanier, W. W. Bhat, T. J. Kinser, B. Vaillancourt, H. Wang, J. C. Wood, J. Jiang, P. S. Soltis, D. E. Soltis, B. Hamberger and C. R. BuellGeneration of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americanaGigaScience9(9)
202010.1007/978-3-030-21001-4_4Hamberger, B., M. M. S. Yuen, E. Buschiazzo, C. Cullis, A. Yuen, C. Ritland, J. Bohlmann and B. HambergerAn Intact, But Dormant LTR Retrotransposon Defines a Moderately Sized Family in White Spruce (Picea glauca)The Spruce GenomeChapter 4 51–63
202010.1021/acssynbio.9b00460Halper, S. M., A. Hossain and H. M. SalisSynthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine LearningACS Synthetic Biology9(7) 1563–71
202010.1074/jbc.H120.015332Hallberg, Z. F. and M. E. TagaTaking the "me" out of meat: A new demethylation pathway dismantles a toxin's precursorJournal of Biological Chemistry295(34) 11982-11983
202010.1002/ecy.3113Hall, S. J., W. Huang, V. I. Timokhin and K. E. HammelLignin lags, leads, or limits the decomposition of litter and soil organic carbonEcology101(9)
202010.1038/s41467-020-15688-wHale, K. R. S., F. S. Valdovinos and N. D. MartinezMutualism increases diversity, stability, and function of multiplex networks that integrate pollinators into food websNature Communications11(1)
202010.1016/j.tree.2019.10.003Haan, N. L., Y. Zhang and D. A. LandisPredicting Landscape Configuration Effects on Agricultural Pest SuppressionTrends in Ecology & Evolution35(2) 175–86
202010.1016/j.biocon.2020.108492Haan, N. L. and D. A. LandisGrassland disturbance effects on first-instar monarch butterfly survival, floral resources, and flower-visiting insectsBiological Conservation243
202010.1038/s41467-020-18706-zGuo, X., Q. Gao, M. Yuan, G. Wang, X. Zhou, et al.Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warmingNature Communications11(1)
202010.1016/j.ymben.2020.05.009Grubbe, W. S., B. J. Rasor, A. Krüger, M. C. Jewett and A. S. KarimCell-free styrene biosynthesis at high titersMetabolic Engineering61 89-95
202010.1104/pp.19.01496Griffiths, M. and L. M. YorkTargeting Root Ion Uptake Kinetics to Increase Plant Productivity and Nutrient Use EfficiencyPlant Physiology182(4) 1854–68
202010.1186/s12866-020-01768-wGrettenberger, C. L., J. R. Havig and T. L. HamiltonMetabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage siteBMC Microbiology20(1) 119
202010.1128/mSystems.00224-20Gordon, G. C., J. C. Cameron, S. T. P. Gupta, M. D. Engstrom, J. L. Reed and B. F. PflegerGenome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002mSystems5(4)
202010.1016/j.ymben.2020.03.001Gopalakrishnan, S., S. Dash and C. MaranasK-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic dataMetabolic Engineering61 197–205
202010.1002/pro.3730Goodsell, D. S., C. Zardecki, L. Di Costanzo, J. M. Duarte, B. P. Hudson, I. Persikova, J. Segura, C. Shao, M. Voigt, J. D. Westbrook, J. Y. Young and S. K. BurleyRCSB Protein Data Bank: Enabling biomedical research and drug discoveryProtein Science29(1) 52–65
202010.1371/JOURNAL.PBIO.3000815Goodsell, D. S., M. Voigt, C. Zardecki and S. K. BurleyIntegrative illustration for coronavirus outreachPLoS Biology18(8)
202010.1016/j.tibs.2020.02.010Goodsell, D. S., A. J. Olson and S. ForliArt and Science of the Cellular MesoscaleTrends in Biochemical Sciences45(6) 472–83
202010.1038/s41388-020-01461-2Goodsell, D. S. and S. K. BurleyRCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case studyOncogene39(43) 6623-6632
202010.1089/cmb.2019.0326Gong, B. and E. PurdomMethCP: Differentially Methylated Region Detection with Change Point ModelsJournal of Computational Biology27(4) 458–71
202010.1093/database/baaa075Gomez-Cano, F., L. Carey, K. Lucas, T. García Navarrete, E. Mukundi, S. Lundback, D. Schnell and E. GrotewoldCamRegBase: A gene regulation database for the biofuel crop, Camelina sativaDatabase2020
202010.1002/csc2.20049Gomez, F. E., J. E. Mullet, A. H. Muliana, K. J. Niklas and W. L. RooneyThe genetic architecture of biomechanical traits in sorghumCrop Science60(1) 82–99
202010.1038/s41594-020-0403-yGlynn, C., M. R. Sawaya, P. Ge, M. Gallagher-Jones, C. W. Short, R. Bowman, M. Apostol, Z. H. Zhou, D. S. Eisenberg and J. A. RodriguezCryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant coreNature Structural and Molecular Biology27(5) 417-423
202010.1074/jbc.RA120.015328Glasgow, E. M., E. I. Kemna, C. A. Bingman, N. Ing, K. Deng, C. M. Bianchetti, T. E. Takasuka, T. R. Northen and B. G. FoxA structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysisJournal of Biological Chemistry295(51) 17752–69
202010.1016/j.synbio.2020.01.003Gilmore, S. P., S. P. Lillington, C. H. Haitjema, R. de Groot and M. A. O'MalleyDesigning chimeric enzymes inspired by fungal cellulosomesSynthetic and Systems Biotechnology5(1) 23–32
202010.1021/acs.est.9b07019Gelfand, I., S. K. Hamilton, A. N. Kravchenko, R. D. Jackson, K. D. Thelen and G. P. RobertsonEmpirical Evidence for the Potential Climate Benefits of Decarbonizing Light Vehicle Transport in the U.S. with Bioenergy from Purpose-Grown Biomass with and without BECCSEnvironmental Science & Technology54(5) 2961–74
202010.3389/fmicb.2020.587127Ge, X., M. P. Thorgersen, F. L. Poole, 2nd, A. M. Deutschbauer, J. M. Chandonia, P. S. Novichkov, S. Gushgari-Doyle, L. M. Lui, T. Nielsen, R. Chakraborty, P. D. Adams, A. P. Arkin, T. C. Hazen and M. W. W. AdamsCharacterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge ReservationFrontiers in Microbiology11 587127
202010.1128/MRA.01149-20Ge, X., M. P. Thorgersen, F. L. Poole, 2nd, A. M. Deutschbauer, J. M. Chandonia, P. S. Novichkov, P. D. Adams, A. P. Arkin, T. C. Hazen and M. W. W. AdamsDraft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated SedimentMicrobiology Resource Announcements9(44)
202010.1039/c9se00912dGaredew, M., D. Young-Farhat, S. Bhatia, P. Hao, J. E. Jackson and C. M. SaffronElectrocatalytic cleavage of lignin model dimers using ruthenium supported on activated carbon clothSustainable Energy and Fuels4(3) 1340-1350
202010.1021/acssynbio.9b00518Garcia, S. and C. T. TrinhHarnessing Natural Modularity of Metabolism with Goal Attainment Optimization to Design a Modular Chassis Cell for Production of Diverse ChemicalsACS Synthetic Biology9(7) 1665–81
202010.3389/fbioe.2020.00772Garcia, S., R. A. Thompson, R. J. Giannone, S. Dash, C. D. Maranas and C. T. TrinhDevelopment of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain DesignFrontiers in Bioengineering and Biotechnology8 772
202010.1128/AEM.01639-20Garcia, C. A., J. A. Narrett and J. G. GardnerTrehalose Degradation by Cellvibrio japonicus Exhibits No Functional Redundancy and Is Solely Dependent on the Tre37A EnzymeApplied and Environmental Microbiology86(22)
202010.1080/09670262.2020.1817569Gao, Y., J. Feng, J. Lv, Q. Liu, F. Nan, X. Liu, C.-J. Liu and S. XieEffects of nitrogen deficiency on the transcriptome of the oleaginous alga Parachlorella kessleri TYEuropean Journal of Phycology56(2) 203–15
202010.1073/pnas.2002780117Gao, Q., G. Wang, K. Xue, Y. Yang, J. Xie, H. Yu, S. Bai, F. Liu, Z. He, D. Ning, S. E. Hobbie, P. B. Reich and J. ZhouStimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland studyProceedings of the National Academy of Sciences of the United States of America117(52) 33317–24
202010.1371/journal.pone.0238327Gao, D., P. R. Barber, J. V. Chacko, M. A. Kader Sagar, C. T. Rueden, A. R. Grislis, M. C. Hiner and K. W. EliceiriFLIMJ: An open-source ImageJ toolkit for fluorescence lifetime image data analysisPLoS One15(12) e0238327
202010.1038/s41467-019-13913-9Gao, C., L. Montoya, L. Xu, M. Madera, J. Hollingsworth, E. Purdom, V. Singan, J. Vogel, R. B. Hutmacher, J. A. Dahlberg, D. Coleman-Derr, P. G. Lemaux and J. W. TaylorFungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamicsNature Communications11(1) 34
202010.1016/j.cbpa.2020.08.005Gambacorta, F. V., J. J. Dietrich, Q. Yan and B. F. PflegerRewiring yeast metabolism to synthesize products beyond ethanolCurrent Opinion in Chemical Biology59 182–92
202010.1073/pnas.1914422117Gallego-Giraldo, L., C. Liu, S. Pose-Albacete, S. Pattathil, A. G. Peralta, J. Young, J. Westpheling, M. G. Hahn, X. Rao, J. P. Knox, B. De Meester, W. Boerjan and R. A. DixonArabidopsis Dehiscence Zone Polygalacturonase 1 (ADPG1) releases latent defense signals in stems with reduced lignin contentProceedings of the National Academy of Sciences of the United States of America117(6) 3281–90
202010.1016/j.str.2020.09.005Gallagher-Jones, M. and J. A. RodriguezStructures from the mesophase: MicroEd targets crystals extracted from LCPStructure28(10) 1084-1086
202010.1107/S2052252520004030Gallagher-Jones, M., K. C. Bustillo, C. Ophus, L. S. Richards, J. Ciston, S. Lee, A. M. Minord and J. A. RodriguezAtomic structures determined from digitally defined nanocrystalline regionsIUCrJ7 490-499
202010.1039/d0gc03218bGalebach, P. H., J. K. Soeherman, E. Gilcher, A. M. Wittrig, J. Johnson, T. Fredriksen, C. R. Wang, M. P. Lanci, J. A. Dumesic and G. W. HuberProduction of renewable alcohols from maple wood using supercritical methanol hydrodeoxygenation in a semi-continuous flowthrough reactorGreen Chemistry22(23) 8462–77
202010.1002/cssc.202000002Gale, M., C. M. Cai and K. L. Gilliard-Abdul-AzizHeterogeneous Catalyst Design Principles for the Conversion of Lignin into High-Value Commodity Fuels and ChemicalsChemSusChem13(8) 1947–66
202010.1039/c9np00071bGalanie, S., D. Entwistle and J. LalondeEngineering biosynthetic enzymes for industrial natural product synthesisNatural Product Reports37(8) 1122–43
202010.1002/pld3.255Gaillard, M., C. Miao, J. C. Schnable and B. BenesVoxel carving-based 3D reconstruction of sorghum identifies genetic determinants of light interception efficiencyPlant Direct4(10) e00255
202010.1007/978-3-030-65414-6_21Gaillard, M., C. Miao, J. Schnable and B. BenesSorghum segmentation by skeleton extractionLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)12540 LNCS 296-311
202010.1080/15592294.2019.1666649Fu, K., G. Bonora and M. PellegriniInteractions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissuesEpigenetics15(3) 272–82
202010.1038/s41396-020-00737-5Fritts, R. K., J. T. Bird, M. G. Behringer, A. Lipzen, J. Martin, M. Lynch and J. B. McKinlayEnhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic communityISME Journal14(11) 2816-2828
202010.1146/annurev-phyto-010820-012740Friesen, M. L.Social Evolution and Cheating in Plant PathogensAnnual Review of Phytopathology58 55–75
202010.1038/s41598-020-64311-xFrausto, R. F., V. S. Swamy, G. S. L. Peh, P. M. Boere, E. M. Hanser, et al.Phenotypic and functional characterization of corneal endothelial cells during in vitro expansionScientific Reports10(1)
202010.1021/jasms.9b00059Frankfater, C., W. R. Henson, A. Juenger-Leif, M. Foston, T. S. Moon, J. Turk, J. L. Kao, A. Haas and F. F. HsuStructural Determination of a New Peptidolipid Family from Rhodococcus opacus and the Pathogen Rhodococcus equi by Multiple Stage Mass SpectrometryJournal of the American Society for Mass Spectrometry31(3) 611–23
202010.1097/01.CCN.0000694084.86350.93Franges, E. Z.Solving the puzzle of Brown-Séquard syndromeNursing Critical Care15(5) 18-23
202010.1128/mBio.02146-20Francoeur, C. B., L. Khadempour, R. D. Moreira-Soto, K. Gotting, A. J. Book, A. A. Pinto-Tomás, K. Keefover-Ring and C. R. CurrieBacteria contribute to plant secondary compound degradation in a generalist herbivore systemmBio11(5) 44944
202010.1111/pce.13887Folk, R. A., C. M. Siniscalchi and D. E. SoltisAngiosperms at the edge: Extremity, diversity, and phylogenyPlant, Cell & Environment43(12) 2871–93
202010.1146/annurev-micro-022620-014327Fitzpatrick, C. R., I. Salas-González, J. M. Conway, O. M. Finkel, S. Gilbert, D. Russ, P. J. P. L. Teixeira and J. L. DanglThe Plant Microbiome: From Ecology to Reductionism and beyondAnnual Review of Microbiology74 81-100
202010.1029/2019WR026058Fisher, J. B., B. Lee, A. J. Purdy, G. H. Halverson, M. B. Dohlen, et al.ECOSTRESS: NASA's Next Generation Mission to Measure Evapotranspiration From the International Space StationWater Resources Research56(4)
202010.1038/s41586-020-2778-7Finkel, O. M., I. Salas-González, G. Castrillo, J. M. Conway, T. F. Law, P. J. P. L. Teixeira, E. D. Wilson, C. R. Fitzpatrick, C. D. Jones and J. L. DanglA single bacterial genus maintains root growth in a complex microbiomeNature587(7832) 103-108
202010.1073/pnas.1920877117Field, J. L., T. L. Richard, E. A. H. Smithwick, H. Cai, M. S. Laser, D. S. LeBauer, S. P. Long, K. Paustian, Z. Qin, J. J. Sheehan, P. Smith, M. Q. Wang and L. R. LyndRobust paths to net greenhouse gas mitigation and negative emissions via advanced biofuelsProceedings of the National Academy of Sciences of the United States of America117(36) 21968–77
202010.5334/DSJ-2020-025Feng, Z., N. Verdiguel, L. Di Costanzo, D. S. Goodsell, J. D. Westbrook, S. K. Burley and C. ZardeckiImpact of the protein data bank across scientific disciplinesData Science Journal19(1) 44940
202010.1002/btpr.3008Fatma, Z., J. C. Schultz and H. ZhaoRecent advances in domesticating non-model microorganismsBiotechnology Progress36(5) e3008
202010.1038/s41598-020-77375-6Fatima, M., X. Zhang, J. Lin, P. Zhou, D. Zhou and R. MingExpression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneumScientific Reports10(1)
202010.1021/acsomega.9b02849Farahi, R. H., A. L. Lereu, A. M. Charrier, U. C. Kalluri, B. H. Davison and A. PassianNanomechanics and Raman Spectroscopy of in Situ Native Carbohydrate Storage Granules for Enhancing Starch Quality and Lignocellulosic Biomass ProductionACS Omega5(6) 2594–602
202010.1021/acssuschemeng.0c02351Fang, Z., S. Nikafshar, E. L. Hegg and M. NejadBiobased Divanillin As a Precursor for Formulating Biobased Epoxy ResinACS Sustainable Chemistry & Engineering8(24) 9095–103
202010.7554/eLife.56717Fan, P., P. Wang, Y. R. Lou, B. J. Leong, B. M. Moore, C. A. Schenck, R. Combs, P. Cao, F. Brandizzi, S. H. Shiu and R. L. LastEvolution of a plant gene cluster in Solanaceae and emergence of metabolic diversityeLife9
202010.1007/s00122-020-03612-1Fan, K. H., K. M. Devos and P. SchliekelmanStrategies for eQTL mapping in allopolyploid organismsTheoretical and Applied Genetics133(8) 2477-2497
202010.1186/s13068-020-01841-6Eugene, A., C. Lapierre and J. RalphImproved analysis of arabinoxylan-bound hydroxycinnamate conjugates in grass cell wallsBiotechnology for Biofuels13(1)
202010.1038/s41467-020-18630-2Espah Borujeni, A., J. Zhang, H. Doosthosseini, A. A. K. Nielsen and C. A. VoigtGenetic circuit characterization by inferring RNA polymerase movement and ribosome usageNature Communications11(1) 5001
202010.1016/j.mec.2019.e00115Eng, T., Y. Sasaki, R. A. Herbert, A. Lau, J. Trinh, Y. Chen, M. Mirsiaghi, C. J. Petzold and A. MukhopadhyayProduction of tetra-methylpyrazine using engineered Corynebacterium glutamicumMetabolic Engineering Communications10 e00115
202010.1111/tpj.14696Ellsworth, P. Z., M. J. Feldman, I. Baxter and A. B. CousinsA genetic link between leaf carbon isotope composition and whole-plant water use efficiency in the C4 grass SetariaPlant Journal102(6) 1234-1248
202010.1186/s12864-020-6615-zEllis, J. C.P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)BMC Genomics21(1) 334
202010.1021/acssuschemeng.0c02880Elder, T., J. C. Del Río, J. Ralph, J. Rencoret, H. Kim, G. T. Beckham and M. F. CrowleyCoupling and Reactions of Lignols and New Lignin Monomers: A Density Functional Theory StudyACS Sustainable Chemistry and Engineering8(30) 11033-11045
202010.1021/acssynbio.9b00402Eiben, C. B., T. Tian, M. G. Thompson, D. Mendez-Perez, N. Kaplan, G. Goyal, J. Chiniquy, N. J. Hillson, T. S. Lee and J. D. KeaslingAdenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel IsopentanolACS Synthetic Biology9(3) 468–74
202010.1094/pbiomes-02-20-0019-rEckshtain-Levi, N., S. L. Harris, R. Q. Roscios and E. A. ShankBacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thalianaPhytobiomes Journal4(4) 303–13
202010.1016/j.ymben.2020.05.006Dudley, Q. M., A. S. Karim, C. J. Nash and M. C. JewettIn vitro prototyping of limonene biosynthesis using cell-free protein synthesisMetabolic Engineering61 251–60
202010.3389/fmicb.2020.01528Dove, N. C., T. J. Rogers, C. Leppanen, D. Simberloff, J. A. Fordyce, V. A. Brown, A. V. LeBude, T. G. Ranney and M. A. CreggerMicrobiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid InfestationFrontiers in Microbiology11 1528
202010.1038/s41396-019-0557-yDoud, D. F. R., R. M. Bowers, F. Schulz, M. De Raad, K. Deng, et al.Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphereThe ISME Journal14(3) 659–75
202010.1038/s41467-020-14981-yDong, O. X., S. Yu, R. Jain, N. Zhang, P. Q. Duong, C. Butler, Y. Li, A. Lipzen, J. A. Martin, K. W. Barry, J. Schmutz, L. Tian and P. C. RonaldMarker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9Nature Communications11(1) 1178
202010.1038/s41467-020-17502-zDomeignoz-Horta, L. A., G. Pold, X. A. Liu, S. D. Frey, J. M. Melillo and K. M. DeAngelisMicrobial diversity drives carbon use efficiency in a model soilNature Communications11(1) 3684
202010.1128/AEM.00880-20Dirks, A. C. and R. D. JacksonCommunity Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for BioenergyApplied and Environmental Microbiology86(19)
202010.3390/insects11040250Dharampal, P. S., L. Diaz-Garcia, M. A. B. Haase, J. Zalapa, C. R. Currie, C. T. Hittinger and S. A. SteffanMicrobial Diversity Associated with the Pollen Stores of Captive-Bred Bumble Bee ColoniesInsects11(4)
202010.1073/pnas.1917110117Demir, B., T. Kropp, K. R. Rivera-Dones, E. B. Gilcher, G. W. Huber, M. Mavrikakis and J. A. DumesicA self-adjusting platinum surface for acetone hydrogenationProceedings of the National Academy of Sciences of the United States of America117(7) 3446–50
202010.1126/sciadv.aax8254Del Valle, I., T. M. Webster, H. Y. Cheng, J. E. Thies, A. Kessler, M. K. Miller, Z. T. Ball, K. R. MacKenzie, C. A. Masiello, J. J. Silberg and J. LehmannSoil organic matter attenuates the efficacy of flavonoid-based plant-microbe communicationScience Advances6(5) eaax8254
202010.1021/acssuschemeng.0c01109Del Río, J. C., J. Rencoret, A. Gutiérrez, T. Elder, H. Kim and J. RalphLignin Monomers from beyond the Canonical Monolignol Biosynthetic Pathway: Another Brick in the WallACS Sustainable Chemistry and Engineering8(13) 4997-5012
202010.1128/MRA.00614-20DeAngelis, K. M. and G. PoldGenome Sequences of Frankineae sp. Strain MT45 and Jatrophihabitans sp. Strain GAS493, Two Actinobacteria Isolated from Forest SoilMicrobiology Resource Announcements9(38)
202010.1111/1751-7915.13575De Vrieze, J., T. De Mulder, S. Matassa, J. Zhou, L. T. Angenent, N. Boon and W. VerstraeteStochasticity in microbiology: managing unpredictability to reach the Sustainable Development GoalsMicrobial Biotechnology13(4) 829–43
202010.1016/j.cbpa.2020.04.001Davis, K. and T. S. MoonTailoring microbes to upgrade ligninCurrent Opinion in Chemical Biology59 23-29
202010.1016/j.cels.2020.05.011Davis, J. E., K. D. Insigne, E. M. Jones, Q. A. Hastings, W. C. Boldridge and S. KosuriDissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter AssaysCell Systems11(1) 75-85.e7
202010.1089/ind.2020.29230.ndaDanielson, N., S. McKay, P. Bloom, J. Dunn, N. Jakel, T. Bauer, J. Hannon, M. C. Jewett and B. ShanksIndustrial Biotechnology - An Industry at an Inflection PointIndustrial Biotechnology16(6) 321-332
202010.1038/s41598-020-72387-8Dalia, T. N., J. L. Chlebek and A. B. DaliaA modular chromosomally integrated toolkit for ectopic gene expression in Vibrio choleraeScientific Reports10(1) 15398
202010.3390/land9100398Dahlin, K. M., D. Akanga, D. L. Lombardozzi, D. E. Reed, G. Shirkey, C. Lei, M. Abraha and J. ChenChallenging a Global Land Surface Model in a Local Socio-Environmental SystemLand9(10) 398
202010.1038/s41598-020-76832-6Daguerre, Y., V. Basso, S. Hartmann-Wittulski, R. Schellenberger, L. Meyer, J. Bailly, A. Kohler, J. M. Plett, F. Martin and C. Veneault-FourreyThe mutualism effector MiSSP7 of Laccaria bicolor alters the interactions between the poplar JAZ6 protein and its associated proteinsScientific Reports10(1) 20362
202010.1021/acs.biochem.0c00126Curran, S. C., J. H. Pereira, M. J. Baluyot, J. Lake, H. Puetz, D. J. Rosenburg, P. Adams and J. D. KeaslingStructure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene ClusterBiochemistry59(16) 1630–9
202010.1002/jrs.6056Cupil_Garcia, V., P. Strobbia, B. M. Crawford, H. N. Wang, H. Ngo, Y. Liu and T. Vo_DinhPlasmonic nanoplatforms: From surface_enhanced Raman scattering sensing to biomedical applicationsJournal of Raman Spectroscopy52(2) 541–53
202010.1117/12.2552993Cupil-Garcia, V., P. Strobbia, Y. Ran, B. M. Crawford, H. N. Wang, R. Zentella, T. P. Sun and T. Vo-DinhFiberoptics SERS sensors using plasmonic nanostar probes for detection of molecular biotargetsProgress in Biomedical Optics and Imaging - Proceedings of SPIE
202010.3389/fenrg.2020.00072Cui, J. X., D. Stevenson, T. Korosh, D. Amador-Noguez, D. G. Olson and L. R. LyndDeveloping a Cell-Free Extract Reaction (CFER) System in Clostridium thermocellum to Identify Metabolic Limitations to Ethanol ProductionFrontiers in Energy Research8
202010.1016/j.mec.2020.e00122Cui, J., M. I. Maloney, D. G. Olson and L. R. LyndConversion of phosphoenolpyruvate to pyruvate in Thermoanaerobacterium saccharolyticumMetabolic Engineering Communications10 e00122
202010.1186/s12864-020-6489-0Cuevas, H. E. and L. K. PromEvaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collectionBMC Genomics21(1) 88
202010.1534/g3.120.401121Cruet-Burgos, C. M., H. E. Cuevas, L. K. Prom, J. E. Knoll, L. R. Stutts and W. VermerrisGenomic Dissection of Anthracnose Colletotrichum sublineolum Resistance Response in Sorghum Differential Line SC112-14G3 Genes|Genomes|Genetics10(4) 1403–12
202010.1104/pp.19.00817Crisp, P. A., R. Hammond, P. Zhou, B. Vaillancourt, A. Lipzen, C. Daum, K. Barry, N. de Leon, C. R. Buell, S. M. Kaeppler, B. C. Meyers, C. N. Hirsch and N. M. SpringerVariation and Inheritance of Small RNAs in Maize Inbreds and F1 HybridsPlant Physiology182(1) 318–31
202010.1007/s12010-019-03130-xCrigler, J., M. A. Eiteman and E. AltmanCharacterization of the Furfural and 5-Hydroxymethylfurfural (HMF) Metabolic Pathway in the Novel Isolate Pseudomonas putida ALS1267Applied Biochemistry and Biotechnology190(3) 918–30
202010.1088/2515-7647/ab9714Crawford, B. M., H. N. Wang, P. Strobbia, R. Zentella, Z. M. Pei, T. P. Sun and T. Vo-DinhPlasmonic Nanobiosensing: from in situ plant monitoring to cancer diagnostics at the point of careJournal of Physics: Photonics2(3)
202010.1111/tpj.14664Cousins, A. B., D. L. Mullendore and B. V. SonawaneRecent developments in mesophyll conductance in C3, C4, and crassulacean acid metabolism plantsThe Plant Journal101(4) 816–30
202010.1021/acssuschemeng.9b07040Cortes-Peña, Y., D. Kumar, V. Singh and J. S. GuestBioSTEAM: A Fast and Flexible Platform for the Design, Simulation, and Techno-Economic Analysis of Biorefineries under UncertaintyACS Sustainable Chemistry and Engineering8(8) 3302-3310
202010.1128/mSystems.00516-19Contador, C. A., S. K. Lo, S. H. J. Chan and H. M. LamMetabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based ModelingmSystems5(1)
202010.3389/fenrg.2020.00093Comer, A. D., J. P. Abraham, A. J. Steiner, T. C. Korosh, A. L. Markley and B. F. PflegerEnhancing photosynthetic production of glycogen-rich biomass for use as a fermentation feedstockFrontiers in Energy Research8
202010.3390/metabo10010030Cocuron, J. C., Z. Ross and A. P. AlonsoLiquid Chromatography Tandem Mass Spectrometry Quantification of 13C-Labeling in SugarsMetabolites10(1)
202010.1146/annurev-arplant-050718-100221Clark, T. J., L. Guo, J. Morgan and J. SchwenderModeling Plant Metabolism: From Network Reconstruction to Mechanistic ModelsAnnual Review of Plant Biology71 303–26
202010.1039/c9gc03524aChundawat, S. P. S., L. D. Sousa, S. Roy, Z. Yang, S. Gupta, R. Pal, C. Zhao, S. H. Liu, L. Petridis, H. O'Neill and S. V. PingaliAmmonia-salt solvent promotes cellulosic biomass deconstruction under ambient pretreatment conditions to enable rapid soluble sugar production at ultra-low enzyme loadingsGreen Chemistry22(1) 204–18
202010.3791/57488Chundawat, S. P. S., R. K. Pal, C. Zhao, T. Campbell, F. Teymouri, et al.Ammonia fiber expansion (AFEX) pretreatment of lignocellulosic biomassJournal of Visualized Experiments2020(158)
202010.1128/MRA.00895-20Chuckran, P. F., M. Huntemann, A. Clum, B. Foster, B. Foster, et al.Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural SoilMicrobiology Resource Announcements9(44)
202010.1016/j.str.2020.08.003Chowdhury, R., M. J. Grisewood, V. S. Boorla, Q. Yan, B. F. Pfleger and C. D. MaranasIPRO+/-: Computational Protein Design Tool Allowing for Insertions and DeletionsStructure28(12) 1344–57.e4
202010.1016/j.csbj.2020.09.019Chowdhury, R., V. S. Boorla and C. D. MaranasComputational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivityComputational and Structural Biotechnology Journal18 2573–82
202010.15252/msb.20199265Choudhury, A., J. A. Fenster, R. G. Fankhauser, J. L. Kaar, O. Tenaillon and R. T. GillCRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coliMolecular Systems Biology16(3) e9265
202010.1021/acssynbio.9b00440Choudhury, A., R. G. Fankhauser, E. F. Freed, E. J. Oh, A. B. Morgenthaler, M. C. Bassalo, S. D. Copley, J. L. Kaar and R. T. GillDeterminants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coliACS Synthetic Biology9(5) 1083–99
202010.3389/fpls.2020.545748Chhetri, H. B., A. Furches, D. Macaya-Sanz, A. R. Walker, D. Kainer, P. Jones, A. E. Harman-Ware, T. J. Tschaplinski, D. Jacobson, G. A. Tuskan and S. P. DiFazioGenome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpaFrontiers in Plant Science11 545748
202010.1021/acscatal.9b03460Chew, A. K., T. W. Walker, Z. Z. Shen, B. Demir, L. Witteman, J. Euclide, G. W. Huber, J. A. Dumesic and R. C. Van LehnEffect of Mixed-Solvent Environments on the Selectivity of Acid-Catalyzed Dehydration ReactionsACS Catalysis10(3) 1679–91
202010.1039/d0sc03261aChew, A. K., S. Jiang, W. Zhang, V. M. Zavala and R. C. Van LehnFast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics simulations and convolutional neural networksChemical Science11(46) 12464–76
202010.1016/j.biortech.2020.123275Cheng, M. H., L. Sun, Y. S. Jin, B. Dien and V. SinghProduction of xylose enriched hydrolysate from bioenergy sorghum and its conversion to _-carotene using an engineered Saccharomyces cerevisiaeBioresource Technology308 123275
202010.1016/j.biortech.2020.124051Cheng, M. H., H. J. Kadhum, G. S. Murthy, B. S. Dien and V. SinghHigh solids loading biorefinery for the production of cellulosic sugars from bioenergy sorghumBioresource Technology318 124051
202010.1038/s41564-020-0757-2Chen, Y., S. Zhang, E. M. Young, T. S. Jones, D. Densmore and C. A. VoigtGenetic circuit design automation for yeastNature Microbiology5(11) 1349–60
202010.1016/j.copbio.2019.12.007Chen, Y., D. Banerjee, A. Mukhopadhyay and C. J. PetzoldSystems and synthetic biology tools for advanced bioproduction hostsCurrent Opinion in Biotechnology64 101–9
202010.1016/j.ymben.2020.03.007Cheah, Y. E., Y. Xu, S. A. Sacco, P. K. Babele, A. O. Zheng, C. H. Johnson and J. D. YoungSystematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942Metabolic Engineering60 56–65
202010.1016/j.copbio.2019.08.013Chatterjee, A., D. M. DeLorenzo, R. Carr and T. S. MoonBioconversion of renewable feedstocks by Rhodococcus opacusCurrent Opinion in Biotechnology64 10–6
202010.1128/AEM.01271-20Charubin, K., H. Streett and E. T. PapoutsakisDevelopment of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag ProteinsApplied and Environmental Microbiology86(20)
202010.1128/mBio.02030-20Charubin, K., S. Modla, J. L. Caplan and E. T. PapoutsakisInterspecies Microbial Fusion and Large-Scale Exchange of Cytoplasmic Proteins and RNA in a Syntrophic Clostridium CoculturemBio11(5)
202010.5194/bg-17-5849-2020Chang, K. Y., W. J. Riley, P. M. Crill, R. F. Grant and S. R. SaleskaHysteretic temperature sensitivity of wetland CH4 fluxes explained by substrate availability and microbial activityBiogeosciences17(22) 5849–60
202010.1002/cssc.202001471Chang, H., G. W. Huber and J. A. DumesicChemical-Switching Strategy for Synthesis and Controlled Release of Norcantharimides from a Biomass-Derived ChemicalChemSusChem13(19) 5213–9
202010.1039/d0gc01576hChang, H., I. Bajaj, G. W. Huber, C. T. Maravelias and J. A. DumesicCatalytic strategy for conversion of fructose to organic dyes, polymers, and liquid fuelsGreen Chemistry22(16) 5285–95
202010.1111/tpj.14671Chakrabarti, M., L. de Lorenzo, S. E. Abdel-Ghany, A. S. N. Reddy and A. G. HuntWide-ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in SorghumPlant Journal102(5) 916-930
202010.1128/mSystems.00252-20Catlett, J. L., J. Catazaro, M. Cashman, S. Carr, R. Powers, M. B. Cohen and N. R. BuanMetabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicronmSystems5(5)
202010.3389/fmicb.2020.00341Casarrubia, S., E. Martino, S. Daghino, A. Kohler, E. Morin, H. R. Khouja, C. Murat, K. W. Barry, E. A. Lindquist, F. M. Martin and S. PerottoModulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillusFrontiers in Microbiology11 341
202010.1038/s41467-020-17837-7Carrasco-López, C., E. M. Zhao, A. A. Gil, N. Alam, J. E. Toettcher and J. L. AvalosDevelopment of light-responsive protein binding in the monobody non-immunoglobulin scaffoldNature Communications11(1)
202010.1016/j.copbio.2020.07.012Carrasco-López, C., S. A. García-Echauri, T. Kichuk and J. L. AvalosOptogenetics and biosensors set the stage for metabolic cybergeneticsCurrent Opinion in Biotechnology65 296-309
202010.1128/MRA.00351-20Carper, D. L., C. W. Schadt, L. H. Burdick, U. C. Kalluri and D. A. PelletierDraft Genome Sequence of Tumebacillus sp. Strain BK434, Isolated from the Roots of Eastern CottonwoodMicrobiology Resource Announcements9(22)
202010.7717/peerj.8534Carper, D. L., T. J. Lawrence, A. A. Carrell, D. A. Pelletier and D. J. WestonDISCo-microbe: design of an identifiable synthetic community of microbesPeerJ8 e8534
202010.1038/s41396-020-0666-7Carlson, H. K., L. M. Lui, M. N. Price, A. E. Kazakov, A. V. Carr, J. V. Kuehl, T. K. Owens, T. Nielsen, A. P. Arkin and A. M. DeutschbauerSelective carbon sources influence the end products of microbial nitrate respirationThe ISME Journal14(8) 2034–45
202010.1104/pp.19.00740Carey, L. M., T. J. Clark, R. R. Deshpande, J. C. Cocuron, E. K. Rustad and Y. Shachar-HillHigh Flux Through the Oxidative Pentose Phosphate Pathway Lowers Efficiency in Developing Camelina SeedsPlant Physiology182(1) 493–506
202010.1038/s41594-020-0435-3Cao, Q., D. R. Boyer, M. R. Sawaya, P. Ge and D. S. EisenbergCryo-EM structure and inhibitor design of human IAPP (amylin) fibrilsNature Structural and Molecular Biology27(7) 653-659
202010.1111/biom.13144Cao, M., W. Zhou, F. J. Breidt and G. PeersLarge scale maximum average power multiple inference on time-course count data with application to RNA-seq analysisBiometrics76(1) 9–22
202010.1016/j.copbio.2020.06.012Cao, M., V. G. Tran and H. ZhaoUnlocking nature's biosynthetic potential by directed genome evolutionCurrent Opinion in Biotechnology66 95-104
202010.1016/j.ymben.2020.01.005Cao, M., Z. Fatma, X. Song, P. H. Hsieh, V. G. Tran, W. L. Lyon, M. Sayadi, Z. Shao, Y. Yoshikuni and H. ZhaoA genetic toolbox for metabolic engineering of Issatchenkia orientalisMetabolic Engineering59 87–97
202010.1021/acssuschemeng.9b07073Cao, H., J. D. Walton, P. Brumm and G. N. PhillipsCrystal Structure of _-Xylosidase from Aspergillus niger in Complex with a Hydrolyzed Xyloglucan Product and New Insights in Accurately Predicting Substrate Specificities of GH31 Family GlycosidasesACS Sustainable Chemistry and Engineering8(6) 2540-2547
202010.1002/pro.3802Cannon, K. A., R. U. Park, S. E. Boyken, U. Nattermann, S. Yi, D. Baker, N. P. King and T. O. YeatesDesign and structure of two new protein cages illustrate successes and ongoing challenges in protein engineeringProtein Science29(4) 919–29
202010.1021/acssynbio.9b00392Cannon, K. A., V. N. Nguyen, C. Morgan and T. O. YeatesDesign and Characterization of an Icosahedral Protein Cage Formed by a Double-Fusion Protein Containing Three Distinct Symmetry ElementsACS Synthetic Biology9(3) 517-524
202010.1021/jasms.0c00030Campuzano, I. D. G., M. Nshanian, C. Spahr, C. Lantz, C. Netirojjanakul, H. Li, P. Wongkongkathep, J. J. Wolff and J. A. LooHigh Mass Analysis with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: From Inorganic Salt Clusters to Antibody Conjugates and beyondJournal of the American Society for Mass Spectrometry31(5) 1155-1162
202010.1016/j.mec.2020.e00132Campos, D. T., C. Zuñiga, A. Passi, J. Del Toro, J. D. Tibocha-Bonilla, A. Zepeda, M. J. Betenbaugh and K. ZenglerModeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ: Genome-scale metabolic modeling of Azotobacter vinelandii DJMetabolic Engineering Communications11
202010.1074/jbc.RA120.014258Cai, Y., X. H. Yu, J. Chai, C. J. Liu and J. ShanklinA conserved evolutionary mechanism permits _9 desaturation of very-long-chain fatty acyl lipidsJournal of Biological Chemistry295(32) 11337–45
202010.1016/j.pbi.2020.03.007Cahoon, E. B. and Y. Li-BeissonPlant unusual fatty acids: learning from the less commonCurrent Opinion in Plant Biology55 66–73
202010.1002/bmb.21428Burley, S. K., Y. Bromberg, P. Craig, S. Duffy, S. Dutta, et al.Virtual Boot Camp: COVID-19 evolution and structural biologyBiochemistry and Molecular Biology Education48(5) 511-513
202010.1371/journal.pone.0234839Buongiorno, J., K. Sipes, K. Wasmund, A. Loy and K. G. LloydWoeseiales transcriptional response to shallow burial in Arctic fjord surface sedimentPLoS One15(8) e0234839
202010.1099/ijsem.0.004316Buhl, M. and M. MarschalPrevotella vespertina sp. nov., isolated from an abscess of a hospital patientInternational Journal of Systematic and Evolutionary Microbiology70(8) 4576–82
202010.1016/j.tplants.2020.03.008Bryant, N. D., Y. Pu, T. J. Tschaplinski, G. A. Tuskan, W. Muchero, U. C. Kalluri, C. G. Yoo and A. J. RagauskasTransgenic Poplar Designed for BiofuelsTrends in Plant Science25(9) 881–96
202010.1002/slct.202000406Bryant, N., C. G. Yoo, Y. Q. Pu and A. J. Ragauskas2D HSQC Chemical Shifts of Impurities from Biomass PretreatmentChemistrySelect5(11) 3359–64
202010.1371/journal.pone.0222691Bruns, T. D., J. A. Chung, A. A. Carver and S. I. GlassmanA simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema speciesPLoS One15(3) e0222691
202010.1039/c9gc03062jBrunecky, R., V. Subramanian, J. M. Yarbrough, B. S. Donohoe, T. B. Vinzant, T. A. Vanderwall, B. C. Knott, Y. B. Chaudhari, Y. J. Bomble, M. E. Himmel and S. R. DeckerSynthetic fungal multifunctional cellulases for enhanced biomass conversionGreen Chemistry22(2) 478–89
202010.1002/jeq2.20082Brown, S., M. Pannu and S. C. FransenGreener gas? Impact of biosolids on carbon intensity of switchgrass ethanolJournal of Environmental Quality49(4) 1032-1043
202010.3389/fmicb.2020.00076Bratburd, J. R., R. A. Arango and H. A. HornDefensive Symbioses in Social Insects Can Inform Human Health and AgricultureFrontiers in Microbiology11 76
202010.3389/fpls.2020.00282Brandon, A. G. and H. V. SchellerEngineering of Bioenergy Crops: Dominant Genetic Approaches to Improve Polysaccharide Properties and Composition in BiomassFrontiers in Plant Science11 282
202010.1007/s00122-020-03659-0Bragg, J., P. Tomasi, L. Zhang, T. Williams, D. Wood, J. T. Lovell, A. Healey, J. Schmutz, J. E. Bonnette, P. Cheng, L. Chanbusarakum, T. Juenger and C. M. TobiasEnvironmentally responsive QTL controlling surface wax load in switchgrassTheoretical and Applied Genetics133(11) 3119–37
202010.1073/pnas.1917914117Boyer, D. R., B. Li, C. Sun, W. Fan, K. Zhou, M. P. Hughes, M. R. Sawaya, L. Jiang and D. S. EisenbergThe _-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structureProceedings of the National Academy of Sciences of the United States of America117(7) 3592–602
202010.1105/TPC.19.00481Boxall, S. F., N. Kadu, L. V. Dever, J. Knerová, J. L. Waller, P. J. D. Gould and J. HartwellKalanchoë PPC1 is essential for crassulacean acid metabolism and the regulation of core circadian clock and guard cell signaling genes[CC-BY]Plant Cell32(4) 1136-1160
202010.1016/j.tibtech.2019.12.024Bowie, J. U., S. Sherkhanov, T. P. Korman, M. A. Valliere, P. H. Opgenorth and H. LiuSynthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical ProductionTrends in Biotechnology38(7) 766–78
202010.1088/1361-6420/ab6e78Borges, C. and G. BirosA Domain Decomposition Preconditioning for an Inverse Volume Scattering ProblemInverse Problems36(3)
202010.1038/s41396-020-0617-3Blazewicz, S. J., B. A. Hungate, B. J. Koch, E. E. Nuccio, E. Morrissey, E. L. Brodie, E. Schwartz, J. Pett-Ridge and M. K. FirestoneTaxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soilThe ISME Journal14(6) 1520–32
202010.1021/jacs.9b09187Blake-Hedges, J. M., J. H. Pereira, P. Cruz-Morales, M. G. Thompson, J. F. Barajas, et al.Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA DehydrogenaseJournal of the American Chemical Society142(2) 835–46
202010.1371/journal.pcbi.1008502Bittrich, S., S. K. Burley and A. S. RoseReal-time structural motif searching in proteins using an inverted index strategyPLoS Computational Biology16(12)
202010.1038/s41564-020-0694-0Bittinger, K., C. Zhao, Y. Li, E. Ford, E. S. Friedman, et al.Bacterial colonization reprograms the neonatal gut metabolomeNature Microbiology5(6) 838–47
202010.1016/j.rhisph.2020.100259Bilyera, N., I. Kuzyakova, A. Guber, B. S. Razavi and Y. KuzyakovHow “hot” are hotspots: Statistically localizing the high-activity areas on soil and rhizosphere imagesRhizosphere16
202010.1002/lno.11301Bier, R. L., J. J. Wernegreen, R. J. Vilgalys, J. C. Ellis and E. S. BernhardtSubsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainageLimnology and Oceanography65(S1) S277–92
202010.1128/mSystems.00645-19Bhattacharjee, A., D. Velickovic, T. W. Wietsma, S. L. Bell, J. K. Jansson, K. S. Hofmockel and C. R. AndertonVisualizing Microbial Community Dynamics via a Controllable Soil EnvironmentmSystems5(1)
202010.1016/j.soilbio.2020.108037Bhattacharjee, A., A. M. Thompson, K. C. Schwarz, M. C. Burnet, Y. M. Kim, et al.Soil microbial EPS resiliency is influenced by carbon source accessibilitySoil Biology and Biochemistry151
202010.1016/j.biortech.2019.122724Bhatia, S. K., S. S. Jagtap, A. A. Bedekar, R. K. Bhatia, A. K. Patel, D. Pant, J. Rajesh Banu, C. V. Rao, Y. G. Kim and Y. H. YangRecent developments in pretreatment technologies on lignocellulosic biomass: Effect of key parameters, technological improvements, and challengesBioresource Technology300 122724
202010.1016/j.pbi.2020.09.003Bhandari, D. D. and F. BrandizziPlant endomembranes and cytoskeleton: moving targets in immunityCurrent Opinion in Plant Biology58 8–16
202010.1016/j.plantsci.2020.110675Beuchat, G., X. Xue and L. Q. ChenReview: The Next Steps in Crop Improvement: Adoption of Emerging Strategies to Identify Bottlenecks in Sugar FluxPlant Science301 110675
202010.1007/s11240-020-01897-0Berim, A. and D. R. GangExtractability, stability, and accumulation of nepetoidins in Ocimum basilicum L. leaves and cell culturesPlant Cell, Tissue and Organ Culture143(1) 75-85
202010.1111/gcbb.12730Berardi, D., E. Brzostek, E. Blanc_Betes, B. Davison, E. H. DeLucia, M. D. Hartman, J. Kent, W. J. Parton, D. Saha and T. W. Hudiburg21st_cent