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.

Year	DOI	Authors	Title	Journal
2021	10.1016/j.bbrc.2021.02.046	Abdelhamid, A. G. and N. K. El-Dougdoug	Comparative genomics of the gut commensal Bifidobacterium bifidum reveals adaptation to carbohydrate utilization	Biochemical and Biophysical Research Communications
2021	10.21203/rs.3.rs-23478/v1	Anne Elizabeth, H.-W., M.-S. David, A. Chanaka Roshan, D. Crissa, H. Kathleen, A. T. Gerald, S. Brian, P. D. Stephen and F. D. Mark	Accurate Determination of Genotypic Variance of Cell Wall Characteristics of a Populus trichocarpa Pedigree Using High-Throughput Pyrolysis-Molecular Beam Mass Spectrometry	Biotechnology for Biofuels
2021	10.1128/MRA.01411-20	Ateba, T. P., K. A. Alayande and M. Mwanza	Metagenomes and Assembled Genomes from Diarrhea-Affected Cattle (Bos taurus)	Microbiology Resource Announcements
2021	10.1016/j.rhisph.2021.100342	Babalola, O. O., O. A. Fasusi, A. E. Amoo and A. S. Ayangbenro	Genomic analysis of a Pseudomonas strain with multiple plant growth promoting properties	Rhizosphere
2021	10.1128/MRA.00029-21	Babalola, O. O., O. A. Fasusi, A. E. Amoo and A. S. Ayangbenro	Draft Genomic Analysis of Pseudomonas sp. Strain OA3, a Potential Plant Growth-Promoting Rhizospheric Bacterium	Microbiology Resource Announcements
2021	10.1128/MRA.00954-20	Babalola, O. O., R. R. Molefe and A. E. Amoo	Metagenome Assembly and Metagenome-Assembled Genome Sequences from the Rhizosphere of Maize Plants in Mafikeng, South Africa	Microbiology Resource Announcements
2021	10.1016/j.scitotenv.2020.144429	Bhatia, 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. Yang	Renewable biohydrogen production from lignocellulosic biomass using fermentation and integration of systems with other energy generation technologies	Science of The Total Environment
2021	10.1128/MRA.00884-20	Bhattacharjee, A., L. N. Anderson, T. Alfaro, A. Porras-Alfaro, A. Jumpponen, K. S. Hofmockel, J. K. Jansson, C. R. Anderton and W. C. Nelson	Draft Genome Sequence of Fusarium sp. Strain DS 682, a Novel Fungal Isolate from the Grass Rhizosphere	Microbiology Resource Announcements
2021	10.1186/s40168-020-00983-x	Blaustein, R. A., L.-M. Michelitsch, A. J. Glawe, H. Lee, S. Huttelmaier, N. Hellgeth, S. Ben Maamar and E. M. Hartmann	Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota	Microbiome
2021	10.1128/MRA.01485-20	Borre, I. and E. C. Sonnenschein	Draft Genome Sequences of Nine Environmental Bacterial Isolates Colonizing Plastic	Microbiology Resource Announcements
2021	10.1128/MRA.01427-20	Bridges, C. M., M. C. Nelson, J. Graf and D. J. Gage	Draft Genome Sequences of Dysgonomonas sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower Termite	Microbiology Resource Announcements
2021	10.1016/j.jpdc.2020.11.006	Brunn, M., N. Himthani, G. Biros, M. Mehl and A. Mang	Fast GPU 3D diffeomorphic image registration	Journal of Parallel and Distributed Computing
2021	10.1073/pnas.2022982118	Busta, L., E. Schmitz, D. K. Kosma, J. C. Schnable and E. B. Cahoon	A co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistry	Proceedings of the National Academy of Sciences
2021	10.1137/19M129961X	Chen, C., S. Reiz, C. D. Yu, H.-J. Bungartz and G. Biros	Fast Approximation of the Gauss--Newton Hessian Matrix for the Multilayer Perceptron	SIAM Journal on Matrix Analysis and Applications
2021	10.1088/1748-9326/abd7af	Chen, L., D. Debnath, J. Zhong, K. Ferin, A. VanLoocke and M. Khanna	The economic and environmental costs and benefits of the renewable fuel standard	Environmental Research Letters
2021	10.1021/acs.est.0c06133	Chen, L., E. Blanc-Betes, T. W. Hudiburg, D. Hellerstein, S. Wallander, E. H. DeLucia and M. Khanna	Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land	Environmental Science & Technology
2021	10.1002/jrs.6056	Cupil-Garcia, V., P. Strobbia, B. M. Crawford, H.-N. Wang, H. Ngo, Y. Liu and T. Vo-Dinh	Plasmonic nanoplatforms: From surface-enhanced Raman scattering sensing to biomedical applications	Journal of Raman Spectroscopy
2021	10.1007/s11120-020-00806-y	Dahlgren, K. K., C. Gates, T. Lee and J. C. Cameron	Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002	Photosynthesis Research
2021	10.1016/j.agee.2020.107150	De Antoni Migliorati, M., W. J. Parton, M. J. Bell, W. Wang and P. R. Grace	Soybean fallow and nitrification inhibitors: Strategies to reduce N2O emission intensities and N losses in Australian sugarcane cropping systems	Agriculture, Ecosystems & Environment
2021	10.1111/pce.13872	Ding, N., R. Huertas, I. Torres-Jerez, W. Liu, B. Watson, W.-R. Scheible and M. Udvardi	Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation	Plant, Cell & Environment
2021	10.1039/D0AN02022B	Do, H., S.-R. Kwon, S. Baek, C. S. Madukoma, M. K. Smiley, L. E. Dietrich, J. D. Shrout and P. W. Bohn	Redox cycling-based detection of phenazine metabolites secreted from Pseudomonas aeruginosa in nanopore electrode arrays	Analyst
2021	10.1093/femsyr/foab002	Domenzain, I., F. Li, E. J. Kerkhoven and V. Siewers	Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species	FEMS Yeast Research
2021	10.1371/journal.pone.0240390	Dong, H., L. V. Clark, X. Jin, K. Anzoua, L. Bagmet, P. Chebukin, E. Dzyubenko, N. Dzyubenko, B. K. Ghimire, K. Heo, D. A. Johnson, H. Nagano, A. Sabitov, J. Peng, T. Yamada, J. H. Yoo, C. Y. Yu, H. Zhao, S. P. Long and E. J. Sacks	Managing flowering time in Miscanthus and sugarcane to facilitate intra- and intergeneric crosses	PLOS ONE
2021	10.1128/MRA.00864-20	Doyle, D. A., K. E. Duncan and R. S. Tanner	Genome Sequence of Clostridium sp. Strain P21, a CO-Fermenting Acetogen Isolated from Old Hay	Microbiology Resource Announcements
2021	10.3390/v13010074	Faleye, T. O. C., E. Driver, D. Bowes, S. Adhikari, D. Adams, A. Varsani, R. U. Halden and M. Scotch	Pan-Enterovirus Amplicon-Based High-Throughput Sequencing Detects the Complete Capsid of a EVA71 Genotype C1 Variant via Wastewater-Based Epidemiology in Arizona	Viruses
2021	10.1039/D0GC03597A	Fang, Z., M. G. Flynn, J. E. Jackson and E. L. Hegg	Thio-assisted reductive electrolytic cleavage of lignin ?-O-4 models and authentic lignin	Green Chemistry
2021	10.1021/acs.est.0c04358	Ferin, K. M., L. Chen, J. Zhong, S. Acquah, E. A. Heaton, M. Khanna and A. VanLoocke	Water Quality Effects of Economically Viable Land Use Change in the Mississippi River Basin under the Renewable Fuel Standard	Environmental Science & Technology
2021	10.1093/molbev/msaa221	Foflonker, F. and C. E. Blaby-Haas	Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery	Molecular Biology and Evolution
2021	10.1016/j.copbio.2020.11.010	Foster, C. J., L. Wang, H. V. Dinh, P. F. Suthers and C. D. Maranas	Building kinetic models for metabolic engineering	Current Opinion in Biotechnology
2021	10.1371/journal.pone.0238327	Gao, D., P. R. Barber, J. V. Chacko, M. A. Kader Sagar, C. T. Rueden, A. R. Grislis, M. C. Hiner and K. W. Eliceiri	FLIMJ: An open-source ImageJ toolkit for fluorescence lifetime image data analysis	PLOS ONE
2021	10.1016/j.mec.2021.e00162	Garcia, D. C., J. L. N. Dinglasan, H. Shrestha, P. E. Abraham, R. L. Hettich and M. J. Doktycz	A lysate proteome engineering strategy for enhancing cell-free metabolite production	Metabolic Engineering Communications
2021	10.3390/genes12020288	Guo, Z., M. Xu, H. Nagano, L. V. Clark, E. J. Sacks and T. Yamada	Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis	Genes
2021	10.1038/s41477-021-00877-2	Horton, P., S. P. Long, P. Smith, S. A. Banwart and D. J. Beerling	Technologies to deliver food and climate security through agriculture	Nature Plants
2021	10.1016/j.micres.2020.126640	Igiehon, N. O., O. O. Babalola, X. Cheseto and B. Torto	Effects of rhizobia and arbuscular mycorrhizal fungi on yield, size distribution and fatty acid of soybean seeds grown under drought stress	Microbiological Research
2021	10.1021/acsomega.1c00997	Joshi, R. P., A. McNaughton, D. G. Thomas, C. S. Henry, S. R. Canon, L. A. McCue and N. Kumar	Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions	ACS Omega
2021	10.1111/gcbb.12777	Kasanke, C. P., Q. Zhao, S. Bell, A. M. Thompson and K. S. Hofmockel	Can switchgrass increase carbon accrual in marginal soils? The importance of site selection	GCB Bioenergy
2021	10.1016/j.jmb.2020.11.020	Kennedy, N. W., S. P. Ikonomova, M. Slininger Lee, H. W. Raeder and D. Tullman-Ercek	Self-assembling shell proteins PduA and PduJ have essential and redundant roles in bacterial microcompartment assembly	Journal of Molecular Biology
2021	10.1111/ajae.12189	Khanna, M., X. Chen, W. Wang and A. Oliver	Repeal of the Clean Power Plan: Social Cost and Distributional Implications	American Journal of Agricultural Economics
2021	10.1111/gcbb.12768	Kim, S. Y., R. A. Slattery and D. R. Ort	A role for differential Rubisco activase isoform expression in C4 bioenergy grasses at high temperature	GCB Bioenergy
2021	10.1002/bit.27576	Kuanyshev, N., C. V. Rao, B. Dien and Y.-S. Jin	Domesticating a food spoilage yeast into an organic acid-tolerant metabolic engineering host: Lactic acid production by engineered Zygosaccharomyces bailii	Biotechnology and Bioengineering
2021	10.1002/bbb.2212	Kurambhatti, C., D. Kumar and V. Singh	Technical and economic feasibility of an integrated ethanol and anthocyanin coproduction process using purple corn stover	Biofuels, Bioproducts and Biorefining
2021	10.1111/omi.12323	Lamont, E. I., A. Gadkari, K. A. Kerns, T. T. To, D. Daubert, G. Kotsakis, B. Bor, X. He and J. S. McLean	Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro	Molecular Oral Microbiology
2021	10.3390/microorganisms9020321	Lee, J. A., A. C. Baugh, N. J. Shevalier, B. Strand, S. Stolyar and C. J. Marx	Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community	Microorganisms
2021	10.1016/j.copbio.2020.10.012	Lee, J. W., S. Yook, H. Koh, C. V. Rao and Y.-S. Jin	Engineering xylose metabolism in yeasts to produce biofuels and chemicals	Current Opinion in Biotechnology
2021	10.1016/j.rser.2020.110613	Leibensperger, C., P. Yang, Q. Zhao, S. Wei and X. Cai	The synergy between stakeholders for cellulosic biofuel development: Perspectives, opportunities, and barriers	Renewable and Sustainable Energy Reviews
2021	10.1146/annurev-ento-040920-061140	Li, H., S. E. Young, M. Poulsen and C. R. Currie	Symbiont-Mediated Digestion of Plant Biomass in Fungus-Farming Insects	Annual Review of Entomology
2021	10.1016/j.copbio.2020.09.011	Liu, D., M. Liberton, J. I. Hendry, J. Aminian-Dehkordi, C. D. Maranas and H. B. Pakrasi	Engineering biology approaches for food and nutrient production by cyanobacteria	Current Opinion in Biotechnology
2021	10.1038/s41598-020-79733-w	Liu, J., A. Cheng, M. Wang, M. Liu, D. Zhu, Q. Yang, Y. Wu, R. Jia, S. Chen, X. Zhao, S. Zhang, J. Huang, X. Ou, S. Mao, Q. Gao, X. Wen, L. Zhang, Y. Liu, Y. Yu, B. Tian, L. Pan, M. Ur Rehman and X. Chen	Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2	Scientific Reports
2021	10.1111/1758-2229.12892	Lloyd, K. G.	Time as a microbial resource	Environmental Microbiology Reports
2021	10.1016/j.biortech.2020.124424	Maitra, S. and V. Singh	Balancing sugar recovery and inhibitor generation during energycane processing: Coupling cryogenic grinding with hydrothermal pretreatment at low temperatures	Bioresource Technology
2021	10.1128/MRA.01380-20	Martin, R. M., M. Kausch, K. Yap, J. D. Wehr, G. L. Boyer and S. W. Wilhelm	Metagenome-Assembled Genome Sequences of Raphidiopsis raciborskii and Planktothrix agardhii from a Cyanobacterial Bloom in Kissena Lake, New York, USA	Microbiology Resource Announcements
2021	10.1038/s41396-020-00757-1	Metcalfe, K. S., R. Murali, S. W. Mullin, S. A. Connon and V. J. Orphan	Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy	The ISME Journal
2021	10.1101/gr.266429.120	Michael, T. P., E. Ernst, N. Hartwick, P. Chu, D. Bryant, S. Gilbert, S. Ortleb, E. L. Baggs, K. S. Sree, K. J. Appenroth, J. Fuchs, F. Jupe, J. P. Sandoval, K. V. Krasileva, L. Borisjuk, T. C. Mockler, J. R. Ecker, R. A. Martienssen and E. Lam	Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control	Genome Research
2021	10.1111/gcbb.12788	Moore, 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. Bernacchi	Ecosystem-scale biogeochemical fluxes from three bioenergy crop candidates: How energy sorghum compares to maize and miscanthus	GCB Bioenergy
2021	10.1093/jxb/erab090	Moore, C. E., K. Meacham-Hensold, P. Lemonnier, R. A. Slattery, C. Benjamin, C. J. Bernacchi, T. Lawson and A. P. Cavanagh	The effect of increasing temperature on crop photosynthesis: from enzymes to ecosystems	Journal of Experimental Botany
2021	10.1016/j.watres.2020.116445	Nguyen Quoc, B., S. Wei, M. Armenta, R. Bucher, P. Sukapanpotharam, D. A. Stahl, H. D. Stensel and M.-K. H. Winkler	Aerobic granular sludge: Impact of size distribution on nitrification capacity	Water Research
2021	10.1111/tpj.15086	Oliver, J., M. Fan, B. McKinley, S. Zemelis-Durfee, F. Brandizzi, C. Wilkerson and J. E. Mullet	The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor	The Plant Journal
2021	10.1007/s10533-020-00742-y	Ostrom, P. H., S. DeCamp, H. Gandhi, J. Haslun and N. E. Ostrom	The influence of tillage and fertilizer on the flux and source of nitrous oxide with reference to atmospheric variation using laser spectroscopy	Biogeochemistry
2021	10.1007/978-1-0716-1032-9_5	Pavan, M.	Setting Up an Automated Biomanufacturing Laboratory	Synthetic Gene Circuits
2021	10.1128/MRA.00002-21	Podar, P. T., K. Peyton, A. Soren, R. L. Wilpiszeski, C. C. Gilmour, D. A. Elias and M. Podar	Complete Genome Sequence of Desulfobulbus oligotrophicus Prop6, an Anaerobic Deltabacterota Strain That Lacks Mercury Methylation Capability	Microbiology Resource Announcements
2021	10.1016/j.electacta.2020.137326	Rago, L., D. Popp, J. T. Heiker and F. Harnisch	Electroactive microorganisms in mouse feces	Electrochimica Acta
2021	10.1016/j.molcel.2020.12.031	Saba, J., X. Cao and R. Landick	Bacterial Transcription Continues to Surprise: Activation by Alarmone-Mediated ?-Factor Tethering	Molecular Cell
2021	10.1088/1748-9326/abd2f3	Saha, D., B. Basso and G. P. Robertson	Machine learning improves predictions of agricultural nitrous oxide (N2O) emissions from intensively managed cropping systems	Environmental Research Letters
2021	10.1007/s12155-021-10272-6	Schetter, A., C.-H. Lin, C. Zumpf, C. Jang, L. Hoffmann, W. Rooney and D. K. Lee	Genotype-Environment-Management Interactions in Biomass Yield and Feedstock Composition of Photoperiod-Sensitive Energy Sorghum	BioEnergy Research
2021	10.1109/TMI.2020.3024264	Scheufele, K., S. Subramanian and G. Biros	Fully Automatic Calibration of Tumor-Growth Models Using a Single mpMRI Scan	IEEE Transactions on Medical Imaging
2021	10.1016/j.watres.2020.116571	Shabtai, I. A., L. M. Lynch and Y. G. Mishael	Designing clay-polymer nanocomposite sorbents for water treatment: A review and meta-analysis of the past decade	Water Research
2021	10.1371/journal.pone.0245069	Sim, M. S., C. T. Skennerton and V. J. Orphan	Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus	PLOS ONE
2021	10.1016/j.polymdegradstab.2021.109481	Soulenthone, P., Y. Tachibana, M. Suzuki, T. Mizuno, Y. Ohta and K.-i. Kasuya	Characterization of a poly(butylene adipate-co-terephthalate) hydrolase from the mesophilic actinobacteria Rhodococcus fascians	Polymer Degradation and Stability
2021	10.1038/s41396-020-00782-0	St. James, A. R., J. B. Yavitt, S. H. Zinder and R. E. Richardson	Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study	The ISME Journal
2021	10.1007/s00248-020-01651-1	St. James, A. R., J. Lin and R. E. Richardson	Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA	Microbial Ecology
2021	10.1071/MF20024	Stoessel, D. J., A. R. van Rooyen, L. B. Beheregaray, S. M. C. Raymond, B. van Wyk, J. Haddy, J. Lieschke and A. R. Weeks	Population genetic structure of estuary perch (Percalates colonorum Gunther) in south-eastern Australia	Marine and Freshwater Research
2021	10.1002/biot.202000142	Sun, L. and Y.-S. Jin	Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae	Biotechnology Journal
2021	10.1016/j.ymben.2020.11.013	Suthers, P. F., C. J. Foster, D. Sarkar, L. Wang and C. D. Maranas	Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms	Metabolic Engineering
2021	10.1021/jasms.0c00251	Weitz, K. K., M. L. Smith, K. K. Hixson, E. A. Hill, J. K. Jansson, K. S. Hofmockel and M. S. Lipton	Real-Time Mass Spectrometry Measurements of Respiration Rates in Biological Systems	Journal of the American Society for Mass Spectrometry
2021	10.1128/mBio.03099-20	Wilhelm, R. C., C. Pepe-Ranney, P. Weisenhorn, M. Lipton and D. H. Buckley	Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil	mBio
2021	10.1128/MRA.01410-20	Xavier, R. K. M., D. Xu, P. J. McCarthy, S. Yang and G. Wang	Genome Sequence of Streptomyces sp. Strain HB-N217, Isolated from the Marine Sponge Forcepia sp	Microbiology Resource Announcements
2021	10.1111/gcbb.12821	Yang, P., X. Cai and M. Khanna	Farmers' heterogeneous perceptions of marginal land for biofuel crops in US Midwestern states considering biophysical and socioeconomic factors	GCB Bioenergy
2021	10.3389/fpls.2020.572137	Yao, T., J. Zhang, M. Xie, G. Yuan, T. J. Tschaplinski, W. Muchero and J.-G. Chen	Transcriptional Regulation of Drought Response in Arabidopsis and Woody Plants	Frontiers in Plant Science
2021	10.1038/s41598-020-79975-8	Yu, K. M. J., B. McKinley, W. L. Rooney and J. E. Mullet	High planting density induces the expression of GA3-oxidase in leaves and GA mediated stem elongation in bioenergy sorghum	Scientific Reports
2021	10.1093/plphys/kiaa109	Yu, X.-H., Y. Cai, J. Keereetaweep, K. Wei, J. Chai, E. Deng, H. Liu and J. Shanklin	Biotin attachment domain-containing proteins mediate hydroxy fatty acid-dependent inhibition of acetyl CoA carboxylase	Plant Physiology
2021	10.1021/acscatal.0c05393	Yun, D., E. Z. Ayla, D. T. Bregante and D. W. Flaherty	Reactive Species and Reaction Pathways for the Oxidative Cleavage of 4-Octene and Oleic Acid with H2O2 over Tungsten Oxide Catalysts	ACS Catalysis
2021	10.1016/j.copbio.2021.01.013	Zaramela, L. S., O. Moyne, M. Kumar, C. Zuniga, J. D. Tibocha-Bonilla and K. Zengler	The sum is greater than the parts: exploiting microbial communities to achieve complex functions	Current Opinion in Biotechnology
2021	10.1002/cbic.202000616	Zegeye, E. K., N. C. Sadler, G. X. Lomas, I. K. Attah, J. K. Jansson, K. S. Hofmockel, C. R. Anderton and A. T. Wright	Activity-Based Protein Profiling of Chitin Catabolism	ChemBioChem
2021	10.3390/plants10030513	Zhai, Z., H. Liu and J. Shanklin	Ectopic Expression of OLEOSIN 1 and Inactivation of GBSS1 Have a Synergistic Effect on Oil Accumulation in Plant Leaves	Plants
2020	10.1093/treephys/tpz020	Abbas, M., I. Peszlen, R. Shi, H. Kim, R. Katahira, K. Kafle, Z. Xiang, X. Huang, D. Min, M. Mohamadamin, C. Yang, X. Dai, X. Yan, S. Park, Y. Li, S. H. Kim, M. Davis, J. Ralph, R. R. Sederoff, V. L. Chiang and Q. Li	Involvement of CesA4, CesA7-A/B and CesA8-A/B in secondary wall formation in Populus trichocarpa wood	Tree Physiology
2020	10.3390/ijms21030772	Abdel-Ghany, S. E., F. Ullah, A. Ben-Hur and A. S. Reddy	Transcriptome analysis of drought-resistant and drought-sensitive sorghum (Sorghum bicolor) genotypes in response to PEG-Induced drought stress	International Journal of Molecular Sciences
2020	10.1016/j.ymben.2020.07.008	Abdel-Mawgoud, A. M. and G. Stephanopoulos	Improving CRISPR/Cas9-mediated genome editing efficiency in Yarrowia lipolytica using direct tRNA-sgRNA fusions	Metabolic Engineering
2020	10.1002/pmic.202000067	Abraham, P. E., A. Matthiadis, R. L. Hettich and U. C. Kalluri	Molecular Remodeling in Populus PdKOR RNAi Roots Profiled Using LC-MS/MS Proteomics	PROTEOMICS
2020	10.1371/journal.pone.0228560	Acosta, K., J. Xu, S. Gilbert, E. Denison, T. Brinkman, S. Lebeis and E. Lam	Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome	PLOS ONE
2020	10.1111/1462-2920.15192	Aigle, A., C. Gubry-Rangin, C. Thion, K. Y. Estera-Molina, H. Richmond, J. Pett-Ridge, M. K. Firestone, G. W. Nicol and J. I. Prosser	Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria	Environmental Microbiology
2020	10.1016/j.xcrm.2020.100077	Alcon-Giner, C., M. J. Dalby, S. Caim, J. Ketskemety, A. Shaw, K. Sim, M. A. E. Lawson, R. Kiu, C. Leclaire, L. Chalklen, M. Kujawska, S. Mitra, F. Fardus-Reid, G. Belteki, K. McColl, J. R. Swann, J. S. Kroll, P. Clarke and L. J. Hall	Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study	Cell Reports Medicine
2020	10.1186/s12870-020-2305-x	Alexandersson, E., S. Kushwaha, A. Subedi, D. Weighill, S. Climer, D. Jacobson and E. Andreasson	Linking crop traits to transcriptome differences in a progeny population of tetraploid potato	BMC Plant Biology
2020	10.1016/j.copbio.2019.11.003	Allen, D. K. and J. D. Young	Tracing metabolic flux through time and space with isotope labeling experiments	Curr Opin Biotechnol
2020	10.1111/gcb.15053	Alster, C. J., J. C. von Fischer, S. D. Allison and K. K. Treseder	Embracing a new paradigm for temperature sensitivity of soil microbes	Global Change Biology
2020	10.3389/feart.2020.557961	AminiTabrizi, R., R. M. Wilson, J. D. Fudyma, S. B. Hodgkins, H. M. Heyman, V. I. Rich, S. R. Saleska, J. P. Chanton and M. M. Tfaily	Controls on Soil Organic Matter Degradation and Subsequent Greenhouse Gas Emissions Across a Permafrost Thaw Gradient in Northern Sweden	Frontiers in Earth Science
2020	10.1016/j.cell.2020.04.046	Anava, S., M. Neuhof, H. Gingold, O. Sagy, A. Munters, E. M. Svensson, E. Afshinnekoo, D. Danko, J. Foox, P. Shor, B. Riestra, D. Huchon, C. E. Mason, N. Mizrahi, M. Jakobsson and O. Rechavi	Illuminating Genetic Mysteries of the Dead Sea Scrolls	Cell
2020	10.1089/ast.2020.2313	Angelos, E., D. K. Ko, S. Zemelis-Durfee and F. Brandizzi	Relevance of the unfolded protein response to spaceflight-induced transcriptional reprogramming in Arabidopsis	Astrobiology
2020	10.1038/s41467-020-18677-1	Angenent-Mari, N. M., A. S. Garruss, L. R. Soenksen, G. Church and J. J. Collins	A deep learning approach to programmable RNA switches	Nature Communications
2020	10.1021/acs.chemrev.9b00717	Anson, C. W. and S. S. Stahl	Mediated Fuel Cells: Soluble Redox Mediators and Their Applications to Electrochemical Reduction of O2 and Oxidation of H2, Alcohols, Biomass, and Complex Fuels	Chemical Reviews
2020	10.1016/j.apenergy.2020.115933	Arora, A. and V. Singh	Biodiesel production from engineered sugarcane lipids under uncertain feedstock compositions: Process design and techno-economic analysis	Applied Energy
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2020	10.1093/nargab/lqaa049	Azodi, C. B., J. P. Lloyd and S.-H. Shiu	The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana	NAR Genomics and Bioinformatics
2020	10.1105/tpc.19.00332	Azodi, C. B., J. Pardo, R. VanBuren, G. de los Campos and S.-H. Shiu	Transcriptome-based prediction of complex traits in maize	Plant Cell
2020	10.1016/j.tig.2020.03.005	Azodi, C. B., J. Tang and S.-H. Shiu	Opening the black box: Interpretable machine learning for geneticists	Trends in Genetics
2020	10.1093/plcell/koaa021	Baetsen-Young, A., H. Chen, S.-H. Shiu and B. Day	Contrasting transcriptional responses to Fusarium virguliforme colonization in symptomatic and asymptomatic hosts	The Plant Cell
2020	10.1007/s12155-020-10090-2	Bahri, B. A., G. Daverdin, X. Xu, J.-F. Cheng, K. W. Barry, E. C. Brummer, A. Missaoui and K. M. Devos	Natural Variation in Lignin and Pectin Biosynthesis-Related Genes in Switchgrass (Panicum virgatum L.) and Association of SNP Variants with Dry Matter Traits	BioEnergy Research
2020	10.1093/bioinformatics/btaa1075	Baisya, D. R. and S. Lonardi	Prediction of histone post-translational modifications using deep learning	Bioinformatics
2020	10.1128/mBio.00351-20	Banerjee, R., E. Weisenhorn, K. J. Schwartz, K. S. Myers, J. D. Glasner, N. T. Perna, J. J. Coon, R. A. Welch and P. J. Kiley	Tailoring a Global Iron Regulon to a Uropathogen	mBio
2020	10.1128/aem.01621-20	Banta, A. B., A. L. Enright, C. Siletti and J. M. Peters	A High-Efficacy CRISPR Interference System for Gene Function Discovery in Zymomonas mobilis	Applied and Environmental Microbiology
2020	10.1002/cpmc.130	Banta, A. B., R. D. Ward, J. S. Tran, E. E. Bacon and J. M. Peters	Programmable gene knockdown in diverse bacteria using Mobile-CRISPRi	Current Protocols in Microbiology
2020	10.1073/pnas.1918539117	Bao, Y., W.-M. Song, P. Wang, X. Yu, B. Li, C. Jiang, S.-H. Shiu, H. Zhang and D. C. Bassham	COST1 regulates autophagy to control plant drought tolerance	Proceedings of the National Academy of Sciences
2020	10.1016/j.soilbio.2020.107819	Barnard, R. L., S. J. Blazewicz and M. K. Firestone	Rewetting of soil: Revisiting the origin of soil CO2 emissions	Soil Biology and Biochemistry
2020	10.1186/s12859-020-3372-6	Barnett, S. E. and D. H. Buckley	Simulating metagenomic stable isotope probing datasets with MetaSIPSim	BMC Bioinformatics
2020	10.1089/crispr.2020.29085.rba	Barrangou, R.	Ushering in the Next CRISPR Decade	The CRISPR Journal
2020	10.3390/genes11010102	Barthel, S., S. Palluk, N. J. Hillson, J. D. Keasling and D. H. Arlow	Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3? Terminal Structures for Enzymatic De Novo DNA Synthesis	Genes
2020	10.1101/2020.01.03.894477	Barua, N., A. M. Herken, K. R. Stern, S. Reese, R. L. Powers, J. L. Morrell-Falvey, T. G. Platt and R. R. Hansen	Simultaneous Discovery of Positive and Negative Interactions Among Root Microbiome Bacteria Using Microwell Recovery Arrays	bioRxiv
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2020	10.1007/978-1-0716-0142-6_4	Basso, V. and C. Veneault-Fourrey	Role of Jasmonates in Beneficial Microbe-Root Interactions	Methods in Molecular Biology
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2020	10.1016/j.copbio.2020.02.001	Belcher, M. S., J. Mahinthakumar and J. D. Keasling	New frontiers: harnessing pivotal advances in microbial engineering for the biosynthesis of plant-derived terpenoids	Current Opinion in Biotechnology
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2020	10.1016/j.plantsci.2020.110675	Beuchat, G., X. Xue and L.-Q. Chen	Review: The Next Steps in Crop Improvement: Adoption of Emerging Strategies to Identify Bottlenecks in Sugar Flux	Plant Science
2020	10.1016/j.pbi.2020.09.003	Bhandari, D. D. and F. Brandizzi	Plant endomembranes and cytoskeleton: moving targets in immunity	Current Opinion in Plant Biology
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2020	10.1038/s41564-020-0694-0	Bittinger, K., C. Zhao, Y. Li, E. Ford, E. S. Friedman, J. Ni, C. V. Kulkarni, J. Cai, Y. Tian, Q. Liu, A. D. Patterson, D. Sarkar, S. H. J. Chan, C. Maranas, A. Saha-Shah, P. Lund, B. A. Garcia, L. M. Mattei, J. S. Gerber, M. A. Elovitz, A. Kelly, P. DeRusso, D. Kim, C. E. Hofstaedter, M. Goulian, H. Li, F. D. Bushman, B. S. Zemel and G. D. Wu	Bacterial colonization reprograms the neonatal gut metabolome	Nature Microbiology
2020	10.1021/jacs.9b09187	Blake-Hedges, J. M., J. H. Pereira, P. Cruz-Morales, M. G. Thompson, J. F. Barajas, J. Chen, R. N. Krishna, L. J. G. Chan, D. Nimlos, C. Alonso-Martinez, E. E. K. Baidoo, Y. Chen, J. W. Gin, L. Katz, C. J. Petzold, P. D. Adams and J. D. Keasling	Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase	Journal of the American Chemical Society
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2020	10.1088/1361-6420/ab6e78	Borges, C. and G. Biros	A domain decomposition preconditioning for an inverse volume scattering problem	Inverse Problems
2020	10.1016/j.tibtech.2019.12.024	Bowie, J. U., S. Sherkhanov, T. P. Korman, M. A. Valliere, P. H. Opgenorth and H. Liu	Synthetic Biochemistry: The bio-inspired cell-free approach to commodity chemical production	Trends in Biotechnology
2020	10.1094/PBIOMES-07-20-0051-R	Bowsher, A. W., G. M. N. Benucci, G. Bonito and A. Shade	Seasonal Dynamics of Core Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf Bacteria	Phytobiomes Journal
2020	10.1073/pnas.1917914117	Boyer, D. R., B. Li, C. Sun, W. Fan, K. Zhou, M. P. Hughes, M. R. Sawaya, L. Jiang and D. S. Eisenberg	The ?-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure	Proceedings of the National Academy of Sciences
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2020	10.3389/fpls.2020.00282	Brandon, A. G. and H. V. Scheller	Engineering of Bioenergy Crops: Dominant Genetic Approaches to Improve Polysaccharide Properties and Composition in Biomass	Frontiers in Plant Science
2020	10.3389/fmicb.2020.00076	Bratburd, J. R., R. A. Arango and H. A. Horn	Defensive Symbioses in Social Insects Can Inform Human Health and Agriculture	Frontiers in Microbiology
2020	10.1039/C9GC03062J	Brunecky, 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. Decker	Synthetic fungal multifunctional cellulases for enhanced biomass conversion	Green Chemistry
2020	10.1371/journal.pone.0222691	Bruns, T. D., J. A. Chung, A. A. Carver and S. I. Glassman	A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species	PLoS ONE
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2020	10.1002/slct.202000406	Bryant, N., C. G. Yoo, Y. Pu and A. J. Ragauskas	2D HSQC Chemical Shifts of Impurities from Biomass Pretreatment	ChemistrySelect
2020	10.1099/ijsem.0.004316	Buhl, M. and M. Marschal	Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient	International Journal of Systematic and Evolutionary Microbiology
2020	10.1371/journal.pone.0234839	Buongiorno, J., K. Sipes, K. Wasmund, A. Loy and K. G. Lloyd	Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment	PLoS ONE
2020	10.1016/j.pbi.2020.03.007	Cahoon, E. B. and Y. Li-Beisson	Plant unusual fatty acids: learning from the less common	Current Opinion in Plant Biology
2020	10.1074/jbc.RA120.014258	Cai, Y., X.-H. Yu, J. Chai, C.-J. Liu and J. Shanklin	A conserved evolutionary mechanism permits ?9 desaturation of very-long-chain fatty acyl lipids	Journal of Biological Chemistry
2020	10.1016/j.ymben.2020.01.005	Cao, M., Z. Fatma, X. Song, P.-H. Hsieh, V. G. Tran, W. L. Lyon, M. Sayadi, Z. Shao, Y. Yoshikuni and H. Zhao	A genetic toolbox for metabolic engineering of Issatchenkia orientalis	Metabolic Engineering
2020	10.1104/pp.19.00740	Carey, L. M., T. J. Clark, R. R. Deshpande, J.-C. Cocuron, E. K. Rustad and Y. Shachar-Hill	High Flux Through the Oxidative Pentose Phosphate Pathway Lowers Efficiency in Developing Camelina Seeds	Plant Physiology
2020	10.1038/s41396-020-0666-7	Carlson, 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. Deutschbauer	Selective carbon sources influence the end products of microbial nitrate respiration	The ISME Journal
2020	10.1128/MRA.00351-20	Carper, D. L., C. W. Schadt, L. H. Burdick, U. C. Kalluri and D. A. Pelletier	Draft Genome Sequence of Tumebacillus sp. Strain BK434, Isolated from the Roots of Eastern Cottonwood	Microbiology Resource Announcements
2020	10.3389/fmicb.2020.00341	Casarrubia, 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. Perotto	Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus	Frontiers in Microbiology
2020	10.1128/mSystems.00252-20	Catlett, J. L., J. Catazaro, M. Cashman, S. Carr, R. Powers, M. B. Cohen and N. R. Buan	Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron	mSystems
2020	10.1002/cssc.202001471	Chang, H., G. W. Huber and J. A. Dumesic	Chemical-Switching Strategy for Synthesis and Controlled Release of Norcantharimides from a Biomass-Derived Chemical	ChemSusChem
2020	10.1039/D0GC01576H	Chang, H., I. Bajaj, G. W. Huber, C. T. Maravelias and J. A. Dumesic	Catalytic strategy for conversion of fructose to organic dyes, polymers, and liquid fuels	Green Chemistry
2020	10.5194/bg-17-5849-2020	Chang, K. Y., W. J. Riley, P. M. Crill, R. F. Grant and S. R. Saleska	Hysteretic temperature sensitivity of wetland CH4 fluxes explained by substrate availability and microbial activity	Biogeosciences
2020	10.1128/aem.01271-20	Charubin, K., H. Streett and E. T. Papoutsakis	Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins	Applied and Environmental Microbiology
2020	10.1128/mBio.02030-20	Charubin, K., S. Modla, J. L. Caplan and E. T. Papoutsakis	Interspecies Microbial Fusion and Large-Scale Exchange of Cytoplasmic Proteins and RNA in a Syntrophic Clostridium Coculture	mBio
2020	10.1016/j.copbio.2019.08.013	Chatterjee, A., D. M. DeLorenzo, R. Carr and T. S. Moon	Bioconversion of renewable feedstocks by Rhodococcus opacus	Current Opinion in Biotechnology
2020	10.1016/j.ymben.2020.03.007	Cheah, Y. E., Y. Xu, S. A. Sacco, P. K. Babele, A. O. Zheng, C. H. Johnson and J. D. Young	Systematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942	Metabolic Engineering
2020	10.1093/bioinformatics/btaa902	Chen, C., J. Hou, X. Shi, H. Yang, J. A. Birchler and J. Cheng	GNET2: an R package for constructing gene regulatory networks from transcriptomic data	Bioinformatics
2020	10.1016/j.copbio.2019.12.007	Chen, Y., D. Banerjee, A. Mukhopadhyay and C. J. Petzold	Systems and synthetic biology tools for advanced bioproduction hosts	Current Opinion in Biotechnology
2020	10.1038/s41564-020-0757-2	Chen, Y., S. Zhang, E. M. Young, T. S. Jones, D. Densmore and C. A. Voigt	Genetic circuit design automation for yeast	Nature Microbiology
2020	10.1016/j.biortech.2020.124051	Cheng, M.-H., H. J. Kadhum, G. S. Murthy, B. S. Dien and V. Singh	High solids loading biorefinery for the production of cellulosic sugars from bioenergy sorghum	Bioresource Technology
2020	10.1016/j.biortech.2020.123275	Cheng, M.-H., L. Sun, Y.-S. Jin, B. Dien and V. Singh	Production of xylose enriched hydrolysate from bioenergy sorghum and its conversion to ?-carotene using an engineered Saccharomyces cerevisiae	Bioresource Technology
2020	10.1039/D0SC03261A	Chew, A. K., S. Jiang, W. Zhang, V. M. Zavala and R. C. Van Lehn	Fast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics simulations and convolutional neural networks	Chemical Science
2020	10.1021/acscatal.9b03460	Chew, A. K., T. W. Walker, Z. Shen, B. Demir, L. Witteman, J. Euclide, G. W. Huber, J. A. Dumesic and R. C. Van Lehn	Effect of Mixed-Solvent Environments on the Selectivity of Acid-Catalyzed Dehydration Reactions	ACS Catalysis
2020	10.3389/fpls.2020.545748	Chhetri, 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. DiFazio	Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa	Frontiers in Plant Science
2020	10.15252/msb.20199265	Choudhury, A., J. A. Fenster, R. G. Fankhauser, J. L. Kaar, O. Tenaillon and R. T. Gill	CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli	Molecular Systems Biology
2020	10.1021/acssynbio.9b00440	Choudhury, 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. Gill	Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli	ACS Synthetic Biology
2020	10.1101/2020.03.30.015891	Chowdhury, R. and C. D. Maranas	Biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity	bioRxiv
2020	10.1016/j.str.2020.08.003	Chowdhury, R., M. J. Grisewood, V. S. Boorla, Q. Yan, B. F. Pfleger and C. D. Maranas	IPRO+/?: Computational Protein Design Tool Allowing for Insertions and Deletions	Structure
2020	10.1128/MRA.00895-20	Chuckran, P. F., M. Huntemann, A. Clum, B. Foster, B. Foster, S. Roux, K. Palaniappan, N. Varghese, S. Mukherjee, T. B. K. Reddy, C. Daum, A. Copeland, N. N. Ivanova, N. C. Kyrpides, T. G. del Rio, E. A. Eloe-Fadrosh, E. M. Morrissey, E. Schwartz, V. Fofanov, B. Hungate and P. Dijkstra	Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil	Microbiology Resource Announcements
2020	10.1039/C9GC03524A	Chundawat, S. P. S., L. d. C. Sousa, S. Roy, Z. Yang, S. Gupta, R. Pal, C. Zhao, S.-H. Liu, L. Petridis, H. O'Neill and S. V. Pingali	Ammonia-salt solvent promotes cellulosic biomass deconstruction under ambient pretreatment conditions to enable rapid soluble sugar production at ultra-low enzyme loadings	Green Chemistry
2020	10.3791/57488	Chundawat, S. P. S., R. K. Pal, C. Zhao, T. Campbell, F. Teymouri, J. Videto, C. Nielson, B. Wieferich, L. Sousa, B. E. Dale, V. Balan, S. Chipkar, J. Aguado, E. Burke and R. G. Ong	Ammonia Fiber Expansion (AFEX) Pretreatment of Lignocellulosic Biomass	JoVE
2020	10.1146/annurev-arplant-050718-100221	Clark, T. J., L. Guo, J. Morgan and J. Schwender	Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models	Annual Review of Plant Biology
2020	10.3390/metabo10010030	Cocuron, J.-C., Z. Ross and A. P. Alonso	Liquid Chromatography Tandem Mass Spectrometry Quantification of 13C-Labeling in Sugars	Metabolites
2020	10.3389/fenrg.2020.00093	Comer, A. D., J. P. Abraham, A. J. Steiner, T. C. Korosh, A. L. Markley and B. F. Pfleger	Enhancing Photosynthetic Production of Glycogen-Rich Biomass for Use as a Fermentation Feedstock	Frontiers in Energy Research
2020	10.1128/mSystems.00516-19	Contador, C. A., S.-K. Lo, S. H. J. Chan and H.-M. Lam	Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling	mSystems
2020	10.1111/tpj.14664	Cousins, A. B., D. L. Mullendore and B. V. Sonawane	Recent developments in mesophyll conductance in C3, C4, and crassulacean acid metabolism plants	The Plant Journal
2020	10.1088/2515-7647/ab9714	Crawford, B. M., H.-N. Wang, P. Strobbia, R. Zentella, Z.-M. Pei, T.-p. Sun and T. Vo-Dinh	Plasmonic Nanobiosensing: from in situ plant monitoring to cancer diagnostics at the point of care	Journal of Physics: Photonics
2020	10.1007/s12010-019-03130-x	Crigler, J., M. A. Eiteman and E. Altman	Characterization of the Furfural and 5-Hydroxymethylfurfural (HMF) Metabolic Pathway in the Novel Isolate Pseudomonas putida ALS1267	Applied Biochemistry and Biotechnology
2020	10.1104/pp.19.00817	Crisp, 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. Springer	Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids	Plant Physiology
2020	10.1534/g3.120.401121	Cruet-Burgos, C. M., H. E. Cuevas, L. K. Prom, J. E. Knoll, L. R. Stutts and W. Vermerris	Genomic dissection of anthracnose Colletotrichum sublineolum resistance response in sorghum differential Line SC112-14	G3: Genes Genomes Genetics
2020	10.1186/s12864-020-6489-0	Cuevas, H. E. and L. K. Prom	Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection	BMC Genomics
2020	10.3389/fenrg.2020.00072	Cui, J., D. Stevenson, T. Korosh, D. Amador-Noguez, D. G. Olson and L. R. Lynd	Developing a Cell-Free Extract Reaction (CFER) System in Clostridium thermocellum to Identify Metabolic Limitations to Ethanol Production	Frontiers in Energy Research
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2020	10.1117/12.2552993	Cupil-Garcia, V., P. Strobbia, Y. Ran, B. M. Crawford, H. N. Wang, R. Zentella, T. P. Sun and T. Vo-Dinh	Fiberoptics SERS sensors using plasmonic nanostar probes for detection of molecular biotargets	Progress in Biomedical Optics and Imaging - Proceedings of SPIE
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2020	10.1128/MRA.00229-20	Jennings, E. C., M. W. Korthauer and J. B. Benoit	Genome Sequence of a Blattabacterium Strain Isolated from the Viviparous Cockroach, Diploptera punctata	Microbiology Resource Announcements
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2020	10.1016/j.tibtech.2020.07.005	Liu, R., L. Liang, E. F. Freed and R. T. Gill	Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing	Trends in Biotechnology
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2020	10.1038/s41540-019-0122-3	Mazharul Islam, M., V. C. Thomas, M. Van Beek, J.-S. Ahn, A. A. Alqarzaee, C. Zhou, P. D. Fey, K. W. Bayles and R. Saha	An integrated computational and experimental study to investigate Staphylococcus aureus metabolism	npj Systems Biology and Applications
2020	10.1038/s41598-020-67878-7	McClure, R. S., J.-Y. Lee, T. R. Chowdhury, E. M. Bottos, R. A. White, Y.-M. Kim, C. D. Nicora, T. O. Metz, K. S. Hofmockel, J. K. Jansson and H.-S. Song	Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations	Scientific Reports
2020	10.3389/fmicb.2020.01987	McClure, R., D. Naylor, Y. Farris, M. Davison, S. J. Fansler, K. S. Hofmockel and J. K. Jansson	Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome	Frontiers in Microbiology
2020	10.1021/acssynbio.9b00407	McConnell, S. A., K. A. Cannon, C. Morgan, R. McAllister, B. R. Amer, R. T. Clubb and T. O. Yeates	Designed protein cages as scaffolds for building multienzyme materials	ACS Synthetic Biology
2020	10.1039/D0GC00661K	Meng, X., Y. Pu, M. Li and A. J. Ragauskas	A biomass pretreatment using cellulose-derived solvent Cyrene	Green Chemistry
2020	10.1016/j.algal.2020.101967	Metcalf, A. J., A. Nagygyor and N. R. Boyle	Rapid Annotation of Photosynthetic Systems (RAPS): automated algorithm to generate genome-scale metabolic networks from algal genomes	Algal Research
2020	10.1111/tpj.14957	Miller, G. P., W. W. Bhat, E. R. Lanier, S. R. Johnson, D. T. Mathieu and B. Hamberger	The biosynthesis of the anti-microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all-cis prenyl intermediate	The Plant Journal
2020	10.1038/s41467-020-18923-6	Mitros, T., A. M. Session, B. T. James, G. A. Wu, M. B. Belaffif, L. V. Clark, S. Shu, H. Dong, A. Barling, J. R. Holmes, J. E. Mattick, J. V. Bredeson, S. Liu, K. Farrar, K. Glowacka, S. Jeżowski, K. Barry, W. B. Chae, J. A. Juvik, J. Gifford, A. Oladeinde, T. Yamada, J. Grimwood, N. H. Putnam, J. De Vega, S. Barth, M. Klaas, T. Hodkinson, L. Li, X. Jin, J. Peng, C. Y. Yu, K. Heo, J. H. Yoo, B. K. Ghimire, I. S. Donnison, J. Schmutz, M. E. Hudson, E. J. Sacks, S. P. Moose, K. Swaminathan and D. S. Rokhsar	Genome biology of the paleotetraploid perennial biomass crop Miscanthus	Nature Communications
2020	10.1007/s00253-020-10469-3	Monge, E. C., M. Levi, J. N. Forbin, M. D. Legesse, B. A. Udo, T. N. deCarvalho and J. G. Gardner	High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates	Applied Microbiology and Biotechnology
2020	10.1111/gcb.14925	Monteiro, L. A., A. M. Allee, E. E. Campbell, L. R. Lynd, J. R. Soares, D. Jaiswal, J. de Castro Oliveira, M. dos Santos Vianna, A. E. Morishige, G. K. D. A. Figueiredo, R. A. C. Lamparelli, N. D. Mueller, J. Gerber, L. A. B. Cortez and J. J. Sheehan	Assessment of yield gaps on global grazed-only permanent pasture using climate binning	Global Change Biology
2020	10.1016/j.chemosphere.2020.126951	Moon, J. W., C. J. Paradis, D. C. Joyner, F. von Netzer, E. L. Majumder, E. R. Dixon, M. Podar, X. Ge, P. J. Walian, H. J. Smith, X. Wu, G. M. Zane, K. F. Walker, M. P. Thorgersen, F. L. Poole Ii, L. M. Lui, B. G. Adams, K. B. De Leon, S. S. Brewer, D. E. Williams, K. A. Lowe, M. Rodriguez, Jr., T. L. Mehlhorn, S. M. Pfiffner, R. Chakraborty, A. P. Arkin, J. D. Wall, M. W. Fields, M. W. W. Adams, D. A. Stahl, D. A. Elias and T. C. Hazen	Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer	Chemosphere
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2020	10.3389/fmicb.2020.00005	Moosburner, M. A., P. Gholami, J. K. McCarthy, M. Tan, V. A. Bielinski and A. E. Allen	Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9	Frontiers in Microbiology
2020	10.1038/s41893-019-0456-2	Moreira, M. M. R., J. E. A. Seabra, L. R. Lynd, S. M. Arantes, M. P. Cunha and J. J. M. Guilhoto	Socio-environmental and land-use impacts of double-cropped maize ethanol in Brazil	Nature Sustainability
2020	10.1128/mra.00956-20	Morrow, M. A., G. Pold and K. M. DeAngelis	Draft Genome Sequence of a Terrestrial Planctomycete, Singulisphaera sp. Strain GP187, Isolated from Forest Soil	Microbiology Resource Announcements
2020	10.1016/j.rser.2020.109764	Mousavi-Avval, S. H. and A. Shah	Techno-economic analysis of pennycress production, harvest and post-harvest logistics for renewable jet fuel	Renewable and Sustainable Energy Reviews
2020	10.1002/was.000400041	Muneeba Khalid, M. J. D., and Scott T. Retterer	Nano-enabled chemical imaging	Wiley Imaging and Microscopy Journal
2020	10.1099/ijsem.0.004360	Muramatsu, S., M. Kanamuro, Y. Sato-Takabe, S. Hirose, Y. Muramatsu, S. Takaichi and S. Hanada	Roseobacter cerasinus sp. nov., isolated from a fish farm	International Journal of Systematic and Evolutionary Microbiology
2020	10.1371/journal.pbio.3000877	Mutalik, 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. Arkin	High-throughput mapping of the phage resistance landscape in E. coli	PLoS Biol
2020	10.1007/s10841-020-00248-w	Myers, A. T., N. L. Haan and D. A. Landis	Video surveillance reveals a community of largely nocturnal Danaus plexippus (L.) egg predators	Journal of Insect Conservation
2020	10.1128/mra.00880-20	Myers, K. S., J. M. Vera, K. C. Lemmer, A. M. Linz, R. Landick, D. R. Noguera and T. J. Donohue	Genome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria, Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444	Microbiology Resource Announcements
2020	10.1128/mra.00587-20	Myers, K. S., M. Place, D. R. Noguera and T. J. Donohue	COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database	Microbiology Resource Announcements
2020	10.1038/s41598-020-73253-3	Nanda, P., P. Patra, M. Das and A. Ghosh	Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri	Scientific Reports
2020	10.1021/acssuschemeng.9b06556	Nandiwale, K. Y., A. M. Danby, A. Ramanathan, R. V. Chaudhari, A. H. Motagamwala, J. A. Dumesic and B. Subramaniam	Enhanced Acid-Catalyzed Lignin Depolymerization in a Continuous Reactor with Stable Activity	ACS Sustainable Chemistry & Engineering
2020	10.1007/s11104-020-04616-y	Nash, J., R. Laushman and C. Schadt	Ectomycorrhizal fungal diversity interacts with soil nutrients to predict plant growth despite weak plant-soil feedbacks	Plant and Soil
2020	10.1146/annurev-environ-012320-082720	Naylor, D., N. Sadler, A. Bhattacharjee, E. B. Graham, C. R. Anderton, R. McClure, M. Lipton, K. S. Hofmockel and J. K. Jansson	Soil Microbiomes Under Climate Change and Implications for Carbon Cycling	Annual Review of Environment and Resources
2020	10.1128/mBio.01349-20	Naylor, D., S. Fansler, C. Brislawn, W. C. Nelson, K. S. Hofmockel, J. K. Jansson and R. McClure	Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules	mBio
2020	10.1128/MRA.00718-20	Nelson, 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. Jansson	Terabase Metagenome Sequencing of Grassland Soil Microbiomes	Microbiology Resource Announcements
2020	10.1093/sysbio/syaa038	Neumann, J. S., R. Desalle, A. Narechania, B. Schierwater and M. Tessler	Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets	Systematic Biology
2020	10.1016/j.bej.2020.107496	Nichols, T. M., N. W. Kennedy and D. Tullman-Ercek	A genomic integration platform for heterologous cargo encapsulation in 1,2-propanediol utilization bacterial microcompartments	Biochemical Engineering Journal
2020	10.3390/genes11060625	Nikolaou, E., A. T. M. Hubbard, J. Botelho, T. A. M. Marschall, D. M. Ferreira and A. P. Roberts	Antibiotic Resistance Is Associated with Integrative and Conjugative Elements and Genomic Islands in Naturally Circulating Streptococcus pneumoniae Isolates from Adults in Liverpool, UK	Genes
2020	10.1021/acssuschemeng.0c00779	Nill, J. D. and T. Jeoh	The Role of Evolving Interfacial Substrate Properties on Heterogeneous Cellulose Hydrolysis Kinetics	ACS Sustainable Chemistry & Engineering
2020	10.1038/s41467-020-18560-z	Ning, D., M. Yuan, L. Wu, Y. Zhang, X. Guo, X. Zhou, Y. Yang, A. P. Arkin, M. K. Firestone and J. Zhou	A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming	Nature Communications
2020	10.1016/j.soilbio.2020.107952	Norman, J. S., D. N. Smercina, J. T. Hileman, L. K. Tiemann and M. L. Friesen	Soil aminopeptidase induction is unaffected by inorganic nitrogen availability	Soil Biology and Biochemistry
2020	10.1126/science.abb6310	North, 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. Tabita	A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis	Science
2020	10.1111/mmi.14459	North, J. A., J. A. Wildenthal, T. J. Erb, B. S. Evans, K. M. Byerly, J. A. Gerlt and F. R. Tabita	A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli	Molecular Microbiology
2020	10.1002/agj2.20184	Novak, J. M., D. W. Watts, P. J. Bauer, D. L. Karlen, P. G. Hunt and U. Mishra	Loamy sand soil approaches organic carbon saturation after 37 years of conservation tillage	Agronomy Journal
2020	10.1038/s41396-019-0582-x	Nuccio, 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-Ridge	Niche differentiation is spatially and temporally regulated in the rhizosphere	ISME Journal
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2020	10.1093/femsyr/foz089	Oh, E. J. and Y.-S. Jin	Engineering of Saccharomyces cerevisiae for efficient fermentation of cellulose	FEMS Yeast Research
2020	10.1021/acssynbio.0c00159	Oh, E. J., R. Liu, L. Liang, E. F. Freed, C. A. Eckert and R. T. Gill	Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform	ACS Synthetic Biology
2020	10.1534/g3.120.401402	Olatoye, M. O., L. V. Clark, N. R. Labonte, H. Dong, M. S. Dwiyanti, K. G. Anzoua, J. E. Brummer, B. K. Ghimire, E. Dzyubenko, N. Dzyubenko, L. Bagmet, A. Sabitov, P. Chebukin, K. Glowacka, K. Heo, X. Jin, H. Nagano, J. Peng, C. Y. Yu, J. H. Yoo, H. Zhao, S. P. Long, T. Yamada, E. J. Sacks and A. E. Lipka	Training Population Optimization for Genomic Selection in Miscanthus	G3 Genes\|Genomes\|Genetics
2020	10.1080/15321819.2020.1804933	Olayinka, 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. Adeniji	A possible risk of environmental exposure to HEV in Ibadan, Oyo State, Nigeria	Journal of Immunoassay and Immunochemistry
2020	10.1111/tpj.15086	Oliver, J., M. Fan, B. McKinley, S. Zemelis-Durfee, F. Brandizzi, C. Wilkerson and J. E. Mullet	The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor	The Plant Journal
2020	10.1371/journal.pcbi.1008137	Ong, W. K., D. K. Courtney, S. Pan, R. B. Andrade, P. J. Kiley, B. F. Pfleger and J. L. Reed	Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4	PLOS Computational Biology
2020	10.1094/PBIOMES-05-20-0044-R	Onufrak, A. J., G. M. Williams, W. E. Klingeman, M. A. Cregger, D. M. Klingeman, J. M. DeBruyn, M. D. Ginzel and D. Hadziabdic	Regional Differences in the Structure of Juglans nigra Phytobiome Reflect Geographical Differences in Thousand Cankers Disease Severity	Phytobiomes Journal
2020	10.1128/aem.01888-19	Oshlag, J. Z., Y. Ma, K. Morse, B. T. Burger, R. A. Lemke, S. D. Karlen, K. S. Myers, T. J. Donohue and D. R. Noguera	Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris	Applied and Environmental Microbiology
2020	10.1016/j.coisb.2020.09.007	Ostrov, N., A. Nyerges, A. Chiappino-Pepe, A. Rudolph, M. Baas-Thomas and G. M. Church	Synthetic genomes with altered genetic codes	Current Opinion in Systems Biology
2020	10.1186/s12864-020-6554-8	Panchy, N. L., J. P. Lloyd and S.-H. Shiu	Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data	BMC Genomics
2020	10.1002/ecy.2887	Papp, K., B. A. Hungate and E. Schwartz	Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP	Ecology
2020	10.1111/gcbb.12684	Parajuli, S., B. Kannan, R. Karan, G. Sanahuja, H. Liu, E. Garcia-Ruiz, D. Kumar, V. Singh, H. Zhao, S. Long, J. Shanklin and F. Altpeter	Towards oilcane: Engineering hyperaccumulation of triacylglycerol into sugarcane stems	GCB Bioenergy
2020	10.1002/cssc.202000268	Park, 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. Singer	Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass	ChemSusChem
2020	10.1111/tpj.14870	Park, S. and S.-Y. Ding	The N-terminal zinc finger of CELLULOSE SYNTHASE6 is critical in defining its functional properties by determining the level of homodimerization in Arabidopsis	The Plant Journal
2020	10.1017/S143192762002190X	Parrell, D., K. Lemmer, T. Donohue and E. Wright	Deletion of the ntrYX Two Component System in Rhodobacter sphaeroides Causes the Generation of Diverse Extracellular Membrane Structures	Microscopy and Microanalysis
2020	10.1128/MRA.00159-20	Pelletier, D. A., L. H. Burdick, M. Podar, C. W. Schadt and U. C. Kalluri	Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots	Microbiology resource announcements
2020	10.1038/s41467-020-15559-4	Peris, D., W. G. Alexander, K. J. Fisher, R. V. Moriarty, M. G. Basuino, E. J. Ubbelohde, R. L. Wrobel and C. T. Hittinger	Synthetic hybrids of six yeast species	Nature Communications
2020	10.1029/2019JG005526	Perryman, C. R., C. K. McCalley, A. Malhotra, M. F. Fahnestock, N. N. Kashi, J. G. Bryce, R. Giesler and R. K. Varner	Thaw Transitions and Redox Conditions Drive Methane Oxidation in a Permafrost Peatland	Journal of Geophysical Research: Biogeosciences
2020	10.1086/706198	Petipas, R. H., A. W. Bowsher, C. S. Bekkering, C. N. Jack, E. E. McLachlan, R. A. I. White, B. S. Younginger, L. K. Tiemann, B. S. Evans and M. L. Friesen	Interactive effects of microbes and nitrogen on Panicum virgatum root functional traits and patterns of phenotypic selection	International Journal of Plant Sciences
2020	10.1002/jbm.a.36811	Pierce, A., Y. Zheng, W. L. Wagner, H. V. Scheller, D. Mohnen, A. Tsuda, M. Ackermann and S. J. Mentzer	Pectin biopolymer mechanics and microstructure associated with polysaccharide phase transitions	Journal of Biomedical Materials Research Part A
2020	10.1111/nph.16759	Plett, J. M., K. L. Plett, J. Wong-Bajracharya, M. de Freitas Pereira, M. D. Costa, A. Kohler, F. Martin and I. C. Anderson	Mycorrhizal effector PaMiSSP10b alters polyamine biosynthesis in Eucalyptus root cells and promotes root colonization	New Phytologist
2020	10.1128/MRA.00617-20	Podar, M., J. Turner, L. H. Burdick and D. A. Pelletier	Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides Rhizosphere	Microbiology Resource Announcements
2020	10.1128/MRA.00644-20	Podar, M., J. Turner, L. H. Burdick and D. A. Pelletier	Complete Genome Sequence of Starkeya sp. Strain ORNL1, a Soil Alphaproteobacterium Isolated from the Rhizosphere of Populus deltoides	Microbiology Resource Announcements
2020	10.1016/j.agrformet.2020.108188	Poe, J., D. E. Reed, M. Abraha, J. Chen, K. M. Dahlin and A. R. Desai	Geospatial coherence of surface-atmosphere fluxes in the upper Great Lakes region	Agricultural and Forest Meteorology
2020	10.1128/mBio.02293-19	Pold, G., L. A. Domeignoz-Horta, E. W. Morrison, S. D. Frey, S. A. Sistla and K. M. DeAngelis	Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria	mBio
2020	10.3389/ffgc.2020.00097	Policelli, N., T. R. Horton, A. T. Hudon, T. R. Patterson and J. M. Bhatnagar	Back to Roots: The Role of Ectomycorrhizal Fungi in Boreal and Temperate Forest Restoration	Frontiers in Forests and Global Change
2020	10.1002/saj2.20159	Purcell, 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. Hungate	Quantitative stable isotope probing with H218O to measure taxon-specific microbial growth	Soil Science Society of America Journal
2020	10.1021/acssuschemeng.0c04433	Ragauskas, A. and X. Meng	ACS Sustainable Chemistry & Engineering Virtual Special Issue on Recent Advances in Biomass Characterization and Modeling	ACS Sustainable Chemistry & Engineering
2020	10.1111/1758-2229.12838	Rajeev, L., M. E. Garber and A. Mukhopadhyay	Tools to map target genes of bacterial two-component system response regulators	Environmental Microbiology Reports
2020	10.1111/nph.16827	Ralph, J.	Tricin and tricin-lignins in Medicago versus in monocots	New Phytologist
2020	10.1016/j.copbio.2020.10.001	Rapp, K. M., J. P. Jenkins and M. J. Betenbaugh	Partners for life: building microbial consortia for the future	Current Opinion in Biotechnology
2020	10.1111/1462-2920.15242	Ray, P., Y. Guo, M.-H. Chi, N. Krom, M. C. Saha and K. D. Craven	Serendipita bescii promotes winter wheat growth and modulates the host root transcriptome under phosphorus and nitrogen starvation	Environmental Microbiology
2020	10.1007/s10021-019-00407-4	Reed, D. E., J. Chen, M. Abraha, G. P. Robertson and K. M. Dahlin	The Shifting Role of mRUE for Regulating Ecosystem Production	Ecosystems
2020	10.1021/acssynbio.0c00394	Reis, A. C. and H. M. Salis	An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models	ACS Synthetic Biology
2020	10.1016/j.isci.2019.100795	Ren, H., C. Shi and H. Zhao	Computational tools for discovering and engineering natural product biosynthetic pathways	iScience
2020	10.1128/MRA.00770-20	Reyes, S. M., E. Bolettieri, D. Allen and A. G. Hay	Genome Sequences of Four Strains of Acinetobacter bereziniae Isolated from Human Milk Pumped with a Personal Breast Pump and Hand-Washed Milk Collection Supplies	Microbiology Resource Announcements
2020	10.1073/pnas.1912434117	Ribeiro, C. L., D. Conde, K. M. Balmant, C. Dervinis, M. G. Johnson, A. P. McGrath, P. Szewczyk, F. Unda, C. A. Finegan, H. W. Schmidt, B. Miles, D. R. Drost, E. Novaes, C. A. Gonzalez-Benecke, G. F. Peter, J. G. Burleigh, T. A. Martin, S. D. Mansfield, G. Chang, N. J. Wickett and M. Kirst	The uncharacterized gene EVE contributes to vessel element dimensions in Populus	Proceedings of the National Academy of Sciences
2020	10.1111/pbi.13510	Rigoulot, S. B., T. M. Schimel, J. H. Lee, R. G. Sears, H. Brabazon, J. S. Layton, L. Li, K. A. Meier, M. R. Poindexter, M. J. Schmid, E. M. Seaberry, J. A. Madajian, M. J. Finander, J. DiBenedetto, A. Occhialini, S. C. Lenaghan and C. N. Stewart Jr	Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants	Plant Biotechnology Journal
2020	10.1021/acssuschemeng.9b04451	Rigual, 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. Singh	Evaluating Protic Ionic Liquid for Woody Biomass One-Pot Pretreatment + Saccharification, Followed by Rhodosporidium toruloides Cultivation	ACS Sustainable Chemistry & Engineering
2020	10.1534/g3.120.401489	Robinson, A. J., D. O. Natvig and P. S. G. Chain	Genomic Analysis of Diverse Members of the Fungal Genus Monosporascus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate	G3 (Bethesda)
2020	10.1002/cbic.201900560	Rodrigues, A. V., D. J. Tantillo, A. Mukhopadhyay, J. D. Keasling and H. R. Beller	Insight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme	ChemBioChem
2020	10.1094/PBIOMES-11-19-0064-FI	Roley, S. S., T. C. Ulbrich and G. P. Robertson	Nitrogen Fixation and Resorption Efficiency Differences Among Twelve Upland and Lowland Switchgrass Cultivars	Phytobiomes Journal
2020	10.1002/saj2.20082	Ruan, L. and G. P. Robertson	No-till establishment improves the climate benefit of bioenergy crops on marginal grasslands	Soil Science Society of America Journal
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2020	10.3390/f11020213	Russell, A. E. and W. J. Parton	Modeling the Effects of Global Change on Ecosystem Processes in a Tropical Rainforest	Forests
2020	10.1128/AEM.00909-20	Russell, J. F., M. L. Russo, X. Wang, N. Hengge, D. Chung, L. Wells, Y. J. Bomble and J. Westpheling	Deletion 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 Substrates	Applied and Environmental Microbiology
2020	10.1002/aic.16994	Ryu, J. and C. T. Maravelias	Efficient generalized shortcut distillation model with improved accuracy for superstructure-based process synthesis	AIChE Journal
2020	10.1016/j.compchemeng.2020.107072	Ryu, J. and C. T. Maravelias	Computationally efficient optimization models for preliminary distillation column design and separation energy targeting	Computers & Chemical Engineering
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2020	10.1038/s41598-020-77684-w	Samira, R., J. A. Kimball, L. F. Samayoa, J. B. Holland, T. M. Jamann, P. J. Brown, G. Stacey and P. J. Balint-Kurti	Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum	Scientific Reports
2020	10.1186/s13068-020-01690-3	Sander, K. B., D. Chung, D. M. Klingeman, R. J. Giannone, M. Rodriguez, J. Whitham, R. L. Hettich, B. H. Davison, J. Westpheling and S. D. Brown	Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii	Biotechnology for Biofuels
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2020	10.1104/pp.19.00760	Schwarz, B., C. B. Azodi, S.-H. Shiu and P. Bauer	Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots	Plant Physiology
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2020	10.1093/femsle/fnaa045	Semrau, J. D., A. A. DiSpirito, P. K. Obulisamy and C. S. Kang-Yun	Methanobactin from methanotrophs: genetics, structure, function and potential applications	FEMS Microbiology Letters
2020	10.3390/metabo10060250	Sengupta, A., P. Pritam, D. Jaiswal, A. Bandyopadhyay, H. B. Pakrasi and P. P. Wangikar	Photosynthetic co-production of succinate and ethylene in a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801	Metabolites
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2020	10.1111/gcbb.12731	Serba, D., D. Walker, J. Jenkins, J. Schmutz, S. Bhamidimarri and M. Saha	Genome?wide QTL detection for biofuel traits in switchgrass ( Panicum virgatum L.)	GCB Bioenergy
2020	10.3389/fcell.2020.566702	Sertbas, M. and K. O. Ulgen	Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens	Frontiers in Cell and Developmental Biology
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2020	10.1021/acs.iecr.9b06086	Shen, Z. and R. C. Van Lehn	Solvent Selection for the Separation of Lignin-Derived Monomers Using the Conductor-like Screening Model for Real Solvents	Industrial & Engineering Chemistry Research
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2020	10.1007/s12010-020-03293-y	Sitepu, I., L. Enriquez, V. Nguyen, R. Fry, B. Simmons, S. Singer, C. Simmons and K. L. Boundy-Mills	Ionic Liquid Tolerance of Yeasts in Family Dipodascaceae and Genus Wickerhamomyces	Applied Biochemistry and Biotechnology
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2020	10.1016/j.bej.2020.107707	Stone, K., M. Hilliard, K. Badr, A. Bradford, Q. P. He and J. Wang	Comparative study of oxygen-limited and methane-limited growth phenotypes of Methylomicrobium buryatense 5GB1	Biochemical Engineering Journal
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2020	10.1007/s00216-020-02544-5	Strobbia, P., R. A. Odion, M. Maiwald, B. Sumpf and T. Vo-Dinh	Direct SERDS sensing of molecular biomarkers in plants under field conditions	Analytical and Bioanalytical Chemistry
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2020	10.1002/biot.202000142	Sun, L. and Y.-S. Jin	Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae	Biotechnology Journal
2020	10.1002/bit.27508	Sun, L., C. A. Atkinson, Y.-G. Lee and Y.-S. Jin	High-level ?-carotene production from xylose by engineered Saccharomyces cerevisiae without overexpression of a truncated HMG1 (tHMG1)	Biotechnology and Bioengineering
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2020	10.3389/fpls.2020.596301	Sun, Y., Z. Qiao, W. Muchero and J. G. Chen	Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface	Front Plant Sci
2020	10.1002/aic.16235	Suthers, P. F. and C. D. Maranas	Challenges of cultivated meat production and applications of genome-scale metabolic modeling	AIChE Journal
2020	10.1016/j.ymben.2020.11.013	Suthers, P. F., C. J. Foster, D. Sarkar, L. Wang and C. D. Maranas	Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms	Metabolic Engineering
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2020	10.1105/tpc.19.00628	Takeuchi, T., B. B. Sears, C. D. Lindeboom, Y.-T. Lin, N. Fekaris, K. Zienkiewicz, A. Zienkiewicz, E. Poliner and C. Benning	Chlamydomonas CHT7 is required for an effective quiescent state by regulating nutrient-responsive cell cycle gene expression	Plant Cell
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2020	10.1002/saj2.20010	Thies, S., D. R. Joshi, S. A. Bruggeman, S. A. Clay, U. Mishra, J. Morile-Miller and D. E. Clay	Fertilizer timing affects nitrous oxide, carbon dioxide, and ammonia emissions from soil	Soil Science Society of America Journal
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2020	10.1093/synbio/ysaa005	Tiedge, K., A. Muchlinski and P. Zerbe	Genomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challenges	Synthetic Biology
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2020	10.1128/MRA.00852-20	Tshipamba, M. E., K. A. Alayande, N. Lubanza and M. Mwanza	Whole-Genome Sequencing of Multidrug-Resistant Campylobacter fetus subsp. fetus NWU_ED24, Isolated from a Bovine Sheath Wash Sample	Microbiology Resource Announcements
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2020	10.1093/jxb/eraa060	Tsogtbaatar, E., J.-C. Cocuron and A. P. Alonso	Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesis	Journal of Experimental Botany
2020	10.1094/PBIOMES-12-19-0069-FI	Ulbrich, T. C., M. Friesen, S. S. Roley, L. K. Tiemann and S. E. Evans	Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars	Phytobiomes Journal
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2020	10.1128/mSystems.00092-20	Veach, A. M., H. Chen, Z. K. Yang, A. D. Labbe, N. L. Engle, T. J. Tschaplinski, C. W. Schadt and M. A. Cregger	Plant Hosts Modify Belowground Microbial Community Response to Extreme Drought	mSystems
2020	10.1128/mSystems.00250-20	Vera, J. M., I. N. Ghosh, Y. Zhang, A. S. Hebert, J. J. Coon and R. Landick	Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters	mSystems
2020	10.1038/s41598-020-71672-w	Vijaya Kumar, S., P. E. Abraham, G. B. Hurst, K. Chourey, A. N. Bible, R. L. Hettich, M. J. Doktycz and J. L. Morrell-Falvey	A carotenoid-deficient mutant of the plant-associated microbe Pantoea sp. YR343 displays an altered membrane proteome	Scientific Reports
2020	10.1093/femsec/fiaa229	Vishnivetskaya, T. A., A. L. Almatari, E. V. Spirina, X. Wu, D. E. Williams, S. M. Pfiffner and E. M. Rivkina	Insights into community of photosynthetic microorganisms from permafrost	FEMS Microbiology Ecology
2020	10.1016/j.indcrop.2020.112906	Viswanathan, M. B., K. Park, M.-H. Cheng, E. B. Cahoon, I. Dweikat, T. Clemente and V. Singh	Variability in structural carbohydrates, lipid composition, and cellulosic sugar production from industrial hemp varieties	Industrial Crops and Products
2020	10.1021/acssynbio.0c00129	Volk, M. J., I. Lourentzou, S. Mishra, L. T. Vo, C. Zhai and H. Zhao	Biosystems design by machine learning	ACS Synthetic Biology
2020	10.1111/gcb.15124	von Haden, A. C., W. H. Yang and E. H. DeLucia	Soils' dirty little secret: Depth-based comparisons can be inadequate for quantifying changes in soil organic carbon and other mineral soil properties	Global Change Biology
2020	10.1128/aem.02299-19	Walker, C., S. Ryu, R. J. Giannone, S. Garcia and C. T. Trinh	Understanding and Eliminating the Detrimental Effect of Thiamine Deficiency on the Oleaginous Yeast Yarrowia lipolytica	Applied and Environmental Microbiology
2020	10.1128/mra.01356-19	Walker, C., S. Ryu, S. Haridas, H. Na, M. Zane, K. LaButti, K. Barry, I. V. Grigoriev and C. T. Trinh	Draft Genome Assemblies of Ionic Liquid-Resistant Yarrowia lipolytica PO1f and Its Superior Evolved Strain, YlCW001	Microbiology Resource Announcements
2020	10.1007/s11244-020-01260-9	Walker, T. W., A. K. Chew, R. C. Van Lehn, J. A. Dumesic and G. W. Huber	Rational design of mixed solvent systems for acid-catalyzed biomass conversion processes using a combined experimental, molecular dynamics and machine learning approach	Topics in Catalysis
2020	10.1126/sciadv.aba7599	Walker, 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. Huber	Recycling of multilayer plastic packaging materials by solvent-targeted recovery and precipitation	Science advances
2020	10.1021/acssuschemeng.0c01538	Walker, T. W., N. Kuch, K. A. Vander Meulen, C. F. M. Clewett, G. W. Huber, B. G. Fox and J. A. Dumesic	Solid-State NMR studies of solvent-mediated, acid-catalyzed woody biomass pretreatment for enzymatic conversion of residual cellulose	ACS Sustainable Chemistry & Engineering
2020	10.1016/j.synbio.2020.01.002	Wang, B. and H. Zhao	Unleashing the power of energy storage: Engineering ?-oxidation pathways for polyketide production	Synthetic and Systems Biotechnology
2020	10.1021/acs.accounts.9b00544	Wang, F. and S. S. Stahl	Electrochemical Oxidation of Organic Molecules at Lower Overpotential: Accessing Broader Functional Group Compatibility with Electron?Proton Transfer Mediators	Accounts of Chemical Research
2020	10.1016/j.jhydrol.2020.124777	Wang, G., W. Huang, G. Zhou, M. A. Mayes and J. Zhou	Modeling the processes of soil moisture in regulating microbial and carbon-nitrogen cycling	Journal of Hydrology
2020	10.3389/fenrg.2020.563352	Wang, J., N. Roberts, M. Hilliard and Q. P. He	A Microalgae-Methanotroph Coculture is a Promising Platform for Fuels and Chemical Production From Wastewater	Frontiers in Energy Research
2020	10.1007/s12155-019-10072-z	Wang, S., G. R. Sanford, G. P. Robertson, R. D. Jackson and K. D. Thelen	Perennial Bioenergy Crop Yield and Quality Response to Nitrogen Fertilization	BioEnergy Research
2020	10.1093/jxb/eraa432	Wang, S., K. Guan, Z. Wang, E. A. Ainsworth, T. Zheng, P. A. Townsend, K. Li, C. Moller, G. Wu and C. Jiang	Unique contributions of chlorophyll and nitrogen to predict crop photosynthetic capacity from leaf spectroscopy	Journal of Experimental Botany
2020	10.1002/aic.16716	Wang, Y. J., X. W. Yu and H. M. Zhao	Biosystems design by directed evolution	AIChE Journal
2020	10.1021/acscatal.0c02489	Wang, Y., X. Huang, J. Hui, L. T. Vo and H. Zhao	Stereoconvergent Reduction of Activated Alkenes by a Nicotinamide Free Synergistic Photobiocatalytic System	ACS Catalysis
2020	10.3389/fenrg.2020.00149	Wang, Y.-Y., P. Sengupta, B. Scheidemantle, Y. Pu, C. E. Wyman, C. M. Cai and A. J. Ragauskas	Effects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane Properties	Frontiers in Energy Research
2020	10.1111/gcb.15365	Waring, B. G., B. N. Sulman, S. Reed, A. P. Smith, C. Averill, C. A. Creamer, D. F. Cusack, S. J. Hall, J. D. Jastrow, A. Jilling, K. M. Kemner, M. Kleber, X.-J. A. Liu, J. Pett-Ridge and M. Schulz	From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world	Global Change Biology
2020	10.1111/tpj.14949	Weiss, 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. Zhang	Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis	The Plant Journal
2020	10.1016/j.drudis.2020.02.002	Westbrook, J. D., R. Soskind, B. P. Hudson and S. K. Burley	Impact of the Protein Data Bank on antineoplastic approvals	Drug Discovery Today
2020	10.1002/bit.27364	Whitehead, T. A., S. Banta, W. E. Bentley, M. J. Betenbaugh, C. Chan, D. S. Clark, C. A. Hoesli, M. C. Jewett, B. Junker, M. Koffas, R. Kshirsagar, A. Lewis, C.-T. Li, C. Maranas, E. Terry Papoutsakis, K. L. J. Prather, S. Schaffer, L. Segatori and I. Wheeldon	The importance and future of biochemical engineering	Biotechnology and Bioengineering
2020	10.1099/ijsem.0.004387	Wilhelm, R. C., K. T. Cyle, C. E. Martinez, D. C. Karasz, J. D. Newman and D. H. Buckley	Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana	International Journal of Systematic and Evolutionary Microbiology
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2020	10.1371/journal.pone.0232437	Wilpiszeski, R. L., C. M. Gionfriddo, A. M. Wymore, J. W. Moon, K. A. Lowe, M. Podar, S. Rafie, M. W. Fields, T. C. Hazen, X. Ge, F. Poole, M. W. W. Adams, R. Chakraborty, Y. Fan, J. D. Van Nostrand, J. Zhou, A. P. Arkin and D. A. Elias	In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations	PLoS One
2020	10.1016/j.soilbio.2019.107678	Woolet, J. and T. Whitman	Pyrogenic organic matter effects on soil bacterial community composition	Soil Biology and Biochemistry
2020	10.1038/s41396-020-00753-5	Wu, B., F. Liu, A. Zhou, J. Li, L. Shu, M. L. Kempher, X. Yang, D. Ning, F. Pan, G. M. Zane, J. D. Wall, J. D. Van Nostrand, P. Juneau, S. Chen, Q. Yan, J. Zhou and Z. He	Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris	The ISME Journal
2020	10.1021/acssuschemeng.9b07226	Wu, J., R. P. Chandra, K. H. Kim, C. S. Kim, Y. Pu, A. J. Ragauskas and J. N. Saddler	Enhancing Enzyme-Mediated Hydrolysis of Mechanical Pulps by Deacetylation and Delignification	ACS Sustainable Chemistry & Engineering
2020	10.1002/bbb.2083	Wu, X., J. Jiang, C. Wang, J. Liu, Y. Pu, A. Ragauskas, S. Li and B. Yang	Lignin-derived electrochemical energy materials and systems	Biofuels, Bioproducts and Biorefining
2020	10.1016/j.cbpa.2020.05.003	Wu, Y., Z. Yang and Y. Lu	Photocaged functional nucleic acids for spatiotemporal imaging in biology	Current Opinion in Chemical Biology
2020	10.1002/pld3.178	Xie, M., J. Zhang, V. R. Singan, M. J. McGranahan, P. R. LaFayette, S. S. Jawdy, N. Engle, C. Doeppke, T. J. Tschaplinski, M. F. Davis, E. Lindquist, K. Barry, J. Schmutz, W. A. Parrott, F. Chen, G. A. Tuskan, J.-G. Chen and W. Muchero	Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect	Plant Direct
2020	10.1016/j.plipres.2020.101069	Xu, C., J. Fan and J. Shanklin	Metabolic and functional connections between cytoplasmic and chloroplast triacylglycerol storage	Progress in Lipid Research
2020	10.1016/j.soilbio.2020.107986	Xu, J., S. S. Roley, M. M. Tfaily, R. K. Chu and J. M. Tiedje	Organic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scales	Soil Biology and Biochemistry
2020	10.1093/nar/gkaa131	Xu, P., C. Modavi, B. Demaree, F. Twigg, B. Liang, C. Sun, W. Zhang and A. R. Abate	Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery	Nucleic Acids Research
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2020	10.1016/bs.mie.2020.04.054	Xue, P., T. Si and H. Zhao	Optically guided mass spectrometry to screen microbial colonies for directed enzyme evolution	Methods in Enzymology
2020	10.1002/bit.27343	Xue, P., T. Si, S. Mishra, L. Zhang, K. Choe, J. V. Sweedler and H. Zhao	A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids	Biotechnology and Bioengineering
2020	10.1104/pp.19.01467	Yamamoto, M., H. Tomiyama, A. Koyama, H. Okuizumi, S. Liu, R. Vanholme, G. Goeminne, Y. Hirai, H. Shi, N. Takata, T. Ikeda, M. Uesugi, H. Kim, S. Sakamoto, N. Mitsuda, W. Boerjan, J. Ralph and S. Kajita	A Century-Old Mystery Unveiled: Sekizaisou is a Natural Lignin Mutant	Plant Physiology
2020	10.1016/j.ymben.2019.04.009	Yan, Q. and B. F. Pfleger	Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals	Metabolic Engineering
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2020	10.1073/pnas.2000053117	Yang, M., N. R. Baral, B. A. Simmons, J. C. Mortimer, P. M. Shih and C. D. Scown	Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels	Proceedings of the National Academy of Sciences
2020	10.1088/1748-9326/ab865f	Yang, P., Q. Zhao and X. Cai	Machine learning based estimation of land productivity in the contiguous US using biophysical predictors	Environmental Research Letters
2020	10.34133/2020/8051764	Yang, X., J. I. Medford, K. Markel, P. M. Shih, H. C. De Paoli, C. T. Trinh, A. J. McCormick, R. Ployet, S. G. Hussey, A. A. Myburg, P. E. Jensen, M. M. Hassan, J. Zhang, W. Muchero, U. C. Kalluri, H. Yin, R. Zhuo, P. E. Abraham, J.-G. Chen, D. J. Weston, Y. Yang, D. Liu, Y. Li, J. Labbe, B. Yang, J. H. Lee, R. W. Cottingham, S. Martin, M. Lu, T. J. Tschaplinski, G. Yuan, H. Lu, P. Ranjan, J. C. Mitchell, S. D. Wullschleger and G. A. Tuskan	Plant Biosystems Design Research Roadmap 1.0	BioDesign Research
2020	10.1016/j.bpj.2020.04.009	Yin, S., M. Tien and H. Yang	Prior-Apprised Unsupervised Learning of Subpixel Curvilinear Features in Low Signal/Noise Images	Biophysical Journal
2020	10.1016/j.biortech.2020.122784	Yoo, C. G., X. Meng, Y. Pu and A. J. Ragauskas	The critical role of lignin in lignocellulosic biomass conversion and recent pretreatment strategies: A comprehensive review	Bioresource Technology
2020	10.1093/plphys/kiaa071	Young, D. Y. and Y. Shachar-Hill	Large fluxes of fatty acids from membranes to triacylglycerol and back during N-deprivation and recovery in Chlamydomonas	Plant Physiology
2020	10.1016/j.jpdc.2019.07.008	Young, M. T., J. Hinkle, R. Kannan and A. Ramanathan	Distributed Bayesian optimization of deep reinforcement learning algorithms	Journal of Parallel and Distributed Computing
2020	10.1007/s00138-020-01088-z	Yu, G., A. Zare, H. Sheng, R. Matamala, J. Reyes-Cabrera, F. B. Fritschi and T. E. Juenger	Root identification in minirhizotron imagery with multiple instance learning	Machine Vision and Applications
2020	10.1038/s41586-020-2468-5	Yu, H. and J. R. Leadbetter	Bacterial chemolithoautotrophy via manganese oxidation	Nature
2020	10.1074/jbc.H120.014701	Yu, X.-H. and J. Shanklin	Solving a furan fatty acid biosynthesis puzzle	Journal of Biological Chemistry
2020	10.1111/gcbb.12728	Zeri, M., W. H. Yang, G. Cunha-Zeri, C. D. Gibson and C. J. Bernacchi	Nitrous oxide fluxes over establishing biofuel crops: Characterization of temporal variability using the cross-wavelet analysis	GCB Bioenergy
2020	10.3389/fpls.2020.00652	Zhang, J., G. A. Tuskan, T. J. Tschaplinski, W. Muchero and J.-G. Chen	Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in Populus	Frontiers in Plant Science
2020	10.1111/pbi.13254	Zhang, J., M. Xie, M. Li, J. Ding, Y. Pu, A. C. Bryan, W. Rottmann, K. A. Winkeler, C. M. Collins, V. Singan, E. A. Lindquist, S. S. Jawdy, L. E. Gunter, N. L. Engle, X. Yang, K. Barry, T. J. Tschaplinski, J. Schmutz, G. A. Tuskan, W. Muchero and J. G. Chen	Overexpression of a Prefoldin beta subunit gene reduces biomass recalcitrance in the bioenergy crop Populus	Plant Biotechnology Journal
2020	10.1186/s12870-020-2275-z	Zhang, X., S. B. Fernandes, C. Kaiser, P. Adhikari, P. J. Brown, S. X. Mideros and T. M. Jamann	Conserved defense responses between maize and sorghum to Exserohilum turcicum	BMC Plant Biology
2020	10.1016/j.biteb.2020.100517	Zhang, 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. Sato	Production of hydrolysates from unmilled AFEX-pretreated switchgrass and comparative fermentation with Zymomonas mobilis	Bioresource Technology Reports
2020	10.1016/j.agee.2020.107085	Zhang, Y., N. L. Haan and D. A. Landis	Landscape composition and configuration have scale-dependent effects on agricultural pest suppression	Agriculture, Ecosystems & Environment
2020	10.3390/microorganisms8040608	Zhao, J., X. Zhao, J. Wang, Q. Gong, X. Zhang and G. Zhang	Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture	Microorganisms
2020	10.1061/(ASCE)WR.1943-5452.0001197	Zhao, Q., X. Cai and Y. Li	Algorithm Design Based on Derived Operation Rules for a System of Reservoirs in Parallel	Journal of Water Resources Planning and Management
2020	10.1016/j.rser.2020.110265	Zhao, Q., X. Cai, W. Mischo and L. Ma	How do the research and public communities view biofuel development?	Renewable and Sustainable Energy Reviews
2020	10.1002/cssc.202001401	Zhao, Z.-M., Z.-H. Liu, Y. Pu, X. Meng, J. Xu, J. S. Yuan and A. J. Ragauskas	Emerging Strategies for Modifying Lignin Chemistry to Enhance Biological Lignin Valorization	ChemSusChem
2020	10.1021/acs.est.0c01028	Zheng, H., K. Kim, A. Kravchenko, M. Rivers and A. Guber	Testing Os staining approach for visualizing soil organic matter patterns in intact samples via X-ray dual-energy tomography scanning	Environmental Science & Technology
2020	10.3390/molecules25092108	Zheng, Y., A. Pierce, W. L. Wagner, H. V. Scheller, D. Mohnen, M. Ackermann and S. J. Mentzer	Water-Dependent Blending of Pectin Films: The Mechanics of Conjoined Biopolymers	Molecules
2020	10.1186/s13059-020-1952-4	Zhou, R., D. Macaya-Sanz, C. H. Carlson, J. Schmutz, J. W. Jenkins, D. Kudrna, A. Sharma, L. Sandor, S. Shu, K. Barry, G. A. Tuskan, T. Ma, J. Liu, M. Olson, L. B. Smart and S. P. DiFazio	A willow sex chromosome reveals convergent evolution of complex palindromic repeats	Genome Biology
2020	10.3390/genes11080843	Zhou, R., D. Macaya-Sanz, J. Schmutz, J. W. Jenkins, G. A. Tuskan and S. P. DiFazio	Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa	Genes
2020	10.1021/jacs.0c00199	Zhou, Y., G. E. Klinger, E. L. Hegg, C. M. Saffron and J. E. Jackson	Multiple mechanisms mapped in aryl alkyl ether cleavage via aqueous electrocatalytic hydrogenation over skeletal nickel	Journal of the American Chemical Society
2020	10.1038/s41467-020-15830-8	Zhu, P., X.-H. Yu, C. Wang, Q. Zhang, W. Liu, S. McSweeney, J. Shanklin, E. Lam and Q. Liu	Structural basis for Ca2+-dependent activation of a plant metacaspase	Nature Communications
2020	10.1111/gcb.15319	Zhu, X., R. D. Jackson, E. H. DeLucia, J. M. Tiedje and C. Liang	The soil microbial carbon pump: From conceptual insights to empirical assessments	Global Change Biology
2020	10.1104/pp.19.00854	Zienkiewicz, 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. Benning	The Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen Availability	Plant Physiology
2019	10.1002/aic.16367	Abernathy, M. H., Y. C. Zhang, W. D. Hollinshead, G. Wang, E. E. K. Baidoo, T. G. Liu and Y. J. J. Tang	Comparative studies of glycolytic pathways and channeling under in vitro and in vivo modes	Aiche Journal
2019	10.1088/1748-9326/aafc10	Abraha, M., I. Gelfand, S. K. Hamilton, J. Q. Chen and G. P. Robertson	Carbon debt of field-scale conservation reserve program grasslands converted to annual and perennial bioenergy crops	Environmental Research Letters
2019	10.1002/hyp.13630	Abraha, M., J. Q. Chen, S. K. Hamilton and G. P. Robertson	Long-term evapotranspiration rates for rainfed corn versus perennial bioenergy crops in a mesic landscape	Hydrological Processes
2019	10.1094/phyto-03-19-0105-r	Abraham, N., P. Chitrampalam, B. Nelson, R. S. Poudel, K. Chittem, P. Borowicz, R. Brueggeman, S. Jain and J. M. LeBoldus	Microscopic, biochemical, and molecular comparisons of moderately resistant and susceptible Populus genotypes inoculated with Sphaerulina musiva	Phytopathology
2019	10.1128/MRA.00595-19	Adeniji, A. A. and O. O. Babalola	Genome Sequence of Lipopeptide- and Antioxidant-Producing Strain Bacillus velezensis NWUMFkBS10.5	Microbiology Resource Announcements
2019	10.1007/s00253-019-09710-5	Adeniji, A. A., D. T. Loots and O. O. Babalola	Bacillus velezensis: phylogeny, useful applications, and avenues for exploitation	Applied Microbiology and Biotechnology
2019	10.1002/mbo3.742	Adeniji, A. A., O. S. Aremu and O. O. Babalola	Selecting lipopeptide-producing, Fusarium-suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5	MicrobiologyOpen
2019	10.1021/acs.jafc.8b06707	Agarwal, U. P., S. A. Ralph, D. Padmakshan, S. Liu and C. E. Foster	Estimation of syringyl units in wood lignins by FT-raman spectroscopy	Journal of Agricultural and Food Chemistry
2019	10.1128/MRA.00362-19	Alayande, K. A., O. A. Aiyegoro and C. N. Ateba	Whole-Genome Sequence of Lactobacillus acidophilus PNW3, Isolated from Weaned Piglets of the Indigenous South African Windsnyer Pig Breed	Microbiology Resource Announcements
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2019	10.1016/j.copbio.2019.11.003	Allen, D. K. and J. D. Young	Tracing metabolic flux through time and space with isotope labeling experiments	Current Opinion in Biotechnology
2019	10.1038/s41477-018-0322-7	Allen, J. M., R. A. Folk, P. S. Soltis, D. E. Soltis and R. P. Guralnick	Biodiversity synthesis across the green branches of the tree of life	Nature Plants
2019	10.1007/s11626-019-00354-3	Altpeter, F., S. Parajuli, B. Kannan, G. B. Luo, R. Karan, H. Liu, E. Garcia-Ruiz, H. M. Zhao and J. Shanklin	Converting Sugarcane into Oilcane by Metabolic Engineering	In Vitro Cellular & Developmental Biology-Animal
2019	10.1007/s11627-019-09993-3	Altpeter, F., T. M. Oz, A. Altpeter, R. Karan and A. Merotto	Precision Nucleotide Editing in Sugarcane Following Homology Directed Repair of Targeted DNA Breaks	In Vitro Cellular & Developmental Biology-Plant
2019	10.1093/femsec/fiz049	Altshuler, I., J. Ronholm, A. Layton, T. C. Onstott, C. W. Greer and L. G. Whyte	Denitrifiers, nitrogen-fixing bacteria and N2O soil gas flux in high Arctic ice-wedge polygon cryosols	FEMS Microbiology Ecology
2019	10.1126/science.aaw1280	Amann, R. I., S. Baichoo, B. J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P. S. G. Chain, R. R. Colwell, D. G. Daffonchio, A. Danchin, V. de Lorenzo, P. C. Dorrestein, R. D. Finn, C. M. Fraser, J. A. Gilbert, S. J. Hallam, P. Hugenholtz, J. P. A. Ioannidis, J. K. Jansson, J. F. Kim, H. P. Klenk, M. G. Klotz, R. Knight, K. T. Konstantinidis, N. C. Kyrpides, C. E. Mason, A. C. McHardy, F. Meyer, C. A. Ouzounis, A. A. N. Patrinos, M. Podar, K. S. Pollard, J. Ravel, A. R. Munoz, R. J. Roberts, R. Rossello-Mora, S. A. Sansone, P. D. Schloss, L. M. Schriml, J. C. Setubal, R. Sorek, R. L. Stevens, J. M. Tiedje, A. Turjanski, G. W. Tyson, D. W. Ussery, G. M. Weinstock, O. White, W. B. Whitman and I. Xenarios	Toward unrestricted use of public genomic data	Science
2019	10.3389/fpls.2019.00129	Amin, A. B., K. N. Rathnayake, W. C. Yim, T. M. Garcia, B. Wone, J. C. Cushman and B. W. M. Wone	Crassulacean acid metabolism abiotic stress-responsive transcription factors: A potential genetic engineering approach for improving crop tolerance to abiotic stress	Frontiers in Plant Science
2019	10.3389/fpls.2019.00915	Amos, R. A., and Mohnen, D.	Critical review of plant cell wall matrix polysaccharide glycosyltransferase activities verified by heterologous protein expression	Frontiers in Plant Science
2019	10.1111/agec.12501	Anand, M., R. Q. Miao and M. Khanna	Adopting bioenergy crops: Does farmers' attitude toward loss matter?	Agricultural Economics
2019	10.1038/s41467-019-09986-1	Anderson, E. M., Stone, M.L., Katahira, R., Reed, M., Muchero, W., Ramirez, K.J., Beckham, G.T., and Roman-Leshkov, Y.	Differences in S/G ratio in natural poplar variants do not predict catalytic depolymerization monomer yields	Nature Communications
2019	10.1104/pp.19.00480	Andersson, B., C. Shen, M. Cantrell, D. S. Dandy and G. Peers	The fluctuating cell-specific light environment and its effects on cyanobacterial physiology	Plant Physiology
2019	10.1021/acssuschemeng.9b04981	Ando, D. and J. Ralph	Method to regioselectively iodine-tag free-phenolic aromatic end-groups in lignin for 1H-13CHSQC NMR analysis	ACS Sustainable Chemistry & Engineering
2019	10.1186/s13068-019-1535-3	Anthony, W. E., R. R. Carr, D. M. DeLorenzo, T. P. Campbell, Z. Y. Shang, M. Foston, T. S. Moon and G. Dantas	Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds	Biotechnology for Biofuels
2019	10.1128/MRA.00136-19	Aremu, B. R., C. Prigent-Combaret and O. O. Babalola	Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16	Microbiology Resource Announcements
2019	10.1186/s12864-019-5629-x	Armaleo, D., O. Muller, F. Lutzoni, O. S. Andresson, G. Blanc, H. B. Bode, F. R. Collart, F. Dal Grande, F. Dietrich, I. V. Grigoriev, S. Joneson, A. Kuo, P. E. Larsen, J. M. Logsdon, D. Lopez, F. Martin, S. P. May, T. R. McDonald, S. S. Merchant, V. Miao, E. Morin, R. Oono, M. Pellegrini, N. Rubinstein, M. V. Sanchez-Puerta, E. Savelkoul, I. Schmitt, J. C. Slot, D. Soanes, P. Szovenyi, N. J. Talbot, C. Veneault-Fourrey and B. B. Xavier	The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata	Bmc Genomics
2019	10.1371/journal.pone.0218316	Aufrecht, J. A., J. D. Fowlkes, A. N. Bible, J. Morrell-Falvey, M. J. Doktycz and S. T. Retterer	Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network	PLOS ONE
2019	10.3389/fenrg.2019.00085	Avci, U., X. L. Zhou, S. Pattathil, L. D. Sousa, M. G. Hahn, B. Dale, Y. Xu and V. Balan	Effects of Extractive Ammonia Pretreatment on the Ultrastructure and Glycan Composition of Corn Stover	Frontiers in Energy Research
2019	10.1534/g3.119.400498	Azodi, C. B., E. Bolger, A. McCarren, M. Roantree, G. de los Campos and S. H. Shiu	Benchmarking parametric and machine learning models for genomic prediction of complex traits	G3-Genes Genomes Genetics
2019	10.1128/MRA.00455-19	Babalola, O. O., A. S. Ayangbenro and O. S. Olanrewaju	Draft Genome Sequences of Three Rhizospheric Plant Growth-Promoting Bacteria	Microbiology Resource Announcements
2019	10.1128/MRA.01706-18	Babalola, O. O., B. R. Aremu and A. S. Ayangbenro	Draft Genome Sequence of Heavy Metal-Resistant Bacillus cereus NWUAB01	Microbiology Resource Announcements
2019	10.1002/wsbm.1472	Babele, P. K. and J. D. Young	Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria	Wiley Interdisciplinary Reviews-Systems Biology and Medicine
2019	10.1016/j.ifacol.2019.06.179	Badr, K., M. Hilliard, N. Roberts, Q. P. He and J. Wang	Photoautotroph-methanotroph coculture - A flexible platform for efficient biological CO2-CH4 Co-utilization	IFAC-PapersOnline
2019	10.1094/PBIOMES-09-19-0050-FI	Bahulikar, R. A., S. R. Chaluvadi, I. Torres-Jerez, J. Mosali, J. L. Bennetzen and M. Udvardi	Nitrogen Fertilization Reduces Nitrogen Fixation Activity of Diverse Diazotrophs in Switchgrass Roots	Phytobiomes Journal
2019	10.1186/s13068-019-1424-9	Bai, W. Q., W. T. Geng, S. J. Wang and F. Z. Zhang	Biosynthesis, regulation, and engineering of microbially produced branched biofuels	Biotechnology for Biofuels
2019	10.1007/978-1-4939-8757-3_1	Baidoo, E. E. K.	Microbial Metabolomics: A General Overview	Microbial Metabolomics: Methods and Protocols
2019	10.1007/978-1-4939-8757-3_2	Baidoo, E. E. K., and Teixeira Benites, V.	Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications	Microbial Metabolomics: Methods and Protocols
2019	10.1371/journal.pgen.1007786	Baker, E. P. and C. T. Hittinger	Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function	PLOS Genetics
2019	10.1126/sciadv.aav1869	Baker, E. P., D. Peris, R. V. Moriarty, X. Y. C. Li, J. C. Fay and C. T. Hittinger	Mitochondrial DNA and temperature tolerance in lager yeasts	Science Advances
2019	10.1007/s00425-018-3053-0	Banerjee, A., J. A. Arnesen, D. Moser, B. B. Motsa, S. R. Johnson and B. Hamberger	Engineering modular diterpene biosynthetic pathways in Physcomitrella patens	Planta
2019	10.1093/bioinformatics/btz021	Banf, M., K. M. Zhao and S. Y. Rhee	METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters	Bioinformatics
2019	10.1039/c8ee03266a	Baral, N. R., Kavvada, O., Mendez-Perez, D., Mukhopadhyay, A., Lee, T. S., Simmons, B. A., and Scown, C. D.	Techno-economic analysis and life-cycle greenhouse gas mitigation cost of five routes to bio-jet fuel blendstocks. Energy and Environmental Science	Energy & Environmental Science
2019	10.1021/acssuschemeng.9b02928	Baral, N. R., O. Kavvada, D. Mendez Perez, A. Mukhopadhyay, T. S. Lee, B. A. Simmons and C. D. Scown	Greenhouse Gas Footprint, Water-Intensity, and Production Cost of Bio-Based Isopentenol as a Renewable Transportation Fuel	ACS Sustainable Chemistry & Engineering
2019	10.1002/bbb.1975	Baral, N. R., R. Davis and T. H. Bradley	Supply and value chain analysis of mixed biomass feedstock supply system for lignocellulosic sugar production	Biofuels, Bioproducts and Biorefining
2019	10.1111/jbi.13641	Barge, E. G., D. R. Leopold, K. G. Peay, G. Newcombe and P. E. Busby	Differentiating spatial from environmental effects on foliar fungal communities of Populus trichocarpa	Journal of Biogeography
2019	10.1093/femsec/fiz194	Barnett, S. E., N. D. Youngblut and D. H. Buckley	Soil characteristics and land-use drive bacterial community assembly patterns	FEMS Microbiology Ecology
2019	10.1089/crispr.2019.29076.rba	Barrangou, R.	Partnering with bioRxiv	The CRISPR Journal
2019	10.1038/s41467-019-10082-7	Barros, J., Escamilla-Trevino, L., Song, L., Rao, X., Serrani-Yance, J.C., Palacios, M.D., Engle, N., Choudhury, F.K., Tschaplinski, T.J., Venables, B.J., Mittler, R., and Dixon, R.A.	4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase	Nature Communications
2019	10.1016/j.copbio.2018.09.003	Barros, J., S. Temple and R. A. Dixon	Development and commercialization of reduced lignin alfalfa	Current Opinion in Biotechnology
2019	10.1038/s41598-019-42271-1	Basso, B., G. Y. Shuai, J. S. Zhang and G. P. Robertson	Yield stability analysis reveals sources of large-scale nitrogen loss from the US Midwest	Scientific Reports
2019	10.1111/pce.13702	Basso, V., A. Kohler, S. Miyauchi, V. Singan, F. Guinet, J. Simura, O. Novak, K. W. Barry, M. Amirebrahimi, J. Block, Y. Daguerre, H. Na, I. V. Grigoriev, F. Martin and C. Veneault-Fourrey	An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots	Plant Cell & Environment
2019	10.1073/pnas.1903229116	Bastiaanse, H., M. Zinkgraf, C. Canning, H. Tsai, M. Lieberman, L. Comai, I. Henry and A. Groover	A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees	Proceedings of the National Academy of Sciences of the United States of America
2019	10.1073/pnas.1904154116	Batista, C. E., J. Ye, I. O. Ribeiro, P. C. Guimaraes, A. S. S. Medeiros, R. G. Barbosa, R. L. Oliveira, S. Duvoisin, Jr., K. J. Jardine, D. Gu, A. B. Guenther, K. A. McKinney, L. D. Martins, R. A. F. Souza and S. T. Martin	Intermediate-scale horizontal isoprene concentrations in the near-canopy forest atmosphere and implications for emission heterogeneity	Proceedings of the National Academy of Sciences of the United States of America
2019	10.1007/s11295-019-1399-5	Bdeir, R., Muchero, W., Yordanov, Y., Tuskan, G.A., Busov, V., and Gailing, O.	Genome-wide association studies of bark texture in Populus trichocarpa	Tree Genetics & Genomes
2019	10.1128/mra.00857-19	Benucci, G. M. N., S. Haridas, K. Labutti, G. Marozzi, L. Antonielli, S. Sanchez, P. Marco, X. Wang, K. Barry, A. Lipzen, M. Chovatia, H. Hundley, L. Baciarelli Falini, C. Murat, F. Martin, E. Albertini, D. Donnini, I. V. Grigoriev and G. Bonito	Draft Genome Sequence of the Ectomycorrhizal Ascomycete Sphaerosporella brunnea	Microbiology Resource Announcements
2019	10.7554/eLife.39733	Bernstein, D. B., F. E. Dewhirst and D. Segre	Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome	eLife
2019	10.1186/s13068-019-1439-2	Bhagia, S., Wyman, C.E., and Kumar, R.	Impacts of cellulase deactivation at the moving air-liquid interface on cellulose conversions at low enzyme loadings	BioTechnology for Biofuels
2019	10.1186/s13068-019-1546-0	Bhalla, A., C. M. Cai, F. Xu, S. K. Singh, N. Bansal, T. Phongpreecha, T. Dutta, C. E. Foster, R. Kumar, B. A. Simmons, S. Singh, C. E. Wyman, E. L. Hegg and D. B. Hodge	Performance of three delignifying pretreatments on hardwoods: hydrolysis yields, comprehensive mass balances, and lignin properties	Biotechnology for Biofuels
2019	10.1002/lno.11301	Bier, R. L., J. J. Wernegreen, R. J. Vilgalys, J. C. Ellis and E. S. Bernhardt	Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage	Limnology and Oceanography
2019	10.1038/s41587-019-0100-8	Bin Jang, H., B. Bolduc, O. Zablocki, J. H. Kuhn, S. Roux, E. M. Adriaenssens, J. R. Brister, A. M. Kropinski, M. Krupovic, R. Lavigne, D. Turner and M. B. Sullivan	Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks	Nature Biotechnology
2019	10.1146/annurev-arplant-050718-095841	Blaby-Haas, C. E. and S. S. Merchant	Comparative and functional algal genomics	Annual Review of Plant Biology
2019	10.1016/j.scitotenv.2019.07.127	Bladon, K. D., S. Bywater-Reyes, J. M. LeBoldus, S. Kerio, C. Segura, G. Ritokova and D. C. Shaw	Increased streamflow in catchments affected by a forest disease epidemic	Science of the Total Environment
2019	10.3389/fmicb.2019.00481	Bonito, G., G. M. N. Benucci, K. Hameed, D. Weighill, P. Jones, K. H. Chen, D. Jacobson, C. Schadt and R. Vilgalys	Fungal-bacterial networks in the Populus rhizobiome are impacted by soil properties and host genotype	Frontiers in Microbiology
2019	10.1038/s41467-019-08486-6	Boock, J. T., A. J. E. Freedman, G. A. Tompsett, S. K. Muse, A. J. Allen, L. A. Jackson, B. Castro-Dominguez, M. T. Timko, K. L. J. Prather and J. R. Thompson	Engineered microbial biofuel production and recovery under supercritical carbon dioxide	Nature Communications
2019	10.1177/0022034519831671	Bor, B., J. K. Bedree, W. Shi, J. S. McLean and X. He	Saccharibacteria (TM7) in the Human Oral Microbiome	Journal of Dental Research
2019	10.1099/ijsem.0.003140	Bortniak, V. L., D. A. Pelletier and J. D. Newman	Chryseobacterium populi sp. nov., isolated from Populus deltoides endosphere	International Journal of Systematic and Evolutionary Microbiology
2019	10.1128/mSystems.00003-19	Bowsher, A. W., P. J. Kearns and A. Shade	16S rRNA/rRNA gene ratios and cell activity staining reveal consistent patterns of microbial activity in plant-associated soil	mSystems
2019	10.1038/s41396-018-0343-2	Boyd, J. A., S. P. Jungbluth, A. O. Leu, P. N. Evans, B. J. Woodcroft, G. L. Chadwick, V. J. Orphan, J. P. Amend, M. S. Rappe and G. W. Tyson	Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi	ISME Journal
2019	10.1038/s41594-019-0322-y	Boyer, D. R., B. S. Li, C. Q. Sun, W. J. Fan, M. R. Sawaya, L. Jiang and D. S. Eisenberg	Structures of fibrils formed by alpha-synuclein hereditary disease mutant H50Q reveal new polymorphs	Nature Structural and Molecular Biology
2019	10.1074/mcp.TIR118.001209	Brademan, D. R., N. M. Riley, N. W. Kwiecien and J. J. Coon	Interactive Peptide Spectral Annotator: A versatile web-based tool for proteomic applications	Molecular & Cellular Proteomics
2019	10.1128/mSystems.00170-18	Bradley, P. H., P. A. Gibney, D. Botstein, O. G. Troyanskaya and J. D. Rabinowitz	Minor isozymes tailor yeast metabolism to carbon availability	mSystems
2019	10.1111/mmi.14380	Brenac, L., E. E. K. Baidoo, J. D. Keasling and I. Budin	Distinct functional roles for hopanoid composition in the chemical tolerance of Zymomonas mobilis	Molecular Microbiology
2019	10.1021/acs.est.9b03763	Breunig, H. M., J. Amirebrahimi, S. Smith and C. D. Scown	Role of Digestate and Biochar in Carbon-Negative Bioenergy	Environmental Science & Technology
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2019	10.1016/j.funeco.2018.12.009	Bruns, T. D.	The developing relationship between the study of fungal communities and community ecology theory	Fungal Ecology
2019	10.1080/00275514.2019.1657354	Bruns, T. D., M. L. Hale and N. H. Nguyen	Rhizopogon olivaceotinctus increases its inoculum potential in heated soil independent of competitive release from other ectomycorrhizal fungi	Mycologia
2019	10.1007/s00425-019-03288-y	Buanafina, M. M. D., M. F. Buanafina, T. Laremore, E. A. Shearer and H. W. Fescemyer	Characterization of feruloyl esterases in maize pollen	Planta
2019	10.1021/acs.biochem.8b00915	Budin, I. and J. D. Keasling	Synthetic Biology for Fundamental Biochemical Discovery	Biochemistry
2019	10.1099/ijsem.0.003715	Buhl, M., C. Dunlap and M. Marschal	Prevotella brunnea sp. nov., isolated from a wound of a patient	International Journal of Systematic and Evolutionary Microbiology
2019	10.1029/2018jg004786	Burke, S. A., M. Wik, A. Lang, A. R. Contosta, M. Palace, M. Crill and R. K. Varner	Long-term measurements of methane ebullition from thaw ponds	Journal of Geophysical Research-Biogeosciences
2019	10.1371/journal.pone.0210792	Cadez, N., N. Bellora, R. Ulloa, C. T. Hittinger and D. Libkind	Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina	PLOS ONE
2019	10.1093/nar/gky1309	Caldwell, B. J., E. Zakharova, G. T. Filsinger, T. M. Wormier, J. P. Hempfling, L. Chun-Der, D. Pei, G. M. Church and C. E. Bell	Crystal structure of the Red C-terminal domain in complex with Exonuclease reveals an unexpected homology with Orf and an interaction with Escherichia coli single stranded DNA binding protein	Nucleic Acids Research
2019	10.1016/j.sbi.2019.03.008	Cannon, K. A., J. M. Ochoa and T. O. Yeates	High-symmetry protein assemblies: patterns and emerging applications	Current Opinion in Structural Biology
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2019	10.1007/s11627-019-09993-3	Cano, S., S. Parajuli, B. Kannan, H. Liu, E. Garcia-Ruiz, H. M. Zhao, J. Shanklin and F. Altpeter	Environmental Impacts on Triacyl Glycerol Accumulation in Vegetative Tissues of Oilcane	In Vitro Cellular & Developmental Biology-Plant
2019	10.1093/bib/bbx088	Cao, H., Q. Ma, X. Chen and Y. Xu	DOOR: a prokaryotic operon database for genome analyses and functional inference	Briefings in Bioinformatics
2019	10.1111/biom.13144	Cao, M., W. Zhou, F. J. Breidt and G. Peers	Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis	Biometrics
2019	10.7554/eLife.50747	Cao, P., S.-J. Kim, A. Xing, C. A. Schenck, L. Liu, N. Jiang, J. Wang, R. L. Last and F. Brandizzi	Homeostasis of branched-chain amino acids is critical for the activity of TOR signaling in Arabidopsis	eLife
2019	10.1038/s41594-019-0248-4	Cao, Q., D. R. Boyer, M. R. Sawaya, P. Ge and D. S. Eisenberg	Cryo-EM structures of four polymorphic TDP-43 amyloid cores	Nature Structural & Molecular Biology
2019	10.1093/aob/mcz047	Carlson, C. H., F. E. Gouker, C. R. Crowell, L. Evans, S. P. DiFazio, C. D. Smart and L. B. Smart	Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.)	Annals of Botany
2019	10.7287/peerj.preprints.27898v1	Carper, D. L., T. J. Lawrence, A. A. Carrell, D. A. Pelletier and D. J. Weston	DISCo-microbe: Design of an identifiable synthetic community of microbes	PeerJ Preprints
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2019	10.1016/j.biortech.2019.122214	Carrozza, C. F., G. Papa, A. Citterio, R. Sebastiano, B. A. Simmons and S. Singh	One-pot bio-derived ionic liquid conversion followed by hydrogenolysis reaction for biomass valorization: A promising approach affecting the morphology and quality of lignin of switchgrass and poplar	Bioresource Technology
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2019	10.1094/MPMI-07-18-0185-R	Cecchini, N. M., S. Roychoudhry, D. J. Speed, K. Steffes, A. Tambe, K. Zodrow, K. Konstantinoff, H. W. Jung, N. L. Engle, T. J. Tschaplinski and J. T. Greenberg	Underground Azelaic Acid-Conferred Resistance to Pseudomonas syringae in Arabidopsis	Molecular Plant-Microbe Interactions
2019	10.1038/s41564-019-0384-y	Ceja-Navarro, J. A., U. Karaoz, M. Bill, Z. Hao, R. A. White, 3rd, A. Arellano, L. Ramanculova, T. R. Filley, T. D. Berry, M. E. Conrad, M. Blackwell, C. D. Nicora, Y. M. Kim, P. N. Reardon, M. S. Lipton, J. N. Adkins, J. Pett-Ridge and E. L. Brodie	Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle	Nature Microbiology
2019	10.1073/pnas.1912498116	Chadwick, G. L., F. J. Otero, J. A. Gralnick, D. R. Bond and V. J. Orphan	NanoSIMS imaging reveals metabolic stratification within current-producing biofilms	Proceedings of the National Academy of Sciences of the United States of America
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2019	10.1039/c9gc01859j	Chang, H., A. H. Motagamwala, G. W. Huber and J. A. Dumesic	Synthesis of biomass-derived feedstocks for the polymers and fuels industries from 5-(hydroxymethyl)furfural (HMF) and acetone	Green Chemistry
2019	10.5194/tc-13-647-2019	Chang, K. Y., W. J. Riley, P. M. Crill, R. F. Grant, V. I. Rich and S. R. Saleska	Large carbon cycle sensitivities to climate across a permafrost thaw gradient in subarctic Sweden	Cryosphere
2019	10.1029/2019JG005355	Chang, K.-Y., W. J. Riley, E. L. Brodie, C. K. McCalley, P. M. Crill and R. F. Grant	Methane production pathway regulated proximally by substrate availability and distally by temperature in a high-latitude Mire Complex	Journal of Geophysical Research: Biogeosciences
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2019	10.1128/mBio.02361-19	Chase, A. B., P. Arevalo, E. L. Brodie, M. F. Polz, U. Karaoz and J. B. H. Martiny	Maintenance of sympatric and allopatric populations in free-living terrestrial bacteria	mBio
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2019	10.1007/s10980-019-00928-2	Chen, J. Q., P. Sciusco, Z. T. Ouyang, R. Zhang, G. M. Henebry, R. John and D. P. Roy	Linear downscaling from MODIS to landsat: connecting landscape composition with ecosystem functions	Landscape Ecology
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2019	10.1371/journal.pone.0211582	Chen, Y., Vu, J., Thompson, M. G., Sharpless, W. A., Chan, L. J. G., Gin, J. W., Petzold, C. J.	A rapid methods development workflow for high-throughput quantitative proteomic applications	PLOS ONE
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2019	10.1002/bbb.1976	Cheng, M. H., H. B. Huang, B. S. Dien and V. Singh	The costs of sugar production from different feedstocks and processing technologies	Biofuels Bioproducts & Biorefining-Biofpr
2019	10.3390/pr7100642	Cheng, M. H., Z. Q. Wang, B. S. Dien, P. J. W. Slininger and V. Singh	Economic Analysis of Cellulosic Ethanol Production from Sugarcane Bagasse Using a Sequential Deacetylation, Hot Water and Disk-Refining Pretreatment	Processes
2019	10.1016/j.bcab.2019.101056	Cheng, M.-H., B. S. Dien and V. Singh	Economics of plant oil recovery: A review	Biocatalysis and Agricultural Biotechnology
2019	10.1021/acs.chemrev.8b00439	Cheng, X. L. and J. C. Smith	Biological Membrane Organization and Cellular Signaling	Chemical Reviews
2019	10.1016/j.ecolmodel.2019.05.007	Cheng, Y., N. J. Bouskill and E. L. Brodie	Model exploration of interactions between algal functional diversity and productivity in chemostats to represent open ponds systems across climate gradients	Ecological Modelling
2019	10.1016/j.molcel.2018.10.037	Cheung, R., K. D. Insigne, D. Yao, C. P. Burghard, J. Wang, Y. H. E. Hsiao, E. M. Jones, D. B. Goodman, X. S. Xiao and S. Kosuri	A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions	Molecular Cell
2019	10.3389/fmicb.2019.02170	Chevrette, M. G., C. Carlos-Shanley, K. B. Louie, B. P. Bowen, T. R. Northen and C. R. Currie	Taxonomic and metabolic incongruence in the ancient genus Streptomyces	Frontiers in Microbiology
2019	10.1111/nph.15777	Chhetri, H. B., Macaya-Sanz, D., Kainer, D., Biswal, A.K., Evans, L.M., Chen, J-G., Collins, C., Hunt, K., Mohanty, S.S., Rosenstiel, T., Ryno, D., Winkeler, K., Yang, X., Jacoson, D., Mohnen, D., Muchero, W., Strauss, S.H., Tschaplinski, T.J., Tuskan, G.A	Multi-trait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits	New Phytologist
2019	10.1094/mpmi-09-18-0247-r	Chowda-Reddy, R. V., N. Palmer, S. Edme, G. Sarath, F. Kovacs, G. Yuen, R. Mitchell and S. Tatineni	A two-amino acid difference in the coat protein of Satellite panicum mosaic virus isolates is responsible for differential synergistic interactions with Panicum mosaic virus	Molecular Plant-Microbe Interactions
2019	10.1021/acs.est.8b06389	Christensen, G. A., C. M. Gionfriddo, A. J. King, J. G. Moberly, C. L. Miller, A. C. Somenahally, S. J. Callister, H. Brewer, M. Podar, S. D. Brown, A. V. Palumbo, C. C. Brandt, A. M. Wymore, S. C. Brooks, C. Hwang, M. W. Fields, J. D. Wall, C. C. Gilmour and D. A. Elias	Determining the Reliability of Measuring Mercury Cycling Gene Abundance with Correlations with Mercury and Methylmercury Concentrations	Environmental Science & Technology
2019	10.1021/acssuschemeng.8b05049	Chung, D., Sarai, N.S., Knott, B.C., Hengge, N., Russell, J.F., Yarbrough, J.M., Brunecky, R., Young, J., Supekar, N., Vander Wall, T., Sammond, D.W., Crowley, M.F., Szymanski, C.M., Wells, L., Azadi, P., Westpheling, J., Himmel, M.E., and Bomble, Y.J.	Glycosylation is vital for industrial performance of hyperactive cellulases	ACS Sustainable Chemistry & Engineering
2019	10.1111/gcbb.12606	Clark, L. V., M. S. Dwiyanti, K. G. Anzoua, J. E. Brummer, B. K. Ghimire, K. Glowacka, M. Hall, K. Heo, X. L. Jin, A. E. Lipka, J. H. Peng, T. Yamada, J. H. Yoo, C. Y. Yu, H. Zhao, S. P. Long and E. J. Sacks	Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential	Global Change Biology Bioenergy
2019	10.1111/gcbb.12620	Clark, L. V., M. S. Dwiyanti, K. G. Anzoua, J. E. Brummer, B. K. Ghimire, K. Glowacka, M. Hall, K. Heo, X. L. Jin, A. E. Lipka, J. H. Peng, T. Yamada, J. H. Yoo, C. Y. Yu, H. Zhao, S. P. Long and E. J. Sacks	Genome-wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America	Global Change Biology Bioenergy
2019	10.1093/aob/mcy161	Clark, L. V., X. L. Jin, K. K. Petersen, K. G. Anzoua, L. Bagmet, P. Chebukin, M. Deuter, E. Dzyubenko, N. Dzyubenko, K. Heo, D. A. Johnson, U. Jorgensen, J. B. Kjeldsen, H. Nagano, J. H. Peng, A. Sabitov, T. Yamada, J. H. Yoo, C. Y. Yu, S. P. Long and E. J. Sacks	Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea	Annals of Botany
2019	10.3390/genes10120996	Cliff, A., J. Romero, D. Kainer, A. Walker, A. Furches and D. Jacobson	A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks	Genes
2019	10.1111/gcbb.12566	Clifton-Brown, J., A. Harfouche, M. D. Casler, H. D. Jones, W. J. Macalpine, D. Murphy-Bokern, L. B. Smart, A. Adler, C. Ashman, D. Awty-Carroll, C. Bastien, S. Bopper, V. Botnari, M. Brancourt-Hulmel, Z. Y. Chen, L. V. Clark, S. Cosentino, S. Dalton, C. Davey, O. Dolstra, I. Donnison, R. Flavell, J. Greef, S. Hanley, A. Hastings, M. Hertzberg, T. W. Hsu, L. S. Huang, A. Iurato, E. Jensen, X. L. Jin, U. Jorgensen, A. Kiesel, D. S. Kim, J. Liu, J. P. McCalmont, B. G. McMahon, M. Mos, P. Robson, E. J. Sacks, A. Sandu, G. Scalici, K. Schwarz, D. Scordia, R. Shafiei, I. Shield, G. Slavov, B. J. Stanton, K. Swaminathan, G. Taylor, A. F. Torres, L. M. Trindade, T. Tschaplinski, G. A. Tuskan, T. Yamada, C. Y. Yu, R. S. Zalesny, J. Q. Zong and I. Lewandowski	Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar	Global Change Biology Bioenergy
2019	10.1016/j.chroma.2018.12.059	Cocuron, J. C., M. I. Casas, F. Yang, E. Grotewold and A. P. Alonso	Beyond the wall: High-throughput quantification of plant soluble and cell-wall bound phenolics by liquid chromatography tandem mass spectrometry	Journal of Chromatography A
2019	10.1104/pp.19.00920	Cocuron, J.-C., M. Koubaa, R. Kimmelfield, Z. Ross and A. P. Alonso	A Combined Metabolomics and Fluxomics Analysis Identifies Steps Limiting Oil Synthesis in Maize Embryos	Plant Physiology
2019	10.3389/fpls.2019.00412	Conde, D., Perales, M., Sreedasyam, A., Tuskan, G.A., Lloret, A., Badenes, M.L., Gonzalez-Melendi, P., Rios, G., and Allona, I.	Engineering tree seasonal cycles of growth through chromatin modification	Frontiers in Plant Science
2019	10.1186/s12864-019-5734-x	Cooper, E. A., Z. W. Brenton, B. S. Flinn, J. Jenkins, S. Shu, D. Flowers, F. Luo, Y. Wang, P. Xia, K. Barry, C. Daum, A. Lipzen, Y. Yoshinaga, J. Schmutz, C. Saski, W. Vermerris and S. Kresovich	A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism	BMC Genomics
2019	10.1105/tpc.18.00676	Cope, K. R., A. Bascaules, T. B. Irving, M. Venkateshwaran, J. Maeda, K. Garcia, T. A. Rush, C. Ma, J. Labbe, S. Jawdy, E. Steigerwald, J. Setzke, E. Fung, K. M. G. Schnell, Y. Q. Wang, N. Schlief, H. Bucking, S. H. Strauss, F. Maillet, P. Jargeat, G. Becard, V. Puech-Pages and J. M. Ane	The ectomycorrhizal fungus Laccaria bicolor produces lipochitooligosaccharides and uses the common symbiosis pathway to colonize Populus roots	Plant Cell
2019	10.1038/s41598-018-37025-4	Corts, A. D., L. C. Thomason, R. T. Gill and J. A. Gralnick	A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides	Scientific Reports
2019	10.1038/s41467-019-10542-0	Couradeau, E., J. Sasse, D. Goudeau, N. Nath, T. C. Hazen, B. P. Bowen, R. Chakraborty, R. R. Malmstrom and T. R. Northen	Probing the active fraction of soil microbiomes using BONCAT-FACS	Nature Communications
2019	10.1094/PBIOMES-12-18-0058-P	Craven, K., and Ray, P.	More than serendipity: the potential to manage soil carbon and emissions while promoting low-input agriculture with serendipitoid mycorrhizae	Phytobiomes Journal
2019	10.1534/g3.119.400350	Cuevas, H. E., L. K. Prom and C. M. Cruet-Burgos	Genome-wide association mapping of anthracnose (Colletotrichum sublineolum) resistance in NPGS Ethiopian sorghum germplasm	G3-Genes Genomes Genetics
2019	10.1016/j.ymben.2018.09.006	Cui, J., D. G. Olson and L. R. Lynd	Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum	Metabolic Engineering
2019	10.1186/s13068-019-1426-7	da Costa, R. M. F., S. Pattathil, U. Avci, A. Winters, M. G. Hahn and M. Bosch	Desirable plant cell wall traits for higher-quality miscanthus lignocellulosic biomass	Biotechnology for Biofuels
2019	10.3390/insects10040087	da Costa, R. R., H. F. Hu, H. J. Li and M. Poulsen	Symbiotic Plant Biomass Decomposition in Fungus-Growing Termites	Insects
2019	10.1063/1.5080158	Daloglu, M. U., A. Ray, M. J. Collazo, C. Brown, D. Tseng, B. Chocarro-Ruiz, L. M. Lechuga, D. Cascio and A. Ozcan	Low-cost and portable UV holographic microscope for high-contrast protein crystal imaging	APL Photonics
2019	10.1111/pbi.13001	Daly, P., C. McClellan, M. Maluk, H. Oakey, C. Lapierre, R. Waugh, J. Stephens, D. Marshall, A. Barakate, Y. Tsuji, G. Goeminne, R. Vanholme, W. Boerjan, J. Ralph and C. Halpin	RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family	Plant Biotechnology Journal
2019	10.1186/s12864-019-5591-7	Das, P., P. Babaei and J. Nielsen	Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome	BMC Genomics
2019	10.1016/j.ymben.2019.06.006	Dash, S., Olson, D.G., Chan, S.H.J., Amador-Noguez, D., Lynd, L.R., and Maranas, C.D.	Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum	Metabolic Engineering
2019	10.1128/MRA.00456-19	Day, L. A., K. B. De Leon, M. L. Kempher, J. Zhou and J. D. Wall	Complete Genome Sequence of Desulfovibrio desulfuricans IC1, a Sulfonate-Respiring Anaerobe	Microbiology Resource Announcements
2019	10.1039/c9gc00564a	De Bruyn, M., C. Sener, D. D. Petrolini, D. J. McClelland, J. Y. He, M. R. Ball, Y. F. Liu, L. Martins, J. A. Dumesic, G. W. Huber and B. M. Weckhuysen	Catalytic hydrogenation of dihydrolevoglucosenone to levoglucosanol with a hydrotalcite/mixed oxide copper catalyst	Green Chemistry
2019	10.1016/j.funbio.2019.09.006	Deaver, N. R., C. Hesse, C. R. Kuske and A. Porras-Alfaro	Presence and distribution of insect-associated and entomopathogenic fungi in a temperate pine forest soil: An integrated approach	Fungal Biology
2019	10.1093/aepp/ppz023	Debnath, D., M. Khanna, D. Rajagopal and D. Zilberman	The Future of biofuels in an electrifying global transportation sector: imperative, prospects and challenges	Applied Economic Perspectives and Policy
2019	10.1021/acssynbio.9b00213	DeLorenzo, D. M. and T. S. Moon	Construction of Genetic Logic Gates Based on the T7 RNA Polymerase Expression System in Rhodococcus opacus PD630	ACS Synthetic Biology
2019	10.3389/fmolb.2019.00064	Demerdash, O., U. R. Shrestha, L. Petridis, J. C. Smith, J. C. Mitchell and A. Ramanathan	Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins	Frontiers in Molecular Biosciences
2019	10.1002/jpln.201800301	Denis, E. H., P. D. Ilhardt, A. E. Tucker, N. L. Huggett, J. J. Rosnow and J. J. Moran	Spatially tracking carbon through the root-rhizosphere-soil system using laser ablation-IRMS	Journal of Plant Nutrition and Soil Science
2019	10.1021/acssynbio.8b00432	diCenzo, G. C., A. Mengoni and M. Fondi	Tn-Core: A Toolbox for Integrating Tn-seq Gene Essentiality Data and Constraint-Based Metabolic Modeling	ACS Synthetic Biology
2019	10.1039/c9gc00252a	Ding, J. H., C. G. Yoo, Y. Q. Pu, X. Z. Meng, S. Bhagia, C. W. Yu and A. J. Ragauskas	Cellulolytic enzyme-aided extraction of hemicellulose from switchgrass and its characteristics	Green Chemistry
2019	10.1016/j.mec.2019.e00101	Dinh, H. V., P. F. Suthers, S. H. J. Chan, Y. Shen, T. Xiao, A. Deewan, S. S. Jagtap, H. Zhao, C. V. Rao, J. D. Rabinowitz and C. D. Maranas	A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data	Metabolic Engineering Communications
2019	10.1128/mra.01464-18	Domeignoz-Horta, L. A., K. M. DeAngelis and G. Pold	Draft genome sequence of Acidobacteria Group 1 Acidipila sp. Strain EB88, isolated from forest soil	Microbiology Resource Announcements
2019	10.1021/acs.analchem.8b03126	Domingo-Almenara, X., J. R. Montenegro-Burke, C. Guijas, E. L. Majumder, H. P. Benton and G. Siuzdak	Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics	Analytical Chemistry
2019	10.1111/gcbb.12615	Dong, H. X., L. V. Clark, A. E. Lipka, J. E. Brummer, K. Glowacka, M. C. Hall, K. Heo, X. L. Jin, J. H. Peng, T. Yamada, B. K. Ghimire, J. H. Yoo, C. Y. Yu, H. Zhao, S. P. Long and E. J. Sacks	Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis	Global Change Biology Bioenergy
2019	10.1111/gcbb.12588	Dong, H. X., S. V. Green, A. Nishiwaki, T. Yamada, J. R. Stewart, M. Deuter and E. J. Sacks	Winter hardiness of Miscanthus (I): Overwintering ability and yield of new Miscanthus xgiganteus genotypes in Illinois and Arkansas	Global Change Biology Bioenergy
2019	10.1111/gcbb.12587	Dong, H. X., S. Y. Liu, L. V. Clark, S. Sharma, J. M. Gifford, J. A. Juvik, A. E. Lipka and E. J. Sacks	Winter hardiness of Miscanthus (II): Genetic mapping for overwintering ability and adaptation traits in three interconnected Miscanthus populations	Global Change Biology Bioenergy
2019	10.1111/mmi.14280	Donohue, T. J.	Shedding light on a Group IV (ECF11) alternative sigma factor	Molecular Microbiology
2019	10.1016/j.indcrop.2018.11.033	Dou, J., H. Bian, D. J. Yelle, M. Ago, K. Vajanto, T. Vuorinen and J. Zhu	Lignin containing cellulose nanofibril production from willow bark at 80 degrees C using a highly recyclable acid hydrotrope	Industrial Crops and Products
2019	10.1016/j.cmet.2019.05.010	Drigo, R. A. E., V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E. Bushong, S. Phan, V. Orphan, C. Lechene, M. H. Ellisman and M. W. Hetzer	Age Mosaicism across Multiple Scales in Adult Tissues	Cell Metabolism
2019	10.7554/eLife.47815	Du, Z. Y., K. Zienkiewicz, N. Vande Pol, N. E. Ostrom, C. Benning and G. M. Bonito	Algal-fungal symbiosis leads to photosynthetic mycelium	eLife
2019	10.1002/ecm.1367	Duhamel, M., J. Wan, L. M. Bogar, R. M. Segnitz, N. C. Duncritts and K. G. Peay	Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance	Ecological Monographs
2019	10.1016/j.biombioe.2019.01.026	Dulys-Nusbaum, E., S. S. H. Klammer and S. M. Swinton	How willing are different types of landowner to supply hardwood timber residues for bioenergy?	Biomass and Bioenergy
2019	10.1111/gcbb.12572	Duncan, D. S., L. G. Oates, I. Gelfand, N. Millar, G. P. Robertson and R. D. Jackson	Environmental factors function as constraints on soil nitrous oxide fluxes in bioenergy feedstock cropping systems	Global Change Biology Bioenergy
2019	10.1128/mSystems.00349-18	Dunivin, T. K., J. Choi, A. Howe and A. Shade	RefSoil+: A reference database for genes and traits of soil plasmids	mSystems
2019	10.1093/nar/gkz085	Egbert, R. G., H. S. Rishi, B. A. Adler, D. M. McCormick, E. Toro, R. T. Gill and A. P. Arkin	A versatile platform strain for high-fidelity multiplex genome editing	Nucleic Acids Research
2019	10.1021/acssynbio.9b00230	Eiben, C. B., T. de Rond, C. Bloszies, J. Gin, J. Chiniquy, E. E. K. Baidoo, C. J. Petzold, N. J. Hillson, O. Fiehn and J. D. Keasling	Mevalonate Pathway Promiscuity Enables Noncanonical Terpene Production	ACS Synthetic Biology
2019	10.1016/j.phytochem.2019.04.003	Elder, T., J. C. del Rio, J. Ralph, J. Rencoret, H. Kim and G. T. Beckham	Radical coupling reactions of piceatannol and monolignols: A density functional theory study	Phytochemistry
2019	10.1002/bit.26847	Emerson, D. F., B. M. Woolston, N. Liu, M. Donnelly, D. H. Currie and G. Stephanopoulos	Enhancing hydrogen-dependent growth of and carbon dioxide fixation by Clostridium ljungdahlii through nitrate supplementation	Biotechnology and Bioengineering
2019	10.1021/acschembio.8b01107	Erbilgin, O., O. Rubel, K. B. Louie, M. Trinh, M. Raad, T. Wildish, D. Udwary, C. Hoover, S. Deutsch, T. R. Northen and B. P. Bowen	MAGI: A Method for Metabolite Annotation and Gene Integration	ACS Chemical Biology
2019	10.1002/ece3.5670	Escalas, A., L. Hale, J. W. Voordeckers, Y. F. Yang, M. K. Firestone, L. Alvarez-Cohen and J. Z. Zhou	Microbial functional diversity: From concepts to applications	Ecology and Evolution
2019	10.1007/s00425-019-03097-3	Evans, B. R., M. Foston, H. M. O'Neill, D. Reeves, C. Rempe, K. McGrath, A. J. Ragauskas and B. H. Davison	Production of deuterated biomass by cultivation of Lemna minor (duckweed) in D2O	Planta
2019	10.1038/s41579-018-0136-7	Evans, P. N., J. A. Boyd, A. O. Leu, B. Woodcroft, D. H. Parks, P. Hugenholtz and G. W. Tyson	An evolving view of methane metabolism in the Archaea	Nature Reviews Microbiology
2019	10.7185/geochemlet.1922	Fahnestock, M. F., J. G. Bryce, C. K. McCalley, M. Montesdeoca, S. Bai, Y. Li, C. T. Driscoll, P. M. Crill, V. I. Rich and R. K. Varner	Mercury reallocation in thawing subarctic peatlands	Geochemical Perspectives Letters
2019	10.1128/MRA.00849-19	Faleye, T. O. C., O. M. Adewumi, O. T. Olayinka and J. A. Adeniji	Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria	Microbiology Resource Announcements
2019	10.3390/plants8070229	Fan, J. L., C. Zhou, L. H. Yu, P. Li, J. Shanklin and C. C. Xu	Diversion of Carbon Flux from Sugars to Lipids Improves the Growth of an Arabidopsis Starchless Mutant	Plants-Basel
2019	10.3390/plants8070229	Fan, J., C. Zhou, L. Yu, P. Li, J. Shanklin and C. Xu	Diversion of carbon flux from sugars to lipids improves the growth of an Arabidopsis starchless mutant	Plants
2019	10.1016/j.apenergy.2019.01.143	Fasahati, P., J. J. Liu, J. B. Ohlrogge and C. M. Saffron	Process design and economics for production of advanced biofuels from genetically modified lipid-producing sorghum	Applied Energy
2019	10.1021/acscatal.9b02737	Fasan, R., S. B. J. Kan and H. M. Zhao	A continuing career in biocatalysis: Frances H. Arnold	ACS Catalysis
2019	10.3389/fmicb.2019.02270	Felczak, M. M., T. B. Jacobson, W. K. Ong, D. Amador-Noguez and M. A. TerAvest	Expression of phosphofructokinase is not sufficient to enable embden-meyerhof-parnas glycolysis in Zymomonas mobilis ZM4	Frontiers in Microbiology
2019	10.1128/mBio.02521-18	Feng, J. J., C. R. Penton, Z. L. He, J. D. Van Nostrand, M. T. M. Yuan, L. Y. Wu, C. Wang, Y. J. Qin, Z. J. Shi, X. Guo, E. A. G. Schuur, Y. Q. Luo, R. Bracho, K. T. Konstantinidis, J. R. Cole, J. M. Tiedje, Y. F. Yang and J. Z. Zhou	Long-term warming in alaska enlarges the diazotrophic community in deep soils	mBio
2019	10.1007/978-1-4939-9721-3_11	Finley, B. K., M. Hayer, R. L. Mau, A. M. Purcell, B. J. Koch, N. C. van Gestel, E. Schwartz and B. A. Hungate	Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing	Methods Mol Biol
2019	10.1016/j.algal.2019.101500	Fisher, C. L., C. S. Ward, P. D. Lane, J. A. Kimbrel, K. L. Sale, R. K. Stuart, X. Mayali and T. W. Lane	Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis	Algal Research
2019	10.1371/journal.pcbi.1007319	Foster, C. J., Gopalakrishnan, S., Antoniewicz, M. A., Maranas, C.D.	From escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline	PLOS Computational Biology
2019	10.1371/journal.pone.0218279	Frausto, R. F., D. D. Chung, P. M. Boere, V. S. Swamy, H. N. V. Duong, L. Kao, R. Azimov, W. L. Zhang, L. Carrigan, D. Wong, M. Morselli, M. Zakharevich, E. M. Hanser, A. C. Kassels, I. Kurtz, M. Pellegrini and A. J. Aldave	ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing	Plos One
2019	10.3389/fpls.2019.01249	Furches, A., Kainer, D., Weighill, D., Large, A., Jones, P., Walker, A.M., Romero, J., Gazolla, J.G.F.M., Joubert, W., Shah, M., Streich, J., Ranjan, P., Schmutz, J., Sreedasyam, A., Macaya-Sanz, D., Zhao, N., Martin, M.Z., Rao, X., Dixon, R.A., DiFazio	Finding new cell wall regulatory genes in Populus trichocarpa using multiple lines of evidence	Frontiers in Plant Science
2019	10.3835/plantgenome2018.09.0069	Gage, J. L., B. Vaillancourt, J. P. Hamilton, N. C. Manrique-Carpintero, T. J. Gustafson, K. Barry, A. Lipzen, W. F. Tracy, M. A. Mikel, S. M. Kaeppler, C. R. Buell and N. de Leon	Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel	Plant Genome
2019	10.1016/j.algal.2019.101598	Gaidarenko, O., C. Sathoff, K. Staub, M. H. Huesemann, M. Vernet and M. Hildebrand	Timing is everything: Diel metabolic and physiological changes in the diatom Cyclotella cryptica grown in simulated outdoor conditions	Algal Research
2019	10.1038/s42003-018-0263-8	Gallagher-Jones, M., C. Ophus, K. C. Bustillo, D. R. Boyer, O. Panova, C. Glynn, C. T. Zee, J. Ciston, K. C. Mancia, A. M. Minor and J. A. Rodriguez	Nanoscale mosaicity revealed in peptide microcrystals by scanning electron nanodiffraction	Communications Biology
2019	10.1038/s41396-018-0264-0	Gao, C., L. Montoya, L. Xu, M. Madera, J. Hollingsworth, E. Purdom, R. B. Hutmacher, J. A. Dahlberg, D. Coleman-Derr, P. G. Lemaux and J. W. Taylor	Strong succession in arbuscular mycorrhizal fungal communities	ISME Journal
2019	10.1016/j.watres.2019.02.020	Gao, H., Y. Mao, X. Zhao, W.-T. Liu, T. Zhang and G. Wells	Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess	Water Research
2019	10.2174/1574893614666190204151746	Gao, Y. B., F. H. Xi, H. X. Zhang, X. Q. Liu, H. Y. Wang, L. Z. Zhao, A. S. N. Reddy and L. F. Gu	Single-Molecule Real-Time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The status of the bioinformatics tools to unravel the transcriptome complexity	Current Bioinformatics
2019	10.1128/mra.01077-19	Garcia, C. A., J. A. Narrett and J. G. Gardner	Complete genome sequences of Cellvibrio japonicus Strains with improved growth when using ?-diglucosides	Microbiology Resource Announcements
2019	10.1021/acschembio.9b00725	Garcia, D. C., X. Cheng, M. L. Land, R. F. Standaert, J. L. Morrell-Falvey and M. J. Doktycz	Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways	ACS Chemical Biology
2019	10.1016/j.biotechadv.2019.06.002	Garcia, S. and C. T. Trinh	Modular design: Implementing proven engineering principles in biotechnology	Biotechnology Advances
2019	10.1016/j.ymben.2018.09.003	Garcia, S. and C. T. Trinh	Multiobjective strain design: A framework for modular cell engineering	Metabolic Engineering
2019	10.3390/pr7060361	Garcia, S. and C. T. Trinh	Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis	Processes
2019	10.1038/s41598-019-53188-0	Gardner, J. J., B. M. S. Hodge and N. R. Boyle	Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems	Scientific Reports
2019	10.1021/acssuschemeng.9b00019	Garedew, M., D. Young-Farhat, J. E. Jackson and C. M. Saffron	Electrocatalytic Upgrading of Phenolic Compounds Observed after Lignin Pyrolysis	Acs Sustainable Chemistry & Engineering
2019	10.1016/j.soilbio.2018.09.036	Geyer, K. M., P. Dijkstra, R. Sinsabaugh and S. D. Frey	Clarifying the interpretation of carbon use efficiency in soil through methods comparison	Soil Biology & Biochemistry
2019	10.1016/j.ymben.2018.12.008	Ghosh, I. N., J. Martien, A. S. Hebert, Y. P. Zhang, J. J. Coon, D. Amador-Noguez and R. Landick	OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate	Metabolic Engineering
2019	10.1021/acssynbio.9b00271	Gilmore, S. P., T. S. Lankiewicz, S. Wilken, J. L. Brown, J. A. Sexton, J. K. Henske, M. K. Theodorou, D. L. Valentine and M. A. O'Malley	Top-down enrichment guides in formation of synthetic microbial consortia for biomass degradation	ACS Synthetic Biology
2019	10.1039/c8gc03606c	Giummarella, N., Y. Q. Pu, A. J. Ragauskas and M. Lawoko	A critical review on the analysis of lignin carbohydrate bonds	Green Chemistry
2019	10.1016/j.jmb.2019.01.024	Glasgow, E. M., K. A. Vander Meulen, T. E. Takasuka, C. M. Bianchetti, L. F. Bergeman, S. Deutsch and B. G. Fox	Extent and origins of functional diversity in a subfamily of glycoside hydrolases	Journal of Molecular Biology
2019	10.1042/etls20180177	Glynn, C. and J. A. Rodriguez	Data-driven challenges and opportunities in crystallography	Emerging Topics in Life Sciences
2019	10.3390/sym11091170	Goodsell, D. S.	Symmetry at the cellular mesoscale	Symmetry-Basel
2019	10.1002/pro.3730	Goodsell, D. S., C. Zardecki, L. Di Costanzo, J. M. Duarte, B. P. Hudson, I. Persikova, J. Segura, C. H. Shao, M. Voigt, J. D. Westbrook, J. Y. Young and S. K. Burley	RCSB Protein Data Bank: Enabling biomedical research and drug discovery	Protein Science
2019	10.1016/j.str.2019.08.011	Goodsell, D. S., L. Autin and A. J. Olson	Illustrate: Software for biomolecular illustration	Structure
2019	10.1101/612994	Gopalakrishnan, S., S. Dash and C. Maranas	K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data	bioRxiv
2019	10.1111/nph.15712	Gou, J., C. Tang, N. Chen, H. Wang, S. Debnath, L. Sun, A. Flanagan, Y. Tang, Q. Jiang, R. D. Allen and Z.-Y. Wang	SPL7 and SPL8 represent a novel flowering regulation mechanism in switchgrass	New Phytologist
2019	10.1128/aem.00048-19	Govindaraju, A., J. B. McKinlay and B. LaSarre	Phototrophic lactate utilization by Rhodopseudomonas palustris Is stimulated by coutilization with additional substrates	Applied and Environmental Microbiology
2019	10.1016/j.plantsci.2019.02.004	Grabber, J. H., C. Davidson, Y. Tobimatsu, H. Kim, F. Lu, Y. Zhu, M. Opietnik, N. Santoro, C. E. Foster, F. Yue, D. Ress, X. Pan and J. Ralph	Structural features of alternative lignin monomers associated with improved digestibility of artificially lignified maize cell walls	Plant Science
2019	10.1038/s41467-019-11974-4	Grady, K. L., J. W. Sorensen, N. Stopnisek, J. Guittar and A. Shade	Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops	Nature Communications
2019	10.1007/s13399-018-0346-2	Graham, B. J. and R. T. Raines	Efficient metal-free conversion of glucose to 5-hydroxymethylfurfural using a boronic acid	Biomass Conversion and Biorefinery
2019	10.1016/j.fuel.2019.03.094	Groendyk, M. and D. A. Rothamer	Optical investigation of mixing-controlled combustion using a novel transgenic plant oil	Fuel
2019	10.1111/ejss.12744	Guber, A. K., A. N. Kravchenko, B. S. Razavi, E. Blagodatskaya and Y. Kuzyakov	Calibration of 2-D soil zymography for correct analysis of enzyme distribution	European Journal of Soil Science
2019	10.3390/e21060591	Guo, H. B., Y. Ma, G. A. Tuskan, H. Qin, X. H. Yang and H. Guo	A suggestion of converting protein intrinsic disorder to structural entropy using Shannon's Information Theory	Entropy
2019	10.3389/fgene.2019.00957	Guo, J. R., J. F. Quensen, Y. N. Sun, Q. Wang, C. T. Brown, J. R. Cole and J. M. Tedje	Review, evaluation, and directions for gene-targeted assembly for ecological analyses of metagenomes	Frontiers in Genetics
2019	10.1038/s41559-019-0848-8	Guo, X., X. S. Zhou, L. Hale, M. T. Yuan, D. L. Ning, J. J. Feng, Z. Shi, Z. X. Li, B. Feng, Q. Gao, L. W. Wu, W. L. Shi, A. F. Zhou, Y. Fu, L. Y. Wu, Z. L. He, J. D. Van Nostrand, G. Z. Qiu, X. D. Liu, Y. Q. Luo, J. M. Tiedje, Y. F. Yang and J. Z. Zhou	Climate warming accelerates temporal scaling of grassland soil microbial biodiversity	Nature Ecology & Evolution
2019	10.1128/MRA.00301-19	Gupta, N., K. A. Skinner, S. Khan, J. N. Edirisinghe and C. S. Henry	Draft Genome Sequence of Enterobacter sp. Strain A8, a Carbazole-Degrading Bacterium	Microbiology Resource Announcements
2019	10.3389/fmolb.2019.00115	Gupta, V. V. S. R., B. Zhang, C. R. Penton, J. Yu and J. M. Tiedje	Diazotroph diversity and nitrogen fixation in summer active perennial grasses in a Mediterranean region agricultural soil	Frontiers in Molecular Biosciences
2019	10.1104/pp.19.00533	Ha, C. M., Fine, D., Bhatia, A., Rao, X., Martin, M.Z., Engle, N.L., Wherritt, D.J., Tschaplinski, T.J. and L. W. Sumner, and Dixon, R.A.	Ectopic defense gene expression is associated with growth defects in medicago thrncatula lignin pathway mutants	Plant Physiology
2019	10.1016/j.biocon.2019.03.007	Haan, N. L. and D. A. Landis	Grassland disturbance increases monarch butterfly oviposition and decreases arthropod predator abundance	Biological Conservation
2019	10.3389/fevo.2019.00191	Haan, N. L. and D. A. Landis	The importance of shifting disturbance regimes in Monarch butterfly decline and recovery	Frontiers in Ecology and Evolution
2019	10.1038/s41396-019-0485-x	Hale, L. R., W. T. Feng, H. Q. Yin, X. Guo, X. S. Zhou, R. Bracho, E. Pegoraro, C. R. Penton, L. Y. Wu, J. Cole, K. T. Konstantinidis, Y. Q. Luo, J. M. Tiedje, E. A. G. Schuur and J. Z. Zhou	Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon	ISME Journal
2019	10.1038/s41467-019-13189-z	HamediRad, M., R. Chao, S. Weisberg, J. Lian, S. Sinha and H. Zhao	Towards a fully automated algorithm driven platform for biosystems design	Nature Communications
2019	10.1021/acssynbio.8b00480	HamediRad, M., S. Weisberg, R. Chao, J. Z. Lian and H. M. Zhao	Highly Efficient Single-Pot Scarless Golden Gate Assembly	Acs Synthetic Biology
2019	10.1093/nar/gkz642	Hancock, S. P., D. Cascio and R. C. Johnson	Cooperative DNA binding by proteins through DNA shape complementarity	Nucleic Acids Research
2019	10.1016/bs.abr.2018.11.008	Harding, S. A. and C.-J. Tsai	Cell wall pectins in tree growth and woody biomass utilization	Advances in Botanical Research
2019	10.1016/j.tibtech.2019.05.007	Harfouche, A. L., D. A. Jacobson, D. Kainer, J. C. Romero, A. H. Harfouche, G. Scarascia Mugnozza, M. Moshelion, G. A. Tuskan, J. J. B. Keurentjes and A. Altman	Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence	Trends in Biotechnology
2019	10.1042/bcj20180615	Hartman, K. and S. G. Tringe	Interactions between plants and soil shaping the root microbiome under abiotic stress	Biochemical Journal
2019	10.1093/femsec/fiz147	Hashmi, I., C. Paul, A. Al-Dourobi, F. Sandoz, P. Deschamps, T. Junier, P. Junier and S. Bindschedler	Comparison of the plant growth-promotion performance of a consortium of Bacilli inoculated as endospores or as vegetative cells	FEMS Microbiol Ecol
2019	10.1128/MRA.01430-18	Hatmaker, E. A., D. M. Klingeman, K. B. O'Dell, L. A. Riley, B. Papanek and A. M. Guss	Complete Genome Sequences of Two Megasphaera elsdenii Strains, NCIMB 702410 and ATCC 25940	Microbiology Resource Announcements
2019	10.1128/MRA.00708-19	Hatmaker, E. A., D. M. Klingeman, R. K. Martin, A. M. Guss and J. G. Elkins	Complete Genome Sequence of Caloramator sp. Strain E03, a Novel Ethanologenic, Thermophilic, Obligately Anaerobic Bacterium	Microbiology Resource Announcements
2019	10.1111/1462-2920.14507	He, X. J., G. Chadwick, C. Kempes, Y. M. Shi, S. McGlynn, V. Orphan and C. Meile	Microbial interactions in the anaerobic oxidation of methane: model simulations constrained by process rates and activity patterns	Environmental Microbiology
2019	10.1007/978-1-4939-8757-3_17	Heinemann, J.	Machine Learning in Untargeted Metabolomics Experiments	Microbial Metabolomics: Methods and Protocols
2019	10.1186/s40168-019-0689-3	Heinken, A., D. A. Ravcheev, F. Baldini, L. Heirendt, R. M. T. Fleming and I. Thiele	Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease	Microbiome
2019	10.1007/s10530-019-02011-y	Helms, J. A., S. E. Ijelu and N. M. Haddad	Range expansion in an introduced social parasite-host species pair	Biological Invasions
2019	10.1104/pp.18.01357	Hendry, J. I., S. Gopalakrishnan, J. Ungerer, H. B. Pakrasi, Y. J. J. Tang and C. D. Maranasa	Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient C-13-Labeling Data	Plant Physiology
2019	10.1002/ajb2.1373	Henning, J. A., D. J. Weston, D. A. Pelletier, C. M. Timm, S. S. Jawdy and A. T. Classen	Relatively rare root endophytic bacteria drive plant resource allocation patterns and tissue nutrient concentration in unpredictable ways	American Journal of Botany
2019	10.1038/s41598-019-50737-5	Hermann, S. L., C. Blackledge, N. L. Haan, A. T. Myers and D. A. Landis	Predators of monarch butterfly eggs and neonate larvae are more diverse than previously recognised	Scientific Reports
2019	10.1038/s42003-019-0481-8	Hestrin, R., E. C. Hammer, C. W. Mueller and J. Lehmann	Synergies between mycorrhizal fungi and soil microbial communities increase plant nitrogen acquisition	Communications Biology
2019	10.1016/j.ymben.2019.08.014	Hing, N. Y. K., F. Y. Liang, P. Lindblad and J. A. Morgan	Combining isotopically non-stationary metabolic flux analysis with proteomics to unravel the regulation of the Calvin-Benson-Bassham cycle in Synechocystis sp. PCC 6803	Metabolic Engineering
2019	10.1186/s13068-019-1353-7	Holwerda, E. K., Worthen, R.S., Kothari, N., Lasky, R.C., Davison, B.H., Fu, C., Wang, Z.Y., Dixon, R.A., Biswal, A.J., Mohnen, D., Nelson, R.S., Baxter, H.L., Mazarei, M., Stewart, C. N., Muchero, W., Tuskan, G.A., Cai, C.M., Gjersing, E.E., Davis, M.F.	Multiple levers for overcoming the recalcitrance of lignocellulosic biomass	Biotechnology for Biofuels
2019	10.1111/tpj.14184	Hoopes, G. M., J. P. Hamilton, J. C. Wood, E. Esteban, A. Pasha, B. Vaillancourt, N. J. Provart and C. R. Buell	An updated gene atlas for maize reveals organ-specific and stress-induced genes	Plant Journal
2019	10.1021/acs.est.9b01834	Huang, W. J., K. E. Hammel, J. L. Hao, A. Thompson, V. I. Timokhin and S. J. Hall	Enrichment of lignin-derived carbon in mineral-associated soil organic matter	Environmental Science & Technology
2019	10.2134/jeq2019.04.0156	Hussain, M. Z., A. K. Bhardwaj, B. Basso, G. P. Robertson and S. K. Hamilton	Nitrate leaching from continuous corn, perennial grasses, and poplar in the us midwest	Journal of Environmental Quality
2019	10.1016/j.agwat.2019.02.049	Hussain, M. Z., S. K. Hamilton, A. K. Bhardwaj, B. Basso, K. D. Thelen and G. P. Robertson	Evapotranspiration and water use efficiency of continuous maize and maize and soybean in rotation in the upper Midwest US	Agricultural Water Management
2019	10.1007/s13361-018-02125-y	Hutchins, P. D., J. D. Russell and J. J. Coon	Mapping lipid fragmentation for tailored mass spectral libraries	Journal of the American Society for Mass Spectrometry
2019	10.1021/acs.analchem.9b01234	Hutchins, P. D., J. D. Russell and J. J. Coon	Accelerating lipidomic method development through in silico simulation	Analytical Chemistry
2019	10.1038/s41467-019-10390-y	Isobe, K., S. D. Allison, B. Khalili, A. C. Martiny and J. B. H. Martiny	Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents	Nature Communications
2019	10.1093/nar/gkz121	Jabre, I., A. S. N. Reddy, M. Kalyna, S. Chaudhary, W. Khokhar, L. J. Byrne, C. M. Wilson and N. H. Syed	Does co-transcriptional regulation of alternative splicing mediate plant stress responses?	Nucleic Acids Research
2019	10.1002/eap.2047	Jach-Smith, L. C. and R. D. Jackson	Inorganic N addition replaces N supplied to switchgrass (Panicum virgatum) by arbuscular mycorrhizal fungi	Ecological Applications
2019	10.1016/j.ymben.2019.05.006	Jacobson, T. B., P. A. Adamczyk, D. M. Stevenson, M. Regner, J. Ralph, J. L. Reed and D. Amador-Noguez	2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis	Metabolic Engineering
2019	10.1016/j.ymben.2019.05.006	Jacobson, T. B., P. A. Adamczyk, D. M. Stevenson, M. Regner, J. Ralph, J. L. Reed and D. Amador-Noguez	H-2 and C-13 metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis	Metabolic Engineering
2019	10.1186/s13068-019-1586-5	Jagtap, S. S., A. A. Bedekar, J. J. Liu, Y. S. Jin and C. V. Rao	Production of galactitol from galactose by the oleaginous yeast Rhodosporidium toruloides IFO0880	Biotechnology for Biofuels
2019	10.1186/s12864-019-6262-4	Jain, R., J. Jenkins, S. Shu, M. Chern, J. A. Martin, D. Copetti, P. Q. Duong, N. T. Pham, D. A. Kudrna, J. Talag, W. S. Schackwitz, A. M. Lipzen, D. Dilworth, D. Bauer, J. Grimwood, C. R. Nelson, F. Xing, W. Xie, K. W. Barry, R. A. Wing, J. Schmutz, G. Li and P. C. Ronald	Genome sequence of the model rice variety KitaakeX	BMC Genomics
2019	10.1038/s41598-019-45532-1	Jia, Q., X. Chen, T. G. Kollner, J. Rinkel, J. Fu, J. Labbe, W. Xiong, J. S. Dickschat, J. Gershenzon and F. Chen	Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi	Scientific Reports
2019	10.1002/cssc.201802016	Jiang, H. J., S. Imberti, B. A. Simmons, R. Atkin and G. G. Warr	Structural Design of Ionic Liquids for Optimizing Aromatic Dissolution	ChemSusChem
2019	10.1007/s00248-019-01368-w	Johansen, R., M. Albright, L. V. Gallegos-Graves, D. Lopez, A. Runde, T. Yoshida and J. Dunbar	Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms	Microbial Ecology
2019	10.1016/j.joule.2019.05.011	Johnson, C. W., D. Salvachua, N. A. Rorrer, B. A. Black, D. R. Vardon, P. C. St John, N. S. Cleveland, G. Dominick, J. R. Elmore, N. Grundl, P. Khanna, C. R. Martinez, W. E. Michener, D. J. Peterson, K. J. Ramirez, P. Singh, T. A. VanderWall, A. N. Wilson, X. N. Yi, M. J. Biddy, Y. J. Bomble, A. M. Guss and G. T. Beckham	Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways	Joule
2019	10.1074/jbc.RA118.006025	Johnson, S. R., W. W. Bhat, J. Bibik, A. Turmo, B. Hamberger, B. Hamberger and G. Evolutionary Mint	A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae)	Journal of Biological Chemistry
2019	10.1111/nph.15778	Johnson, S. R., W. W. Bhat, R. Sadre, G. P. Miller, A. S. Garcia and B. Hamberger	Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution	New Phytologist
2019	10.1073/pnas.1901307116	Johnston, E. R., J. K. Hatt, Z. L. He, L. Y. Wu, X. Guo, Y. Q. Luo, E. A. G. Schuur, J. M. Tiedje, J. Z. Zhou and K. T. Konstantinidis	Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths	Proceedings of the National Academy of Sciences of the United States of America
2019	10.3389/fpls.2019.00862	Jones, P., B. J. Garcia, A. Furches, G. A. Tuskan and D. Jacobson	Plant Host-Associated Mechanisms for Microbial Selection	Frontiers in Plant Science
2019	10.1007/978-1-4939-8757-3_3	Joshua, C. J.	Metabolomics: A Microbial Physiology and Metabolism Perspective	Microbial Metabolomics: Methods and Protocols
2019	10.1016/j.jconhyd.2019.04.006	Jung, H. and C. Meile	Upscaling of microbially driven first-order reactions in heterogeneous porous media	Journal of Contaminant Hydrology
2019	10.1186/s13068-019-1386-y	Kahn, A., S. Morais, A. P. Galanopoulou, D. Chung, N. S. Sarai, N. Hengge, D. G. Hatzinikolaou, M. E. Himmel, Y. J. Bomble and E. A. Bayer	Creation of a functional hyperthermostable designer cellulosome	Biotechnology for Biofuels
2019	10.1111/nph.15887	Kainer, D., A. Padovan, J. Degenhardt, S. Krause, P. Mondal, W. J. Foley and C. Kulheim	High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus	New Phytologist
2019	10.1016/j.ymben.2019.09.003	Kang, A., D. Mendez-Perez, E.-B. Goh, E. E. K. Baidoo, V. T. Benites, H. R. Beller, J. D. Keasling, P. D. Adams, A. Mukhopadhyay and T. S. Lee	Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli	Metabolic Engineering
2019	10.1128/MRA.01562-18	Kang, S., S. Denman and C. McSweeney	Draft Genome Sequence and Annotation of Oribacterium sp. Strain C9, Isolated from a Cattle Rumen	Microbiology Resource Announcements
2019	None	Kannan, B., A. Altpeter, T. H. Nguyen, P. South, S. Long and F. Altpeter	Over-expression of Miscanthus Pyruvate Orthophosphate Dikinase (PPDK) in Energycane for Improving Cold Tolerance and Biomass Yield	In Vitro Cellular & Developmental Biology-Plant
2019	10.1007/s12155-019-10066-x	Kar, S., T. Y. Weng, T. Nakashima, A. Villanueva-Morales, J. R. Stewart, E. J. Sacks, Y. Terajima and T. Yamada	Field performance of Saccharum x Miscanthus intergeneric hybrids (miscanes) under cool climatic conditions of northern Japan	BioEnergy Research
2019	10.3389/fpls.2019.01166	Karunanithi, P. S. and P. Zerbe	Terpene synthases as metabolic gatekeepers in the evolution of plant terpenoid chemical diversity	Frontiers in Plant Science
2019	10.1016/j.plantsci.2019.01.006	Kausch, A. P., K. Nelson-Vasilchik, J. Hague, M. Mookkan, H. Quemada, S. Dellaporta, C. Fragoso and Z. Y. J. Zhang	Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing	Plant Science
2019	10.1128/mra.01683-18	Kee, H. L., I. V. Mikheyeva, R. L. Mickol, S. C. Dawson, D. K. Newman and J. R. Leadbetter	Draft genome sequence of the iridescent marine bacterium Tenacibaculum discolor Strain IMLK18	Microbiology Resource Announcements
2019	10.1016/j.biortech.2019.02.051	Kellock, M., H. Maaheimo, K. Marjamaa, J. Rahikainen, H. Zhang, U. Holopainen-Mantila, J. Ralph, T. Tamminen, C. Felby and K. Kruus	Effect of hydrothermal pretreatment severity on lignin inhibition in enzymatic hydrolysis	Bioresource Technology
2019	10.1080/07060661.2019.1626910	Kerio, 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. LeBoldus	From genomes to forest management - tackling invasive Phytophthora species in the era of genomics	Canadian Journal of Plant Pathology
2019	10.1128/mSphere.00435-19	Khalili, B., C. Weihe, S. Kimball, K. T. Schmidt and J. B. H. Martiny	Optimization of a method to quantify soil bacterial abundance by flow cytometry	mSphere
2019	10.3389/fpls.2019.00366	Khasanova, A., J. T. Lovell, J. Bonnette, X. Y. Weng, J. Jenkins, Y. Yoshinaga, J. Schmutz and T. E. Juenger	The genetic architecture of shoot and root trait divergence between mesic and xeric ecotypes of a perennial grass	Frontiers in Plant Science
2019	10.3389/fpls.2019.01160	Khokhar, W., M. A. Hassan, A. S. N. Reddy, S. Chaudhary, I. Jabre, L. J. Byrne and N. H. Syed	Genome-wide identification of splicing quantitative trait loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana	Frontiers in Plant Science
2019	10.1002/biot.201800441	Kim, J., M. Tremaine, J. A. Grass, H. M. Purdy, R. Landick, P. J. Kiley and J. L. Reed	Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose-Derived Sugars	Biotechnology Journal
2019	10.1073/pnas.1904636116	Kim, K. H., A. Eudes, K. Jeong, C. G. Yoo, C. S. Kim and A. Ragauskas	Integration of renewable deep eutectic solvents with engineered biomass to achieve a closed-loop biorefinery	Proceedings of the National Academy of Sciences of the United States of America
2019	10.1007/s10295-019-02150-0	Kim, S. K., D. Chung, M. E. Himmel, Y. J. Bomble and J. Westpheling	Heterologous co-expression of two beta-glucanases and a cellobiose phosphorylase resulted in a significant increase in the cellulolytic activity of the Caldicellulosiruptor bescii exoproteome	Journal of Industrial Microbiology & Biotechnology
2019	10.1111/gcbb.12613	Kim, S., B. E. Dale, M. Jin, K. D. Thelen, X. Zhang, P. Meier, A. D. Reddy, C. D. Jones, R. C. Izaurralde, V. Balan, T. Runge and M. Sharara	Integration in a depot-based decentralized biorefinery system: Corn stover-based cellulosic biofuel	Global Change Biology Bioenergy
2019	10.1021/acs.est.8b02808	Kim, S., B. E. Dale, X. S. Zhang, C. D. Jones, A. D. Reddy and R. C. Izaurralde	The renewable fuel standard may limit overall greenhouse gas savings by corn stover-based cellulosic biofuels in the us midwest: Effects of the regulatory approach on projected emissions	Environmental Science & Technology
2019	10.1002/ece3.5523	Kim, T., S. Bartel and C. Gratton	Grassland harvesting alters ant community trophic structure: An isotopic study in tallgrass prairies	Ecology and Evolution
2019	10.1038/s41598-019-54802-x	Kimball, J., Y. Y. Cui, D. Q. Chen, P. Brown, W. L. Rooney, G. Stacey and P. J. Balint-Kurti	Identification of QTL for Target Leaf Spot resistance in Sorghum bicolor and investigation of relationships between disease resistance and variation in the MAMP response	Scientific Reports
2019	10.1007/s00122-019-03371-8	King, K., H. Li, J. L. Kang and C. F. Lu	Mapping quantitative trait loci for seed traits in Camelina sativa	Theoretical and Applied Genetics
2019	10.1002/cssc.201901742	Klinger, G. E., Y. T. Zhou, P. C. Hao, J. Robbins, J. M. Aquilina, J. E. Jackson and E. L. Hegg	Biomimetic reductive cleavage of keto aryl ether bonds by small-molecule thiols	ChemSusChem
2019	10.1038/s41598-018-38124-y	Knoot, C. J. and H. B. Pakrasi	Diverse hydrocarbon biosynthetic enzymes can substitute for olefin synthase in the cyanobacterium Synechococcus sp. PCC 7002	Scientific Reports
2019	10.1016/j.soilbio.2018.12.013	Koechli, C., A. N. Campbell, C. Pepe-Ranney and D. H. Buckley	Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing	Soil Biology & Biochemistry
2019	10.1186/s12864-019-5522-7	Kolbe, A. R., A. J. Studer, O. E. Cornejo and A. B. Cousins	Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO2	BMC Genomics
2019	10.1038/s41396-019-0472-2	Kolody, B. C., J. P. McCrow, L. Z. Allen, F. O. Aylward, K. M. Fontanez, A. Moustafa, M. Moniruzzaman, F. P. Chavez, C. A. Scholin, E. E. Allen, A. Z. Worden, E. F. Delong and A. E. Allen	Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection	ISME Journal
2019	10.1016/j.cell.2019.01.034	Kominek, J., D. T. Doering, D. A. Opulente, X. X. Shen, X. F. Zhou, J. DeVirgilio, A. B. Hulfachor, M. Groenewald, M. A. McGee, S. D. Karlen, C. P. Kurtzman, A. Rokas and C. T. Hittinger	Eukaryotic acquisition of a bacterial operon	Cell
2019	10.1002/aic.16731	Kong, L. X. and C. T. Maravelias	From graphical to model-based distillation column design: A McCabe-Thiele-inspired mathematical programming approach	AIChE Journal
2019	10.1074/jbc.RA118.006548	Kontur, W. S., C. N. Olmsted, L. M. Yusko, A. V. Niles, K. A. Walters, E. T. Beebe, K. A. Vander Meulen, S. D. Karlen, D. L. Gall, D. R. Noguera and T. J. Donohue	A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's (R)-aryl ether bond reveals the diversity of bacterial -etherases	Journal of Biological Chemistry
2019	10.1096/fasebj.2019.33.1_supplement.781.8	Kontur, W. S., D. R. Noguera and T. J. Donohue	Bacterial glutathione s-transferases (gsts) involved in breaking the ?-aryl ether bond of lignin reveal novel catalytic abilities and reaction mechanisms within the GST superfamily	The FASEB Journal
2019	10.1128/mSystems.00588-19	Kothari, A., D. Soneja, A. Tang, H. K. Carlson, A. M. Deutschbauer and A. Mukhopadhyay	Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates	mSystems
2019	10.1128/mBio.02899-18	Kothari, A., Y. W. Wu, J. M. Chandonia, M. Charrier, L. Rajeev, A. M. Rocha, D. C. Joyner, T. C. Hazen, S. W. Singer and A. Mukhopadhyay	Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes	mBio
2019	10.1186/s13068-018-1216-7	Kothari, N., Holwerda, E.K., Cai, C.M., Kumar, R., and Wyman, C.E.	Biomass augmentation through thermochemical pretreatments greatly enhances digestion of switchgrass by Clostridium thermocellum	Biotechnology for Biofuels
2019	10.1039/c9gc00262f	Kothari, N., S. Bhagia, M. Zaher, Y. Q. Pu, A. Mittal, C. G. Yoo, M. E. Himmel, A. J. Ragauskas, R. Kumar and C. E. Wyman	Cellulose hydrolysis by Clostridium thermocellum is agnostic to substrate structural properties in contrast to fungal cellulases	Green Chemistry
2019	10.1080/08927014.2019.1646731	Krantz, G. P., K. Lucas, E. L. Wunderlich, L. T. Hoang, R. Avci, G. Siuzdak and M. W. Fields	Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm	Biofouling
2019	10.1016/j.cub.2019.06.056	Krassowski, T., J. Kominek, X. X. Shen, D. A. Opulente, X. F. Zhou, A. Rokas, C. T. Hittinger and K. H. Wolfe	Multiple reinventions of mating-type switching during budding yeast evolution	Current Biology
2019	10.1016/j.soilbio.2019.06.002	Kravchenko, A. N., A. K. Guber, B. S. Razavi, J. Koestel, E. V. Blagodatskaya and Y. Kuzyakov	Spatial patterns of extracellular enzymes: Combining X-ray computed micro-tomography and 2D zymography	Soil Biology & Biochemistry
2019	10.1038/s41467-019-11057-4	Kraychenko, A. N., A. K. Guber, B. S. Razavi, J. Koestel, M. Y. Quigley, G. P. Robertson and Y. Kuzyakov	Microbial spatial footprint as a driver of soil carbon stabilization	Nature Communications
2019	10.1016/j.bbamem.2019.05.009	Kumar, S. V., G. Taylor, S. Hasim, C. P. Collier, A. T. Farmer, S. R. Campagna, A. N. Bible, M. J. Doktycz and J. Morrell-Falvey	Loss of carotenoids from membranes of Pantoea sp. YR343 results in altered lipid composition and changes in membrane biophysical properties	Biochimica et Biophysica Acta (BBA) - Biomembranes
2019	10.3390/pr7090578	Kurambhatti, C., D. Kumar and V. Singh	Impact of fractionation process on the technical and economic viability of corn dry grind ethanol process	Processes
2019	10.1002/ecs2.2687	Kuske, C. R., R. L. Sinsabaugh, L. V. Gallegos-Graves, M. B. N. Albright, R. Mueller and J. Dunbar	Simple measurements in a complex system: soil community responses to nitrogen amendment in a Pinus taeda forest	Ecosphere
2019	10.1016/j.biotechadv.2018.12.003	Kwak, S., J. H. Jo, E. J. Yun, Y. S. Jin and J. H. Seo	Production of biofuels and chemicals from xylose using native and engineered yeast strains	Biotechnology Advances
2019	10.1038/s41477-019-0469-x	Labbe, J., W. Muchero, O. Czarnecki, J. Wang, X. Wang, A. C. Bryan, K. Zheng, Y. Yang, M. Xie, J. Zhang, D. Wang, P. Meidl, H. Wang, J. L. Morrell-Falvey, K. R. Cope, L. G. S. Maia, J. M. Ane, R. Mewalal, S. S. Jawdy, L. E. Gunter, W. Schackwitz, J. Martin, F. Le Tacon, T. Li, Z. Zhang, P. Ranjan, E. Lindquist, X. Yang, D. A. Jacobson, T. J. Tschaplinski, K. Barry, J. Schmutz, J. G. Chen and G. A. Tuskan	Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase	Nature Plants
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2019	10.3389/fpls.2019.00165	Lakusta, A. M., M. Kwon, E. G. Kwon, S. Stonebloom, H. V. Scheller and D. K. Ro	Molecular Studies of the Protein Complexes Involving Cis-Prenyltransferase in Guayule (Parthenium argentatum), an Alternative Rubber-Producing Plant	Frontiers in Plant Science
2019	10.3389/fmicb.2019.02216	Lal, P. B., F. M. Wells, Y. C. Lyu, I. N. Ghosh, R. Landick and P. J. Kiley	A Markerless method for genome engineering in Zymomonas mobilis ZM4	Frontiers in Microbiology
2019	10.1038/s41598-019-47957-0	Lam, P. Y., Y. Tobimatsu, N. Matsumoto, S. Suzuki, W. Lan, Y. Takeda, M. Yamamura, M. Sakamoto, J. Ralph, C. Lo and T. Umezawa	OsCAldOMT1 is a bifunctional O-methyltransferase involved in the biosynthesis of tricin-lignins in rice cell walls	Scientific Reports
2019	10.1002/bit.27202	Lane, S., Y. F. Zhang, E. J. Yun, L. Ziolkowski, G. C. Zhang, Y. S. Jin and J. L. Avalos	Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae	Biotechnology and Bioengineering
2019	10.1038/s41559-019-0998-8	Langdon, Q. K., D. Peris, E. P. Baker, D. A. Opulente, H. V. Nguyen, U. Bond, P. Goncalves, J. P. Sampaio, D. Libkind and C. T. Hittinger	Fermentation innovation through complex hybridization of wild and domesticated yeasts	Nature Ecology & Evolution
2019	10.1128/MRA.00432-19	Langley, S., T. Eng, K. H. Wan, R. A. Herbert, A. P. Klein, Y. Yoshikuni, S. G. Tringe, J. B. Brown, S. E. Celniker, J. C. Mortimer and A. Mukhopadhyay	Complete Genome Sequence of Agrobacterium sp. Strain 33MFTa1.1, Isolated from Thlaspi arvense Roots	Microbiology Resource Announcements
2019	10.3389/ffgc.2019.00008	Lantz, A. T., C. Solomon, L. Gog, A. M. McClain, S. M. Weraduwage, J. A. Cruz and T. D. Sharkey	Isoprene suppression by CO2 is not due to triose phosphate utilization (TPU) limitation	Frontiers in Forests and Global Change
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2019	10.1021/acs.jafc.9b05840	Lapierre, C., A. Voxeur, S. Boutet and J. Ralph	Arabinose conjugates diagnostic of ferulate-ferulate and ferulate-monolignol cross-coupling are released by mild acidolysis of grass cell walls	Journal of Agricultural and Food Chemistry
2019	10.1038/s41579-019-0255-9	Lawson, C. E., W. R. Harcombe, R. Hatzenpichler, S. R. Lindemann, F. E. Loffler, M. A. O'Malley, H. G. Martin, B. F. Pfleger, L. Raskin, O. S. Venturelli, D. G. Weissbrodt, D. R. Noguera and K. D. McMahon	Common principles and best practices for engineering microbiomes	Nature Reviews Microbiology
2019	10.1146/annurev-arplant-042817-040305	Leakey, A. D. B., J. N. Ferguson, C. P. Pignon, A. Wu, Z. Jin, G. L. Hammer and D. B. Lobell	Water use efficiency as a constraint and target for improving the resilience and productivity of C3 and C4 crops	Annual Review of Plant Biology
2019	10.1038/s41564-019-0423-8	Lee, H. H., N. Ostrov, B. G. Wong, M. A. Gold, A. S. Khalil and G. M. Church	Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi	Nature Microbiology
2019	10.1038/s41467-019-10258-1	Lee, H. H., R. Kalhor, N. Goela, J. Bolot and G. M. Church	Terminator-free template-independent enzymatic DNA synthesis for digital information storage	Nature Communications
2019	10.1128/AEM.01983-18	Lee, L. L., W. S. Hart, V. V. Lunin, M. Alahuhta, Y. J. Bomble, M. E. Himmel, S. E. Blumer-Schuette, M. W. W. Adams and R. M. Kelly	Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (T?pirins) from Extremely Thermophilic Caldicellulosiruptor Species	Applied and Environmental Microbiology
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2019	10.3791/58882	Levine, M. Z., N. E. Gregorio, M. C. Jewett, K. R. Watts and J. P. Oza	Escherichia coli-based cell-free protein synthesis: Protocols for a robust, flexible, and accessible platform technology	JoVE
2019	10.1371/journal.pone.0210243	Leynaud-Kieffer, L. M. C., Curran, S. C., Kim, I., Magnuson, J. K., Gladden, J. M., Baker, S. E., and Simmons, B. A.	A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable	PLOS ONE
2019	10.1038/s41540-019-0110-7	Li, C. T., J. Yelsky, Y. Q. Chen, C. Zuniga, R. Eng, L. Q. Jiang, A. Shapiro, K. W. Huang, K. Zengler and M. J. Betenbaugh	Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity	npj Systems Biology and Applications
2019	10.1093/bib/bby022	Li, G., H. Cao and Y. Xu	Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes	Briefings in Bioinformatics
2019	10.1038/s41396-019-0422-z	Li, J. H., R. L. Mau, P. Dijkstra, B. J. Koch, E. Schwartz, X. J. A. Liu, E. M. Morrissey, S. J. Blazewicz, J. Pett-Ridge, B. W. Stone, M. Hayer and B. A. Hungate	Predictive genomic traits for bacterial growth in culture versus actual growth in soil	ISME Journal
2019	10.1111/gcb.14517	Li, J. W., G. S. Wang, M. A. Mayes, S. D. Allison, S. D. Frey, Z. Shi, X. M. Hu, Y. Q. Luo and J. M. Melillo	Reduced carbon use efficiency and increased microbial turnover with soil warming	Global Change Biology
2019	10.1038/s42003-018-0265-6	Li, M., C. G. Yoo, Y. Pu, A. K. Biswal, A. K. Tolbert, D. Mohnen and A. J. Ragauskas	Downregulation of pectin biosynthesis gene GAUT4 leads to reduced ferulate and lignin-carbohydrate cross-linking in switchgrass	Communications Biology
2019	10.3390/plants8040085	Li, S., G. Courbet, A. Ourry and E. A. Ainsworth	Elevated ozone concentration reduces photosynthetic carbon gain but does not alter leaf structural traits, nutrient composition or biomass in switchgrass	Plants
2019	10.1126/sciadv.aav1848	Li, X. Y. C., D. Peris, C. T. Hittinger, E. A. Sia and J. C. Fay	Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast	Science Advances
2019	10.1039/c9gc00986h	Li, Y. D., B. Demir, L. M. V. Ramos, M. J. Chen, J. A. Dumesice and O. Ralph	Kinetic and mechanistic insights into hydrogenolysis of lignin to monomers in a continuous flow reactor	Green Chemistry
2019	10.1111/gcb.14628	Li, Y., K. Y. Guan, G. D. Schnitkey, E. DeLucia and B. Peng	Excessive rainfall leads to maize yield loss of a comparable magnitude to extreme drought in the United States	Global Change Biology
2019	10.3389/fmicb.2019.02706	Li, Z., Q. Yao, X. Guo, A. Crits-Christoph, M. A. Mayes, W. J. H. IV, S. L. Lebeis, J. F. Banfield, G. B. Hurst, R. L. Hettich and C. Pan	Genome-Resolved proteomic stable isotope probing of soil microbial communities Using 13CO2 and 13C-methanol	Frontiers in Microbiology
2019	10.1094/MPMI-05-18-0133-R	Liao, H. L., G. Bonito, J. A. Rojas, K. Hameed, S. Wu, C. W. Schadt, J. Labbe, G. A. Tuskan, F. Martin, I. V. Grigoriev and R. Vilgalys	Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition	Molecular Plant-Microbe Interactions
2019	10.3389/fpls.2019.00101	Lim, S. D., S. Lee, W. G. Choi, W. C. Yim and J. C. Cushman	Laying the Foundation for Crassulacean Acid Metabolism (CAM) Biodesign: Expression of the C4 metabolism cycle genes of CAM in Arabidopsis	Frontiers in Plant Science
2019	10.1007/s12042-019-09238-y	Lin, J. S., M. T. Zhu, M. X. Cai, W. P. Zhang, M. Fatima, H. F. Jia, F. F. Li and R. Ming	Identification and expression analysis of TCP genes in Saccharum spontaneum L	Tropical Plant Biology
2019	10.1093/jxb/erz415	Liu, D., M. Chen, B. Mendoza, H. Cheng, R. Hu, L. Li, C. T. Trinh, G. A. Tuskan and X. Yang	CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants	Journal of Experimental Botany
2019	10.1021/acssynbio.9b00110	Liu, F., J. W. Mao, T. Lu and Q. Hua	Synthetic, Context-Dependent Microbial Consortium of Predator and Prey	ACS Synthetic Biology
2019	10.1038/s41467-019-09288-6	Liu, J. J., G. C. Zhang, S. Kwak, E. J. Oh, E. J. Yun, K. Chomvong, J. H. D. Cate and Y. S. Jin	Overcoming the thermodynamic equilibrium of an isomerization reaction through oxidoreductive reactions for biotransformation	Nature Communications
2019	10.1371/journal.pcbi.1006848	Liu, J. K., C. Lloyd, M. M. Al-Bassam, A. Ebrahim, J. N. Kim, C. Olson, A. Aksenov, P. Dorrestein and K. Zengler	Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen	PLOS Computational Biology
2019	10.1038/s41396-018-0255-1	Liu, N., H. J. Li, M. G. Chevrette, L. Zhang, L. Cao, H. K. Zhou, X. G. Zhou, Z. H. Zhou, P. B. Pope, C. R. Currie, Y. P. Huang and Q. Wang	Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite	Isme Journal
2019	10.1038/s41467-019-13500-y	Liu, R. M., L. L. Liang, E. Freed, H. Chang, E. Oh, Z. Y. Liu, A. Garst, C. A. Eckert and R. T. Gill	Synthetic chimeric nucleases function for efficient genome editing	Nature Communications
2019	10.1016/j.ymben.2018.07.007	Liu, R. M., L. Y. Liang, A. Choudhury, A. D. Garst, C. A. Eckert, E. J. Oh, J. Winkler and R. T. Gill	Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production	Metabolic Engineering
2019	10.1111/oik.05548	Liu, S., J. Streich, J. O. Borevitz, K. J. Rice, T. Li, B. Li and K. J. Bradford	Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations	Oikos
2019	10.3389/fpls.2018.01902	Liu, W., Xiang, Y., Zhang, X., Han, G., Sun, X., Sheng, Y., Zhang, A.	Over-Expression of a Maize N-Acetylglutamate Kinase Gene (ZmNAGK) Improves Drought Tolerance in Tobacco	Frontiers in Plant Science
2019	10.1021/acssuschemeng.9b02800	Liu, X. R., Y. D. Li, C. M. Ewulonu, J. Ralph, F. Xu, Q. L. Zhang, M. Wu and Y. Huang	Mild Alkaline pretreatment for isolation of native-like lignin and lignin-containing cellulose nanofibers (LCNF) from crop waste	ACS Sustainable Chemistry & Engineering
2019	10.1093/nar/gkz772	Liu, X. Y., S. T. P. Gupta, D. Bhimsaria, J. L. Reed, J. A. Rodriguez-Martinez, A. Z. Ansari and S. Raman	De novo design of programmable inducible promoters	Nucleic Acids Research
2019	10.1038/s41467-019-09836-0	Liu, Y. X., D. T. Huynh and T. O. Yeates	A 3.8 angstrom resolution cryo-EM structure of a small protein bound to an imaging scaffold	Nature Communications
2019	10.1021/acssynbio.8b00485	Liu, Y., R. Landick and S. Raman	A Regulatory NADH/NAD plus Redox Biosensor for Bacteria	Acs Synthetic Biology
2019	10.1038/s41598-019-47797-y	Lloyd, J. P., M. J. Bowman, C. B. Azodi, R. P. Sowers, G. D. Moghe, K. L. Childs and S. H. Shiu	Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae	Scientific Reports
2019	10.3389/fmicb.2019.00124	Lohberger, A., J. E. Spangenberg, Y. Ventura, S. Bindschedler, E. P. Verrecchia, R. Bshary and P. Junier	Effect of Organic Carbon and Nitrogen on the Interactions of Morchella spp. and Bacteria Dispersing on Their Mycelium	Front Microbiol
2019	10.1007/s10021-019-00439-w	Looby, C. I., E. C. Hollenbeck and K. K. Treseder	Fungi in the canopy: how soil fungi and extracellular enzymes differ between canopy and ground soils	Ecosystems
2019	10.1073/pnas.1821543116	Lowry, D. B., J. T. Lovell, L. Zhang, J. Bonnette, P. A. Fay, R. B. Mitchell, J. Lloyd-Reilley, A. R. Boe, Y. Q. Wu, F. M. Rouquette, R. L. Wynia, X. Y. Weng, K. D. Behrman, A. Healey, K. Barrym, A. Lipzen, D. Bauer, A. Sharma, J. Jenkins, J. Schmutz, F. B. Fritschi and T. E. Juenger	QTL x environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient	Proceedings of the National Academy of Sciences of the United States of America
2019	10.1016/j.biortech.2019.121589	Lu, K., N. Hao, X. Meng, Z. Luo, G. A. Tuskan and A. J. Ragauskas	Investigating the correlation of biomass recalcitrance with pyrolysis oil using poplar as the feedstock	Bioresource Technology
2019	10.1093/bioinformatics/btz592	Ma, F. and M. Pellegrini	ACTINN: automated identification of cell types in single cell RNA sequencing	Bioinformatics
2019	10.1186/s12864-018-5393-3	Ma, F. Y., B. K. Fuqua, Y. Hasin, C. Yukhtman, C. D. Vulpe, A. J. Lusis and M. Pellegrini	A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods	Bmc Genomics
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2019	10.1099/ijsem.0.004720	Mahmoud, H., L. Jose and S. Eapen	Grimontia sedimenti sp. nov., isolated from benthic sediments near coral reefs south of Kuwait	Int J Syst Evol Microbiol
2019	10.1016/j.copbio.2018.10.014	Mahon, E. L. and S. D. Mansfield	Tailor-made trees: engineering lignin for ease of processing and tomorrow's bioeconomy	Current Opinion in Biotechnology
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2019	10.1128/mSystems.00284-18	Martien, J. I., A. S. Hebert, D. M. Stevenson, M. R. Regner, D. B. Khana, J. J. Coon and D. Amador-Noguez	Systems-level analysis of oxygen exposure in Zymomonas mobilis: Implications for isoprenoid production	mSystems
2019	10.1016/j.syapm.2018.12.003	Martinez, M. A., B. J. Woodcroft, J. C. Ignacio Espinoza, A. A. Zayed, C. M. Singleton, J. A. Boyd, Y.-F. Li, S. Purvine, H. Maughan, S. B. Hodgkins, D. Anderson, M. Sederholm, B. Temperton, B. Bolduc, S. R. Saleska, G. W. Tyson, V. I. Rich, S. R. Saleska, G. W. Tyson and V. I. Rich	Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus cryosericota phylum nov., Ca. cryosericia class nov., Ca. cryosericales ord. nov., Ca. cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. c. hinesii sp. nov., Ca. c. odellii sp. nov., Ca. c. terrychapinii sp. nov	Systematic and Applied Microbiology
2019	10.1128/mSystems.00016-19	Martino, C., J. T. Morton, C. A. Marotz, L. R. Thompson, A. Tripathi, R. Knight and K. Zengler	A novel sparse compositional technique reveals microbial perturbations	mSystems
2019	10.1038/s41396-019-0410-3	Martiny, A. C.	High proportions of bacteria are culturable across major biomes	ISME Journal
2019	10.1038/s41467-018-08246-y	Matheus Carnevali, P. B., Schulz, F., Castelle, C. J., Kantor, R. S., Shih, P. M., Sharon, I., Banfield, J. F.	Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria	Nature Communications
2019	10.1128/MRA.01518-18	Matu, A., A. Lum Nde, L. Oosthuizen, A. Hitzeroth, M. Badenhorst, L. Duba, M. Gidaga, J. Klinck, I.-M. Kriek, P. J. Lekoma, L. Nel, S. M. dos Ramos, J. Rossouw, N. Salomane, N. Segone, S. Serobe, T. Tiyani, C. J. Hugo and J. D. Newman	Draft Genome Sequences of Seven Chryseobacterium Type Strains	Microbiology Resource Announcements
2019	10.1007/978-1-4939-9721-3_6	Mayali, X., P. K. Weber, E. Nuccio, J. Lietard, M. Somoza, S. J. Blazewicz and J. Pett-Ridge	Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS	Methods in Molecular Biology
2019	10.1186/s12870-019-1653-x	Mazaheri, M., M. Heckwolf, B. Vaillancourt, J. L. Gage, B. Burdo, S. Heckwolf, K. Barry, A. Lipzen, C. B. Ribeiro, T. J. Y. Kono, H. F. Kaeppler, E. P. Spalding, C. N. Hirsch, C. R. Buell, N. de Leon and S. M. Kaeppler	Genome-wide association analysis of stalk biomass and anatomical traits in maize	BMC Plant Biology
2019	10.1039/c9gc00589g	McClelland, D. J., P. H. Galebach, A. H. Motagamwala, A. M. Wittrig, S. D. Karlen, J. S. Buchanan, J. A. Dumesic and G. W. Huber	Supercritical methanol depolymerization and hydrodeoxygenation of lignin and biomass over reduced copper porous metal oxides	Green Chemistry
2019	10.1128/MRA.01538-18	McComb, E., J. Holm, B. Ma and J. Ravel	Complete Genome Sequence of Lactobacillus crispatus CO3MRSI1	Microbiology Resource Announcements
2019	10.1002/bit.26976	McTaggart, T. L., D. Bever, S. Bassett and N. A. Da Silva	Synthesis of polyketides from low cost substrates by the thermotolerant yeast Kluyveromyces marxianus	Biotechnology and Bioengineering
2019	10.1016/j.ymben.2019.06.003	Mehrer, C. R., J. M. Rand, M. R. Incha, T. B. Cook, B. Demir, A. H. Motagamwala, D. Kim, J. A. Dumesic and B. F. Pfleger	Growth-coupled bioconversion of levulinic acid to butanone	Metabolic Engineering
2019	10.1002/pld3.181	Mei, Y., B. M. Beernink, E. E. Ellison, E. Konecna, A. K. Neelakandan, D. F. Voytas and S. A. Whitham	Protein expression and gene editing in monocots using foxtail mosaic virus vectors	Plant Direct
2019	10.2138/gselements.15.2.111	Meile, C. and T. D. Scheibe	Reactive transport modeling of microbial dynamics	Elements: An International Magazine of Mineralogy, Geochemistry, and Petrology
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2019	10.3389/fmicb.2019.00515	Mewalal, R., H. Yin, R. Hu, S. Jawdy, P. Vion, G. A. Tuskan, F. Le Tacon, J. L. Labbe and X. Yang	Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis	Frontiers in Microbiology
2019	10.1186/s40694-019-0071-z	Millet, L. J., J. Aufrecht, J. Labbe, J. Uehling, R. Vilgalys, M. L. Estes, C. Miquel Guennoc, A. Deveau, S. Olsson, G. Bonito, M. J. Doktycz and S. T. Retterer	Increasing access to microfluidics for studying fungi and other branched biological structures	Fungal Biology and Biotechnology
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2019	10.1007/s11627-019-09993-3	Mohan, C., D. D. Wang and F. Altpeter	Establishing a Rapid Readout System for Genome Editing of Sugarcane	In Vitro Cellular & Developmental Biology-Plant
2019	10.1002/slct.201802187	Mohapatra, S., C. Mishra, B. B. Merritt, S. Pattathil and H. Thatoi	Evaluating the Role of Ultrasonication-Assisted Alkali Pretreatment and Enzymatic Hydrolysis on Cellwall Polysaccharides of Pennisetum Grass Varieties as Potential Biofuel Feedstock	ChemistrySelect
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2019	10.1016/j.pbi.2019.05.004	Muller, L. M. and M. J. Harrison	Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis	Current Opinion in Plant Biology
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2019	10.1111/nph.15479	Murik, O., L. Tirichine, J. Prihoda, Y. Thomas, W. L. Araujo, A. E. Allen, A. R. Fernie and C. Bowler	Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom	New Phytologist
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2019	10.1111/tpj.14223	Na, G., X. P. Mu, P. Grabowski, J. Schmutz and C. F. Lu	Enhancing microRNA167A expression in seed decreases the alpha-linolenic acid content and increases seed size in Camelina sativa	Plant Journal
2019	10.1039/c8cc07482h	Nagy, G., D. Velickovic, R. K. Chu, A. A. Carrell, D. J. Weston, Y. M. Ibrahim, C. R. Anderton and R. D. Smith	Towards resolving the spatial metabolome with unambiguous molecular annotations in complex biological systems by coupling mass spectrometry imaging with structures for lossless ion manipulations	Chemical Communications
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2019	10.1038/s41598-019-38836-9	Ng, C. Y., L. Wang, A. Chowdhury and C. D. Maranas	Pareto Optimality Explanation of the Glycolytic Alternatives in Nature	Scientific Reports
2019	10.1016/j.apenergy.2019.03.020	Ng, R. T. L., P. Fasahati, K. F. Huang and C. T. Maravelias	Utilizing stillage in the biorefinery: Economic, technological and energetic analysis	Applied Energy
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2019	10.1186/s12864-019-6329-2	Nguyen, N. D., I. K. Blaby and D. Wang	ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks	BMC Genomics
2019	10.1016/bs.mie.2018.12.009	Nichols, T. M., N. W. Kennedy and D. Tullman-Ercek	Cargo encapsulation in bacterial microcompartments: Methods and analysis	Methods in Enzymology
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2019	10.1073/pnas.1904623116	Ning, D. L., Y. Deng, J. M. Tiedje and J. Z. Zhou	A general framework for quantitatively assessing ecological stochasticity	Proceedings of the National Academy of Sciences of the United States of America
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2019	10.1007/s13361-018-2027-6	Nshanian, M., C. Lantz, P. Wongkongkathep, T. Schrader, F. G. Klarner, A. Blumke, C. Despres, M. Ehrmann, C. Smet-Nocca, G. Bitan and J. A. Loo	Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator	Journal of the American Society for Mass Spectrometry
2019	10.1080/15427528.2019.1566186	Obeng, E., A. K. Obour, N. O. Nelson, J. A. Moreno, I. A. Ciampitti, D. Wang and T. P. Durrett	Seed yield and oil quality as affected by Camelina cultivar and planting date	Journal of Crop Improvement
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2019	10.1093/femsyr/foz032	Opulente, D. A., Q. K. Langdon, K. V. Buh, M. A. B. Haase, K. Sylvester, R. V. Moriarty, M. Jarzyna, S. L. Considine, R. M. Schneider and C. T. Hittinger	Pathogenic budding yeasts isolated outside of clinical settings	FEMS Yeast Research
2019	10.1128/jb.00410-18	Orr, J. S., D. G. Christensen, A. J. Wolfe and C. V. Rao	Extracellular acidic pH inhibits acetate consumption by decreasing gene transcription of the tricarboxylic acid cycle and the glyoxylate shunt	Journal of Bacteriology
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2019	10.1371/journal.pone.0210558	Oyetunde, T., D. Liu, H. G. Martin and Y. J. J. Tang	Machine learning framework for assessment of microbial factory performance	Plos One
2019	10.1093/femsle/fnz125	Pacheco, A. R. and D. Segre	A multidimensional perspective on microbial interactions	FEMS Microbiology Letters
2019	10.1038/s41467-018-07946-9	Pacheco, A. R., M. Moel and D. Segre	Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems	Nature Communications
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2019	10.1186/s12862-019-1398-z	Panchy, N. L., C. B. Azodi, E. F. Winship, R. C. O'Malley and S. H. Shiu	Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication	BMC Evolutionary Biology
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2019	10.1016/j.soilbio.2018.12.016	Papp, K., B. A. Hungate and E. Schwartz	mRNA, rRNA and DNA quantitative stable isotope probing with H2O18O indicates use of old rRNA among soil Thaumarchaeota	Soil Biology & Biochemistry
2019	10.1002/cbic.201800650	Pappireddi, N., L. Martin and M. Wuhr	A review on quantitative multiplexed proteomics	ChemBioChem
2019	10.1111/gcbb.12585	Parish, A. L., A. D. Kendall, A. M. Thompson, R. S. Stenjem and D. W. Hyndman	Cellulosic biofuel crops alter evapotranspiration and drainage fluxes: Direct quantification using automated equilibrium tension lysimeters	GCB Bioenergy
2019	10.1038/s41589-019-0364-9	Park, J. O., L. B. Tanner, M. H. Wei, D. B. Khana, T. B. Jacobson, Z. Y. Zhang, S. A. Rubin, S. H. J. Li, M. B. Higgins, D. M. Stevenson, D. Amador-Noguez and J. D. Rabinowitz	Near-equilibrium glycolysis supports metabolic homeostasis and energy yield	Nature Chemical Biology
2019	10.1038/s42255-019-0077-0	Park, J. O., N. Liu, K. M. Holinski, D. F. Emerson, K. Qiao, B. M. Woolston, J. Xu, Z. Lazar, M. A. Islam and C. Vidoudez	Synergistic substrate cofeeding stimulates reductive metabolism	Nature Metabolism
2019	10.1093/jxb/erz369	Park, S., B. Song, W. Shen and S.-Y. Ding	A mutation in the catalytic domain of cellulose synthase 6 halts its transport to the Golgi apparatus	Journal of Experimental Botany
2019	10.1039/c9cp01431d	Paslack, C., J. C. Smith, M. Heyden and L. V. Schafer	Hydration-mediated stiffening of collective membrane dynamics by cholesterol	Physical Chemistry Chemical Physics
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2019	10.1021/jacs.8b10242	Patri, A. S., B. Mostofian, Y. Q. Pu, N. Ciaffone, M. Soliman, M. D. Smith, R. Kumar, X. L. Cheng, C. E. Wyrnan, L. Tetard, A. J. Ragauskas, J. C. Smith, L. Petridis and C. M. Cai	A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction	Journal of the American Chemical Society
2019	10.1186/s13068-019-1515-7	Patri, A. S., L. McAlister, C. M. Cai, R. Kumar and C. E. Wyman	CELF significantly reduces milling requirements and improves soaking effectiveness for maximum sugar recovery of Alamo switchgrass over dilute sulfuric acid pretreatment	Biotechnology for Biofuels
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2019	10.1016/j.soilbio.2018.10.009	Pegoraro, E., M. Mauritz, R. Bracho, C. Ebert, P. Dijkstra, B. A. Hungate, K. T. Konstantinidis, Y. Q. Luo, C. Schadel, J. M. Tiedje, J. Z. Zhou and E. A. G. Schuur	Glucose addition increases the magnitude and decreases the age of soil respired carbon in a long-term permafrost incubation study	Soil Biology & Biochemistry
2019	10.1111/1462-2920.14727	Pellegrin, C., Y. Daguerre, J. Ruytinx, F. Guinet, M. Kemppainen, N. F. D. Frey, V. Puech-Pages, A. Hecker, A. G. Pardo, F. M. Martin and C. Veneault-Fourrey	Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis	Environmental Microbiology
2019	10.1002/cbic.201800580	Pelot, K. A., D. M. Hagelthorn, Y. J. Hong, D. J. Tantillo and P. Zerbe	Diterpene synthase-catalyzed biosynthesis of distinct clerodane stereoisomers	ChemBioChem
2019	10.3390/ijms20184363	Pereira, P. N. and J. C. Cushman	Exploring the relationship between Crassulacean Acid Metabolism (CAM) and mineral nutrition with a special focus on nitrogen	International Journal of Molecular Sciences
2019	10.1039/c8gc03504k	Perez, J. M., W. S. Kontur, M. Alherech, J. Coplien, S. D. Karlen, S. S. Stahl, T. J. Donohue and D. R. Noguera	Funneling aromatic products of chemically depolymerized lignin into 2-pyrone-4-6-dicarboxylic acid with Novosphingobium aromaticivorans	Green Chemistry
2019	10.1016/j.copbio.2018.09.011	Perkins, M., R. A. Smith and L. Samuels	The transport of monomers during lignification in plants: anything goes but how?	Current Opinion in Biotechnology
2019	10.1111/gcbb.12599	Pignon, C. P., I. Spitz, E. J. Sacks, U. Jorgensen, K. Korup and S. P. Long	Siberian Miscanthus sacchariflorus accessions surpass the exceptional chilling tolerance of the most widely cultivated clone of Miscanthus x giganteus	Global Change Biology Bioenergy
2019	10.1002/9781119409144.ch136	Pingault, L., Z. Qiao and M. Libault	Comparative genomic and transcriptomic analyses of legume genes controlling the nodulation process	The Model Legume Medicago Truncatula
2019	10.1016/j.phytochem.2019.01.014	Piva, L. R. O., K. J. Jardine, B. O. Gimenez, R. de Oliveira Perdiz, V. S. Menezes, F. M. Durgante, L. O. Cobello, N. Higuchi and J. Q. Chambers	Volatile monoterpene 'fingerprints' of resinous Protium tree species in the Amazon rainforest	Phytochemistry
2019	10.1128/MRA.01065-19	Podar, M., J. Turner, L. H. Burdick and D. A. Pelletier	Complete Genome Sequence of Terriglobus albidus Strain ORNL, an Acidobacterium Isolated from the Populus deltoides Rhizosphere	Microbiology Resource Announcements
2019	10.5194/bg-16-4875-2019	Pold, G., S. A. Sistla and K. M. DeAngelis	Metabolic tradeoffs and heterogeneity in microbial responses to temperature determine the fate of litter carbon in simulations of a warmer world	Biogeosciences
2019	10.3389/fmicb.2019.02594	Poudel, S., R. J. Giannone, A. T. Farmer, S. R. Campagna, A. N. Bible, J. L. Morrell-Falvey, J. G. Elkins and R. L. Hettich	Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Paenibacillus polymyxa Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility	Frontiers in Microbiology
2019	10.1021/acs.jpcb.9b06243	Prates, E. T., M. F. Crowley, M. S. Skaf and G. T. Beckham	Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG	The Journal of Physical Chemistry B
2019	10.1128/mSystems.00072-19	Price, M. N. and A. P. Arkin	Curated BLAST for Genomes	mSystems
2019	10.1128/mSystems.00297-18	Price, M. N., J. Ray, A. T. Iavarone, H. K. Carlson, E. M. Ryan, R. R. Malmstrom, A. P. Arkin and A. M. Deutschbauer	Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism	mSystems
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2019	10.1093/molbev/msz185	Priyann, A., B. J. Woodcroft, V. Rai, I. Moghul, A. Munagala, F. Ter, H. Chowdhary, I. Pieniak, L. J. Maynard, M. A. Gibbins, H. Moon, A. Davis-Richardson, M. Uludag, N. S. Watson-Haigh, R. Challis, H. Nakamura, E. Favreau, E. A. Gomez, T. Pluskal, G. Leonard, W. Rumpf and Y. Wurm	Sequenceserver: A modern graphical user interface for custom BLAST databases	Molecular Biology and Evolution
2019	10.1021/jacs.9b07243	Rafiee, M., M. Alherech, S. D. Karlen and S. S. Stahl	Electrochemical aminoxyl-mediated oxidation of primary alcohols in lignin to carboxylic acids: Polymer modification and depolymerization	Journal of the American Chemical Society
2019	10.1371/journal.pone.0214960	Rajeev, L., E. G. Luning, G. M. Zane, T. R. Juba, A. E. Kazakov, P. S. Novichkov, J. D. Wall and A. Mukhopadhyay	LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species	PLoS One
2019	10.1016/j.copbio.2019.02.019	Ralph, J., C. Lapierre and W. Boerjan	Lignin structure and its engineering	Current Opinion in Biotechnology
2019	10.1007/978-3-030-10777-2_1	Ramin, K. I. and S. D. Allison	Carbon cycle implications of soil microbial interactions	Understanding Terrestrial Microbial Communities
2019	10.3389/fmicb.2019.02956	Ramin, K. I. and S. D. Allison	Bacterial tradeoffs in growth rate and extracellular enzymes	Frontiers in Microbiology
2019	10.1534/g3.118.200969	Ramstein, G. P. and M. D. Casler	Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample	G3-Genes Genomes Genetics
2019	10.1093/abbs/gmz080	Rao, X., and Dixon, R.A.	Co-expression networks for plant biology: why and how	Acta Biochimica et Biophysica Sinica
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2019	10.1111/1758-2229.12757	Ray, P., Abraham, P.E., Guo, Y., Giannone, R.J., Engle, N.L., Yang, Z.K., Jacobson, D.J., Hettich, R.L., Tschaplinski, T.J., and Craven, K.D.	Scavenging organic nitrogen and remodeling lipid metabolism are key survival strategies adopted by the endophytic fugi, Serendipita vermifera and Serendipita bescii to alleviate nitrogen and phosphorous starvation in vitro	Environmental Microbiology Reports
2019	10.21203/rs.2.15334/v1	Razar, R., K. Devos and A. Missaoui	Analysis of Segregation Ratio Distortion and Linkage Mapping in Two Switchgrass F1 Populations: Lowland-lowland and Lowland-upland Using Genotyping by Sequencing Data	Research Square
2019	10.1016/j.rhisph.2019.100161	Razavi, B. S., X. C. Zhang, N. Bilyera, A. Guber and M. Zarebanadkouki	Soil zymography: Simple and reliable? Review of current knowledge and optimization of the method	Rhizosphere
2019	10.1007/s10021-019-00407-4	Reed, D. E., J. Chen, M. Abraha, G. P. Robertson and K. M. Dahlin	The Shifting role of mRUE for regulating ecosystem production	Ecosystems
2019	10.1038/s41598-019-50125-z	Reese, K. L., C. L. Fisher, P. D. Lane, J. D. Jaryenneh, M. W. Moorman, A. D. Jones, M. Frank and T. W. Lane	Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes	Scientific Reports
2019	10.1038/s41587-019-0286-9	Reis, A. C., S. M. Halper, G. E. Vezeau, D. P. Cetnar, A. Hossain, P. R. Clauer and H. M. Salis	Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays	Nature Biotechnology
2019	10.1104/pp.19.00344	Rencoret, J., D. Neiva, G. Marques, A. Gutierrez, H. Kim, J. Gominho, H. Pereira, J. Ralph and J. C. del Rio	Hydroxystilbene glucosides are incorporated into Norway Spruce bark lignin	Plant Physiology
2019	10.1016/j.tplants.2019.01.006	Rhee, S. Y., K. D. Birnbaum and D. W. Ehrhardt	Towards building a plant cell atlas	Trends in Plant Science
2019	10.1007/s11103-019-00861-7	Rigoulot, S. B., H. E. Petzold, S. P. Williams, A. M. Brunner and E. P. Beers	Populus trichocarpa clade A PP2C protein phosphatases: their stress-induced expression patterns, interactions in core abscisic acid signaling, and potential for regulation of growth and development	Plant Molecular Biology
2019	10.1007/s10295-019-02218-x	Riley, L. A., L. Ji, R. J. Schmitz, J. Westpheling and A. M. Guss	Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems	Journal of Industrial Microbiology & Biotechnology
2019	10.1002/ppp3.29	Rodriguez-Zaccaro, F. D. and A. Groover	Wood and water: How trees modify wood development to cope with drought	Plants, People, Planet
2019	10.1186/s12934-019-1083-3	Roell, G. W., J. Zha, R. R. Carr, M. A. Koffas, S. S. Fong and Y. J. J. Tang	Engineering microbial consortia by division of labor	Microbial Cell Factories
2019	10.1016/j.ymben.2019.06.013	Roell, G. W., R. R. Carr, T. Campbell, Z. Y. Shang, W. R. Henson, J. J. Czajka, H. G. Martin, F. Z. Zhang, M. Foston, G. Dantas, T. S. Moon and Y. J. J. Tang	A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630	Metabolic Engineering
2019	10.1016/j.soilbio.2018.11.006	Roley, S. S., C. Xue, S. K. Hamilton, J. M. Tiedje and G. P. Robertson	Isotopic evidence for episodic nitrogen fixation in switchgrass (Panicum virgatum L.)	Soil Biology & Biochemistry
2019	10.1038/s42003-019-0577-1	Roth, M. S., D. J. Westcott, M. Iwai and K. K. Niyogi	Hexokinase is necessary for glucose-mediated photosynthesis repression and lipid accumulation in a green alga	Communications Biology
2019	10.1105/tpc.18.00742	Roth, M. S., S. D. Gallaher, D. J. Westcott, M. Iwai, K. B. Louie, M. Mueller, A. Walter, F. Foflonker, B. P. Bowen, N. N. Ataii, J. H. Song, J. H. Chen, C. E. Blaby-Haas, C. Larabell, M. Auer, T. R. Northen, S. S. Merchant and K. K. Niyogi	Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis	Plant Cell
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2019	10.1128/mra.01178-19	Rusley, C., T. C. Onstott, T. A. Vishnivetskaya, A. Layton, A. Chauhan, S. M. Pfiffner, L. G. Whyte and M. C. Y. Lau	Metagenome-assembled genome of USC? AHI, a potential high-affinity methanotroph from Axel Heiberg Island, Canadian High Arctic	Microbiology Resource Announcements
2019	10.1021/acs.iecr.8b04083	Ryu, J. and C. T. Maravelias	Simultaneous process and heat exchanger network synthesis using a discrete temperature grid	Industrial & Engineering Chemistry Research
2019	10.1038/s41467-019-08515-4	Sadre, R., P. Y. Kuo, J. X. Chen, Y. Yang, A. Banerjee, C. Benning and B. Hamberger	Cytosolic lipid droplets as engineered organelles for production and accumulation of terpenoid biomaterials in leaves	Nature Communications
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2019	10.1016/j.fuel.2018.09.037	Sakai, S. and D. Rothamer	Impact of ethanol blending on particulate emissions from a spark-ignition direct-injection engine	Fuel
2019	10.1007/s10529-018-2622-4	Sake, C. L., A. J. Metcalf and N. R. Boyle	The challenge and potential of photosynthesis: unique considerations for metabolic flux measurements in photosynthetic microorganisms	Biotechnology Letters
2019	10.1105/tpc.18.00952	Salome, P. A. and S. S. Merchant	A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism	Plant Cell
2019	10.21769/BioProtoc.3304	Samira, R., X. Zhang, J. Kimball, Y. Cui, G. Stacey and P. Balint-Kurti	Quantifying MAMP-induced production of reactive oxygen species in sorghum and maize	Bio-101
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2019	10.1039/C8SE00287H	Satari, B., K. Karimi and R. Kumar	Cellulose solvent-based pretreatment for enhanced second-generation biofuel production: a review	Sustainable Energy & Fuels
2019	10.1128/jb.00768-18	Schilling, B., N. Basisty, D. G. Christensen, D. Sorensen, J. S. Orr, A. J. Wolfe and C. V. Rao	Global lysine acetylation in Escherichia coli results from growth conditions that favor acetate fermentation	Journal of Bacteriology
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2019	10.1016/j.mib.2019.09.008	Shade, A. and N. Stopnisek	Abundance-occupancy distributions to prioritize plant core microbiome membership	Current Opinion in Microbiology
2019	10.1007/s10021-019-00363-z	Shcherbak, I. and G. P. Robertson	Nitrous Oxide (N2O) emissions from subsurface soils of agricultural ecosystems	Ecosystems
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2019	10.1021/acssuschemeng.9b01166	Shen, W., C. Collings, M. Y. Li, J. Markovicz, J. Ralph, S. D. Mansfield and S. Y. Ding	Imaging changes in cell walls of engineered poplar by stimulated raman scattering and atomic force microscopy	ACS Sustainable Chemistry & Engineering
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2019	10.3390/s19204446	Shuai, G., A. R. Martinez-Feria, J. Zhang, S. Li, R. Price and B. Basso	Capturing maize stand heterogeneity across yield-stability zones using unmanned aerial vehicles (UAV)	Sensors
2019	10.1128/mBio.01580-18	Siegel, S. D., B. R. Amer, C. G. Wu, M. R. Sawaya, J. E. Gosschalk, R. T. Clubb and H. Ton-That	Structure and Mechanism of LcpA, a Phosphotransferase That Mediates Glycosylation of a Gram-Positive Bacterial Cell Wall-Anchored Protein	mBio
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2019	10.3389/fmicb.2019.02181	Singer, E., J. Bonnette, T. Woyke and T. E. Juenger	Conservation of endophyte bacterial community structure across two Panicum grass species	Frontiers in Microbiology
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2019	10.1111/1758-2229.12725	Sirois, S. H. and D. H. Buckley	Factors governing extracellular DNA degradation dynamics in soil	Environmental Microbiology Reports
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2019	10.1111/nph.15585	Sonawane, B. V. and A. B. Cousins	Uncertainties and limitations of using carbon-13 and oxygen-18 leaf isotope exchange to estimate the temperature response of mesophyll CO2 conductance in C-3 plants	New Phytologist
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2019	10.1016/j.carbpol.2019.115119	Sowinski, E. E., S. Gilbert, E. Lam and N. C. Carpita	Linkage structure of cell-wall polysaccharides from three duckweed species	Carbohydrate Polymers
2019	10.1002/eap.1828	Spiesman, B. J., A. Bennett, R. Isaacs and C. Gratton	Harvesting effects on wild bee communities in bioenergy grasslands depend on nesting guild	Ecological Applications
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2019	10.1021/acssynbio.8b00381	Stark, J. C., A. Huang, K. J. Hsu, R. S. Dubner, J. Forbrook, S. Marshalla, F. Rodriguez, M. Washington, G. A. Rzimicky, P. Q. Nguyen, B. Hasselbacher, R. Jabri, R. Kamran, V. Koralewski, W. Wightkin, T. Martinez and M. C. Jewett	BioBits Health: Classroom activities exploring engineering, biology, and human health with fluorescent readouts	ACS Synthetic Biology
2019	10.1073/pnas.1908291116	Starr, E. P., E. E. Nuccio, J. Pett-Ridge, J. F. Banfield and M. K. Firestone	Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil	Proceedings of the National Academy of Sciences
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2019	10.1016/j.agwat.2019.04.008	Stenjem, R. S., A. M. Thompson, K. G. Karthikeyan, B. J. Lepore, A. D. Kendall and D. W. Hyndman	Quantity and quality of water percolating below the root zone of three biofuel feedstock crop systems	Agricultural Water Management
2019	10.1038/s41598-019-42469-3	Stone, K. A., Q. P. He and J. Wang	Two experimental protocols for accurate measurement of gas component uptake and production rates in bioconversion processes	Scientific Reports
2019	10.1186/s12870-019-1653-x	Stonebloom, S. h., and Scheller, H. V.	Transcriptome analysis of rubber biosynthesis in guayule (Parthenium argentatum gray)	BMC Plant Biology
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2019	10.1002/bit.26993	Straub, C. T., P. A. Khatibi, J. K. Otten, M. W. W. Adams and R. M. Kelly	Lignocellulose solubilization and conversion by extremely thermophilic Caldicellulosiruptor bescii improves by maintaining metabolic activity	Biotechnology and Bioengineering
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2019	10.1128/aem.00622-19	Streett, H. E., K. M. Kalis and E. T. Papoutsakis	A Strongly fluorescing anaerobic reporter and protein-tagging system for Clostridium organisms based on the Fluorescence-Activating and Absorption-Shifting Tag Protein (FAST)	Applied and Environmental Microbiology
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2019	10.1128/mSystems.00230-18	Succurro, A., D. Segre and O. Ebenhoh	Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth	mSystems
2019	10.1021/acssynbio.9b00217	Sun, L., S. Kwak and Y. S. Jin	Vitamin A Production by Engineered Saccharomyces cerevisiae from Xylose via Two-Phase in Situ Extraction	Acs Synthetic Biology
2019	10.1111/nph.15472	Sun, X. P., W. B. Chen, S. Ivanov, A. M. MacLean, H. Wight, T. Ramaraj, J. Mudge, M. J. Harrison and Z. J. Fei	Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts	New Phytologist
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2019	10.3389/fmicb.2019.01986	Tatli, M., A. S. Hebert, J. J. Coon and D. Amador-Noguez	Genome wide phosphoproteome analysis of Zymomonas mobilis under anaerobic, aerobic, and N-2-fixing conditions	Frontiers in Microbiology
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2019	10.1128/mSystems.00263-18	Thommes, M., T. Y. Wang, Q. Zhao, I. C. Paschalidis and D. Segre	Designing Metabolic Division of Labor in Microbial Communities	mSystems
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2019	10.1128/AEM.00896-19	Thorgersen, M. P., X. Ge, F. L. Poole, M. N. Price, A. P. Arkin and M. W. W. Adams	Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation	Applied and Environmental Microbiology
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2019	10.1038/s41598-018-37979-5	Tian, L., N. D. Cervenka, A. M. Low, D. G. Olson and L. R. Lynd	A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol	Scientific Reports
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2019	10.1021/acssynbio.8b00429	Tian, T., Kang, J. W., Kang, A., and Lee, T. S.	Redirecting metabolic flux via combinatorial multiplex CRISPRi-mediated repression for isopentenol production in Escherichia coli	ACS Synthetic Biology
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2019	10.1128/mSphere.00345-19	Tran, V. G., M. F. Cao, Z. Fatma, X. F. Song and H. M. Zhao	Development of a CRISPR/Cas9-Based Too for Gene Deletion in Issatchenkia orientalis	Msphere
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2019	10.1021/acs.biochem.7b01069	Urtecho, G., A. D. Tripp, K. D. Insigne, H. Kim and S. Kosuri	Systematic Dissection of Sequence Elements Controlling sigma 70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli	Biochemistry
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2019	10.1038/s41467-019-08448-y	Valliere, M. A., T. P. Korman, N. B. Woodall, G. A. Khitrov, R. E. Taylor, D. Baker and J. U. Bowie	A cell-free platform for the prenylation of natural products and application to cannabinoid production	Nature Communications
2019	10.1128/mBio.02287-19	Van Goethem, M. W., T. L. Swenson, G. Trubl, S. Roux and T. R. Northen	Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust	mBio
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2019	10.1038/s41598-019-43026-8	Woolf, D. and J. Lehmann	Microbial models with minimal mineral protection can explain long-term soil organic carbon persistence	Scientific Reports
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2019	10.1111/pbi.12992	Yang, X. P., J. Song, J. Todd, Z. Peng, D. Paudel, Z. L. Luo, X. K. Ma, Q. You, E. Hanson, Z. F. Zhao, Y. Zhao, J. Zhang, R. Ming and J. P. Wang	Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a 'sweet' crop with 'bitter' genomes	Plant Biotechnology Journal
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2019	10.1111/nph.15346	Yip, D. Z., A. M. Veach, Z. K. Yang, M. A. Cregger and C. W. Schadt	Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides)	New Phytologist
2019	10.1038/s41598-019-47529-2	Yoo, C. Y., N. Mano, A. Finkler, H. Weng, I. S. Day, A. S. N. Reddy, B. W. Poovaiah, H. Fromm, P. M. Hasegawa and M. V. Mickelbart	A Ca2+/CaM-regulated transcriptional switch modulates stomatal development in response to water deficit	Scientific Reports
2019	10.1016/j.cub.2019.07.086	Yoshida, S., S. Kim, E. K. Wafula, J. Tanskanen, Y.-M. Kim, L. Honaas, Z. Yang, T. Spallek, C. E. Conn, Y. Ichihashi, K. Cheong, S. Cui, J. P. Der, H. Gundlach, Y. Jiao, C. Hori, J. K. Ishida, H. Kasahara, T. Kiba, M.-S. Kim, N. Koo, A. Laohavisit, Y.-H. Lee, S. Lumba, P. McCourt, J. C. Mortimer, J. M. Mutuku, T. Nomura, Y. Sasaki-Sekimoto, Y. Seto, Y. Wang, T. Wakatake, H. Sakakibara, T. Demura, S. Yamaguchi, K. Yoneyama, R.-i. Manabe, D. C. Nelson, A. H. Schulman, M. P. Timko, C. W. dePamphilis, D. Choi and K. Shirasu	Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism	Current Biology
2019	10.1080/15592324.2018.1561121	Yu, L., J. Fan and C. Xu	Peroxisomal fatty acid ?-oxidation negatively impacts plant survival under salt stress	Plant Signaling & Behavior
2019	10.1104/pp.19.00396	Yu, X. H., Y. H. Cai, J. Chai, J. Schwender and J. Shanklin	Expression of a Lychee PHOSPHATIDYLCHOLINE:DIACYLGLYCEROL CHOLINEPHOSPHOTRANSFERASE with an Escherichia coli CYCLOPROPANE SYNTHASE Enhances Cyclopropane Fatty Acid Accumulation in Camelina Seeds	Plant Physiology
2019	10.1038/s41396-019-0356-5	Yu, X. Q., M. F. Polz and E. J. Alm	Interactions in self-assembled microbial communities saturate with diversity	ISME Journal
2019	10.1107/s2052252518017621	Zee, C. T., C. Glynn, M. Gallagher-Jones, J. Miao, C. G. Santiago, D. Cascio, T. Gonen, M. R. Sawaya and J. A. Rodriguez	Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ	Iucrj
2019	10.1016/j.watres.2019.114917	Zelaya, A. J., A. E. Parker, K. L. Bailey, P. Zhang, J. Van Nostrand, D. Ning, D. A. Elias, J. Zhou, T. C. Hazen, A. P. Arkin and M. W. Fields	High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer	Water Research
2019	10.1038/s41592-019-0465-0	Zengler, K., K. Hofmockel, N. S. Baliga, S. W. Behie, H. C. Bernstein, J. B. Brown, J. R. Dinneny, S. A. Floge, S. P. Forry, M. Hess, S. A. Jackson, C. Jansson, S. R. Lindemann, J. Pett-Ridge, C. Maranas, O. S. Venturelli, M. D. Wallenstein, E. A. Shank and T. R. Northen	EcoFABs: advancing microbiome science through standardized fabricated ecosystems	Nature Methods
2019	10.1111/pbi.12962	Zhang, J. S., Q. Zhang, L. T. Li, H. B. Tang, Q. Zhang, Y. Chen, J. Arrow, X. T. Zhang, A. Q. Wang, C. Y. Miao and R. Ming	Recent polyploidization events in three Saccharum founding species	Plant Biotechnology Journal
2019	10.1016/j.ibiod.2019.104731	Zhang, J. W., D. H. Hu, G. Orr and J. Schilling	Fluorescence in situ mRNA hybridization for gene expression detection in a wood decay fungus	International Biodeterioration & Biodegradation
2019	10.1016/j.fgb.2018.11.005	Zhang, J. W., H. D. Mitchell, L. M. Markillie, M. J. Gaffrey, G. Orr and J. Schilling	Reference genes for accurate normalization of gene expression in wood-decomposing fungi	Fungal Genetics and Biology
2019	10.1128/mBio.02176-19	Zhang, J. W., K. A. T. Silverstein, J. D. Castano, M. Figueroa and J. S. Schilling	Gene regulation shifts shed light on fungal adaption in plant biomass decomposers	mBio
2019	10.1111/gcbb.12609	Zhang, L., T. E. Juenger, D. B. Lowry and K. D. Behrman	Climatic impact, future biomass production, and local adaptation of four switchgrass cultivars	Global Change Biology Bioenergy
2019	10.1016/j.jbiotec.2018.10.012	Zhang, S., S. S. Jagtap, A. Deewan and C. V. Rao	pH selectively regulates citric acid and lipid production in Yarrowia lipolytica W29 during nitrogen-limited growth on glucose	Journal of Biotechnology
2019	10.1007/s12042-019-09239-x	Zhang, W. P., J. S. Lin, F. Dong, Q. Ma, S. L. Wu, X. Y. Ma, M. Fatima, H. F. Jia and R. Ming	Genomic and allelic analyses of laccase genes in sugarcane (Saccharum spontaneum L.)	Tropical Plant Biology
2019	10.1021/acs.est.9b01345	Zhang, X., J. Xia, J. Pu, C. Cai, G. W. Tyson, Z. Yuan and S. Hu	Biochar-mediated anaerobic oxidation of methane	Environmental Science & Technology
2019	10.1186/s13068-019-1560-2	Zhang, Y. F., S. Lane, J. M. Chen, S. K. Hammer, J. Luttinger, L. F. Yang, Y. S. Jin and J. L. Avalos	Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in Saccharomyces cerevisiae	Biotechnology for Biofuels
2019	10.3389/fmicb.2019.02596	Zhang, Y. P., J. M. Vera, D. Xie, J. Serate, E. Pohlmann, J. D. Russell, A. S. Hebert, J. J. Coon, T. K. Sato and R. Landick	Multiomic fermentation using chemically defined synthetic hydrolyzates revealed multiple effects of lignocellulose-derived inhibitors on cell physiology and xylose utilization in Zymomonas mobilis	Frontiers in Microbiology
2019	10.1038/s41598-018-37988-4	Zhang, Y., C. E. Blaby-Haas, S. Steimle, A. F. Verissimo, V. A. Garcia-Angulo, H. G. Koch, F. Daldal and B. Khalfaoui-Hassani	Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria	Scientific Reports
2019	10.1128/MRA.00793-19	Zhang, Y., Y.-T. Liao, A. Salvador, X. Sun and V. C. H. Wu	Complete Genome Sequence of a Shiga Toxin-Converting Bacteriophage, Escherichia Phage Lys12581Vzw, Induced from an Outbreak Shiga Toxin-Producing Escherichia coli Strain	Microbiology Resource Announcements
2019	10.3389/fpls.2019.01275	Zhao, K. M., F. Lin, S. P. Romero-Gamboa, P. Saha, H. J. Goh, G. An, K. H. Jung, S. P. Hazen and L. E. Bartley	Rice genome-scale network integration reveals transcriptional regulators of grass cell wall synthesis	Frontiers in Plant Science
2019	10.3389/fgene.2019.00253	Zhao, L. Z., H. X. Zhang, M. V. Kohnen, K. Prasad, L. F. Gu and A. S. N. Reddy	Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing	Frontiers in Genetics
2019	10.1007/s11103-019-00856-4	Zhao, Y., J. Y. Kim, R. Karan, J. H. Jung, B. Pathak, B. Williamson, B. Kannan, D. D. Wang, C. Y. Fan, W. J. Yu, S. J. Dong, V. Srivastava and F. Altpeter	Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane	Plant Molecular Biology
2019	10.1007/s11103-019-00856-4	Zhao, Y., J. Y. Kim, R. Karan, J. H. Jung, B. Pathak, B. Williamson, B. Kannan, D. Wang, C. Fan, W. Yu, S. Dong, V. Srivastava and F. Altpeter	Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane	Plant Molecular Biology
2019	10.1111/tpj.14340	Zhuo, C., X. Rao, R. Azad, R. Pandey, X. Xiao, A. Harkelroad, X. Wang, F. Chen and R. A. Dixon	Enzymatic basis for C-lignin monomer biosynthesis in the seed coat of Cleome hassleriana	Plant Journal
2019	10.1111/1462-2920.14608	Zimmerman, A. E., C. Bachy, X. F. Ma, S. Roux, H. B. Jang, M. B. Sullivan, J. R. Waldbauer and A. Z. Worden	Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies	Environmental Microbiology
2019	10.1038/s41564-019-0621-4	Zuniga, C., C. T. Li, G. Yu, M. M. Al-Bassam, T. T. Li, L. Q. Jiang, L. S. Zaramela, M. Guarnieri, M. J. Betenbaugh and K. Zengler	Author Correction: Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities	Nature Microbiology
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2018	10.1016/j.synbio.2017.12.001	Abdel-Mawgoud, A. M. and G. Stephanopoulos	Simple glycolipids of microbes: Chemistry, biological activity and metabolic engineering	Synthetic and Systems Biotechnology
2018	10.1016/j.ymben.2018.07.016	Abdel-Mawgoud, A. M., K. A. Markham, C. M. Palmer, N. Liu, G. Stephanopoulos and H. S. Alper	Metabolic engineering in the host Yarrowia lipolytica	Metabolic Engineering
2018	10.1002/aic.16367	Abernathy, M. H., Y. C. Zhang, W. D. Hollinshead, G. Wang, E. E. K. Baidoo, T. G. Liu and Y. J. J. Tang	Comparative studies of glycolytic pathways and channeling under in vitro and in vivo modes	AIChE Journal
2018	10.1002/eap.1745	Abraha, M., I. Gelfand, S. K. Hamilton, J. Q. Chen and G. P. Robertson	Legacy effects of land use on soil nitrous oxide emissions in annual crop and perennial grassland ecosystems	Ecological Applications
2018	10.1016/j.agrformet.2018.02.016	Abraha, M., S. K. Hamilton, J. Q. Chen and G. P. Robertson	Ecosystem carbon exchange on conversion of Conservation Reserve Program grasslands to annual and perennial cropping systems	Agricultural and Forest Meteorology
2018	10.1111/ppa.12913	Abraham, N. D., P. Chitrampal, S. Kerio and J. M. LeBoldus	Multiplex qPCR for detection and quantification of Sphaerulina musiva in Populus stems	Plant Pathology
2018	10.1371/journal.pone.0190019	Abraham, P. E., B. J. Garcia, L. E. Gunter, S. S. Jawdy, N. Engle, X. Yang, D. A. Jacobson, R. L. Hettich, G. A. Tuskan and T. J. Tschaplinski	Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves	PLOS ONE
2018	10.1039/c7mt00349h	Ackerman, C. M., P. K. Weber, T. Xiao, B. Thai, T. J. Kuo, E. Zhang, J. Pett-Ridge and C. J. Chang	Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease	Metallomics
2018	10.1080/00275514.2018.1446650	Aime, M. C., H. Urbina, J. A. Liber, G. Bonito and R. Oono	Two new endophytic Atractiellomycetes, Atractidochium hillariae and Proceropycnis hameedii	Mycologia
2018	10.1038/s41467-017-02362-x	Akhil Kumar , L. W., Chiam Yu Ng, Costas D. Maranas	Pathway design using de novo steps through uncharted biochemical spaces	Nature Communications
2018	10.1038/s41467-018-06993-6	Al-Bassam, M. M., J. N. Kim, L. S. Zaramela, B. P. Kellman, C. Zuniga, J. M. Wozniak, D. J. Gonzalez and K. Zengler	Optimization of carbon and energy utilization through differential translational efficiency	Nature Communications
2018	10.1128/AEM.00598-18	Albright, M. B. N., R. Johansen, D. Lopez, L. V. Gallegos-Graves, B. Steven, C. R. Kuske and J. Dunbar	Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil	Applied and Environmental Microbiology
2018	10.1002/bit.26530	Alonso-Gutierrez, J., D. Koma, Q. Hu, Y. Yang, L. J. G. Chan, C. J. Petzold, P. D. Adams, C. E. Vickers, L. K. Nielsen, J. D. Keasling and T. S. Lee	Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway	Biotechnology and Bioengineering
2018	10.1074/jbc.RA118.004463	Amos, R. A., Pattathil, S., Yang, J-Y., Atmodjo, M.A., Urbanowicz, B.R., Moremen, K.W., and Mohnen, D.	A two-phase model for the non-processive biosynthesis of homogalacturonan polysaccharides by the GAUT1:GAUT7 complex	Journal of Biological Chemistry
2018	10.1074/jbc.RA118.004463	Amos, R. A., S. Pattathil, J.-Y. Yang, M. A. Atmodjo, B. R. Urbanowicz, K. W. Moremen and D. Mohnen	A two-phase model for the non-processive biosynthesis of homogalacturonan polysaccharides by the GAUT1:GAUT7 complex	Journal of Biological Chemistry
2018	10.1007/978-1-4939-7295-1_21	Ando, D. and H. Garcia Martin	Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering	Synthetic Metabolic Pathways: Methods and Protocols
2018	10.1038/s41467-018-05738-9	Anthony, K. W., T. S. von Deimling, I. Nitze, S. Frolking, A. Emond, R. Daanen, P. Anthony, P. Lindgren, B. Jones and G. Grosse	21st-century modeled permafrost carbon emissions accelerated by abrupt thaw beneath lakes	Nature Communications
2018	10.1038/nbt.4163	Arkin, A. P., R. W. Cottingham, C. S. Henry, N. L. Harris, R. L. Stevens, S. Maslov, P. Dehal, D. Ware, F. Perez, S. Canon, M. W. Sneddon, M. L. Henderson, W. J. Riehl, D. Murphy-Olson, S. Y. Chan, R. T. Kamimura, S. Kumari, M. M. Drake, T. S. Brettin, E. M. Glass, D. Chivian, D. Gunter, D. J. Weston, B. H. Allen, J. Baumohl, A. A. Best, B. Bowen, S. E. Brenner, C. C. Bun, J. M. Chandonia, J. M. Chia, R. Colasanti, N. Conrad, J. J. Davis, B. H. Davison, M. DeJongh, S. Devoid, E. Dietrich, I. Dubchak, J. N. Edirisinghe, G. Fang, J. P. Faria, P. M. Frybarger, W. Gerlach, M. Gerstein, A. Greiner, J. Gurtowski, H. L. Haun, F. He, R. Jain, M. P. Joachimiak, K. P. Keegan, S. Kondo, V. Kumar, M. L. Land, F. Meyer, M. Mills, P. S. Novichkov, T. Oh, G. J. Olsen, R. Olson, B. Parrello, S. Pasternak, E. Pearson, S. S. Poon, G. A. Price, S. Ramakrishnan, P. Ranjan, P. C. Ronald, M. C. Schatz, S. M. D. Seaver, M. Shukla, R. A. Sutormin, M. H. Syed, J. Thomason, N. L. Tintle, D. Wang, F. Xia, H. Yoo, S. Yoo and D. Yu	KBase: The United States Department of Energy Systems Biology Knowledgebase	Nature Biotechnology
2018	10.1186/s13068-018-1039-6	Attia, M. A., C. E. Nelson, W. A. Offen, N. Jain, G. J. Davies, J. G. Gardner and H. Brumer	In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions	Biotechnology for Biofuels
2018	doi:10.3791/57170	Au - Gao, J., J. Au - Sasse, K. M. Au - Lewald, K. Au - Zhalnina, L. T. Au - Cornmesser, T. A. Au - Duncombe, Y. Au - Yoshikuni, J. P. Au - Vogel, M. K. Au - Firestone and T. R. Au - Northen	Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions	JoVE
2018	10.1002/adbi.201800048	Aufrecht, J. A., C. M. Timm, A. Bible, J. L. Morrell-Falvey, D. A. Pelletier, M. J. Doktycz and S. T. Retterer	Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat	Advanced Biosystems
2018	10.1111/1462-2920.14273	Bachy, C., C. J. Charlesworth, A. M. Chan, J. F. Finke, C.-H. Wong, C.-L. Wei, S. Sudek, M. L. Coleman, C. A. Suttle and A. Z. Worden	Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions	Environmental Microbiology
2018	10.3389/fpls.2018.01669	Badmi, R., R. S. Payyavula, G. Bali, H.-B. Guo, S. S. Jawdy, L. E. Gunter, X. Yang, K. A. Winkeler, C. Collins, W. H. Rottmann, K. Yee, M. Rodriguez, R. W. Sykes, S. R. Decker, M. F. Davis, A. J. Ragauskas, G. A. Tuskan and U. C. Kalluri	A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in Populus	Frontiers in Plant Science
2018	10.1186/s12862-018-1193-2	Bahri, B. A., G. Daverdin, X. Xu, J.-F. Cheng, K. W. Barry, E. C. Brummer and K. M. Devos	Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)	BMC Evolutionary Biology
2018	10.1007/s00253-018-9265-1	Baker, S. E.	Protein hyperproduction in fungi by design	Applied Microbiology and Biotechnology
2018	10.1002/pld3.41	Banan, D., R. E. Paul, M. J. Feldman, M. W. Holmes, H. Schlake, I. Baxter, H. Jiang and A. D. B. Leakey	High-fidelity detection of crop biomass quantitative trait loci from low-cost imaging in the field	Plant Direct
2018	10.1093/jxb/ery225	Bansal, S., H. J. Kim, G. Na, M. E. Hamilton, E. B. Cahoon, C. Lu and T. P. Durrett	Towards the synthetic design of camelina oil enriched in tailored acetyl-triacylglycerols with medium-chain fatty acids	Journal of Experimental Botany
2018	10.1038/nbt.4132	Bao, Z. H., M. HamediRad, P. Xue, H. Xiao, I. Tasan, R. Chao, J. Liang and H. M. Zhao	Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision	Nature Biotechnology
2018	10.1021/acs.est.8b05176	Baral, N. R., C. Quiroz-Arita and T. H. Bradley	Probabilistic Lifecycle Assessment of Butanol Production from Corn Stover Using Different Pretreatment Methods	Environmental Science & Technology
2018	10.1016/j.copbio.2018.09.003	Barros, J., Temple, S., Dixon, R.A.	Development and commercialization of reduced lignin alfalfa	Current Opinion in Biotechnology
2018	10.1002/pmic.201800123	Basisty, N., J. G. Meyer, L. Wei, B. W. Gibson and B. Schilling	Simultaneous quantification of the acetylome and succinylome by 'One-Pot' affinity enrichment	Proteomics
2018	10.15252/msb.20188371	Bassalo, M. C., A. D. Garst, A. Choudhury, W. C. Grau, E. J. Oh, E. Spindler, T. Lipscomb and R. T. Gill	Deep scanning lysine metabolism in Escherichia coli	Molecular Systems Biology
2018	10.1111/pbi.12747	Baxter, H. L., M. Mazarei, A. Dumitrache, J. M. Natzke, M. Rodriguez Jr, J. Gou, C. Fu, R. W. Sykes, G. B. Turner, M. F. Davis, S. D. Brown, B. H. Davison, Z.-Y. Wang and C. N. Stewart Jr	Transgenic miR156 switchgrass in the field: growth, recalcitrance and rust susceptibility	Plant Biotechnology Journal
2018	10.1038/s41589-018-0017-4	Beller, H. R., A. V. Rodrigues, K. Zargar, Y.-W. Wu, A. K. Saini, R. M. Saville, J. H. Pereira, P. D. Adams, S. G. Tringe, C. J. Petzold and J. D. Keasling	Discovery of enzymes for toluene synthesis from anoxic microbial communities	Nature Chemical Biology
2018	10.1002/bit.26518	Bergenholm, D., M. Gossing, Y. J. Wei, V. Siewers and J. Nielsen	Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids	Biotechnology and Bioengineering
2018	10.1007/s00253-018-9043-0	Berim, A. and D. R. Gang	Production of methoxylated flavonoids in yeast using ring A hydroxylases and flavonoid O-methyltransferases from sweet basil	Applied Microbiology and Biotechnology
2018	10.7717/peerj.5727	Berry, J. C., N. Fahlgren, A. A. Pokorny, R. S. Bart and K. M. Veley	An automated, high-throughput method for standardizing image color profiles to improve image-based plant phenotyping	PeerJ
2018	10.3389/fpls.2018.01732	Bewg, W. P., D. Ci and C.-J. Tsai	Genome Editing in Trees: From Multiple Repair Pathways to Long-Term Stability	Frontiers in Plant Science
2018	10.1002/bit.26582	Bhagia, S., J. F. S. Ferreira, N. Kothari, A. Nunez, X. Liu, N. da Silva Dias, D. L. Suarez, R. Kumar and C. E. Wyman	Sugar yield and composition of tubers from Jerusalem Artichoke (Helianthus tuberosus) irrigated with saline waters	Biotechnology and Bioengineering
2018	10.1038/s41598-018-19848-3	Bhagia, S., R. Dhir, R. Kumar and C. E. Wyman	Deactivation of Cellulase at the Air-Liquid Interface Is the Main Cause of Incomplete Cellulose Conversion at Low Enzyme Loadings	Scientific Reports
2018	10.1038/s41598-018-31269-w	Bhagia, S., X. Meng, B. R. Evans, J. R. Dunlap, G. Bali, J. Chen, K. S. Reeves, H. C. Ho, B. H. Davison, Y. Pu and A. J. Ragauskas	Ultrastructure and Enzymatic Hydrolysis of Deuterated Switchgrass	Scientific Reports
2018	10.1016/j.biortech.2018.08.034	Bhagia, S., Y. Pu, B. R. Evans, B. H. Davison and A. J. Ragauskas	Hemicellulose characterization of deuterated switchgrass	Bioresource Technology
2018	10.1186/s13068-018-1124-x	Bhalla, A., P. Fasahati, C. A. Particka, A. E. Assad, R. J. Stoklosa, N. Bansal, R. Semaan, C. M. Saffron, D. B. Hodge and E. L. Hegg	Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline-oxidative pretreatment of hybrid poplar	Biotechnology for Biofuels
2018	10.1038/nbt.4067	Biswal, A. K., Atmodjo, M.A., Li, M., Baxter, H.L., Yoo, C.G., Pu, Y.J., Lee, Y-C., Mazarei, M., Black, I.M., Zhang, J-Y., Ramanna, H., Bray, A.L., King, Z.R., LaFayette, P.R., Pattathil, S., Donohoe, B.S., Mohanty, S.S., Ryno, D., Yee, K., Thompson, O.A.,	Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis	Nature Biotechnology
2018	10.1038/nbt.4067	Biswal, A. K., M. A. Atmodjo, M. Li, H. L. Baxter, C. G. Yoo, Y. Pu, Y.-C. Lee, M. Mazarei, I. M. Black, J.-Y. Zhang, H. Ramanna, A. L. Bray, Z. R. King, P. R. LaFayette, S. Pattathil, B. S. Donohoe, S. S. Mohanty, D. Ryno, K. Yee, O. A. Thompson, M. Rodriguez, A. Dumitrache, J. Natzke, K. Winkeler, C. Collins, X. Yang, L. Tan, R. W. Sykes, E. L. Gjersing, A. Ziebell, G. B. Turner, S. R. Decker, M. G. Hahn, B. H. Davison, M. K. Udvardi, J. R. Mielenz, M. F. Davis, R. S. Nelson, W. A. Parrott, A. J. Ragauskas, C. Neal Stewart and D. Mohnen	Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis	Nature Biotechnology
2018	10.1186/s13068-017-1002-y	Biswal, A. K., M. A. Atmodjo, S. Pattathil, R. A. Amos, X. Yang, K. Winkeler, C. Collins, S. S. Mohanty, D. Ryno, L. Tan, I. Gelineo-Albersheim, K. Hunt, R. W. Sykes, G. B. Turner, A. Ziebell, M. F. Davis, S. R. Decker, M. G. Hahn and D. Mohnen	Working towards recalcitrance mechanisms: increased xylan and homogalacturonan production by overexpression of GAlactUronosylTransferase12 (GAUT12) causes increased recalcitrance and decreased growth in Populus	Biotechnology for Biofuels
2018	10.1128/genomeA.01411-17	Biswas, R., M. Huntemann, A. Clum, M. Pillay, K. Palaniappan, N. Varghese, N. Mikhailova, D. Stamatis, T. B. K. Reddy, C. Daum, N. Shapiro, N. Ivanova, N. C. Kyrpides, T. Woyke and A. M. Guss	Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate- and Butanol-Producing Thermophile	Genome Announcements
2018	10.1007/978-1-4939-7724-6_10	Blaby-Haas, C. E., M. D. Page and S. S. Merchant	Using YFP as a Reporter of Gene Expression in the Green Alga Chlamydomonas reinhardtii	Methods in Molecular Biology
2018	10.1128/mSystems.00045-18	Blair, P. M., M. L. Land, M. J. Piatek, D. A. Jacobson, T. Y. S. Lu, M. J. Doktycz and D. A. Pelletier	Exploration of the Biosynthetic Potential of the Populus Microbiome	mSystems
2018	10.1111/mmi.13903	Blake, A. D., N. R. Beri, H. S. Guttman, R. Cheng and J. G. Gardner	The complex physiology of Cellvibrio japonicus xylan degradation relies on a single cytoplasmic -xylosidase for xylo-oligosaccharide utilization	Molecular Microbiology
2018	10.1007/978-3-319-93594-2_10	Borland, A. M., A. Leverett, N. Hurtado-Castano, R. Hu and X. Yang	Functional Anatomical Traits of the Photosynthetic Organs of Plants with Crassulacean Acid Metabolism	The Leaf: A Platform for Performing Photosynthesis
2018	10.1039/C7GC03239K	Bouxin, F. P., H. Strub, T. Dutta, J. Aguilhon, T. J. Morgan, F. Mingardon, M. Konda, S. Singh, B. Simmons and A. George	Elucidating transfer hydrogenation mechanisms in non-catalytic lignin depolymerization	Green Chemistry
2018	10.1007/s11104-017-3497-1	Bowsher, A. W., S. Evans, L. K. Tiemann and M. L. Friesen	Effects of soil nitrogen availability on rhizodeposition in plants: a review	Plant and Soil
2018	10.1093/nar/gky174	Boyd, J. A., B. J. Woodcroft and G. W. Tyson	GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes	Nucleic Acids Research
2018	10.1016/j.resconrec.2018.08.022	Breunig, H. M., T. Huntington, L. Jin, A. Robinson and C. D. Scown	Temporal and geographic drivers of biomass residues in California	Resources, Conservation and Recycling
2018	10.1016/j.semcdb.2017.08.051	Brophy, J. A. N., T. LaRue and J. R. Dinneny	Understanding and engineering plant form	Seminars in Cell & Developmental Biology
2018	10.1186/s13068-018-1014-2	Brunecky, R., D. Chung, N. S. Sarai, N. Hengge, J. F. Russell, J. Young, A. Mittal, P. Pason, T. Vander Wall, W. Michener, T. Shollenberger, J. Westpheling, M. E. Himmel and Y. J. Bomble	High activity CAZyme cassette for improving biomass degradation in thermophiles	Biotechnology for Biofuels
2018	10.1073/pnas.1811971115	Brunk, E., R. L. Chang, J. Xia, H. Hefzi, J. T. Yurkovich, D. Kim, E. Buckmiller, H. H. Wang, B. K. Cho, C. Yang, B. O. Palsson, G. M. Church and N. E. Lewis	Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1111/nph.14913	Bruns, T. D., N. Corradi, D. Redecker, J. W. Taylor and M. Opik	Glomeromycotina: what is a species and why should we care?	New Phytologist
2018	10.1126/science.aau0382	Brunson, J. K., S. M. K. McKinnie, J. R. Chekan, J. P. McCrow, Z. D. Miles, E. M. Bertrand, V. A. Bielinski, H. Luhavaya, M. Obornik, G. J. Smith, D. A. Hutchins, A. E. Allen and B. S. Moore	Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom	Science
2018	10.1534/g3.118.200188	Bryan, A. C., J. Zhang, J. Guo, P. Ranjan, V. Singan, K. Barry, J. Schmutz, D. Weighill, D. Jacobson, S. Jawdy, G. A. Tuskan, J.-G. Chen and W. Muchero	A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein	G3 Genes\|Genomes\|Genetics
2018	10.1126/science.aat7925	Budin, I., T. de Rond, Y. Chen, L. J. G. Chan, C. J. Petzold and J. D. Keasling	Viscous control of cellular respiration by membrane lipid composition	Science
2018	10.1016/j.coche.2018.10.003	Bundy, B. C., J. P. Hunt, M. C. Jewett, J. R. Swartz, D. W. Wood, D. D. Frey and G. Rao	Cell-free biomanufacturing	Current Opinion in Chemical Engineering
2018	10.3389/fpls.2018.01505	Busov, V. B.	Manipulation of growth and architectural characteristics in trees for increased woody biomass production	Frontiers in Plant Science
2018	10.1038/s41437-018-0058-1	Butler, J. B., J. S. Freeman, B. M. Potts, R. E. Vaillancourt, D. Grattapaglia, O. B. Silva-Junior, B. A. Simmons, A. L. Healey, J. Schmutz, K. W. Barry, D. J. Lee, R. J. Henry, G. J. King, A. Baten and M. Shepherd	Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus	Heredity
2018	10.1038/s41396-018-0109-x	Cai, C., A. O. Leu, G.-J. Xie, J. Guo, Y. Feng, J.-X. Zhao, G. W. Tyson, Z. Yuan and S. Hu	A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction	ISME Journal
2018	10.1016/j.celrep.2018.03.083	Cano, M., S. C. Holland, J. Artier, R. L. Burnap, M. Ghirardi, J. A. Morgan and J. P. Yu	Glycogen synthesis and metabolite overflow contribute to energy balancing in cyanobacteria	Cell Reports
2018	10.1145/3238147.3240466	Cashman, M., M. B. Cohen, P. Ranjan and R. W. Cottingham	Navigating the maze: the impact of configurability in bioinformatics software	Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering
2018	10.1002/pld3.85	Casto, A. L., B. A. McKinley, K. M. J. Yu, W. L. Rooney and J. E. Mullet	Sorghum stem aerenchyma formation is regulated by SbNAC_D during internode development	Plant Direct
2018	10.1038/s41396-018-0210-1	Chadwick, G. L., J. Hemp, W. W. Fischer and V. J. Orphan	Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications	ISME Journal
2018	10.1093/bioinformatics/bty446	Chan, S. H. J., L. Wang, S. Dash and C. D. Maranas	Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints	Bioinformatics
2018	10.1111/1462-2920.14405	Chase, A. B., Z. Gomez-Lunar, A. E. Lopez, J. Li, S. D. Allison, A. C. Martiny and J. B. H. Martiny	Emergence of soil bacterial ecotypes along a climate gradient	Environmental Microbiology
2018	10.1039/C8NR06470A	Chaves-Lopez, C., H. N. Nguyen, R. C. Oliveira, E. T. Nadres, A. Paparella and D. F. Rodrigues	A morphological, enzymatic and metabolic approach to elucidate apoptotic-like cell death in fungi exposed to h- and ?-molybdenum trioxide nanoparticles	Nanoscale
2018	10.1016/j.copbio.2018.02.013	Cheah, Y. E. and J. D. Young	Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice	Current Opinion in Biotechnology
2018	10.1093/bioinformatics/bty015	Chen, C. P. J. and Z. W. Zhang	iPat: intelligent prediction and association tool for genomic research	Bioinformatics
2018	10.1104/pp.110.155119	Chen, F.	Lignin biosynthesis and control of lignin composition	Plant Physiology
2018	10.1002/biot.201700648	Cheng, F., X. L. Tang and T. Kardashliev	Transcription Factor-Based Biosensors in High-Throughput Screening: Advances and Applications	Biotechnol J
2018	10.1371/journal.pone.0194663	Christensen, G. A., J. Moon, A. M. Veach, J. J. Mosher, A. M. Wymore, J. D. van Nostrand, J. Zhou, T. C. Hazen, A. P. Arkin and D. A. Elias	Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition	PLOS ONE
2018	10.1016/j.ymben.2018.03.017	Clark, R. L., L. L. McGinley, H. M. Purdy, T. C. Korosh, J. L. Reed, T. W. Root and B. F. Pfleger	Light-optimized growth of cyanobacterial cultures: Growth phases and productivity of biomass and secreted molecules in light-limited batch growth	Metabolic Engineering
2018	10.1111/gcbb.12566	Clifton-Brown, J., et al.	Breeding progress and preparedness for mass-scale deployment of perenial lignocellulosic biomass crops switchgrass, miscanthus, willow, and poplar	GCB Bioenergy
2018	10.1111/mmi.14393	Close D, C. S., Wang X, Giannone RJ, Engle NL, Tschaplinski TJ, Hedstrom L, Parks JM, Michener JK	Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis	Molecular Microbiology
2018	10.1016/j.tplants.2017.09.008	Coelho, C. P., P. Huang, D.-Y. Lee and T. P. Brutnell	Making roots, shoots, and seeds: IDD gene family diversification in plants	Trends in Plant Science
2018	10.3389/fenrg.2018.00053	Coffman, P., N. McCaffrey, J. Gardner, S. Bhagia, R. Kumar, C. E. Wyman and D. Tanjore	In Situ Rheological Method to Evaluate Feedstock Physical Properties Throughout Enzymatic Deconstruction	Frontiers in Energy Research
2018	10.1186/s12859-018-2402-0	Colby, S. M., R. S. McClure, C. C. Overall, R. S. Renslow and J. E. McDermott	Improving network inference algorithms using resampling methods	BMC Bioinformatics
2018	10.1002/aic.16354	Conway, J. M., J. R. Crosby, A. P. Hren, R. T. Southerland, L. L. Lee, V. V. Lunin, P. Alahuhta, M. E. Himmel, Y. J. Bomble, M. W. W. Adams and R. M. Kelly	Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species	AIChE Journal
2018	10.1128%2FgenomeA.00581-18	Cook, L. E., S. S. Gang, A. Ihlan, M. Maune, R. S. Tanner, M. J. McInerney, G. Weinstock, E. A. Lobos and R. P. Gunsalus	Genome Sequence of Acetomicrobium hydrogeniformans OS1	Genome Announcements
2018	10.1021/acsinfecdis.8b00036	Cooper SJ, K. G., Wolloscheck D, Walker JK, Rybenkov VV, Parks JM, Zgurskaya HI	Molecular Properties that Define the Activities of Antibiotics in Escherichia coli and Pseudomonas aeruginosa	ACS Infectious Diseases
2018	10.7554/eLife.32110	Coradetti, S. T., D. Pinel, G. M. Geiselman, M. Ito, S. J. Mondo, M. C. Reilly, Y. F. Cheng, S. Bauer, I. V. Grigoriev, J. M. Gladden, B. A. Simmons, R. B. Brem, A. P. Arkin and J. M. Skerker	Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides	Elife
2018	10.1128/jb.00020-18	Corzett, C. H., J. Elsherbini, D. M. Chien, J.-H. Hehemann, A. Henschel, S. P. Preheim, X. Yu, E. J. Alm and M. F. Polz	Evolution of a vegetarian vibrio: metabolic specialization of Vibrio breoganii to macroalgal substrates	Journal of Bacteriology
2018	10.1038/s41540-018-0054-3	Costello, Z. and H. G. Martin	A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data	npj Systems Biology and Applications
2018	10.3389/fenvs.2018.00065	Couradeau, E., V. J. M. N. L. Felde, D. Parkinson, D. Uteau, A. Rochet, C. Cuellar, G. Winegar, S. Peth, T. R. Northen and F. Garcia-Pichel	In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation	Frontiers in Environmental Science
2018	10.1073/pnas.1809611115	Coutinho, B. G., E. Mevers, A. L. Schaefer, D. A. Pelletier, C. S. Harwood, J. Clardy and E. P. Greenberg	A plant-responsive bacterial-signaling system senses an ethanolamine derivative	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1186/s40168-018-0413-8	Cregger, M. A., A. M. Veach, Z. K. Yang, M. J. Crouch, R. Vilgalys, G. A. Tuskan and C. W. Schadt	The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome	Microbiome
2018	10.3835/plantgenome2017.11.0099	Cuevas, H. E., L. K. Prom, E. A. Cooper, J. E. Knoll and X. Z. Ni	Genome-wide association mapping of anthracnose (Colletotrichum sublineolum) resistance in the US sorghum association panel	Plant Genome
2018	10.1016/j.ymben.2018.09.006	Cui, J., Olson, D.G., Lynd, L.R.	Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum	Metabolic Engineering
2018	10.1088/1748-9326/aae6e3	Cui, X., O. Kavvada, T. Huntington and C. D. Scown	Strategies for near-term scale-up of cellulosic biofuel production using sorghum and crop residues in the US	Environmental Research Letters
2018	10.1021/acschembio.8b00422	Curran, S. C., A. Hagen, S. Poust, L. J. G. Chan, B. M. Garabedian, T. de Rond, M.-J. Baluyot, J. T. Vu, A. K. Lau, S. Yuzawa, C. J. Petzold, L. Katz and J. D. Keasling	Probing the Flexibility of an Iterative Modular Polyketide Synthase with Non-Native Substrates in Vitro	ACS Chemical Biology
2018	10.1073/pnas.1807804115	Czajka, J. J., M. H. Abernathy, V. T. Benites, E. E. K. Baidoo, J. W. Deming and Y. J. Tang	Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H	Proceedings of the National Academy of Sciences
2018	10.1021/acssuschemeng.8b01763	Das, L., M. Li, J. Stevens, W. Li, Y. Pu, A. J. Ragauskas and J. Shi	Characterization and Catalytic Transfer Hydrogenolysis of Deep Eutectic Solvent Extracted Sorghum Lignin to Phenolic Compounds	ACS Sustainable Chemistry & Engineering
2018	10.1021/acssuschemeng.8b01763	Das, L., M. Li, J. Stevens, W. Q. Li, Y. Q. Pu, A. J. Ragauskas and J. Shi	Characterization and Catalytic Transfer Hydrogenolysis of Deep Eutectic Solvent Extracted Sorghum Lignin to Phenolic Compounds	ACS Sustainable Chemistry & Engineering
2018	10.1371/journal.pone.0208560	Dash, M., Y. S. Yordanov, T. Georgieva, H. R. Wei and V. Busov	Gene network analysis of poplar root transcriptome in response to drought stress identifies a PtaJAZ3PtaRAP2.6-centered hierarchical network	PLOS ONE
2018	10.1126/science.aas9793	Davis, S. J., N. S. Lewis, M. Shaner, S. Aggarwal, D. Arent, I. L. Azevedo, S. M. Benson, T. Bradley, J. Brouwer, Y.-M. Chiang, C. T. M. Clack, A. Cohen, S. Doig, J. Edmonds, P. Fennell, C. B. Field, B. Hannegan, B.-M. Hodge, M. I. Hoffert, E. Ingersoll, P. Jaramillo, K. S. Lackner, K. J. Mach, M. Mastrandrea, J. Ogden, P. F. Peterson, D. L. Sanchez, D. Sperling, J. Stagner, J. E. Trancik, C.-J. Yang and K. Caldeira	Net-zero emissions energy systems	Science
2018	10.3389/fmicb.2018.00141	de Freitas Pereira, M., C. Veneault-Fourrey, P. Vion, F. Guinet, E. Morin, K. W. Barry, A. Lipzen, V. Singan, S. Pfister, H. Na, M. Kennedy, S. Egli, I. Grigoriev, F. Martin, A. Kohler and M. Peter	Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum	Frontiers in Microbiology
2018	10.1016/bs.coac.2018.06.006	de Raad, M., T. R. Northen and B. P. Bowen	Chapter Thirteen - Analysis and Interpretation of Mass Spectrometry Imaging Datasets	Comprehensive Analytical Chemistry
2018	10.3389/fenrg.2018.00120	Decker, S. R., A. E. Harman-Ware, R. M. Happs, E. J. Wolfrum, G. A. Tuskan, D. Kainer, G. B. Oguntimein, M. Rodriguez, D. Weighill, P. Jones and D. Jacobson	High Throughput Screening Technologies in Biomass Characterization	Frontiers in Energy Research
2018	10.1111/1462-2920.14342	Dekas, A. E., D. A. Fike, G. L. Chadwick, A. Green-Saxena, J. Fortney, S. A. Connon, K. S. Dawson and V. J. Orphan	Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading	Environmental Microbiology
2018	10.1021/acs.jafc.8b00880	del Rio, J. C., J. Rencoret, A. Gutierrez, H. Kim and J. Ralph	Structural characterization of lignin from maize (Zea mays L.) fibers: Evidence for diferuloylputrescine incorporated into the lignin polymer in maize kernels	Journal of Agricultural and Food Chemistry
2018	10.1038/s41598-018-24486-w	DeLorenzo, D. M. and T. S. Moon	Selection of stable reference genes for RT-qPCR in Rhodococcus opacus PD630	Scientific Reports
2018	10.1021/acssynbio.7b00416	DeLorenzo, D. M., A. G. Rottinghaus, W. R. Henson and T. S. Moon	Molecular toolkit for gene expression control and genome modification in Rhodococcus opacus PD630	ACS Synthetic Biology
2018	10.1038/s41467-018-03293-x	Denby, C. M., R. A. Li, V. T. Vu, Z. Costello, W. Lin, L. J. G. Chan, J. Williams, B. Donaldson, C. W. Bamforth, C. J. Petzold, H. V. Scheller, H. G. Martin and J. D. Keasling	Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer	Nature Communications
2018	10.3390/genes9080379	diCenzo, G. C., K. Debiec, J. Krzysztoforski, W. Uhrynowski, A. Mengoni, C. Fagorzi, A. Gorecki, L. Dziewit, T. Bajda, G. Rzepa and L. Drewniak	Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14	Genes (Basel)
2018	10.3389/fenrg.2018.00129	Dien, B. S., R. B. Mitchell, M. J. Bowman, V. L. Jin, J. Quarterman, M. R. Schmer, V. Singh and P. J. Slininger	Bioconversion of Pelletized Big Bluestem, Switchgrass, and Low-Diversity Grass Mixtures Into Sugars and Bioethanol	Frontiers in Energy Research
2018	10.1104/pp.17.00905	Ding, X. S., S. W. Mannas, B. A. Bishop, X. Rao, M. Lecoultre, S. Kwon and R. S. Nelson	An Improved Brome mosaic virus Silencing Vector: Greater Insert Stability and More Extensive VIGS	Plant Physiology
2018	10.1099/ijsem.0.002942	Dobritsa, A. P., K. K. Kutumbaka and M. Samadpour	Reclassification of Eubacterium combesii and discrepancies in the nomenclature of botulinum neurotoxin-producing clostridia: Challenging Opinion 69. Request for an Opinion	International Journal of Systematic and Evolutionary Microbiology
2018	10.1111/gcbb.12472	Dong, H. X., S. Y. Liu, L. V. Clark, S. Sharma, J. M. Gifford, J. A. Juvik, A. E. Lipka and E. J. Sacks	Genetic mapping of biomass yield in three interconnected Miscanthus populations	Global Change Biology Bioenergy
2018	10.1002/yea.3292	Dossani, Z. Y., A. Reider Apel, H. Szmidt-Middleton, N. J. Hillson, S. Deutsch, J. D. Keasling and A. Mukhopadhyay	A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering	Yeast
2018	10.1021/acs.jafc.8b02014	Dou, J. Z., H. Kim, Y. D. Li, D. Padmakshan, F. X. Yue, J. Ralph and T. Vuorinen	Structural characterization of lignins from willow bark and wood	Journal of Agricultural and Food Chemistry
2018	10.1371/journal.pone.0199125	Du, N., P. Gholami, D. I. Kline, C. L. DuPont, A. G. Dickson, D. Mendola, T. Martz, A. E. Allen and B. G. Mitchell	Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures	PLOS ONE
2018	10.1186/s13068-018-1172-2	Du, Z. Y., J. Alvaro, B. Hyden, K. Zienkiewicz, N. Benning, A. Zienkiewicz, G. Bonito and C. Benning	Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata	Biotechnology for Biofuels
2018	10.1021/acs.analchem.8b01989	Duncombe, T. A., M. D. Raad, B. P. Bowen, A. K. Singh and T. R. Northen	Insulator Nanostructure Desorption Ionization Mass Spectrometry	Analytical Chemistry
2018	10.1021/acssuschemeng.7b02991	Dutta, T., G. Papa, E. Wang, J. Sun, N. G. Isern, J. R. Cort, B. A. Simmons and S. Singh	Characterization of Lignin Streams during Bionic Liquid-Based Pretreatment from Grass, Hardwood, and Softwood	ACS Sustainable Chemistry & Engineering
2018	10.1093/pcp/pcy180	Ebert, B., Birdseye, D., Liwanag, A. J. M., Laursen, T., Rennie, E. A., Guo, X., Scheller, H. V.	The Three Members of the Arabidopsis thaliana Glycosyltransferase Family 92 are Functional beta-1,4-Galactan Synthases	Plant Cell Physiolology
2018	10.1038/s41477-018-0235-5	Ebert, B., C. Rautengarten, H. E. McFarlane, T. Rupasinghe, W. Zeng, K. Ford, H. V. Scheller, A. Bacic, U. Roessner, S. Persson and J. L. Heazlewood	A Golgi UDP-GlcNAc transporter delivers substrates for N-linked glycans and sphingolipids	Nature Plants
2018	10.1093/pcp/pcy180	Ebert, B., D. Birdseye, A. J. M. Liwanag, T. Laursen, E. A. Rennie, X. Guo, M. Catena, C. Rautengarten, S. H. Stonebloom, P. Gluza, V. R. Pidatala, M. C. F. Andersen, R. Cheetamun, J. C. Mortimer, J. L. Heazlewood, A. Bacic, M. H. Clausen, W. G. T. Willats and H. V. Scheller	The Three Members of the Arabidopsis Glycosyltransferase Family 92 are Functional ?-1,4-Galactan Synthases	Plant and Cell Physiology
2018	10.1038/s41477-018-0235-5	Ebert, B., Rautengarten, C., McFarlane, H.E., Rupasinghe, T., Zeng, W., Ford, K., Scheller, H.V., Bacic, A., Roessner, U., Persson, S., and Heazlewood, J.	A Golgi UDP-GlcNAc transporter delivers substrates for N-linked glycans and sphingolipids	Nature Plants
2018	10.1007/978-1-4939-7528-0_5	Edirisinghe, J. N., J. P. Faria, N. L. Harris, B. H. Allen and C. S. Henry	Reconstruction and Analysis of Central Metabolism in Microbes	Metabolic Network Reconstruction and Modeling: Methods and Protocols
2018	10.1107/s2059798318006678	Ellinghaus, T. L., J. H. Pereira, R. P. McAndrew, D. H. Welner, A. M. DeGiovanni, J. M. Guenther, H. M. Tran, T. Feldman, B. A. Simmons, K. L. Sale and P. D. Adams	Engineering glycoside hydrolase stability by the introduction of zinc binding	Acta Crystallogr D Struct Biol
2018	10.1107/S2059798318006678	Ellinghaus, T. L., Pereira, J. h., McAndrew, R. P., Welner, D. h., DeGiovanni, A. M., Guenther, J. M., Adams, P. D.	Engineering glycoside hydrolase stability by the introduction of zinc binding	Acta Crystallographica Section D Structural Biology
2018	10.1111/nph.15173	Ellsworth, P. V., P. Z. Ellsworth, N. K. Koteyeva and A. B. Cousins	Cell wall properties in Oryza sativa influence mesophyll CO2 conductance	New Phytologist
2018	10.1038/s41564-018-0190-y	Emerson, J. B., S. Roux, J. R. Brum, B. Bolduc, B. J. Woodcroft, H. B. Jang, C. M. Singleton, L. M. Soden, A. E. Naas, J. A. Boyd, S. B. Hodgkins, R. M. Wilson, G. Trubl, C. S. Li, S. Frokings, P. B. Pope, K. C. Wrighton, P. M. Crill, J. P. Chanton, S. R. Saleska, G. W. Tyson, V. I. Rich and M. B. Sullivan	Host-linked soil viral ecology along a permafrost thaw gradient	Nature Microbiology
2018	10.1186/s12934-018-1006-8	Eng, T., P. Demling, R. A. Herbert, Y. Chen, V. Benites, J. Martin, A. Lipzen, E. E. K. Baidoo, L. M. Blank, C. J. Petzold and A. Mukhopadhyay	Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC	Microbial Cell Factories
2018	10.1021/acs.jproteome.7b00708	Estenson, K., G. B. Hurst, R. F. Standaert, A. N. Bible, D. Garcia, K. Chourey, M. J. Doktycz and J. L. Morrell-Falvey	Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343	Journal of Proteome Research
2018	10.1104/pp.18.00978	Fan, M. Z., K. Herburger, J. K. Jensen, S. Zemelis-Durfee, F. Brandizzi, S. C. Fry and C. G. Wilkerson	A trihelix family transcription factor is associated with key genes in mixed-linkage glucan accumulation	Plant Physiology
2018	10.1042/BST20170246	Faria, J. P., M. Rocha, I. Rocha and C. S. Henry	Methods for automated genome-scale metabolic model reconstruction	Biochemical Society Transactions
2018	10.3389/fpls.2018.00384	Faria-Blanc, N., J. C. Mortimer and P. Dupree	A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis	Frontiers in Plant Science
2018	10.1016/j.joule.2018.09.007	Fasahati, P. and C. T. Maravelias	Advanced biofuels of the future: Atom-Economical or energy-economical?	Joule
2018	10.1104/pp.18.00146	Feldman, M. J., P. Z. Ellsworth, N. Fahlgren, M. A. Gehan, A. B. Cousins and I. Baxter	Components of water use efficiency have unique genetic signatures in the model C4 Grass Setaria	Plant Physiology
2018	10.1007/s00122-017-3033-y	Fernandes, S. B., K. O. G. Dias, D. F. Ferreira and P. J. Brown	Efficiency of multi-trait, indirect, and trait-assisted genomic selection for improvement of biomass sorghum	Theoretical and Applied Genetics
2018	10.3389/fpls.2018.00005	Filichkin, S. A., M. Hamilton, P. D. Dharmawardhana, S. K. Singh, C. Sullivan, A. Ben-Hur, A. S. N. Reddy and P. Jaiswal	Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching	Frontiers in Plant Science
2018	10.1128/mBio.01993-17	Filippova, E. V., B. Zemaitaitis, T. Aung, A. J. Wolfe and W. F. Anderson	Structural basis for DNA recognition by the two-component response regulator RcsB	mBio
2018	10.1111/1758-2229.12619	Flowers, J. J., M. A. Richards, N. Baliga, B. Meyer and D. A. Stahl	Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris	Environmental Microbiology Reports
2018	10.1007/s00253-017-8724-4	Franco, L. C., S. Steinbeisser, G. M. Zane, J. D. Wall and M. W. Fields	Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris	Applied Microbiology and Biotechnology
2018	10.1186/s12864-018-4911-7	Franke, K. R., S. A. Schmidt, S. Park, D. H. Jeong, M. Accerbi and P. J. Green	Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops	BMC Genomics
2018	10.1002/bit.26727	Freed, E., J. Fenster, S. L. Smolinski, J. Walker, C. A. Henard, R. Gill and C. A. Eckert	Building a genome engineering toolbox in nonmodel prokaryotic microbes	Biotechnology and Bioengineering
2018	10.3389/fmicb.2018.02152	Freedman, A. J. E., K. C. Peet, J. T. Boock, K. Penn, K. L. J. Prather and J. R. Thompson	Isolation, development, and genomic analysis of Bacillus megaterium SR7 for growth and metabolite production under supercritical carbon dioxide	Frontiers in Microbiology
2018	10.1111/nph.15258	Gallego-Giraldo, L., S. Pose, S. Pattathil, A. G. Peralta, M. G. Hahn, B. G. Ayre, J. Sunuwar, J. Hernandez, M. Patel, J. Shah, X. Rao, J. P. Knox and R. A. Dixon	Elicitors and defense gene induction in plants with altered lignin compositions	New Phytologist
2018	10.3791/57170	Gao, J., J. Sasse, K. M. Lewald, K. Zhalnina, L. T. Cornmesser, T. A. Duncombe, Y. Yoshikuni, J. P. Vogel, M. K. Firestone and T. R. Northen	Ecosystem Fabrication (EcoFAB) protocols for the construction of laboratory ecosystems designed to study plant-microbe interactions	JoVE
2018	10.1002/cssc.201800598	Gao, R. L., Y. D. Li, H. Kim, J. K. Mobley and J. Ralph	Selective Oxidation of Lignin Model Compounds	ChemSusChem
2018	10.1111/mmi.13909	Garber, M. E., L. Rajeev, A. E. Kazakov, J. Trinh, D. Masuno, M. G. Thompson, N. Kaplan, J. Luk, P. S. Novichkov and A. Mukhopadhyay	Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs	Molecular Microbiology
2018	10.1093/synbio/ysy006	Garcia, D. C., B. P. Mohr, J. T. Dovgan, G. B. Hurst, R. F. Standaert and M. J. Doktycz	Elucidating the potential of crude cell extracts for producing pyruvate from glucose	Synthetic Biology
2018	10.1038/s41564-018-0124-8	Garza, D. R., M. C. van Verk, M. A. Huynen and B. E. Dutilh	Towards predicting the environmental metabolome from metagenomics with a mechanistic model	Nature Microbiology
2018	10.1021/acs.analchem.7b02786	Gates, S. D., R. C. Condit, N. Moussatche, B. J. Stewart, A. J. Malkin and P. K. Weber	High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM	Analytical Chemistry
2018	10.1016/j.ymben.2018.03.004	George, K. W., M. G. Thompson, J. Kim, E. E. K. Baidoo, G. Wang, V. T. Benites, C. J. Petzold, L. J. G. Chan, S. Yilmaz, P. Turhanen, P. D. Adams, J. D. Keasling and T. S. Lee	Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli	Metabolic Engineering
2018	10.1186/s13068-018-1248-z	Ghosh, S., E. K. Holwerda, R. S. Worthen, L. R. Lynd and B. P. Epps	Rheological properties of corn stover slurries during fermentation by Clostridium thermocellum	Biotechnology for Biofuels
2018	10.1091/mbc.E17-11-0666	Gibney, P. A., A. Schieler, J. C. Chen, J. M. Bacha-Hummel, M. Botstein, M. Volpe, S. J. Silverman, Y. F. Xu, B. D. Bennett, J. D. Rabinowitz and D. Botstein	Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast	Molecular Biology of the Cell
2018	10.1080/01490451.2017.1321068	Glass, J. B., S. Chen, K. S. Dawson, D. R. Horton, S. Vogt, E. D. Ingall, B. S. Twining and V. J. Orphan	Trace metal imaging of sulfate-reducing bacteria and methanogenic archaea at single-cell resolution by synchrotron X-Ray fluorescence imaging	Geomicrobiology Journal
2018	10.1128/mSphere.00148-18	Glassman, S. I. and J. B. H. Martiny	Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units	mSphere
2018	10.1073/pnas.1811269115	Glassman, S. I., C. Weihe, J. Li, M. B. N. Albright, C. I. Looby, A. C. Martiny, K. K. Treseder, S. D. Allison and J. B. H. Martiny	Decomposition responses to climate depend on microbial community composition	Proceedings of the National Academy of Sciences
2018	10.1002/bit.26558	Goh, E.-B., Y. Chen, C. J. Petzold, J. D. Keasling and H. R. Beller	Improving methyl ketone production in Escherichia coli by heterologous expression of NADH-dependent FabG	Biotechnology and Bioengineering
2018	10.1074/jbc.RA117.001681	Goins CM, D. S., Smith MD, Parks JM, Ronning DR	Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into Antigen 85 catalysis	Journal of Biological Chemistry
2018	10.1093/bioinformatics/bty227	Goren, E., P. Liu, C. Wang and C. Wang	BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates	Bioinformatics
2018	10.1093/femsyr/foy096	Gossing, M., A. Smialowska and J. Nielsen	Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae	FEMS Yeast Research
2018	10.1186/s12864-018-5179-7	Gould, B. A., J. D. Palacio-Mejia, J. Jenkins, S. Mamidi, K. Barry, J. Schmutz, T. E. Juenger and D. B. Lowry	Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae)	BMC Genomics
2018	10.1021/acssynbio.8b00243	Goyal, G., Z. Costello, J. Alonso-Gutierrez, A. Kang, T. S. Lee, H. Garcia Martin and N. J. Hillson	Parallel Integration and Chromosomal Expansion of Metabolic Pathways	ACS Synthetic Biology
2018	10.1007/s10295-018-2049-x	Groom, J., D. Chung, S.-K. Kim, A. Guss and J. Westpheling	Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences	Journal of Industrial Microbiology and Biotechnology
2018	10.1016/j.ijggc.2018.11.003	Gundersen, C. B., T. Andersen, R. D. Vogt and S. D. Allison	Growth response of environmental bacteria under exposure to nitramines from CO2-capture	International Journal of Greenhouse Gas Control
2018	10.1155/2018/9784161	Guo, H. B., Y. Ma, G. A. Tuskan, X. H. Yang and H. Guo	Classification of complete proteomes of different organisms and protein sets based on their protein distributions in terms of some key attributes of proteins	International Journal of Genomics
2018	10.1038/s41564-018-0178-7	Guo, J., S. Wilken, V. Jimenez, C. J. Choi, C. Ansong, R. Dannebaum, L. Sudek, D. S. Milner, C. Bachy, E. N. Reistetter, V. A. Elrod, D. Klimov, S. O. Purvine, C.-L. Wei, G. Kunde-Ramamoorthy, T. A. Richards, U. Goodenough, R. D. Smith, S. J. Callister and A. Z. Worden	Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation	Nature Microbiology
2018	10.1016/j.ymben.2018.07.003	Guo, L. Y., P. Wang, R. Jaini, N. Dudareva, C. Chapple and J. A. Morgan	Dynamic modeling of subcellular phenylpropanoid metabolism in Arabidopsis lignifying cells	Metabolic Engineering
2018	10.1038/s41558-018-0254-2	Guo, X., J. J. Feng, Z. Shi, X. S. Zhou, M. T. Yuan, X. Y. Tao, L. Hale, T. Yuan, J. J. Wang, Y. J. Qin, A. F. Zhou, Y. Fu, L. Y. Wu, Z. L. He, J. D. Van Nostrand, D. L. Ning, X. D. Liu, Y. Q. Luo, J. M. Tiedje, Y. F. Yang and J. Z. Zhou	Climate warming leads to divergent succession of grassland microbial communities	Nature Climate Change
2018	10.3389/fmicb.2018.00954	Guo, X., X. S. Zhou, L. Hale, M. T. Yuan, J. J. Feng, D. L. Ning, Z. Shi, Y. J. Qin, F. F. Liu, L. Y. Wu, Z. L. He, J. D. Van Nostrand, X. D. Liu, Y. Q. Luo, J. M. Tiedje and J. Z. Zhou	Taxonomic and functional responses of soil microbial communities to annual removal of aboveground plant biomass	Frontiers in Microbiology
2018	10.1007/s10533-018-0489-z	Hagerty, S. B., S. D. Allison and J. P. Schimel	Evaluating soil microbial carbon use efficiency explicitly as a function of cellular processes: implications for measurements and models	Biogeochemistry
2018	10.1002/bit.26570	HamediRad, M., J. Lian, H. Li and H. Zhao	RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization	Biotechnology and Bioengineering
2018	10.1002/hyp.11447	Hamilton, S. K., M. Z. Hussain, C. Lowrie, B. Basso and G. P. Robertson	Evapotranspiration is resilient in the face of land cover and climate change in a humid temperate catchment	Hydrological Processes
2018	10.1111/tpj.14047	Handakumbura, P. P., K. Brow, I. P. Whitney, K. M. Zhao, K. A. Sanguinet, S. J. Lee, J. Olins, S. P. Romero-Gamboa, M. J. Harrington, C. J. Bascom, K. J. M. MacKinnon, M. T. Veling, L. F. Liu, J. E. Lee, J. P. Vogel, R. C. O'Malley, M. Bezanilla, L. E. Bartley and S. P. Hazen	SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae	Plant Journal
2018	10.1073/pnas.1810949115	Harcombe, W. R., J. M. Chacon, E. M. Adamowicz, L. M. Chubiz and C. J. Marx	Evolution of bidirectional costly mutualism from byproduct consumption	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1021/acs.energyfuels.8b02113	Harman-Ware, A. E. and J. R. Ferrell	Methods and Challenges in the Determination of Molecular Weight Metrics of Bio-oils	Energy & Fuels
2018	10.1007/978-3-319-44535-9_11-1	Hazen, T. C.	In Situ: Groundwater Bioremediation	Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation
2018	10.1007/978-3-319-44535-9_5-1	Hazen, T. C.	Cometabolic Bioremediation	Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation
2018	10.1128/mBio.02435-17	He, Z., P. Zhang, L. Wu, A. M. Rocha, Q. Tu, Z. Shi, B. Wu, Y. Qin, J. Wang, Q. Yan, D. Curtis, D. Ning, J. D. Van Nostrand, L. Wu, Y. Yang, D. A. Elias, D. B. Watson, M. W. W. Adams, M. W. Fields, E. J. Alm, T. C. Hazen, P. D. Adams, A. P. Arkin and J. Zhou	Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning	mBio
2018	10.1021/acs.analchem.8b02233	Hebert, A. S., S. Prasad, M. W. Belford, D. J. Bailey, G. C. McAlister, S. E. Abbatiello, R. Huguet, E. R. Wouters, J. J. Dunyach, D. R. Brademan, M. S. Westphall and J. J. Coon	Comprehensive single-shot proteomics with FAIMS on a hybrid orbitrap mass spectrometer	Analytical Chemistry
2018	10.1038/s41467-018-07649-1	Heckmann, D., D. C. Zielinski and B. O. Palsson	Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates	Nature Communications
2018	10.1016/j.bej.2017.11.015	Henske, J. K., S. D. Springer, M. A. O'Malley and A. Butler	Substrate-based differential expression analysis reveals control of biomass degrading enzymes in Pycnoporus cinnabarinus	Biochemical Engineering Journal
2018	10.1002/bit.26515	Henske, J. K., S. E. Wilken, K. V. Solomon, C. R. Smallwood, V. Shutthanandan, J. E. Evans, M. K. Theodorou and M. A. O'Malley	Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose	Biotechnology and Bioengineering
2018	10.1002/aic.16395	Henske, J. K., S. P. Gilmore, C. H. Haitjema, K. V. Solomon and M. A. O'Malley	Biomass-degrading enzymes are catabolite repressed in anaerobic gut fungi	AIChE Journal
2018	10.1186/s13068-018-1337-z	Henson, W. R., F. F. Hsu, G. Dantas, T. S. Moon and M. Foston	Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion	Biotechnology for Biofuels
2018	10.1016/j.ymben.2018.06.009	Henson, W. R., T. Campbell, D. M. DeLorenzo, Y. Gao, B. Berla, S. J. Kim, M. Foston, T. S. Moon and G. Dantas	Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus	Metabolic Engineering
2018	10.1534/genetics.118.301161	Higgins, D. A., M. K. M. Young, M. Tremaine, M. Sardi, J. M. Fletcher, M. Agnew, L. Liu, Q. Dickinson, D. Peris, R. L. Wrobel, C. T. Hittinger, A. P. Gasch, S. W. Singer, B. A. Simmons, R. Landick, M. P. Thelen and T. K. Sato	Natural variation in the multidrug efflux pump SGE1 underlies ionic liquid tolerance in yeast	Genetics
2018	10.1038/s41467-018-06050-2	Hodgkins, S. B., C. J. Richardson, R. Dommain, H. J. Wang, P. H. Glaser, B. Verbeke, B. R. Winkler, A. R. Cobb, V. I. Rich, M. Missilmani, N. Flanagan, M. Ho, A. M. Hoyt, C. F. Harvey, S. R. Vining, M. A. Hough, T. R. Moore, P. J. H. Richard, F. B. De la Cruz, J. Toufaily, R. Hamdan, W. T. Cooper and J. P. Chanton	Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance	Nature Communications
2018	10.1073/pnas.1813192115	Hogle, S. L., C. L. Dupont, B. M. Hopkinson, A. L. King, K. N. Buck, K. L. Roe, R. K. Stuart, A. E. Allen, E. L. Mann, Z. I. Johnson and K. A. Barbeau	Pervasive iron limitation at subsurface chlorophyll maxima of the California Current	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1186/s13068-018-1245-2	Hon, S., E. K. Holwerda, R. S. Worthen, M. I. Maloney, L. Tian, J. Cui, P. P. Lin, L. R. Lynd and D. G. Olson	Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production	Biotechnology for Biofuels
2018	10.1038/nchembio.2552	Hsu, T. M., D. H. Welner, Z. N. Russ, B. Cervantes, R. L. Prathuri, P. D. Adams and J. E. Dueber	Employing a biochemical protecting group for a sustainable indigo dyeing strategy	Nature Chemical Biology
2018	10.1371/journal.pone.0199681	Hu, G. F., Y. M. Liu, T. Q. Duo, B. Y. Zhao, G. W. Cui, J. Ji, X. Kuang, E. H. Ervin and X. Z. Zhang	Antioxidant metabolism variation associated with alkali-salt tolerance in thirty switchgrass (Panicum virgatum) lines	PLOS ONE
2018	10.1126/sciadv.aat5105	Huang, A., P. Q. Nguyen, J. C. Stark, M. K. Takahashi, N. Donghia, T. Ferrante, A. J. Dy, K. J. Hsu, R. S. Dubner, K. Pardee, M. C. Jewett and J. J. Collins	BioBits (TM) Explorer: A modular synthetic biology education kit	Science Advances
2018	10.1186/s13068-018-1104-1	Hwang, H. J., S. Y. Lee and P. C. Lee	Engineering and application of synthetic nar promoter for fine-tuning the expression of metabolic pathway genes in Escherichia coli	Biotechnology for Biofuels
2018	10.1104/pp.18.00396	Ishikawa, T., L. Fang, E. A. Rennie, J. Sechet, J. Yan, B. Jing, W. Moore, E. B. Cahoon, H. V. Scheller, M. Kawai-Yamada and J. C. Mortimer	GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) Is a GlcNAc-Containing Glycosylinositol Phosphorylceramide Glycosyltransferase	Plant Physiology
2018	10.1111/tpj.14021	Iwai, M., M. S. Roth and K. K. Niyogi	Subdiffraction-resolution live-cell imaging for visualizing thylakoid membranes	Plant Journal
2018	10.3389/fpls.2018.00985	Jaganathan, D., K. Ramasamy, G. Sellamuthu, S. Jayabalan and G. Venkataraman	CRISPR for Crop Improvement: An Update Review	Frontiers in Plant Science
2018	10.1007/s00253-018-9294-9	Jagtap, S. S. and C. V. Rao	Microbial conversion of xylose into useful bioproducts	Applied Microbiology and Biotechnology
2018	10.1016/j.cell.2018.03.055	Jang, C., L. Chen and J. D. Rabinowitz	Metabolomics and Isotope Tracing	Cell
2018	10.1093/jxb/ery213	Jansson, C., J. Vogel, S. Hazen, T. Brutnell and T. Mockler	Climate-smart crops with enhanced photosynthesis	Journal of Experimental Botany
2018	10.1039/c8ee00460a	Jayakody, L. N., C. W. Johnson, J. M. Whitham, R. J. Giannone, B. A. Black, N. S. Cleveland, D. M. Klingeman, W. E. Michener, J. L. Olstad, D. R. Vardon, R. C. Brown, S. D. Brown, R. L. Hettich, A. M. Guss and G. T. Beckham	Thermochemical wastewater valorization via enhanced microbial toxicity tolerance	Energy & Environmental Science
2018	10.1002/cssc.201802016	Jiang, H. J., Imberti, S., Simmons, B. A., Atkin, R., and Warr, G.	Structural Design of Ionic Liquids for Optimizing Aromatic Dissolution	ChemSusChem
2018	10.1002/jcc.25192	Johnson QR, L. R., Shen T	CAMERRA An Analysis Tool for the Computation of Allosteric Mechanism by Evaluating Residue-Residue Associations	Journal of Computational Chemistry
2018	10.1039/c7cp07126d	Johnson, Q. R., B. Mostofian, G. Fuente Gomez, J. C. Smith and X. Cheng	Effects of carotenoids on lipid bilayers	Physical Chemistry Chemical Physics
2018	10.1128/aem.00597-18	Jones, A. J., A. G. Fast, M. Clupper and E. T. Papoutsakis	Small and Low but Potent: the Complex Regulatory Role of the Small RNA SolB in Solventogenesis in Clostridium acetobutylicum	Applied and Environmental Microbiology
2018	10.5194/bg-15-2219-2018	Jose, N. A., R. Lau, T. L. Swenson, N. Klitgord, F. Garcia-Pichel, B. P. Bowen, R. Baran and T. R. Northen	Flux balance modeling to predict bacterial survival during pulsed-activity events	Biogeosciences
2018	10.1109/SC.2018.00060	Joubert, W., D. Weighill, D. Kainer, S. Climer, A. Justice, K. Fagnan and D. Jacobson	Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for Chronic Pain and Opioid Addiction	SC18: International Conference for High Performance Computing, Networking, Storage and Analysis
2018	10.1016/j.parco.2018.03.009	Joubert, W., J. Nance, D. Weighill and D. Jacobson	Parallel accelerated vector similarity calculations for genomics applications	Parallel Computing
2018	10.1038/s41467-018-05525-6	Juarez, J. F., B. Lecube-Azpeitia, S. L. Brown, C. D. Johnston and G. M. Church	Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators	Nature Communications
2018	10.1002/slct.201801837	Jung, S., H. L. Trajano, C. G. Yoo, M. B. Foston, F. Hu, A. K. Tolbert, C. E. Wyman and A. J. Ragauskas	Topochemical Understanding of Lignin Distribution During Hydrothermal Flowthrough Pretreatment	ChemistrySelect
2018	10.1534/g3.118.200443	Kainer, D., E. A. Stone, A. Padovan, W. J. Foley and C. Kulheim	Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybractea	G3: Genes, Genomes and Genetics
2018	10.1039/c7em00533d	Kanzler, C. R., P. Lian, E. L. Trainer, X. Yang, N. Govind, J. M. Parks and A. M. Graham	Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions	Environmental Science: Processes & Impacts
2018	10.1128/mBio.01366-16	Karaoz, U., E. Couradeau, U. N. da Rocha, H. C. Lim, T. Northen, F. Garcia-Pichel and E. L. Brodie	Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity	mBio
2018	10.1016/j.ymben.2017.11.005	Karim, A. S., J. T. Heggestad, S. A. Crowe and M. C. Jewett	Controlling cell-free metabolism through physiochemical perturbations	Metabolic Engineering
2018	10.1186/s12918-018-0593-7	Karp, P. D., D. Weaver and M. Latendresse	How accurate is automated gap filling of metabolic models?	BMC Systems Biology
2018	10.1021/acssynbio.7b00287	Kasey, C. M., M. Zerrad, Y. Li, T. A. Cropp and G. J. Williams	Development of Transcription Factor-Based Designer Macrolide Biosensors for Metabolic Engineering and Synthetic Biology	ACS Synthetic Biology
2018	10.1002/cpmc.64	Kelley, B. R., J. C. Ellis, D. Hyatt, D. Jacobson and J. Johnson	Isolation and Whole-Genome Sequencing of Environmental Campylobacter	Current Protocols in Microbiology
2018	10.1039/C7GC03459H	Kent, M. S., J. Zeng, N. Rader, I. C. Avina, C. T. Simoes, C. K. Brenden, M. L. Busse, J. Watt, N. H. Giron, T. M. Alam, M. D. Allendorf, B. A. Simmons, N. S. Bell and K. L. Sale	Efficient conversion of lignin into a water-soluble polymer by a chelator-mediated Fenton reaction: optimization of H2O2 use and performance as a dispersant	Green Chemistry
2018	10.1128/mBio.00065-18	Khalfaoui-Hassani, B., H. Wu, C. E. Blaby-Haas, Y. Zhang, F. Sandri, A. F. Verissimo, H. G. Koch and F. Daldal	Widespread Distribution and Functional Specificity of the Copper Importer CcoA: Distinct Cu Uptake Routes for Bacterial Cytochrome c Oxidases	mBio
2018	10.1186/s12864-018-4609-x	Khosravi, C., E. Battaglia, R. S. Kun, S. Dalhuijsen, J. Visser, M. V. Aguilar-Pontes, M. Zhou, H. M. Heyman, Y. M. Kim, S. E. B. Ronald and R. P. de Vries	Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans	BMC Genomics
2018	10.1109/NYSDS.2018.8538944	Kim, C., P. Yin, C. X. Soto, I. K. Blaby and S. Yoo	Multimodal biological analysis using NLP and expression profile	2018 New York Scientific Data Summit (NYSDS)
2018	10.1039/C7GC03029K	Kim, K. H., T. Dutta, J. Sun, B. Simmons and S. Singh	Biomass pretreatment using deep eutectic solvents from lignin derived phenols	Green Chemistry
2018	10.1111/tpj.13830	Kim, S. J., S. Zemelis-Durfee, J. K. Jensen, C. G. Wilkerson, K. Keegstra and F. Brandizzi	In the grass species Brachypodium distachyon, the production of mixed-linkage (1,3;1,4)-beta-glucan (MLG) occurs in the Golgi apparatus	Plant Journal
2018	10.1016/j.ymben.2018.09.002	Kim, S. K. and J. Westpheling	Engineering a spermidine biosynthetic pathway in Clostridium thermocellum results in increased resistance to furans and increased ethanol production	Metabolic Engineering
2018	10.1002/bbb.1899	Kim, S., X. S. Zhang, B. E. Dale, A. D. Reddy, C. D. Jones and R. C. Izaurralde	EISA (Energy Independence and Security Act) compliant ethanol fuel from corn stover in a depot-based decentralized system	Biofuels Bioproducts & Biorefining-Biofpr
2018	10.1128/AEM.02348-17	Kim, S.-K., M. E. Himmel, Y. J. Bomble and J. Westpheling	Expression of a Cellobiose Phosphorylase from Thermotoga maritima in Caldicellulosiruptor bescii Improves the Phosphorolytic Pathway and Results in a Dramatic Increase in Cellulolytic Activity	Applied and Environmental Microbiology
2018	10.3389/fmicb.2018.01492	Kimbrel, J. A., N. Ballor, Y.-W. Wu, M. M. David, T. C. Hazen, B. A. Simmons, S. W. Singer and J. K. Jansson	Microbial Community Structure and Functional Potential Along a Hypersaline Gradient	Frontiers in Microbiology
2018	10.1002/ecs2.2090	Koch, B. J., T. A. McHugh, M. Hayer, E. Schwartz, S. J. Blazewicz, P. Dijkstra, N. van Gestel, J. C. Marks, R. L. Mau, E. M. Morrissey, J. Pett-Ridge and B. A. Hungate	Estimating taxon-specific population dynamics in diverse microbial communities	Ecosphere
2018	10.1016/j.chembiol.2018.04.014	Kohler, A. C., B. A. Simmons and K. L. Sale	Structure-based Engineering of a Plant-Fungal Hybrid Peroxidase for Enhanced Temperature and pH Tolerance	Cell Chemical Biology
2018	10.1111/nph.14942	Kolbe, A. R. and A. B. Cousins	Mesophyll conductance in Zea mays responds transiently to CO2 availability: implications for transpiration efficiency in C4 crops	New Phytologist
2018	10.1071/FP17265	Kolbe, A. R., A. J. Studer and A. B. Cousins	Biochemical and transcriptomic analysis of maize diversity to elucidate drivers of leaf carbon isotope composition	Functional Plant Biology
2018	10.1021/acs.iecr.8b00065	Kong, L. X. and C. T. Maravelias	An optimization-based approach for simultaneous chemical process and heat exchanger network synthesis	Industrial & Engineering Chemistry Research
2018	10.1074/jbc.RA117.001268	Kontur, W. S., C. A. Bingman, C. N. Olmsted, D. R. Wassarman, A. Ulbrich, D. L. Gall, R. W. Smith, L. M. Yusko, B. G. Fox, D. R. Noguera, J. J. Coon and T. J. Donohue	Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the ?-aryl ether bond of lignin	Journal of Biological Chemistry
2018	10.1186/s12866-018-1256-y	Kosina, S. M., A. M. Greiner, R. K. Lau, S. Jenkins, R. Baran, B. P. Bowen and T. R. Northen	Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes	BMC Microbiology
2018	10.1186/s13068-018-1216-7	Kothari, N., E. K. Holwerda, C. M. Cai, R. Kumar and C. E. Wyman	Biomass augmentation through thermochemical pretreatments greatly enhances digestion of switchgrass by Clostridium thermocellum	Biotechnology for Biofuels
2018	10.1016/j.str.2018.01.006	Kovalevsky A, A. M., Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R	'To Be or Not to Be' Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation	Structure
2018	10.1016/j.soilbio.2018.01.033	Koyama, A., B. Harlow, C. R. Kuske, J. Belnap and R. D. Evans	Plant and microbial biomarkers suggest mechanisms of soil organic carbon accumulation in a Mojave Desert ecosystem under elevated CO2	Soil Biology and Biochemistry
2018	10.1073/pnas.1806268115	Krause, D. J., J. Kominek, D. A. Opulente, X. X. Shen, X. F. Zhou, Q. K. Langdon, J. DeVirgilio, A. B. Hulfachor, C. P. Kurtzman, A. Rokas and C. T. Hittinge	Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1111/gcbb.12552	Kravchenko, A. N., A. K. Guber, M. Y. Quigley, J. Koestel, H. Gandhi and N. E. Ostrom	X-ray computed tomography to predict soil N2O production via bacterial denitrification and N2O emission in contrasting bioenergy cropping systems	Global Change Biology Bioenergy
2018	10.1007/s10570-017-1542-0	Kruer-Zerhusen, N., B. Cantero-Tubilla and D. B. Wilson	Characterization of cellulose crystallinity after enzymatic treatment using Fourier transform infrared spectroscopy (FTIR)	Cellulose
2018	10.1093/molbev/msy102	Kuang, M. C., J. Kominek, W. G. Alexander, J. F. Cheng, R. L. Wrobel and C. T. Hittinger	Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution	Molecular Biology and Evolution
2018	10.1038/s41467-017-02362-x	Kumar, A., L. Wang, C. Y. Ng and C. D. Maranas	Pathway design using de novo steps through uncharted biochemical spaces	Nature Communications
2018	10.1073/pnas.1715137115	Kunjapur, A. M., D. A. Stork, E. Kuru, O. Vargas-Rodriguez, M. Landon, D. Soll and G. M. Church	Engineering posttranslational proofreading to discriminate nonstandard amino acids	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1016/j.biortech.2018.09.120	Kurambhatti, C. V., D. Kumar, K. D. Rausch, M. E. Tumbleson and V. Singh	Increasing ethanol yield through fiber conversion in corn dry grind process	Bioresource Technology
2018	10.3390/en11112921	Kurambhatti, V. C., D. Kumar, D. K. Rausch, E. M. Tumbleson and V. Singh	Ethanol production from corn fiber separated after liquefaction in the dry grind process	Energies
2018	10.1007/s12275-018-8024-4	La Reau, A. J. and G. Suen	The Ruminococci: key symbionts of the gut ecosystem	Journal of Microbiology
2018	10.3390/polym10080916	Lan, W., F. X. Yue, J. Rencoret, J. C. del Rio, W. Boerjan, F. C. Lu and J. Ralph	Elucidating tricin-lignin structures: Assigning correlations in HSQC spectra of monocot lignins	Polymers
2018	10.1016/j.biortech.2018.04.013	Lane, S., J. Dong and Y.-S. Jin	Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae	Bioresource Technology
2018	10.1021/acscatal.7b04114	Langan PS, V. V., Cooper SJ, Weiss KL, Ginell SL, Parks JM, Coates L	Substrate Binding Induces Conformational Changes in a Class A ?-lactamase That Prime It for Catalysis	ACS Catalysis
2018	10.1093/molbev/msy166	Langdon, Q. K., D. Peris, B. Kyle and C. T. Hittinger	spplDer: A species identification tool to investigate hybrid genomes with high-throughput sequencing	Molecular Biology and Evolution
2018	10.1021/acs.jafc.8b01618	Lapierre, C., A. Voxeur, S. D. Karlen, R. F. Helm and J. Ralph	Evaluation of feruloylated and p-coumaroylated arabinosyl units in grass Arabinoxylans by acidolysis in dioxane/methanol	Journal of Agricultural and Food Chemistry
2018	10.1111/tpj.13860	Laursen, T., S. H. Stonebloom, V. R. Pidatala, D. S. Birdseye, M. H. Clausen, J. C. Mortimer and H. V. Scheller	Bifunctional glycosyltransferases catalyze both extension and termination of pectic galactan oligosaccharides	The Plant Journal
2018	10.1016/j.tibtech.2018.06.007	Lazar, Z., N. Liu and G. Stephanopoulos	Holistic approaches in lipid production by Yarrowia lipolytica	Trends in Biotechnology
2018	10.1111/tpj.13782	LeBlanc, C., F. Zhang, J. Mendez, Y. Lozano, K. Chatpar, V. F. Irish and Y. Jacob	Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress	The Plant Journal
2018	10.1371/journal.pone.0202792	Lee, J. Z., R. C. Everroad, U. Karaoz, A. M. Detweiler, J. Pett-Ridge, P. K. Weber, L. Prufert-Bebout and B. M. Bebout	Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat	PLOS One
2018	10.1016/j.mec.2018.e00076	Lee, J.-W., N. P. Niraula and C. T. Trinh	Harnessing a P450 fatty acid decarboxylase from Macrococcus caseolyticus for microbial biosynthesis of odd chain terminal alkenes	Metabolic Engineering Communications
2018	10.1128/AEM.02694-17	Lee, L. L., S. E. Blumer-Schuette, J. A. Izquierdo, J. V. Zurawski, A. J. Loder, J. M. Conway, J. G. Elkins, M. Podar, A. Clum, P. C. Jones, M. J. Piatek, D. A. Weighill, D. A. Jacobson, M. W. W. Adams and R. M. Kelly	Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses	Applied and Environmental Microbiology
2018	10.1186/s12934-018-0863-5	Lei, C., J. Wang, Y. Liu, X. Liu, G. Zhao and J. Wang	A feedback regulatory model for RifQ-mediated repression of rifamycin export in Amycolatopsis mediterranei	Microbial Cell Factories
2018	10.1038/s41588-017-0012-9	Levy, A., I. Salas Gonzalez, M. Mittelviefhaus, S. Clingenpeel, S. Herrera Paredes, J. Miao, K. Wang, G. Devescovi, K. Stillman, F. Monteiro, B. Rangel Alvarez, D. S. Lundberg, T.-Y. Lu, S. Lebeis, Z. Jin, M. McDonald, A. P. Klein, M. E. Feltcher, T. G. Rio, S. R. Grant, S. L. Doty, R. E. Ley, B. Zhao, V. Venturi, D. A. Pelletier, J. A. Vorholt, S. G. Tringe, T. Woyke and J. L. Dangl	Genomic features of bacterial adaptation toplants	Nature Genetics
2018	10.1016/j.chom.2018.09.005	Levy, A., J. M. Conway, J. L. Dangl and T. Woyke	Elucidating bacterial gene functions in the plant microbiome	Cell Host & Microbe
2018	10.1104/pp.18.00200	Li, A., S. Jia, A. Yobi, Z. Ge, S. J. Sato, C. Zhang, R. Angelovici, T. E. Clemente and D. R. Holding	Editing of an Alpha-Kafirin gene family increases, digestibility and protein quality in sorghum	Plant Physiology
2018	10.3389/fpls.2018.01406	Li, J. T., Y. Y. Shi, A. N. Veeranampalayam-Sivakumar and D. P. Schachtman	Elucidating sorghum biomass, nitrogen and chlorophyll contents with spectral and morphological traits derived from unmanned aircraft system	Frontiers in Plant Science
2018	10.1021/acssuschemeng.7b03602	Li, M., C. G. Yoo, Y. Pu and A. J. Ragauskas	31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments	ACS Sustainable Chemistry & Engineering
2018	10.1039/c8gc00953h	Li, N., Y. D. Li, C. G. Yoo, X. H. Yang, X. L. Lin, J. Ralph and X. J. Pan	An uncondensed lignin depolymerized in the solid state and isolated from lignocellulosic biomass: a mechanistic study	Green Chemistry
2018	10.1021/acs.est.8b02314	Li, W., H. Li, Y.-d. Liu, P. Zheng and J. P. Shapleigh	Salinity-Aided Selection of Progressive Onset Denitrifiers as a Means of Providing Nitrite for Anammox	Environmental Science & Technology
2018	10.1186/s13068-018-1305-7	Li, W., K. Amos, M. Li, Y. Pu, S. Debolt, A. J. Ragauskas and J. Shi	Fractionation and characterization of lignin streams from unique high-lignin content endocarp feedstocks	Biotechnology for Biofuels
2018	10.1126/sciadv.aau2968	Li, Y. D., S. Li, H. Kim, A. H. Motagamwala, J. K. Mobley, F. Yue, Y. Tobimatsu, D. Havkin-Frenkel, F. Chen, R. A. Dixon, J. S. Luterbacher, J. A. Dumesic and J. Ralph	An 'ideal lignin' facilitates full biomass utilization	Science Advances
2018	10.1007/s10295-018-2003-y	Li, Z., Y. P. Shen, X. L. Jiang, L. S. Feng and J. Z. Liu	Metabolic evolution and a comparative omics analysis of Corynebacterium glutamicum for putrescine production	J Ind Microbiol Biotechnol
2018	10.1021/acs.jpca.8b01751	Lian P, J. R., Parks JM, Smith JC	Quantum Chemical Calculation of pKas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines and Thiols in Aqueous Solution	Journal of Physical Chemistry A
2018	10.1002/biot.201700601	Lian, J. Z., M. HamediRad and H. M. Zhao	Advancing metabolic engineering of Saccharomyces cerevisiae using the CRISPR/Cas system	Biotechnology Journal
2018	10.1016/j.ymben.2018.04.011	Lian, J. Z., S. Mishra and H. M. Zhao	Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications	Metabolic Engineering
2018	10.1002/bit.26569	Lian, J., Z. Bao, S. Hu and H. Zhao	Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains	Biotechnology and Bioengineering
2018	10.1111/gcb.14325	Liang, J. Y., J. Y. Xia, Z. Shi, L. F. Jiang, S. Ma, X. J. Lu, M. Mauritz, S. M. Natali, E. Pegoraro, C. R. Penton, C. Plaza, V. G. Salmon, G. Celis, J. R. Cole, K. T. Konstantinidis, J. M. Tiedje, J. Z. Zhou, E. A. G. Schuur and Y. Q. Luo	Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra	Global Change Biology
2018	10.1038/s41467-018-05667-7	Liang, J. Y., Z. G. Zhou, C. F. Huo, Z. Shi, J. R. Cole, L. Huang, K. T. Konstantinidis, X. M. Li, B. Liu, Z. K. Luo, C. R. Penton, E. A. G. Schuur, J. M. Tiedje, Y. P. Wang, L. Y. Wu, J. Y. Xia, J. Z. Zhou and Y. Q. Luo	More replenishment than priming loss of soil organic carbon with additional carbon input	Nature Communications
2018	10.1016/j.gee.2018.07.002	Liang, L., Yan, J., He, Q., Luong, T., Pray, T. R., Simmons, B. A., and Sun, N.	Scale-up of Biomass Conversion using 1-Ethyl-3-methylimidazolium Acetate as the Solvent	Green Energy & Environment
2018	10.1186/s13068-018-1238-1	Liang, X., J. M. Whitham, E. K. Holwerda, X. Shao, L. Tian, Y.-W. Wu, V. Lombard, B. Henrissat, D. M. Klingeman, Z. K. Yang, M. Podar, T. L. Richard, J. G. Elkins, S. D. Brown and L. R. Lynd	Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times	Biotechnology for Biofuels
2018	10.1073/pnas.1808351115	Liao, L., A. L. Schaefer, B. G. Coutinho, P. J. B. Brown and E. P. Greenberg	An aryl-homoserine lactone quorum-sensing signal produced by a dimorphic prosthecate bacterium	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1128/genomeA.00337-18	Liao, Y.-T., F. Liu, X. Sun, R. W. Li and V. C. H. Wu	Complete Genome Sequence of Escherichia coli Phage vB_EcoS Sa179lw, Isolated from Surface Water in a Produce-Growing Area in Northern California	Genome Announcements
2018	10.1111/pbi.12898	Lim, S. D., W. C. Yim, D. G. Liu, R. B. Hu, X. H. Yang and J. C. Cushman	A Vitis vinifera basic helix-loop-helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield	Plant Biotechnology Journal
2018	10.1073/pnas.1802191115	Lin, P. P., A. J. Jaeger, T. Y. Wu, S. C. Xu, A. S. Lee, F. K. Gao, P. W. Chen and J. C. Liao	Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1063/1.5004141	Lindsay RJ, S. J., Lohry DP, McGee TS, Ritchie JS, Johnson QR, Shen T	Characterizing protein conformations by correlation analysis of coarse-grained contact matricesPhysical Chemistry Chemical	Journal of Chemical Physics
2018	10.1093/nar/gky604	Lindsay, R. J., B. Pham, T. Shen and R. P. McCord	Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework	Nucleic Acids Research
2018	10.1038/s41586-018-0413-7	Litman, Z. C., Y. Wang, H. Zhao and J. F. Hartwig	Cooperative asymmetric reactions combining photocatalysis and enzymatic catalysis	Nature
2018	10.1186/s13068-018-1272-z	Liu, C.-L., T. Tian, J. Alonso-Gutierrez, B. Garabedian, S. Wang, E. E. K. Baidoo, V. Benites, Y. Chen, C. J. Petzold, P. D. Adams, J. D. Keasling, T. Tan and T. S. Lee	Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli	Biotechnology for Biofuels
2018	10.1016/j.plantsci.2018.06.012	Liu, D. G., K. J. Palla, R. B. Hu, R. C. Moseley, C. Mendoza, M. Chen, P. E. Abraham, J. L. Labbe, U. C. Kalluri, T. J. Tschaplinski, J. C. Cushman, A. M. Borland, G. A. Tuskan and X. H. Yang	Perspectives on the basic and applied aspects of crassulacean acid metabolism (CAM) research	Plant Science
2018	10.1021/acssuschemeng.7b03612	Liu, D., J. Sun, B. A. Simmons and S. Singh	N-Heterocyclic Carbene Promoted Decarboxylation of Lignin-Derived Aromatic Acids	ACS Sustainable Chemistry & Engineering
2018	10.1002/cssc.201701902	Liu, D., K. H. Kim, J. Sun, B. A. Simmons and S. Singh	Cascade Production of Lactic Acid from Universal Types of Sugars Catalyzed by Lanthanum Triflate	ChemSusChem
2018	10.1021/acssuschemeng.8b00384	Liu, E., M. Li, L. Das, Y. Pu, T. Frazier, B. Zhao, M. Crocker, A. J. Ragauskas and J. Shi	Understanding Lignin Fractionation and Characterization from Engineered Switchgrass Treated by an Aqueous Ionic Liquid	ACS Sustainable Chemistry & Engineering
2018	10.1016/j.copbio.2017.12.006	Liu, H. and A. M. Deutschbauer	Rapidly moving new bacteria to model-organism status	Current Opinion in Biotechnology
2018	10.1128/mSystems.00143-17	Liu, H., M. N. Price, R. J. Waters, J. Ray, H. K. Carlson, J. S. Lamson, R. Chakraborty, A. P. Arkin and A. M. Deutschbauer	Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria	mSystems
2018	10.1105/tpc.18.00194	Liu, M. J., K. Sugimoto, S. Uygun, N. Panchy, M. S. Campbell, M. Yandell, G. A. Howe and S. H. Shiu	Regulatory divergence in wound-responsive gene expression between domesticated and wild tomato	Plant Cell
2018	10.1016/j.ymben.2018.04.007	Liu, R. M., L. Y. Liang, A. Choudhury, M. C. Bassalo, A. D. Garst, K. Tarasava and R. T. Gill	Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production	Metabolic Engineering
2018	10.1111/oik.05548	Liu, S., Streich, J., Borevita, J.O., Rice, K.J., Li, T., Li, B.	Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations	Oikos
2018	10.1186/s13068-018-1119-7	Liu, W., M. Mazarei, R. Ye, Y. Peng, Y. Shao, H. L. Baxter, R. W. Sykes, G. B. Turner, M. F. Davis, Z.-Y. Wang, R. A. Dixon and C. N. Stewart	Switchgrass (Panicum virgatum L.) promoters for green tissue-specific expression of the MYB4 transcription factor for reduced-recalcitrance transgenic switchgrass	Biotechnology for Biofuels
2018	10.1186/s40168-017-0392-1	Liu, Y. F., D. D. Galzerani, S. M. Mbadinga, L. S. Zaramela, J. D. Gu, B. Z. Mu and K. Zengler	Metabolic capability and in situ activity of microorganisms in an oil reservoir	Microbiome
2018	10.1021/acssynbio.8b00331	Lobs, A. K., C. Schwartz, S. Thorwall and I. Wheeldon	Highly multiplexed CRISPRi repression of respiratory functions enhances mitochondrial localized ethyl acetate biosynthesis in Kluyveromyces marxianus	ACS Synthetic Biology
2018	10.1111/nph.15001	Looney, B. P., P. Meidl, M. J. Piatek, O. Miettinen, F. M. Martin, P. B. Matheny and J. L. Labbe	Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates	New Phytologist
2018	10.1038/s41467-018-07669-x	Love, J. T., J. Jenkins, D. B. Lowry, S. Mamidi, A. Sreedasyam, X. Y. Weng, K. Barry, J. Bonnette, B. Campitelli, C. Daum, S. P. Gordon, B. A. Gould, A. Khasanova, A. Lipzen, A. MacQueen, J. D. Palacio-Mejia, C. Plott, E. V. Shakirov, S. Q. Shu, Y. Yoshinaga, M. Zane, D. Kudrna, J. D. Talag, D. Rokhsar, J. Grimwood, J. Schmutz and T. E. Juenger	The genomic landscape of molecular responses to natural drought stress in Panicum hallii	Nature Communications
2018	10.1002/cpch.38	Lubner, J. M., J. L. Balsbaugh, G. M. Church, M. F. Chou and D. Schwartz	Characterizing protein kinase substrate specificity using the Proteomic Peptide Library (ProPeL) approach	Current Protocols in Chemical Biology
2018	10.3390/proteomes6040036	Luxmi, R., C. Blaby-Haas, D. Kumar, N. Rauniyar, S. M. King, R. E. Mains and B. A. Eipper	Proteases Shape the Chlamydomonas Secretome: Comparison to Classical Neuropeptide Processing Machinery	Proteomes
2018	10.1038/s41467-017-02571-4	Martin-Platero, A. M., B. Cleary, K. Kauffman, S. P. Preheim, D. J. McGillicuddy, E. J. Alm and M. F. Polz	High resolution time series reveals cohesive but short-lived communities in coastal plankton	Nature Communications
2018	10.3389/fbioe.2018.00117	Martins-Santana, L., L. C. Nora, A. Sanches-Medeiros, G. L. Lovate, M. H. A. Cassiano and R. Silva-Rocha	Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production	Frontiers in bioengineering and biotechnology
2018	10.1093/femsec/fiy047	Mayali, X. and P. K. Weber	Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community	FEMS Microbiology Ecology
2018	10.1111/tpj.13781	McCormick, R. F., S. K. Truong, A. Sreedasyam, J. Jenkins, S. Q. Shu, D. Sims, M. Kennedy, M. Amirebrahimi, B. D. Weers, B. McKinley, A. Mattison, D. T. Morishige, J. Grimwood, J. Schmutz and J. E. Mullet	The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization	Plant Journal
2018	10.1128/aem.00404-18	McCully, A. L., M. G. Behringer, J. R. Gliessman, E. V. Pilipenko, J. L. Mazny, M. Lynch, D. A. Drummond and J. B. McKinlay	An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris	Applied and Environmental Microbiology
2018	10.1128/aem.00399-18	McGlynn, S. E., G. L. Chadwick, A. O'Neill, M. Mackey, A. Thor, T. J. Deerinck, M. H. Ellisman and V. J. Orphan	Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners as revealed by integrated multimodal analytical microscopy	Applied and Environmental Microbiology
2018	10.1002/pld3.74	McKinley, B. A., A. L. Casto, W. L. Rooney and J. E. Mullet	Developmental dynamics of stem starch accumulation in Sorghum bicolor	Plant Direct
2018	10.1371/journal.pone.0195863	McKinley, B. A., S. N. Olson, K. B. Ritter, D. W. Herb, S. D. Karien, F. H. Lu, J. Ralph, W. L. Rooney and J. E. Mullet	Variation in energy sorghum hybrid TX08001 biomass composition and lignin chemistry during development under irrigated and non-irrigated field conditions	PLOS ONE
2018	10.1038/nature25982	McQuaid, J. B., A. B. Kustka, M. Obornik, A. Horak, J. R. McCrow, B. J. Karas, H. Zheng, T. Kindeberg, A. J. Andersson, K. A. Barbeau and A. E. Allen	Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms	Nature
2018	10.1002/biot.201600433	Meadows, C. W., A. Kang and T. S. Lee	Metabolic Engineering for Advanced Biofuels Production and Recent Advances Toward Commercialization	Biotechnology Journal
2018	10.1186/s13068-018-1342-2	Meadows, C. W., F. Mingardon, B. M. Garabedian, E. E. K. Baidoo, V. T. Benites, A. V. Rodrigues, R. Abourjeily, A. Chanal and T. S. Lee	Discovery of novel geranylgeranyl reductases and characterization of their substrate promiscuity	Biotechnology for Biofuels
2018	10.1111/1462-2920.14246	Meinhardt, K. A., N. Stopnisek, M. W. Pannu, S. E. Strand, S. C. Fransen, K. L. Casciotti and D. A. Stahl	Ammonia-oxidizing bacteria are the primary N2O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil	Environmental Microbiology
2018	10.1093/bioinformatics/btx564	Mendoza, B. J. and C. T. Trinh	Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms	Bioinformatics
2018	10.1021/acssuschemeng.8b01028	Meng, X., A. Parikh, B. Seemala, R. Kumar, Y. Pu, P. Christopher, C. E. Wyman, C. M. Cai and A. J. Ragauskas	Chemical Transformations of Poplar Lignin during Cosolvent Enhanced Lignocellulosic Fractionation Process	ACS Sustainable Chemistry & Engineering
2018	10.1021/acssuschemeng.7b03285	Meng, X., Y. Pu, P. Sannigrahi, M. Li, S. Cao and A. J. Ragauskas	The Nature of Hololignin	ACS Sustainable Chemistry & Engineering
2018	10.1371/journal.pone.0198584	Metz, Z. P., T. Ding and D. J. Baumler	Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes	PLOS ONE
2018	10.1186/s13068-018-1033-z	Milano, E. R., C. E. Payne, E. Wolfrum, J. Lovell, J. Jenkins, J. Schmutz and T. E. Juenger	Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii	Biotechnology for Biofuels
2018	10.1016/j.soilbio.2018.06.006	Minerovic, A. J., O. J. Valverde-Barrantes and C. B. Blackwood	Physical and microbial mechanisms of decomposition vary in importance among root orders and tree species with differing chemical and morphological traits	Soil Biology & Biochemistry
2018	10.1093/femsec/fiy093	Miquel Guennoc, C., C. Rose, J. Labbe and A. Deveau	Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls?	FEMS Microbiology Ecology
2018	10.1126/science.aat8474	Mirts, E. N., I. D. Petrik, P. Hosseinzadeh, M. J. Nilges and Y. Lu	A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme	Science
2018	10.1111/1462-2920.14051	Morrissey, E. M., R. L. Mau, E. Schwartz, B. J. Koch, M. Hayer and B. A. Hungate	Taxonomic patterns in the nitrogen assimilation of soil prokaryotes	Environmental Microbiology
2018	10.1177/1535370218793890	Mortimer, J. C.	Plant synthetic biology could drive a revolution in biofuels and medicine	Experimental Biology and Medicine
2018	10.2174/0929866526666181128125725	Morton, S. A., Gupta, S., Petzold, C. J., and Ralston, C.	Recent Advances in X-Ray Hydroxl Radical Footprinting at the Advanced Light Source Synchrotron	Protein & Peptide Letters
2018	10.15252/msb.20188605	Moser, F., A. E. Borujeni, A. N. Ghodasara, E. Cameron, Y. Park and C. A. Voigt	Dynamic control of endogenous metabolism with combinatorial logic circuits	Molecular Systems Biology
2018	10.1073/pnas.1804428115	Muchero, W., K. L. Sondreli, J. G. Chen, B. R. Urbanowicz, J. Zhang, V. Singan, Y. Yang, R. S. Brueggeman, J. Franco-Coronado, N. Abraham, J. Y. Yan, K. W. Moremen, A. J. Weisberg, J. H. Chang, E. Lindquist, K. Barry, P. Ranjan, S. Jawdy, J. Schmutz, G. A. Tuskan and J. M. LeBoldus	Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1186/s13068-018-1334-2	Na, G., N. Aryal, A. Fatihi, J. L. Kang and C. F. Lu	Seed-specific suppression of ADP-glucose pyrophosphorylase in Camelina sativa increases seed size and weight	Biotechnology for Biofuels
2018	10.1128/mSphere.00593-18	Neumann, A. P. and G. Suen	The phylogenomic diversity of herbivore-associated Fibrobacter spp. is correlated to lignocellulose-degrading potential	mSphere
2018	10.1186/s13068-018-1290-x	Neumann, A. P., P. J. Weimer and G. Suen	A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates	Biotechnology for Biofuels
2018	10.3389/fmicb.2018.01645	Newcombe, G., A. Harding, M. Ridout and P. E. Busby	A hypothetical bottleneck in the plant microbiome	Frontiers in Microbiology
2018	10.1145/3233547.3233622	Nguyen, N., I. Blaby and D. Wang	A Manifold Learning Based Approach to Reveal the Functional Linkages across Multiple Gene Networks	Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
2018	10.1016/j.ebiom.2018.04.005	Nickerson, K. P., S. Senger, Y. Zhang, R. Lima, S. Patel, L. Ingano, W. A. Flavahan, D. K. V. Kumar, C. M. Fraser, C. S. Faherty, M. B. Sztein, M. Fiorentino and A. Fasano	Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue	EBioMedicine
2018	10.3389/fmicb.2018.00853	Noirot-Gros, M. F., S. Shinde, P. E. Larsen, S. Zerbs, P. J. Korajczyk, K. M. Kemner and P. H. Noirot	Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation	Front Microbiology
2018	10.1128/MRA.01047-18	O'Dell, K. B., Hatmaker, E.A., Guss, A.M., Mormile, M.R.	Complete genome sequence of salinispaera sp. Strain LB1, a moderately halo-acidophilic bacterium isolated from Lake Brown, western Australia	Microbiology Resource Announcements
2018	10.1007/s10529-017-2467-2	Oguntimein, G. B., M. Rodriguez, A. Dumitrache, T. Shollenberger, S. R. Decker, B. H. Davison and S. D. Brown	Anaerobic microplate assay for direct microbial conversion of switchgrass and Avicel using Clostridium thermocellum	Biotechnology Letters
2018	10.3389/fpls.2018.01895	Olins, J. R., L. Lin, S. J. Lee, G. M. Trabucco, K. J. M. MacKinnon and S. P. Hazen	Secondary wall regulating NACs differentially bind at the promoter at a CELLULOSE SYNTHASE A4 Cis-eQTL	Frontiers in Plant Science
2018	10.25585/1488039	Olson, D.	Identification of secondary mutations in organisms engineered for biofuel production
2018	10.3389/fenrg.2018.00052	Ong, R. G., S. Shinde, L. da Costa Sousa and G. R. Sanford	Pre-senescence harvest of switchgrass inhibits xylose utilization by engineered yeast	Frontiers in Energy Research
2018	10.1186/s12915-018-0498-3	Opulente, D. A., E. J. Rollinson, C. Bernick-Roehr, A. B. Hulfachor, A. Rokas, C. P. Kurtzman and C. T. Hittinger	Factors driving metabolic diversity in the budding yeast subphylum	BMC Biology
2018	10.1002/rcm.8157	Ostrom, N. E., H. Gandhi, T. B. Coplen, S. Toyoda, J. K. Bohlke, W. A. Brand, K. L. Casciotti, J. Dyckmans, A. Giesemann, J. Mohn, R. Well, L. F. Yu and N. Yoshida	Preliminary assessment of stable nitrogen and oxygen isotopic composition of USGS51 and USGS52 nitrous oxide reference gases and perspectives on calibration needs	Rapid Communications in Mass Spectrometry
2018	10.1111/gbi.12295	Otwell, A. E., S. J. Callister, R. W. Sherwood, S. Zhang, A. R. Goldman, R. D. Smith and R. E. Richardson	Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA	Geobiology
2018	10.1016/j.soilbio.2018.08.024	Ouyang, Y., S. E. Evans, M. L. Friesen and L. K. Tiemann	Effect of nitrogen fertilization on the abundance of nitrogen cycling genes in agricultural soils: A meta-analysis of field studies	Soil Biology & Biochemistry
2018	10.1016/j.biotechadv.2018.04.008	Oyetunde, T., F. S. Bao, J.-W. Chen, H. G. Martin and Y. J. Tang	Leveraging knowledge engineering and machine learning for microbial bio-manufacturing	Biotechnology Advances
2018	10.1016/j.plaphy.2017.11.021	Ozseyhan, M. E., J. L. Kang, X. P. Mu and C. F. Lu	Mutagenesis of the FAE1 genes significantly changes fatty acid composition in seeds of Camelina sativa	Plant Physiology and Biochemistry
2018	10.1016/j.bbrc.2018.06.051	Ozseyhan, M. E., P. C. Li, G. Na, Z. J. Li, C. L. Wang and C. F. Lu	Improved fatty acid profiles in seeds of Camelina sativa by artificial microRNA mediated FATB gene suppression	Biochemical and Biophysical Research Communications
2018	10.1038/nbt.4173	Palluk, S., D. H. Arlow, T. de Rond, S. Barthel, J. S. Kang, R. Bector, H. M. Baghdassarian, A. N. Truong, P. W. Kim, A. K. Singh, N. J. Hillson and J. D. Keasling	De novo DNA synthesis using polymerase-nucleotide conjugates	Nature Biotechnology
2018	10.1128/aem.02441-17	Papp, K., B. A. Hungate and E. Schwartz	Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H-2 O-18	Applied and Environmental Microbiology
2018	10.1038/s41396-018-0233-7	Papp, K., R. L. Mau, M. Hayer, B. J. Koch, B. A. Hungate and E. Schwartz	Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA	ISME Journal
2018	10.1016/j.jconhyd.2018.08.009	Paradis, C. J., J.-W. Moon, D. A. Elias, L. D. McKay and T. C. Hazen	In situ decay of polyfluorinated benzoic acids under anaerobic conditions	Journal of Contaminant Hydrology
2018	10.1007/s10040-017-1672-3	Paradis, C. J., L. D. McKay, E. Perfect, J. D. Istok and T. C. Hazen	Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application	Hydrogeology Journal
2018	10.1371/journal.pbio.2003962	Paredes, S. H., T. X. Gao, T. F. Law, O. M. Finkel, T. Mucyn, P. Teixeira, I. S. Gonzalez, M. E. Feltcher, M. J. Powers, E. A. Shank, C. D. Jones, V. Jojic, J. L. Dangl and G. Castrillo	Design of synthetic bacterial communities for predictable plant phenotypes	PLOS Biology
2018	10.1016/j.tibtech.2017.10.013	Park, Y.-K., J.-M. Nicaud and R. Ledesma-Amaro	The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications	Trends in Biotechnology
2018	10.1021/acs.jctc.7b01236	Pavlova, A., J. M. Parks and J. C. Gumbart	Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations	Journal of Chemical Theory and Computation
2018	10.1111/1365-2745.12915	Peay, K. G.	Timing of mutualist arrival has a greater effect on Pinus muricata seedling growth than interspecific competition	Journal of Ecology
2018	10.1038/s41570-018-0050-6	Petridis, L. and J. C. Smith	Molecular-level driving forces in lignocellulosic biomass deconstruction for bioenergy	Nature Reviews Chemistry
2018	10.1111/tpj.13831	Petzold, H. E., B. Chanda, C. S. Zhao, S. B. Rigoulot, E. P. Beers and A. M. Brunner	DIVARICATA AND RADIALIS INTERACTING FACTOR (DRIF) also interacts with WOX and KNOX proteins associated with wood formation in Populus trichocarpa	Plant Journal
2018	10.1371/journal.pone.0195980	Pi M, K. K., Ye R, Hwang D, Miller DD, Smith JC, Baudry J, Quarles LD	Computationally identified novel agonists for GPRC6A	PLOS ONE
2018	10.1002/mnfr.201700770	Pi M, K. K., Ye R, Smith JC, Baudry J, Quarles LD	GPCR6A is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea	Molecular Nutrition & Food Research
2018	10.1002/cppb.20078	Pingault, L., P. Zogli, J. Brooks and M. Libault	Enhancing phenotyping and molecular analysis of plant root system using ultrasound aeroponic technology	Current Protocols in Chemical Biology
2018	10.1128/genomeA.01451-17	Pold, G., E. M. Conlon, M. Huntemann, M. Pillay, N. Mikhailova, D. Stamatis, T. B. K. Reddy, C. Daum, N. Shapiro, N. Kyrpides, T. Woyke and K. M. DeAngelis	Genome sequence of Verrucomicrobium sp. strain GAS474, a novel bacterium isolated from soil	Genome Announcements
2018	10.1128/genomeA.01452-17	Pold, G., M. Huntemann, M. Pillay, N. Mikhailova, D. Stamatis, T. Reddy, C. Daum, N. Shapiro, N. Kyrpides and T. Woyke	Draft genome sequences of three strains of a novel Rhizobiales species isolated from forest soil	Genome Announcements
2018	10.1128/mSphere.00541-18	Pomraning, K. R., E. L. Bredeweg, E. J. Kerkhoven, K. Barry, S. Haridas, H. Hundley, K. LaButti, A. Lipzen, M. Yan, J. K. Magnuson, B. A. Simmons, I. V. Grigoriev, J. Nielsen and S. E. Baker	Regulation of yeast-to-hyphae transition in Yarrowia lipolytica	mSphere
2018	10.3389/fmicb.2018.03043	Porcar, M., K. B. Louie, S. M. Kosina, M. W. Van Goethem, B. P. Bowen, K. Tanner and T. R. Northen	Microbial Ecology on Solar Panels in Berkeley, CA, United States	Frontiers in Microbiology
2018	10.1186/s13068-018-1076-1	Poudel, S., R. J. Giannone, M. Basen, I. Nookaew, F. L. Poole, 2nd, R. M. Kelly, M. W. W. Adams and R. L. Hettich	The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate	Biotechnology for Biofuels
2018	10.1371/journal.pone.0204525	Pozzo, T., S. M. Higdon, S. Pattathil, M. G. Hahn and A. B. Bennett	Characterization of novel glycosyl hydrolases discovered by cell wall glycan directed monoclonal antibody screening and metagenome analysis of maize aerial root mucilage	PLOS ONE
2018	10.1155/2018/4961726	Presley, G. N., B. K. Ndimba and J. S. Schilling	Brown rot-type fungal decomposition of sorghum bagasse: variable success and mechanistic implications	International Journal of Microbiology
2018	10.1128/AEM.00159-18	Presley, G. N., E. Panisko, S. O. Purvine and J. S. Schilling	Comparing the temporal process of wood metabolism among white and brown rot fungi by coupling secretomics with enzyme activities	Applied and Environmental Microbiology
2018	10.1128/aem.00159-18	Presley, G. N., E. Panisko, S. O. Purvine and J. S. Schilling	Coupling secretomics with enzyme activities to compare the temporal processes of wood metabolism among white and brown rot fungi	Applied and Environmental Microbiology
2018	10.1016/j.fgb.2016.08.004	Presley, G. N., J. W. Zhang and J. S. Schilling	A genomics-informed study of oxalate and cellulase regulation by brown rot wood-degrading fungi	Fungal Genetics and Biology
2018	10.1038/s41586-018-0124-0	Price, M. N., K. M. Wetmore, R. J. Waters, M. Callaghan, J. Ray, H. Liu, J. V. Kuehl, R. A. Melnyk, J. S. Lamson, Y. Suh, H. K. Carlson, Z. Esquivel, H. Sadeeshkumar, R. Chakraborty, G. M. Zane, B. E. Rubin, J. D. Wall, A. Visel, J. Bristow, M. J. Blow, A. P. Arkin and A. M. Deutschbauer	Mutant phenotypes for thousands of bacterial genes of unknown function	Nature
2018	10.1186/s12870-018-1316-3	Qi, P., D. Gimode, D. Saha, S. Schroder, D. Chakraborty, X. W. Wang, M. M. Dida, R. L. Malmberg and K. M. Devos	UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study	BMC Plant Biology
2018	10.1002/pmic.201700479	Qian C, C. H., Johs A, Lu X, An J, Pierce EM, Parks JM, Elias DA, Hettich RL, Gu B	Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes	Proteomics
2018	10.3389/fenrg.2018.00118	Ragauskas, A. J. and C. G. Yoo	Editorial: Advancements in Biomass Recalcitrance: The Use of Lignin for the Production of Fuels and Chemicals	Frontiers in Energy Research
2018	10.1002/aic.16396	Ralston, M. T. and E. T. Papoutsakis	RNAseq-based transcriptome assembly of Clostridium acetobutylicum for functional genome annotation and discovery	AIChE Journal
2018	10.1016/j.cherd.2018.07.015	Ramapriya, G. M., W. Y. Won and C. T. Maravelias	A superstructure optimization approach for process synthesis under complex reaction networks	Chemical Engineering Research & Design
2018	10.3389/fpls.2018.00399	Rao, X. and R. A. Dixon	Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses	Frontiers in Plant Science
2018	10.1111/pbi.13000	Rao, X., Chen, X., Shen, H., Ma, Q., Tang, Y., Pena, M., York, W., Frazier, T.P., Lenaghan S., Xiao, X., Chen, F., Dixon, R.A.	Gene regulatory networks of lignin biosynthesis in switchgrass (Panicum virgatum)	Plant Biotechnology Journal
2018	10.1038/s41598-018-23106-x	Rastogi, A., U. Maheswari, R. G. Dorrell, F. R. J. Vieira, F. Maumus, A. Kustka, J. McCarthy, A. E. Allen, P. Kersey, C. Bowler and L. Tirichine	Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms	Scientific Reports
2018	10.4236/jsbs.2018.81001	Rasyidah Mohamad Razar, A. M.	Phenotyping Winter Dormancy in Switchgrass to Extend the Growing Season and Improve Biomass Yield	Journal of Sustainable Bioenergy Systems
2018	10.1094/PBIOMES-04-17-0017-A	Ray, P., M.-H. Chi, Y. Guo, C. Chen, C. Adam, A. Kuo, K. LaButti, A. Lipzen, K. W. Barry, I. V. Grigoriev, Y. Tang and K. D. Craven	Genome Sequence of the Plant Growth Promoting Fungus Serendipita vermifera subsp. bescii: The First Native Strain from North America	Phytobiomes Journal
2018	10.3389/fpls.2017.02236	Ray, P., Y. Guo, J. Kolape and K. D. Craven	Non-targeted Colonization by the Endomycorrhizal Fungus, Serendipita vermifera, in Three Weeds Typically Co-occurring with Switchgrass	Frontiers in Plant Science
2018	10.1002/cssc.201800617	Regner, M., A. Bartuce, D. Padmakshan, J. Ralph and S. D. Karlen	Reductive cleavage method for quantitation of monolignols and low-abundance monolignol conjugates	ChemSusChem
2018	10.1007/s00253-017-8717-3	Reilly, M. C., J. Kim, J. Lynn, B. A. Simmons, J. M. Gladden, J. K. Magnuson and S. E. Baker	Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger	Applied Microbiology and Biotechnology
2018	10.1007/978-1-4939-7877-9_10	Reilly, M. C., S. Amaike Campen, B. A. Simmons, S. E. Baker, J. M. Gladden and J. K. Magnuson	Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger	Cellulases: Methods and Protocols
2018	10.1146/annurev-anchem-061417-125635	Retterer, S. T., J. L. Morrell-Falvey and M. J. Doktycz	Nano-Enabled Approaches to Chemical Imaging in Biosystems	Annual Review of Analytical Chemistry
2018	10.1128/aem.00014-18	Rodriguez-R, L. M., J. C. Castro, N. C. Kyrpides, J. R. Cole, J. M. Tiedje and K. T. Konstantinidis	How much Do rRNA gene surveys underestimate extant bacterial diversity?	Applied and Environmental Microbiology
2018	10.1128/mSystems.00039-18	Rodriguez-R, L. M., S. Gunturu, J. M. Tiedje, J. R. Cole and K. T. Konstantinidis	Nonpareil 3: Fast estimation of metagenomic coverage and sequence diversity	mSystems
2018	10.1002/ecs2.2524	Rogers, T. J., C. Leppanen, V. Brown, J. A. Fordyce, A. LeBude, T. Ranney, D. Simberloff and M. A. Cregger	Exploring variation in phyllosphere microbial communities across four hemlock species	Ecosphere
2018	10.1038/s41467-018-05857-3	Ruegg, T. L., J. H. Pereira, J. C. Chen, A. DeGiovanni, P. Novichkov, V. K. Mutalik, G. P. Tomaleri, S. W. Singer, N. J. Hillson, B. A. Simmons, P. D. Adams and M. P. Thelen	Jungle Express is a versatile repressor system for tight transcriptional control	Nature Communications
2018	10.1002/cbic.201700638	Ruprecht, C., P. Dallabernardina, P. J. Smith, B. R. Urbanowicz and F. Pfrengle	Analyzing Xyloglucan Endotransglycosylases by Incorporating Synthetic Oligosaccharides into Plant Cell Walls	ChemBioChem
2018	10.1186/s13068-018-1266-x	Russell, J., S.-K. Kim, J. Duma, H. Nothaft, M. E. Himmel, Y. J. Bomble, C. M. Szymanski and J. Westpheling	Deletion of a single glycosyltransferase in Caldicellulosiruptor bescii eliminates protein glycosylation and growth on crystalline cellulose	Biotechnology for Biofuels
2018	10.1007/s11103-017-0696-3	Sade, N., M. D. R. Wilhelmi, X. J. Ke, Y. Brotman, M. Wright, I. Khan, W. De Souza, E. Bassil, C. M. Tobias, R. Thilmony, J. P. Vogel and E. Blumwald	Salt tolerance of two perennial grass Brachypodium sylvaticum accessions	Plant Molecular Biology
2018	10.1186/s13068-018-1178-9	Sammond, D. W., N. Kastelowitz, B. S. Donohoe, M. Alahuhta, V. V. Lunin, D. Chung, N. S. Sarai, H. Yin, A. Mittal, M. E. Himmel, A. M. Guss and Y. J. Bomble	An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme	Biotechnology for Biofuels
2018	10.1111/1462-2920.14357	Samo, T. J., J. A. Kimbrel, D. J. Nilson, J. Pett-Ridge, P. K. Weber and X. Mayali	Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions	Environmental Microbiology
2018	10.1007/s00294-018-0835-7	Sardi, M. and A. P. Gasch	Genetic background effects in quantitative genetics: gene-by-system interactions	Current Genetics
2018	10.1534/g3.118.200677	Sardi, M., M. Krause, J. Heilberger and A. P. Gasch	Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis	G3-Genes Genomes Genetics
2018	10.1039/C8SE00287H	Satari, B., Karimi, K., Kumar, R.	Cellulose solvents-based pretreatment for enhanced second-generation biofuels production: A review	Sustainable Energy and Fuels
2018	10.1021/acs.est.8b04481	Satchwell, A. J., C. D. Scown, S. J. Smith, J. Amirebrahimi, L. Jin, T. W. Kirchstetter, N. J. Brown and C. V. Preble	Accelerating the Deployment of Anaerobic Digestion to Meet Zero Waste Goals	Environmental Science & Technology
2018	10.1016/j.biotechadv.2018.08.009	Satlewal, A., R. Agrawal, S. Bhagia, J. Sangoro and A. J. Ragauskas	Natural deep eutectic solvents for lignocellulosic biomass pretreatment: Recent developments, challenges and novel opportunities	Biotechnology Advances
2018	10.1128/mSystems.00221-18	Scarborough, M. J., C. E. Lawson, J. J. Hamilton, T. J. Donohue and D. R. Noguera	Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome	mSystems
2018	10.1186/s13068-018-1193-x	Scarborough, M. J., G. Lynch, M. Dickson, M. McGee, T. J. Donohue and D. R. Noguera	Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production	Biotechnology for Biofuels
2018	10.1111/tpj.14088	Sechet, J., S. Htwe, B. Urbanowicz, A. Agyeman, W. Feng, T. Ishikawa, M. Colomes, K. S. Kumar, M. Kawai-Yamada, J. R. Dinneny, M. A. O'Neill and J. C. Mortimer	Suppression of Arabidopsis GGLT1 affects growth by reducing the L-galactose content and borate cross-linking of rhamnogalacturonan-II	The Plant Journal
2018	10.1016/j.tree.2018.08.005	Shade, A., R. R. Dunn, S. A. Blowes, P. Keil, B. J. M. Bohannan, M. Herrmann, K. Kusel, J. T. Lennon, N. J. Sanders, D. Storch and J. Chase	Macroecology to unite all life, large and small	Trends in Ecology & Evolution
2018	10.1016/j.cell.2018.10.023	Shen, X. X., D. A. Opulente, J. Kominek, X. Zhou, J. L. Steenwyk, K. V. Buh, M. A. B. Haase, J. H. Wisecaver, M. Wang, D. T. Doering, J. T. Boudouris, R. M. Schneider, Q. K. Langdon, M. Ohkuma, R. Endoh, M. Takashima, R. Manabe, N. Cadez, D. Libkind, C. A. Rosa, J. DeVirgilio, A. B. Hulfachor, M. Groenewald, C. P. Kurtzman, C. T. Hittinger and A. Rokas	Tempo and mode of genome evolution in the budding yeast subphylum	Cell
2018	10.1007/s10295-018-2004-x	Shi, S. B., E. L. Ang and H. M. Zhao	In vivo biosensors: mechanisms, development, and applications	Journal of Industrial Microbiology & Biotechnology
2018	10.1016/j.soilbio.2018.09.013	Shi, S. J., D. J. Herman, Z. L. He, J. Pett-Ridge, L. Y. Wu, J. Z. Zhou and M. K. Firestone	Plant roots alter microbial functional genes supporting root litter decomposition	Soil Biology & Biochemistry
2018	10.1111/gcb.14333	Shi, Z., Y. Lin, K. R. Wilcox, L. Souza, L. F. Jiang, J. Jiang, C. G. Jung, X. Xu, M. T. Yuan, X. Guo, L. Y. Wu, J. Z. Zhou and Y. Q. Luo	Successional change in species composition alters climate sensitivity of grassland productivity	Global Change Biology
2018	10.1039/C8GC00353J	Shinde, S. D., X. Meng, R. Kumar and A. J. Ragauskas	Recent advances in understanding the pseudo-lignin formation in a lignocellulosic biorefinery	Green Chemistry
2018	10.1021/jacs.8b05544	Si, T., Q. Tian, Y. Min, L. Zhang, J. V. Sweedler, W. A. van der Donk and H. Zhao	Rapid screening of lanthipeptide analogs via in-colony removal of leader peptides in Escherichia coli	Journal of the American Chemical Society
2018	10.1038/s41396-018-0065-5	Singleton, C. M., C. K. McCalley, B. J. Woodcroft, J. A. Boyd, P. N. Evans, S. B. Hodgkins, J. P. Chanton, S. Frolking, P. M. Crill, S. R. Saleska, V. I. Rich and G. W. Tyson	Methanotrophy across a natural permafrost thaw environment	ISME Journal
2018	10.1128/mBio.00815-18	Smith, G. J., J. C. Angle, L. M. Solden, M. A. Borton, T. H. Morin, R. A. Daly, M. D. Johnston, K. C. Stefanik, R. Wolfe, B. Gil and K. C. Wrighton	Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland	mBio
2018	10.1038/s41396-018-0086-0	Smith, G. R., B. S. Steidinger, T. D. Bruns and K. G. Peay	Competition-colonization tradeoffs structure fungal diversity	ISME Journal
2018	10.1146/annurev-biophys-070317-033358	Smith, J. C., P. Tan, L. Petridis and L. Hong	Dynamic Neutron Scattering by Biological Systems	Annual Review of Biophysics
2018	10.1016/j.fgb.2018.09.004	Solomon, K. V., J. K. Henske, S. P. Gilmore, A. Lipzen, I. V. Grigoriev, D. Thompson and M. A. O'Malley	Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts	Fungal Genetics and Biology
2018	10.1186/s13068-018-1023-1	Song, B., B. Y. Li, X. Y. Wang, W. Shen, S. J. Park, C. Collings, A. R. Feng, S. J. Smith, J. D. Walton and S. Y. Ding	Real-time imaging reveals that lytic polysaccharide monooxygenase promotes cellulase activity by increasing cellulose accessibility	Biotechnology for Biofuels
2018	10.3390/pr6050041	Song, H.-S.	Special Issue: Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics	Processes
2018	10.1039/c8sc03208d	Song, Y., J. K. Mobley, A. H. Motagamwala, M. Isaacs, J. A. Dumesic, J. Ralph, A. F. Lee, K. Wilson and M. Crocker	Gold-catalyzed conversion of lignin to low molecular weight aromatics	Chemical Science
2018	10.7717/peerj.5614	Speth, D. R. and V. J. Orphan	Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales	PeerJ
2018	10.1002/anie.201708867	Stadlmeier, M., J. Bogena, M. Wallner, M. Wuhr and T. Carell	A Sulfoxide-based isobaric labelling reagent for accurate quantitative mass spectrometry	Angewandte Chemie-International Edition
2018	10.1016/j.meteno.2018.04.002	Standaert, R. F., R. J. Giannone and J. K. Michener	Identification of parallel and divergent optimization solutions for homologous metabolic enzymes	Metabolic Engineering Communications
2018	10.1111/gbi.12311	Stanton, C. L., C. T. Reinhard, J. F. Kasting, N. E. Ostrom, J. A. Haslun, T. W. Lyons and J. B. Glass	Nitrous oxide from chemodenitrification: A possible missing link in the Proterozoic greenhouse and the evolution of aerobic respiration	Geobiology
2018	10.1186/s40168-018-0499-z	Starr, E. P., S. J. Shi, S. J. Blazewicz, A. J. Probst, D. J. Herman, M. K. Firestone and J. F. Banfield	Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon	Microbiome
2018	10.1093/femsec/fiy130	Stedtfeld, R. D., X. P. Guo, T. M. Stedtfeld, H. J. Sheng, M. R. Williams, K. Hauschild, S. Gunturu, L. Tift, F. Wang, A. Howes, B. L. Chai, D. Q. Yin, J. R. Cole, J. M. Tiedje and S. A. Hashsham	Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements	FEMS Microbiology Ecology
2018	10.3389/fmicb.2018.02382	Steven, B., J. Belnap and C. R. Kuske	Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing	Frontiers in Microbiology
2018	10.1021/acssuschemeng.8b02741	Stone, M. L., E. M. Anderson, K. M. Meek, M. Reed, R. Katahira, F. Chen, R. A. Dixon, G. T. Beckham and Y. Roman-Leshkoy	Reductive Catalytic Fractionation of C-Lignin	ACS Sustainable Chemistry & Engineering
2018	10.1111/tpj.14067	Stranne, M., Y. Ren, L. Fimognari, D. Birdseye, J. Yan, M. Bardor, J.-C. Mollet, T. Komatsu, J. Kikuchi, H. V. Scheller and Y. Sakuragi	TBL10 is required for O-acetylation of pectic rhamnogalacturonan-I in Arabidopsis thaliana	The Plant Journal
2018	10.1111/nph.15076	Strullu-Derrien, C., M. A. Selosse, P. Kenrick and F. M. Martin	The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics	New Phytologist
2018	10.1002/cssc.201701798	Sun, J., D. Liu, R. P. Young, A. G. Cruz, N. G. Isern, T. Schuerg, J. R. Cort, B. A. Simmons and S. Singh	Solubilization and Upgrading of High Polyethylene Terephthalate Loadings in a Low-Costing Bifunctional Ionic Liquid	ChemSusChem
2018	10.1039/C8GC00518D	Sundstrom, E., J. Yaegashi, J. Yan, F. Masson, G. Papa, A. Rodriguez, M. Mirsiaghi, L. Liang, Q. He, D. Tanjore, T. R. Pray, S. Singh, B. Simmons, N. Sun, J. Magnuson and J. Gladden	Demonstrating a separation-free process coupling ionic liquid pretreatment, saccharification, and fermentation with Rhodosporidium toruloides to produce advanced biofuels	Green Chemistry
2018	10.1038/s41467-017-02356-9	Swenson, T. L., U. Karaoz, J. M. Swenson, B. P. Bowen and T. R. Northen	Linking soil biology and chemistry in biological soil crust using isolate exometabolomics	Nature Communications
2018	10.1111/tpj.13988	Takeda, Y., Y. Tobimatsu, S. D. Karlen, T. Koshiba, S. Suzuki, M. Yamamura, S. Murakami, M. Mukai, T. Hattori, K. Osakabe, J. Ralph, M. Sakamoto and T. Umezawa	Downregulation of p-COUMAROYL ESTER 3-HYDROXYLASE in rice leads to altered cell wall structures and improves biomass saccharification	Plant Journal
2018	10.1007/978-3-319-93594-2_9	Taniguchi, M. and A. B. Cousins	Significance of and C4 Cellular Leaf Structure Levels at the Tissue	The Leaf: A Platform for Performing Photosynthesis
2018	10.1002/biot.201700586	Tarasava, K., E. J. Oh, C. A. Eckert and R. T. Gill	CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes	Biotechnology Journal
2018	10.1002/bit.26589	Tarasava, K., R. Liu, A. Garst and R. T. Gill	Combinatorial pathway engineering using type I-E CRISPR interference	Biotechnology and Bioengineering
2018	10.1007/s00572-018-0865-5	Tarkka, M. T., B. Drigo and A. Deveau	Mycorrhizal microbiomes	Mycorrhiza
2018	10.1038/s41467-018-03089-z	Taş, N., E. Prestat, S. Wang, Y. Wu, C. Ulrich, T. Kneafsey, S. G. Tringe, M. S. Torn, S. S. Hubbard and J. K. Jansson	Landscape topography structures the soil microbiome in arctic polygonal tundra	Nature Communications
2018	10.3389/fpls.2018.01250	Taylor, M., C. E. Tornqvist, X. W. Zhao, P. Grabowski, R. Doerge, J. X. Ma, J. Volenec, J. Evans, G. P. Ramstein, M. D. Sanciangco, C. R. Buell, M. D. Casler and Y. W. Jiang	Genome-Wide association study in pseudo-F2 populations of switchgrass identifies genetic loci affecting heading and anthesis dates	Frontiers in Plant Science
2018	10.1371/journal.pone.0204298	Teter, J., S. Yeh, M. Khanna and G. Berndes	Water impacts of U.S. biofuels: Insights from an assessment combining economic and biophysical models	PLOS ONE
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2018	10.1093/bioinformatics/bty445	Tian, M. Y. and J. L. Reed	Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis	Bioinformatics
2018	10.1186/s13068-018-1244-3	Tibocha-Bonilla, J. D., C. Zuniga, R. D. Godoy-Silva and K. Zengler	Advances in metabolic modeling of oleaginous microalgae	Biotechnology for Biofuels
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2018	10.1016/j.apsoil.2018.08.001	Torres-Cruz, T. J., C. Hesse, C. R. Kuske and A. Porras-Alfaro	Presence and distribution of heavy metal tolerant fungi in surface soils of a temperate pine forest	Applied Soil Ecology
2018	10.1111/1365-2745.12919	Treseder, K. K., E. B. Allen, L. M. Egerton-Warburton, M. M. Hart, J. N. Klironomos, H. Maherali and L. Tedersoo	Arbuscular mycorrhizal fungi as mediators of ecosystem responses to nitrogen deposition: A trait-based predictive framework	Journal of Ecology
2018	10.1128/mSystems.00076-18	Trubl, G., H. B. Jang, S. Roux, J. B. Emerson, N. Solonenko, D. R. Vik, L. Solden, J. Ellenbogen, A. T. Runyon, B. Bolduc, B. J. Woodcroft, S. R. Saleska, G. W. Tyson, K. C. Wrighton, M. B. Sullivan and V. I. Rich	Soil viruses are underexplored players in ecosystem carbon processing	mSystems
2018	10.1111/1462-2920.14104	Tsementzi, D., J. Castro Gordillo, M. Mahagna, Y. Gottlieb and K. T. Konstantinidis	Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis	Environmental Microbiology
2018	10.3389/fpls.2018.01799	Tuskan, G. A., A. T. Groover, J. Schmutz , S. P. DiFazio, A. Myburg, D. Grattapaglia, L. B. Smart, T. Yin, J.-M. Aury, A. Kremer, T. Leroy, G. Le Provost, C. Plomion, J. E. Carlson, J. Randall, J. Westbrook, J. Grimwood, W. Muchero, D. Jacobson and J. K. Michener	Hardwood Tree Genomics: Unlocking Woody Plant Biology	Frontiers in Plant Science
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2018	10.1186/s12864-017-4393-z	Ullah, F., M. Hamilton, A. S. N. Reddy and A. Ben-Hur	Exploring the relationship between intron retention and chromatin accessibility in plants	BMC Genomics
2018	10.1038/s41477-018-0222-x	Ulvskov, P. and H. V. Scheller	Cell walls have a new family	Nature Plants
2018	10.1038/s41467-018-04593-y	Valdovinos, F. S., E. L. Berlow, P. M. de Espanes, R. Ramos-Jiliberto, D. P. Vazquez and N. D. Martinez	Species traits and network structure predict the success and impacts of pollinator invasions	Nature Communications
2018	10.1007/s11104-018-3692-8	Veach, A. M., D. Yip, N. L. Engle, Z. K. Yang, A. Bible, J. Morrell-Falvey, T. J. Tschaplinski, U. C. Kalluri and C. W. Schadt	Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants	Plant and Soil
2018	10.1111/cbdd.13110	Velazquez, H. A., D. Riccardi, Z. Xiao, L. D. Quarles, C. R. Yates, J. Baudry and J. C. Smith	Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23	Chemical Biology & Drug Design
2018	10.1021/acssuschemeng.8b05665	Vermaas, J. V., Dellon, L., Broadbelt, L.J., Beckham, G.T., and Crowley, M.F.	Automated transformation of lignin topologies into atomic structures with LigninBuilder	ACS Sustainable Chemistry & Engineering
2018	10.1021/acssuschemeng.8b03794	Villegas Calvo, M., B. Colombo, L. Corno, G. Eisele, C. Cosentino, G. Papa, B. Scaglia, R. Pilu, B. Simmons and F. Adani	Bioconversion of Giant Cane for Integrated Production of Biohydrogen, Carboxylic Acids, and Polyhydroxyalkanoates (PHAs) in a Multistage Biorefinery Approach	ACS Sustainable Chemistry & Engineering
2018	10.1104/pp.18.00584	Voiniciuc, C., K. A. Engle, M. Gunl, S. Dieluweit, M. H. Schmidt, J. Y. Yang, K. W. Moremen, D. Mohnen and B. Usadel	Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage	Plant Physiology
2018	10.1039/C7GC03796A	Vural, D., C. Gainaru, H. O'Neill, Y. Pu, M. D. Smith, J. M. Parks, S. V. Pingali, E. Mamontov, B. H. Davison, A. P. Sokolov, A. J. Ragauskas, J. C. Smith and L. Petridis	Impact of hydration and temperature history on the structure and dynamics of lignin	Green Chemistry
2018	10.1016/j.bpj.2018.02.024	Vural, D., J. C. Smith and H. R. Glyde	Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins	Biophysical Journal
2018	10.1039/C8CP03144D	Vural, D., J. C. Smith and L. Petridis	Dynamics of the lignin glass transition	Physical Chemistry Chemical Physics
2018	10.1128/MRA.01040-18	Walker, C., S. Ryu, H. Na, M. Zane, K. LaButti, A. Lipzen, S. Haridas, K. Barry, I. V. Grigoriev, J. Quarterman, P. Slininger, B. Dien and C. T. Trinh	Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates	Microbiology Resource Announcements
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2018	10.1021/acssynbio.7b00296	Wang, L. and C. D. Maranas	MinGenome: An in silico top-down approach for the synthesis of minimized genomes	ACS Synthetic Biology
2018	10.1042/Bst20170272	Wang, L., C. Y. Ng, S. Dash and C. D. Maranas	Exploring the combinatorial space of complete pathways to chemicals	Biochemical Society Transactions
2018	10.1186/s13007-018-0318-3	Wang, P., L. Y. Guo, R. Jaini, A. Klempien, R. M. McCoy, J. A. Morgan, N. Dudareva and C. Chapple	A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems	Plant Methods
2018	10.1021/acssuschemeng.8b05144	Wang, S., Cheng, G., Dong, J., Tian, T., Lee, T. S., Mukhopadhyay, A., Singer, S. W.	Tolerance Characterization and Isoprenol Production of Adapted Escherichia coli in the Presence of Ionic Liquids	ACS Sustainable Chemistry & Engineering
2018	10.1021/acssuschemeng.7b04908	Wang, S., W. Zhao, T. S. Lee, S. W. Singer, B. A. Simmons, S. Singh, Q. Yuan and G. Cheng	Dimethyl Sulfoxide Assisted Ionic Liquid Pretreatment of Switchgrass for Isoprenol Production	ACS Sustainable Chemistry & Engineering
2018	10.1016/j.ymben.2018.04.001	Wang, X., Q. N. He, Y. F. Yang, J. W. Wang, K. Haning, Y. Hu, B. Wu, M. X. He, Y. P. Zhang, J. Bao, L. M. Contreras and S. H. Yang	Advances and prospects in metabolic engineering of Zymomonas mobilis	Metabolic Engineering
2018	10.1080/10409238.2018.1431201	Wang, Y., H. Ren and H. Zhao	Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production	Critical Reviews in Biochemistry and Molecular Biology
2018	10.1186/s13068-018-1134-8	Wang, Y., S. Zhang, Z. Zhu, H. Shen, X. Lin, X. Jin, X. Jiao and Z. K. Zhao	Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides	Biotechnology for Biofuels
2018	10.1021/acssuschemeng.7b04546	Wang, Y.-Y., M. Li, C. E. Wyman, C. M. Cai and A. J. Ragauskas	Fast Fractionation of Technical Lignins by Organic Cosolvents	ACS Sustainable Chemistry & Engineering
2018	10.1073/pnas.1715530115	Wannier, T. M., A. M. Kunjapur, D. P. Rice, M. J. McDonald, M. M. Desai and G. M. Church	Adaptive evolution of genomically recoded Escherichia coli	Proceedings of the National Academy of Sciences of the United States of America
2018	10.1186/s12934-018-1045-1	Wehrs, M., J.-P. Prahl, J. Moon, Y. Li, D. Tanjore, J. D. Keasling, T. Pray and A. Mukhopadhyay	Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae	Microbial Cell Factories
2018	10.1186/s12934-018-0866-2	Wei, Y. J., D. Bergenholm, M. Gossing, V. Siewers and J. Nielsen	Expression of cocoa genes in Saccharomyces cerevisiae improves cocoa butter production	Microbial Cell Factories
2018	10.3389/fenrg.2018.00030	Weighill, D., P. Jones, M. Shah, P. Ranjan, W. Muchero, J. Schmutz, A. Sreedasyam, D. Macaya-Sanz, R. Sykes, N. Zhao, M. Z. Martin, S. DiFazio, T. J. Tschaplinski, G. Tuskan and D. Jacobson	Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery	Frontiers in Energy Research
2018	10.1186/s13068-018-1095-y	Whitham, J. M., J.-W. Moon, M. Rodriguez, N. L. Engle, D. M. Klingeman, T. Rydzak, M. M. Abel, T. J. Tschaplinski, A. M. Guss and S. D. Brown	Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics	Biotechnology for Biofuels
2018	10.1111/1462-2920.14366	Whitman, T., R. Neurath, A. Perera, I. Chu-Jacoby, D. L. Ning, J. Z. Zhou, P. Nico, J. Pett-Ridge and M. Firestone	Microbial community assembly differs across minerals in a rhizosphere microcosm	Environmental Microbiology
2018	10.1111/gcb.13979	Wieder, W. R., M. D. Hartman, B. N. Sulman, Y. P. Wang, C. D. Koven and G. B. Bonan	Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models	Global Change Biology
2018	10.1021/acssynbio.8b00222	Wiegand, D. J., H. H. Lee, N. Ostrov and G. M. Church	Establishing a cell-free Vibrio natriegens expression system	ACS Synthetic Biology
2018	10.1029/2017jg004298	Wik, M., J. E. Johnson, P. M. Crill, J. P. DeStasio, L. Erickson, M. J. Halloran, M. F. Fahnestock, M. K. Crawford, S. C. Phillips and R. K. Varner	Sediment characteristics and methane ebullition in three subarctic lakes	Journal of Geophysical Research-Biogeosciences
2018	10.1111/1462-2920.14309	Wilhelm, R. C., B. T. Hanson, S. Chandra and E. Madsen	Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater	Environmental Microbiology
2018	10.3390/pr6010007	Wilken, S., M. Saxena, L. R. Petzold and M. A. O'Malley	In Silico identification of microbial partners to form consortia with anaerobic fungi	Processes
2018	10.1016/j.mec.2018.e00073	Williams-Rhaesa, A. M., G. M. Rubinstein, I. M. Scott, G. L. Lipscomb, I. I. F. L. Poole, R. M. Kelly and M. W. W. Adams	Engineering redox-balanced ethanol production in the cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii	Metabolic Engineering Communications
2018	10.1007/s00792-018-1023-x	Williams-Rhaesa, A. M., N. K. Awuku, G. L. Lipscomb, F. L. Poole, G. M. Rubinstein, J. M. Conway, R. M. Kelly and M. W. W. Adams	Native xylose-inducible promoter expands the genetic tools for the biomass-degrading, extremely thermophilic bacterium Caldicellulosiruptor bescii	Extremophiles
2018	10.1038/s41586-018-0338-1	Woodcroft, B. J., C. M. Singleton, J. A. Boyd, P. N. Evans, J. B. Emerson, A. A. F. Zayed, R. D. Hoelzle, T. O. Lamberton, C. K. McCalley, S. B. Hodgkins, R. M. Wilson, S. O. Purvine, C. D. Nicora, C. S. Li, S. Frolking, J. P. Chanton, P. M. Cril, S. R. Saleska, V. I. Rich and G. W. Tyson	Genome-centric view of carbon processing in thawing permafrost	Nature
2018	10.1186/s13068-018-1285-7	Wu, W. Z. and C. T. Maravelias	Synthesis and techno-economic assessment of microbial-based processes for terpenes production	Biotechnology for Biofuels
2018	10.1002/bit.26779	Wu, W. Z., M. R. Long, X. L. Zhang, J. L. Reed and C. T. Maravelias	A framework for the identification of promising bio-based chemicals	Biotechnology and Bioengineering
2018	10.1073/pnas.1720129115	Wu, W., F. Liu and S. Singh	Toward engineering E. coli with an autoregulatory system for lignin valorization	Proceedings of the National Academy of Sciences
2018	10.3389/fmicb.2018.01234	Wu, X., L. Wu, Y. Liu, P. Zhang, Q. Li, J. Zhou, N. J. Hess, T. C. Hazen, W. Yang and R. Chakraborty	Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession	Frontiers in Microbiology
2018	10.1002/pld3.70	Xia, J., Y. Zhao, P. Burks, M. Pauly and P. J. Brown	A sorghum NAC gene is associated with variation in biomass properties and yield potential	Plant Direct
2018	10.1172/JCI93725	Xiao Z, B. J., Cao L, Huang J, Chen H, Yates CR, Li W, Dong B, Waters CM, Smith JC, Quarles LD	Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis	Journal of Clinical Investigation
2018	10.1186/s13068-018-1224-7	Xiao, Y., X. J. He, Y. Ojeda-Lassalle, C. Poovaiah and H. D. Coleman	Expression of a hyperthermophilic endoglucanase in hybrid poplar modifies the plant cell wall and enhances digestibility	Biotechnology for Biofuels
2018	10.3389/fpls.2018.01427	Xie, M., J. Zhang, T. J. Tschaplinski, G. A. Tuskan, J.-G. Chen and W. Muchero	Regulation of Lignin Biosynthesis and Its Role in Growth-Defense Tradeoffs	Frontiers in Plant Science
2018	10.1105/tpc.18.00168	Xie, M., W. Muchero, A. C. Bryan, K. Yee, H.-B. Guo, J. Zhang, T. J. Tschaplinski, V. R. Singan, E. Lindquist, R. S. Payyavula, J. Barros-Rios, R. Dixon, N. Engle, R. W. Sykes, M. Davis, S. S. Jawdy, L. E. Gunter, O. Thompson, S. P. DiFazio, L. M. Evans, K. Winkeler, C. Collins, J. Schmutz, H. Guo, U. Kalluri, M. Rodriguez, K. Feng, J.-G. Chen and G. A. Tuskan	A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus	The Plant Cell
2018	10.3389/fpls.2018.01427	Xie, M., Zhang, J., Tschaplinski, T.J., Tuskan, G.A., Chen, J-G., Muchero, W.	Regulation of lignin biosynthesis and its role in growth-defense tradeoffs	Frontiers in Plant Science
2018	10.1111/1462-2920.13937	Xie, Z.-X., F. Chen, S.-F. Zhang, M.-H. Wang, H. Zhang, L.-F. Kong, M.-H. Dai, H.-S. Hong, L. Lin and D.-Z. Wang	Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea	Environmental Microbiology
2018	10.1021/acssuschemeng.8b01271	Xu, F., J. Sun, M. Wehrs, K. H. Kim, S. S. Rau, A. M. Chan, B. A. Simmons, A. Mukhopadhyay and S. Singh	Biocompatible Choline-Based Deep Eutectic Solvents Enable One-Pot Production of Cellulosic Ethanol	ACS Sustainable Chemistry & Engineering
2018	10.1073/pnas.1717308115	Xu, L., D. Naylor, Z. Dong, T. Simmons, G. Pierroz, K. K. Hixson, Y.-M. Kim, E. M. Zink, K. M. Engbrecht, Y. Wang, C. Gao, S. DeGraaf, M. A. Madera, J. A. Sievert, J. Hollingsworth, D. Birdseye, H. V. Scheller, R. Hutmacher, J. Dahlberg, C. Jansson, J. W. Taylor, P. G. Lemaux and D. Coleman-Derr	Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria	Proceedings of the National Academy of Sciences
2018	10.1007/s00299-018-2253-1	Xu, W., W. Liu, R. Ye, M. Mazarei, D. Huang, X. Zhang and C. N. Stewart	A profilin gene promoter from switchgrass (Panicum virgatum L.) directs strong and specific transgene expression to vascular bundles in rice	Plant Cell Reports
2018	10.1021/acschembio.8b00804	Xu, Y. F., W. Y. Lu, J. C. Chen, S. A. Johnson, P. A. Gibney, D. G. Thomas, G. Brown, A. L. May, S. R. Campagna, A. F. Yakunin, D. Botstein and J. D. Rabinowitz	Discovery and functional characterization of a yeast sugar alcohol phosphatase	ACS Chemical Biology
2018	10.1007/s10570-017-1549-6	Yang H, W. T., Oehme D, Petridis L, Hong M, Kubicki JD	Structural factors affecting 13C NMR chemical shifts of cellulose a computational study	Cellulose
2018	10.1002/bbb.1825	Yang, B., L. Tao and C. E. Wyman	Strengths, challenges, and opportunities for hydrothermal pretreatment in lignocellulosic biorefineries	Biofuels, Bioproducts and Biorefining
2018	10.1093/jxb/erx241	Yang, J. and M. Udvardi	Senescence and nitrogen use efficiency in perennial grasses for forage and biofuel production	Journal of Experimental Botany
2018	10.1186/s13068-018-1116-x	Yang, S. H., J. M. Vera, J. Grass, G. Savvakis, O. V. Moskvin, Y. F. Yang, S. J. McIlwain, Y. C. Lyu, I. Zinonos, A. S. Hebert, J. J. Coon, D. M. Bates, T. K. Sato, S. D. Brown, M. E. Himmel, M. Zhang, R. Landick, K. M. Pappas and Y. P. Zhang	Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032	Biotechnology for Biofuels
2018	10.1186/s13068-018-1087-y	Yao, L., C. G. Yoo, X. Meng, M. Li, Y. Pu, A. J. Ragauskas and H. Yang	A structured understanding of cellobiohydrolase I binding to poplar lignin fractions after dilute acid pretreatment	Biotechnology for Biofuels
2018	10.3389/fenrg.2018.00001	Yao, L., H. Yang, C. G. Yoo, X. Meng, Y. Pu, N. Hao and A. J. Ragauskas	Characteristics of Lignin Fractions from Dilute Acid Pretreated Switchgrass and Their Effect on Cellobiohydrolase from Trichoderma longibrachiatum	Frontiers in Energy Research
2018	10.1016/j.biortech.2018.05.057	Yao, L., H. Yang, C. G. Yoo, Y. Pu, X. Meng, W. Muchero, G. A. Tuskan, T. Tschaplinski and A. J. Ragauskas	Understanding the influences of different pretreatments on recalcitrance of Populus natural variants	Bioresource Technology
2018	10.1186/s12864-018-4964-7	Yin, H. F., H. B. Guo, D. J. Weston, A. M. Borland, P. Ranjan, P. E. Abraham, S. S. Jawdy, J. Wachira, G. A. Tuskan, T. J. Tschaplinski, S. D. Wullschleger, H. Guo, R. L. Hettich, S. M. Gross, Z. Wang, A. Visel and X. H. Yang	Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave	BMC Genomics
2018	10.1002/9781119312994.apr0435	Yin, Y., D. Mohnen, I. Gelineo-Albersheim, Y. Xu and M. G. Hahn	Glycosyltransferases of the GT8 Family	Annual Plant Reviews online
2018	10.1021/acssuschemeng.7b03586	Yoo, C. G., A. Dumitrache, W. Muchero, J. Natzke, H. Akinosho, M. Li, R. W. Sykes, S. D. Brown, B. Davison, G. A. Tuskan, Y. Pu and A. J. Ragauskas	Significance of Lignin S/G Ratio in Biomass Recalcitrance of Populus trichocarpa Variants for Bioethanol Production	ACS Sustainable Chemistry & Engineering
2018	10.1007/s11240-018-1389-6	Yoo, J. H., E. S. Seong, B. K. Ghimire, K. Heo, X. Jin, T. Yamada, L. V. Clark, E. J. Sacks and C. Y. Yu	Establishment of Miscanthus sinensis with decreased lignin biosynthesis by Agrobacterium-mediated transformation using antisense COMT gene	Plant Cell Tissue and Organ Culture
2018	10.1371/journal.pone.0189616	Youngblut, N. D., S. E. Barnett and D. H. Buckley	HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments	PLOS ONE
2018	10.3389/fmicb.2018.00570	Youngblut, N. D., S. E. Barnett and D. H. Buckley	SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments	Frontiers in Microbiology
2018	10.3389/fmicb.2018.02917	Yu, H., D. Susanti, S. E. McGlynn, C. T. Skennerton, K. Chourey, R. Iyer, S. Scheller, P. L. Tavormina, R. L. Hettich, B. Mukhopadhyay and V. J. Orphan	Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea	Frontiers in Microbiology
2018	10.1111/gcb.13820	Yuan, M. M. M., J. Zhang, K. Xue, L. Y. Wu, Y. Deng, J. Deng, L. R. Hale, X. S. Zhou, Z. L. He, Y. F. Yang, J. D. Van Nostrand, E. A. G. Schuur, K. T. Konstantinidis, C. R. Penton, J. R. Cole, J. M. Tiedje, Y. Q. Luo and J. Z. Zhou	Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil	Global Change Biology
2018	10.1021/acssuschemeng.7b04546	Yun-Yan Wang, M. L., Charles E. Wyman, Charles M. Cai, Arthur J. Ragauskas	Fast Fractionation of Technical Lignins by Organic Cosolvents	ACS Sustainable Chemistry & Engineering
2018	10.1016/bs.mie.2018.04.027	Yuzawa, S., A. Zargar, B. Pang, L. Katz and J. D. Keasling	Commodity Chemicals From Engineered Modular Type I Polyketide Synthases	Methods in Enzymology
2018	10.1007/s10295-018-2021-9	Yuzawa, S., T. W. H. Backman, J. D. Keasling and L. Katz	Synthetic biology of polyketide synthases	Journal of Industrial Microbiology and Biotechnology
2018	10.1038/s41579-018-0004-5	Zengler, K. and L. S. Zaramela	The social network of microorganisms - how auxotrophies shape complex communities	Nature Reviews Microbiology
2018	10.1038/s41564-018-0129-3	Zhalnina, K., K. B. Louie, Z. Hao, N. Mansoori, U. N. da Rocha, S. J. Shi, H. J. Cho, U. Karaoz, D. Loque, B. P. Bowen, M. K. Firestone, T. R. Northen and E. L. Brodie	Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly	Nature Microbiology
2018	10.1128/mBio.01175-18	Zhalnina, K., K. Zengler, D. Newman and T. R. Northen	Need for laboratory ecosystems to unravel the structures and functions of soil microbial communities mediated by chemistry	mBio
2018	10.1111/nph.15113	Zhang, F., G. E. Anasontzis, A. Labourel, C. Champion, M. Haon, M. Kemppainen, C. Commun, A. Deveau, A. Pardo, C. Veneault-Fourrey, A. Kohler, M. N. Rosso, B. Henrissat, J. G. Berrin and F. Martin	The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted beta-1,4 endoglucanase that plays a key role in symbiosis development	New Phytologist
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2018	10.1039/C8SE00471D	Zhang, J., Li, M., Bryan, A.C., Yoo, C.G., Rottmann, W., Winkeler, K.A., Collins, C.M., Singan, V., Lindquist, E.A., Jawdy, S.S., Gunter, L.E., Engle, N.L., Yang, X., Barry, K., Tschaplinski, T.J., Schmutz, J., Pu, Y., Ragauskas, A.J., Tuskan, G.A., Muche	Overexpression of a serine hydroxymethyltransferase increases biomass production and reduces recalcitrance in the bioenergy crop Populus	Sustainable Energy and Fuels
2018	10.3389/fpls.2018.01535	Zhang, J., Xie, M., Tuskan, G.A., Muchero, W., and Chen, J-G.	Recent advances in the transcriptional regulation of secondary cell wall biosynthesis in the woody plants	Frontiers in Plant Science
2018	10.1111/nph.15297	Zhang, J., Y. Yang, K. Zheng, M. Xie, K. Feng, S. S. Jawdy, L. E. Gunter, P. Ranjan, V. R. Singan, N. Engle, E. Lindquist, K. Barry, J. Schmutz, N. Zhao, T. J. Tschaplinski, J. LeBoldus, G. A. Tuskan, J.-G. Chen and W. Muchero	Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus	New Phytologist
2018	10.1007/s12155-017-9878-8	Zhang, L., T. E. Juenger, J. M. Osorio and K. D. Behrman	Sensitivity analysis of the APEX model for assessing sustainability of switchgrass grown for biofuel production in central Texas	BioEnergy Research
2018	10.1038/s41467-018-04513-0	Zhang, M., C. Gao, X. Guo, S. Guo, Z. Kang, D. Xiao, J. Yan, F. Tao, W. Zhang, W. Dong, P. Liu, C. Yang, C. Ma and P. Xu	Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving l-2-hydroxyglutarate	Nature Communications
2018	10.1111/gcbb.12533	Zhang, Y. P., L. G. Oates, J. Serate, D. Xie, E. Pohlmann, Y. V. Bukhman, S. D. Karlen, M. K. Young, A. Higbee, D. Eilert, G. R. Sanford, J. S. Piotrowski, D. Cavalier, J. Ralph, J. J. Coon, T. K. Sato and R. G. Ong	Diverse lignocellulosic feedstocks can achieve high field-scale ethanol yields while providing flexibility for the biorefinery and landscape-level environmental benefits	Global Change Biology Bioenergy
2018	10.1371/journal.pone.0195143	Zheng, T., A. A. Lanahan, L. R. Lynd and D. G. Olson	The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum	PLOS ONE
2018	10.1038/s41593-018-0125-1	Zheng, Y., W. Shen, J. Zhang, B. Yang, Y.-N. Liu, H. Qi, X. Yu, S.-Y. Lu, Y. Chen, Y.-Z. Xu, Y. Li, F. H. Gage, S. Mi and J. Yao	CRISPR interference-based specific and efficient gene inactivation in the brain	Nature Neuroscience
2018	10.1038/s41560-018-0197-x	Zhou, Y. J., E. J. Kerkhoven and J. Nielsen	Barriers and opportunities in bio-based production of hydrocarbons	Nature Energy
2018	10.1007/s10681-018-2137-z	Zhu, F., C. M. Wai, J. S. Zhang, T. C. Jones, C. Nagai and R. Ming	Differential expression of hormone related genes between extreme segregants of a Saccharum interspecific F2 population	Euphytica
2018	10.1186/s13068-018-1049-4	Zhu, Y., L. Xie, G. Q. Chen, M. Y. Lee, D. Loque and H. V. Scheller	A transgene design for enhancing oil content in Arabidopsis and Camelina seeds	Biotechnology for Biofuels
2018	10.1104/pp.17.00605	Zuniga, C., J. Levering, M. R. Antoniewicz, M. T. Guarnieri, M. J. Betenbaugh and K. Zengler	Predicting dynamic metabolic demands in the photosynthetic eukaryote Chlorella vulgaris	Plant Physiology
2018	10.1186/s13068-018-1167-z	Zuo, C., M. Blow, A. Sreedasyam, R. C. Kuo, G. K. Ramamoorthy, I. Torres-Jerez, G. Li, M. Wang, D. Dilworth, K. Barry, M. Udvardi, J. Schmutz, Y. Tang and Y. Xu	Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing	Biotechnology for Biofuels
2017	10.1111/1751-7915.12463	Adams, M. W. W. and R. M. Kelly	The renaissance of life near the boiling point - at last, genetics and metabolic engineering	Microbial biotechnology
2017	10.1021/acssuschemeng.7b01203	Akinosho, H. O., C. G. Yoo, A. Dumitrache, J. Natzke, W. Muchero, S. D. Brown and A. J. Ragauskas	Elucidating the Structural Changes to Populus Lignin during Consolidated Bioprocessing with Clostridium thermocellum	ACS Sustainable Chemistry & Engineering
2017	10.1021/acssuschemeng.7b00449	Akinosho, H., A. Dumitrache, J. Natzke, W. Muchero, S. S. Jawdy, G. A. Tuskan, S. D. Brown and A. J. Ragauskas	Effects of Biomass Accessibility and Klason Lignin Contents during Consolidated Bioprocessing in Populus trichocarpa	ACS Sustainable Chemistry & Engineering
2017	10.1002/slct.201701572	Akinosho, H., K. Yee, M. Rodriguez, W. Muchero, C. G. Yoo, M. Li, O. Thompson, Y. J. Pu, S. D. Brown, J. R. Mielenz and A. J. Ragauskas	Lignin Exhibits Recalcitrance-Associated Features Following the Consolidated Bioprocessing of Populus trichocarpa Natural Variants
2017	10.1002/cpmc.37	Allen, B., M. Drake, N. Harris and T. Sullivan	Using KBase to Assemble and Annotate Prokaryotic Genomes	Current Protocols in Microbiology
2017	10.1016/j.soilbio.2017.01.001	Allison, S. D. and M. L. Goulden	Consequences of drought tolerance traits for microbial decomposition in the DEMENT model	Soil Biology and Biochemistry
2017	10.1371/journal.pone.0189604	Amaike Campen, S., J. Lynn, S. J. Sibert, S. Srikrishnan, P. Phatale, T. Feldman, J. M. Guenther, J. Hiras, Y. T. A. Tran, S. W. Singer, P. D. Adams, K. L. Sale, B. A. Simmons, S. E. Baker, J. K. Magnuson and J. M. Gladden	Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger	PLOS ONE
2017	10.1038/s41467-017-01753-4	Angle, J. C., T. H. Morin, L. M. Solden, A. B. Narrowe, G. J. Smith, M. A. Borton, C. Rey-Sanchez, R. A. Daly, G. Mirfenderesgi, D. W. Hoyt, W. J. Riley, C. S. Miller, G. Bohrer and K. C. Wrighton	Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions	Nature Communications
2017	10.1016/j.jprot.2017.06.004	Aryal, U. K., Z. McBride, D. Chen, J. Xie and D. B. Szymanski	Analysis of protein complexes in Arabidopsis leaves using size exclusion chromatography and label-free protein correlation profiling	J Proteomics
2017	10.3791/55971	Aufrecht, J. A., J. M. Ryan, S. Hasim, D. P. Allison, A. Nebenfuhr, M. J. Doktycz and S. T. Retterer	Imaging the Root Hair Morphology of Arabidopsis Seedlings in a Two-layer Microfluidic Platform	Journal of Visualized Experiments
2017	10.1016/j.plantsci.2017.07.007	Aznar-Moreno, J. A. and T. P. Durrett	Review: Metabolic engineering of unusual lipids in the synthetic biology era	Plant Science
2017	10.1039/C6EE03748H	Balch, M. L., E. K. Holwerda, M. F. Davis, R. W. Sykes, R. M. Happs, R. Kumar, C. E. Wyman and L. R. Lynd	Lignocellulose fermentation and residual solids characterization for senescent switchgrass fermentation by Clostridium thermocellum in the presence and absence of continuous in situ ball-milling	Energy & Environmental Science
2017	10.1016/j.bbagrm.2016.09.003	Banf, M. and S. Y. Rhee	Computational inference of gene regulatory networks: Approaches, limitations and opportunities	Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
2017	10.1038/srep41174	Banf, M. and S. Y. Rhee	Enhancing gene regulatory network inference through data integration with markov random fields	Scientific Reports
2017	10.1021/acschembio.6b00890	Baran, R., R. Lau, B. P. Bowen, S. Diamond, N. Jose, F. Garcia-Pichel and T. R. Northen	Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D2O) Stable Isotope Probing	ACS Chemical Biology
2017	10.1016/j.cell.2017.10.034	Barbieri, E. M., P. Muir, B. O. Akhuetie-Oni, C. M. Yellman and F. J. Isaacs	Precise editing at DNA replication forks enables multiplex genome engineering in eukaryotes	Cell
2017	10.1128/aem.03389-16	Becker, S., A. Scheffel, M. F. Polz and J.-H. Hehemann	Accurate quantification of laminarin in marine organic matter with enzymes from marine microbes	Applied and Environmental Microbiology
2017	10.1016/j.carbpol.2016.11.085	Bhagia, S., R. Kumar and C. E. Wyman	Effects of dilute acid and flowthrough pretreatments and BSA supplementation on enzymatic deconstruction of poplar by cellulase and xylanase	Carbohydrate Polymers
2017	10.1186/s13068-017-0866-1	Biswal, A. K., L. Tan, M. A. Atmodjo, J. DeMartini, I. Gelineo-Albersheim, K. Hunt, I. M. Black, S. S. Mohanty, D. Ryno, C. E. Wyman and D. Mohnen	Comparison of four glycosyl residue composition methods for effectiveness in detecting sugars from cell walls of dicot and grass tissues	Biotechnology for Biofuels
2017	10.1186/s13068-016-0684-x	Biswas, R., C. M. Wilson, R. J. Giannone, D. M. Klingeman, T. Rydzak, M. B. Shah, R. L. Hettich, S. D. Brown and A. M. Guss	Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism	Biotechnology for Biofuels
2017	10.1007/978-3-319-66365-4_1	Blaby, I. K. and C. E. Blaby-Haas	Genomics and Functional Genomics in Chlamydomonas reinhardtii	Chlamydomonas: Molecular Genetics and Physiology
2017	10.1016/j.pbi.2017.06.005	Blaby-Haas, C. E. and S. S. Merchant	Regulating cellular trace metal economy in algae	Current Opinion in Plant Biology
2017	10.1128/microbiolspec.FUNK-0081-2016	Blackwell, M.	Made for Each Other: Ascomycete Yeasts and Insects	Microbiology Spectrum
2017	10.1038/nature24627	Blees, A., D. Januliene, T. Hofmann, N. Koller, C. Schmidt, S. Trowitzsch, A. Moeller and R. Tampe	Structure of the human MHC-I peptide-loading complex	Nature
2017	10.1111/1751-7915.12494	Blumer-Schuette, S. E., J. V. Zurawski, J. M. Conway, P. Khatibi, D. L. Lewis, Q. Li, V. L. Chiang and R. M. Kelly	Caldicellulosiruptor saccharolyticus transcriptomes reveal consequences of chemical pretreatment and genetic modification of lignocellulose	Microbial Biotechnology
2017	10.7717/peerj.3243	Bolduc, B., H. B. Jang, G. Doulcier, Z. Q. You, S. Roux and M. B. Sullivan	vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria	PeerJ
2017	10.1038/ismej.2016.89	Bolduc, B., K. Youens-Clark, S. Roux, B. L. Hurwitz and M. B. Sullivan	iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure	ISME Journal
2017	10.1016/j.cbpa.2017.10.013	Bomble, Y. J., C.-Y. Lin, A. Amore, H. Wei, E. K. Holwerda, P. N. Ciesielski, B. S. Donohoe, S. R. Decker, L. R. Lynd and M. E. Himmel	Lignocellulose deconstruction in the biosphere	Current Opinion in Chemical Biology
2017	10.1080/00275514.2016.1271689	Bonito, G., K. Hameed, M. Toome-Heller, R. Healy, C. Reid, H. L. Liao, M. C. Aime, C. Schadt and R. Vilgalys	Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from the Populus root microbiome	Mycologia
2017	10.1038/srep46249	Bordbar, A., J. T. Yurkovich, G. Paglia, O. Rolfsson, O. E. Sigurjonsson and B. O. Palsson	Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics	Scientific Reports
2017	10.1073/pnas.1703088114	Brawley, S. H., N. A. Blouin, E. Ficko-Blean, G. L. Wheeler, M. Lohr, H. V. Goodson, J. W. Jenkins, C. E. Blaby-Haas, K. E. Helliwell, C. X. Chan, T. N. Marriage, D. Bhattacharya, A. S. Klein, Y. Badis, J. Brodie, Y. Cao, J. Collen, S. M. Dittami, C. M. M. Gachon, B. R. Green, S. J. Karpowicz, J. W. Kim, U. J. Kudahl, S. Lin, G. Michel, M. Mittag, B. Olson, J. L. Pangilinan, Y. Peng, H. Qiu, S. Shu, J. T. Singer, A. G. Smith, B. N. Sprecher, V. Wagner, W. Wang, Z. Y. Wang, J. Yan, C. Yarish, S. Zauner-Riek, Y. Zhuang, Y. Zou, E. A. Lindquist, J. Grimwood, K. W. Barry, D. S. Rokhsar, J. Schmutz, J. W. Stiller, A. R. Grossman and S. E. Prochnik	Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)	Proceedings of the National Academy of Sciences of the United States of America
2017	10.1186/s13068-016-0687-7	Bredeweg, E. L., K. R. Pomraning, Z. Y. Dai, J. Nielsen, E. J. Kerkhoven and S. E. Baker	A molecular genetic toolbox for Yarrowia lipolytica	Biotechnology for Biofuels
2017	10.1021/acs.est.6b04591	Breunig, H. M., L. Jin, A. Robinson and C. D. Scown	Bioenergy Potential from Food Waste in California	Environmental Science & Technology
2017	10.1038/s41598-017-08985-w	Brunecky, R., B. S. Donohoe, J. M. Yarbrough, A. Mittal, B. R. Scott, H. Ding, L. E. Taylor Ii, J. F. Russell, D. Chung, J. Westpheling, S. A. Teter, M. E. Himmel and Y. J. Bomble	The Multi Domain Caldicellulosiruptor bescii CelA Cellulase Excels at the Hydrolysis of Crystalline Cellulose	Scientific Reports
2017	10.1186/s13068-017-0951-5	Brunecky, R., M. Alahuhta, D. W. Sammond, Q. Xu, M. Chen, D. B. Wilson, J. W. Brady, M. E. Himmel, Y. J. Bomble and V. V. Lunin	Natural diversity of glycoside hydrolase family 48 exoglucanases: insights from structure	Biotechnology for Biofuels
2017	10.1007/7397_2016_30	Brunner, A. M., E. Varkonyi-Gasic and R. C. Jones	Phase Change And Phenology In Trees	Comparative and Evolutionary Genomics of Angiosperm Trees
2017	10.1016/j.tibtech.2017.08.011	Campbell, K., J. Xia and J. Nielsen	The Impact of Systems Biology on Bioprocessing	Trends in Biotechnology
2017	10.1038/srep44150	Cao, H., D. Wei, Y. Yang, Y. Shang, G. Li, Y. Zhou, Q. Ma and Y. Xu	Systems-level understanding of ethanol-induced stresses and adaptation in E. coli	Scientific Reports
2017	10.1093/gbe/evx174	Carlson, C. H., Y. Choi, A. P. Chan, M. J. Serapiglia, C. D. Town and L. B. Smart	Dominance and sexual dimorphism pervade the Salix purpurea L. transcriptome	Genome Biology and Evolution
2017	10.1101/160747	Cecil, J. H. and J. K. Michener	Rapid, parallel identification of pathways for catabolism of lignin-derived aromatic compounds	bioRxiv
2017	10.1186/s40793-017-0233-7	Chakraborty, R., H. Woo, P. Dehal, R. Walker, M. Zemla, M. Auer, L. A. Goodwin, A. Kazakov, P. Novichkov, A. P. Arkin and T. C. Hazen	Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site	Standards in Genomic Sciences
2017	10.1021/acs.estlett.6b00460	Chen H, J. R., Mann BF, Chu RK, Tolic N, Parks JM, Gu B	Identification of Mercury and Dissolved Organic Matter Complexes Using Ultrahigh Resolution Mass Spectrometry	Environmental Science & Technology Letters
2017	10.1038/srep43925	Chen, X., W.-C. Chou, Q. Ma and Y. Xu	SeqTU: A Web Server for Identification of Bacterial Transcription Units	Scientific Reports
2017	10.1038/ismej.2017.48	Cheng, L., N. F. Zhang, M. T. Yuan, J. Xiao, Y. J. Qin, Y. Deng, Q. C. Tu, K. Xue, J. D. Van Nostrand, L. Y. Wu, Z. L. He, X. H. Zhou, M. B. Leigh, K. T. Konstantinidis, E. A. G. Schuur, Y. Q. Luo, J. M. Tiedje and J. Z. Zhou	Warming enhances old organic carbon decomposition through altering functional microbial communities	ISME Journal
2017	10.1371/journal.pone.0176085	Choi, J., A. Rajagopal, Y. F. Xu, J. D. Rabinowitz and E. K. O'Shea	A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae	PLOS ONE
2017	10.1186/s13068-017-0849-2	Choi, J., D. M. Klingeman, S. D. Brown and C. D. Cox	The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum	Biotechnology for Biofuels
2017	10.1016/B978-0-12-803725-6.00010-8	Chow, N. and J. D. Wu	The Cellulosome: A supramolecular assembly of microbial biomass-degrading enzymes	Biotechnology of Microbial Enzymes
2017	10.1371/journal.pone.0178650	Chowdhary, J., F. E. Loffler and J. C. Smith	Community detection in sequence similarity networks based on attribute clustering	PLOS ONE
2017	10.1128/aem.03034-16	Christensen, D. G., J. S. Orr, C. V. Rao and A. J. Wolfe	Increasing Growth yield and decreasing acetylation in Escherichia coli by optimizing the carbon-to-magnesium ratio in peptide-based media	Applied and Environmental Microbiology
2017	10.1128/mBio.02045-16	Chu, N. D., S. A. Clarke, S. Timberlake, M. F. Polz, A. D. Grossman and E. J. Alm	A Mobile Element in mutS Drives Hypermutation in a Marine Vibrio	mBio
2017	10.1128/jb.00827-16	Chubiz, L. M. and C. J. Marx	Growth trade-offs accompany the emergence of glycolytic metabolism in Shewanella oneidensis MR-1	Journal of Bacteriology
2017	10.1038/npjsba.2016.35	Chubukov, V., J. J. Desmarais, G. Wang, L. J. G. Chan, E. E. K. Baidoo, C. J. Petzold, J. D. Keasling and A. Mukhopadhyay	Engineering glucose metabolism of Escherichia coli under nitrogen starvation	npj Systems Biology and Applications
2017	10.1016/j.jaridenv.2017.03.005	Chung, Y. A., R. L. Sinsabaugh, C. R. Kuske, S. C. Reed and J. A. Rudgers	Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass	Journal of Arid Environments
2017	10.1111/1755-0998.12639	Clark, L. V. and A. D. Schreier	Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables	Molecular Ecology Resources
2017	10.1016/j.chroma.2017.02.028	Cocuron, J. C., E. Tsogtbaatar and A. P. Alonso	High-throughput quantification of the levels and labeling abundance of free amino acids by liquid chromatography tandem mass spectrometry	Journal of Chromatography A
2017	10.1371/journal.pbio.2002860	Cole, B. J., M. E. Feltcher, R. J. Waters, K. M. Wetmore, T. S. Mucyn, E. M. Ryan, G. Y. Wang, S. Ul-Hasan, M. McDonald, Y. Yoshikuni, R. R. Malmstrom, A. M. Deutschbauer, J. L. Dang and A. Visel	Genome-wide identification of bacterial plant colonization genes	PLOS Biology
2017	10.1016/j.meteno.2017.07.002	Comer, A. D., M. R. Long, J. L. Reed and B. F. Pfleger	Flux balance analysis indicates that methane is the lowest cost feedstock for microbial cell factories	Metabolic Engineering Communications
2017	10.1128/AEM.01828-17	Conway, J. M., B. S. McKinley, N. L. Seals, D. Hernandez, P. A. Khatibi, S. Poudel, R. J. Giannone, R. L. Hettich, A. M. Williams-Rhaesa, G. L. Lipscomb, M. W. W. Adams and R. M. Kelly	Functional Analysis of the Glucan Degradation Locus in Caldicellulosiruptor bescii Reveals Essential Roles of Component Glycoside Hydrolases in Plant Biomass Deconstruction	Applied and Environmental Microbiology
2017	10.1088/1361-648X/aa4e68	Cortini R, C. X., Smith JC, and Kornyshev AA	The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations	Journal of Physics: Condensed Matter
2017	10.1002/wsbm.1377	Counts, J. A., B. M. Zeldes, L. L. Lee, C. T. Straub, M. W. W. Adams and R. M. Kelly	Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms	WIREs Systems Biology and Medicine
2017	10.1128/genomeA.00653-17	Crofts, T. S., B. Wang, A. Spivak, T. A. Gianoulis, K. J. Forsberg, M. K. Gibson, L. A. Johnsky, S. M. Broomall, C. N. Rosenzweig, E. W. Skowronski, H. S. Gibbons, M. O. A. Sommer and G. Dantas	Draft Genome Sequences of Three ?-Lactam-Catabolizing Soil Proteobacteria	Genome Announcements
2017	10.1371/journal.pone.0172135	Cuvelier, M. L., J. Guo, A. C. Ortiz, M. J. Van Baren, M. A. Tariq, F. Partensky and A. Z. Worden	Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress	PLOS ONE
2017	10.1111/nph.14306	da Costa, R. M. F., S. Pattathil, U. Avci, S. J. Lee, S. P. Hazen, A. Winters, M. G. Hahn and M. Bosch	A cell wall reference profile for Miscanthus bioenergy crops highlights compositional and structural variations associated with development and organ origin	New Phytologist
2017	10.1186/s12864-017-4114-7	Daguerre, Y., E. Levati, J. Ruytinx, E. Tisserant, E. Morin, A. Kohler, B. Montanini, S. Ottonello, A. Brun, C. Veneault-Fourrey and F. Martin	Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor	BMC Genomics
2017	10.1074/jbc.M116.774588	Dajnowicz S, P. J., Hu X, Gesler K, Kovalevsky AY, Mueser TC	Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5?-phosphate in aspartate aminotransferase	Journal of Biological Chemistry
2017	10.1016/j.vaccine.2016.11.065	Dale, J. B., P. R. Smeesters, H. S. Courtney, T. A. Penfound, C. M. Hohn, J. C. Smith and J. Y. Baudry	Structure-based design of broadly protective group a streptococcal M protein-based vaccines	Vaccine
2017	10.1039/C7OB02605F	Dallabernardina, P., C. Ruprecht, P. J. Smith, M. G. Hahn, B. R. Urbanowicz and F. Pfrengle	Automated glycan assembly of galactosylated xyloglucan oligosaccharides and their recognition by plant cell wall glycan-directed antibodies	Organic & Biomolecular Chemistry
2017	10.1186/s13068-017-0700-9	Daly, P., J. M. van Munster, M. J. Blythe, R. Ibbett, M. Kokolski, S. Gaddipati, E. Lindquist, V. R. Singan, K. W. Barry, A. Lipzen, C. Y. Ngan, C. J. Petzold, L. J. G. Chan, S. T. Pullan, S. Delmas, P. R. Waldron, I. V. Grigoriev, G. A. Tucker, B. A. Simmons and D. B. Archer	Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments	Biotechnology for Biofuels
2017	10.1093/femsyr/fox076	D'Ambrosio, V. and M. K. Jensen	Lighting up yeast cell factories by transcription factor-based biosensors	FEMS Yeast Research
2017	10.1111/tpj.13413	Dash, M., Y. S. Yordanov, T. Georgieva, T. J. Tschaplinski, E. Yordanova and V. Busov	Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress	Plant Journal
2017	10.1186/s13068-017-0792-2	Dash, S., A. Khodayari, J. Zhou, E. K. Holwerda, D. G. Olson, L. R. Lynd and C. D. Maranas	Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations	Biotechnology for Biofuels
2017	10.1016/j.protis.2016.10.005	Davis, A., R. Abbriano, S. R. Smith and M. Hildebrand	Clarification of photorespiratory processes and the role of malic enzyme in diatoms	Protist
2017	10.1038/nchembio.2471	de Rond, T., P. Stow, I. Eigl, R. E. Johnson, L. J. G. Chan, G. Goyal, E. E. K. Baidoo, N. J. Hillson, C. J. Petzold, R. Sarpong and J. D. Keasling	Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme	Nature Chemical Biology
2017	10.1111/gcbb.12407	DeBruyn, J. M., D. A. Bevard, M. E. Essington, J. Y. McKnight, S. M. Schaeffer, H. L. Baxter, M. Mazarei, D. G. J. Mann, R. A. Dixon, F. Chen, C. Zhuo, Z.-Y. Wang and C. N. Stewart Jr	Field-grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential	GCB Bioenergy
2017	10.1016/j.ymben.2017.03.002	Degreif, D., T. de Rond, A. Bertl, J. D. Keasling and I. Budin	Lipid engineering reveals regulatory roles for membrane fluidity in yeast flocculation and oxygen-limited growth	Metabolic Engineering
2017	10.1021/acssynbio.7b00192	DeLorenzo, D. M., W. R. Henson and T. S. Moon	Development of chemical and metabolite sensors for Rhodococcus opacus PD630	ACS Synthetic Biology
2017	10.1002/2016ms000817	Deng, J., C. K. McCalley, S. Frolking, J. Chanton, P. Crill, R. Varner, G. Tyson, V. Rich, M. Hines, S. R. Saleska and C. S. Li	Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling	Journal of Advances in Modeling Earth Systems
2017	10.1073/pnas.1700764114	Diner, R. E., C. M. Nodding, N. C. Lian, A. K. Kang, J. B. McQuaid, J. Jablanovic, J. L. Espinoza, N. A. Nguyen, M. A. Anzelmatti, J. Jansson, V. A. Bielinski, B. J. Karas, C. L. Dupont, A. E. Allen and P. D. Weyman	Diatom centromeres suggest a mechanism for nuclear DNA acquisition	Proceedings of the National Academy of Sciences of the United States of America
2017	10.1099/ijsem.0.002202	Dobritsa, A. P., E. V. Linardopoulou and M. Samadpour	Transfer of 13 species of the genus Burkholderia to the genus Caballeronia and reclassification of Burkholderia jirisanensis as Paraburkholderia jirisanensis comb. nov	International Journal of Systematic and Evolutionary Microbiology
2017	10.1111/1462-2920.13670	Dore, J., A. Kohler, A. Dubost, H. Hundley, V. Singan, Y. Peng, A. Kuo, I. V. Grigoriev, F. Martin, R. Marmeisse and G. Gay	The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation	Environmental Microbiology
2017	10.1371/journal.pone.0174345	Douglas, S. M., L. M. Chubiz, W. R. Harcombe and C. J. Marx	Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation	PLOS ONE
2017	10.1039/C7GC00346C	Dumitrache, A., A. Tolbert, J. Natzke, S. D. Brown, B. H. Davison and A. J. Ragauskas	Cellulose and lignin colocalization at the plant cell wall surface limits microbial hydrolysis of Populus biomass	Green Chemistry
2017	10.1038/srep43583	Dumitrache, A., D. M. Klingeman, J. Natzke, M. Rodriguez Jr, R. J. Giannone, R. L. Hettich, B. H. Davison and S. D. Brown	Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells	Scientific Reports
2017	10.1111/pbi.12666	Dumitrache, A., J. Natzke, M. Rodriguez Jr, K. L. Yee, O. A. Thompson, C. R. Poovaiah, H. Shen, M. Mazarei, H. L. Baxter, C. Fu, Z.-Y. Wang, A. K. Biswal, G. Li, A. C. Srivastava, Y. Tang, C. N. Stewart Jr, R. A. Dixon, R. S. Nelson, D. Mohnen, J. Mielenz, S. D. Brown and B. H. Davison	Transgenic switchgrass (Panicum virgatum L.) targeted for reduced recalcitrance to bioconversion: a 2-year comparative analysis of field-grown lines modified for target gene or genetic element expression	Plant Biotechnology Journal
2017	10.1021/acssuschemeng.7b02123	Dutta, T., N. G. Isern, J. Sun, E. Wang, S. Hull, J. R. Cort, B. A. Simmons and S. Singh	Survey of Lignin-Structure Changes and Depolymerization during Ionic Liquid Pretreatment	ACS Sustainable Chemistry & Engineering
2017	10.3389/fmicb.2017.01657	Edwards, J. E., R. J. Forster, T. M. Callaghan, V. Dollhofer, S. S. Dagar, Y. F. Cheng, J. Chang, S. Kittelmann, K. Fliegerova, A. K. Puniya, J. K. Henske, S. P. Gilmore, M. A. O'Malley, G. W. Griffith and H. Smidt	PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: Insights, challenges and opportunities	Frontiers in Microbiology
2017	10.1093/jxb/erx185	Ellsworth, P. Z., P. V. Ellsworth and A. B. Cousins	Relationship of leaf oxygen and carbon isotopic composition with transpiration efficiency in the C4 grasses Setaria viridis and Setaria italica	Journal of Experimental Botany
2017	10.1186/s12859-017-1478-2	Erbilgin, O., B. P. Bowen, S. M. Kosina, S. Jenkins, R. K. Lau and T. R. Northen	Dynamic substrate preferences predict metabolic properties of a simple microbial consortium	BMC Bioinformatics
2017	10.1038/nature21056	Esteva, A., B. Kuprel, R. A. Novoa, J. Ko, S. M. Swetter, H. M. Blau and S. Thrun	Dermatologist-level classification of skin cancer with deep neural networks	Nature
2017	10.1111/nph.14154	Fahrenkrog, A. M., L. G. Neves, M. F. R. Resende Jr, A. I. Vazquez, G. de los Campos, C. Dervinis, R. Sykes, M. Davis, R. Davenport, W. B. Barbazuk and M. Kirst	Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides	New Phytologist
2017	10.1002/ece3.3466	Fahrenkrog, A. M., L. G. Neves, M. F. R. Resende Jr, C. Dervinis, R. Davenport, W. B. Barbazuk and M. Kirst	Population genomics of the eastern cottonwood (Populus deltoides)	Ecology and Evolution
2017	10.1073/pnas.1702581114	Fang, X., A. Sastry, N. Mih, D. Kim, J. Tan, J. T. Yurkovich, C. J. Lloyd, Y. Gao, L. Yang and B. O. Palsson	Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities	Proceedings of the National Academy of Sciences of the United States of America
2017	10.1038/s41598-017-00234-4	Farahi, R. H., A. M. Charrier, A. Tolbert, A. L. Lereu, A. Ragauskas, B. H. Davison and A. Passian	Plasticity, elasticity, and adhesion energy of plant cell walls: nanometrology of lignin loss using atomic force microscopy	Scientific Reports
2017	10.1016/j.mbs.2016.08.004	Faraji, M. and E. O. Voit	Nonparametric dynamic modeling	Mathematical Biosciences
2017	10.1093/bioinformatics/btx126	Faraji, M. and E. O. Voit	Stepwise inference of likely dynamic flux distributions from metabolic time series data	Bioinformatics
2017	10.3390/pr5040061	Faraji, M. and E. O. Voit	Improving Bioenergy Crops through Dynamic Metabolic Modeling	Processes
2017	10.1007/s10681-017-2068-0	Felderhoff, T. J., J. W. Olmstead and W. Vermerris	A cost-benefit analysis to select the most effective method for positional cloning: genotyping by sequencing versus allele-specific PCR	Euphytica
2017	10.1371/journal.pgen.1006841	Feldman, M. J., R. E. Paul, D. Banan, J. F. Barrett, J. Sebastian, M.-C. Yee, H. Jiang, A. E. Lipka, T. P. Brutnell, J. R. Dinneny, A. D. B. Leakey and I. Baxter	Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria	PLOS Genetics
2017	10.1111/gcb.13755	Feng, W. T., J. Y. Liang, L. E. Hale, C. G. Jung, J. Chen, J. Z. Zhou, M. G. Xu, M. T. Yuan, L. Y. Wu, R. Bracho, E. Pegoraro, E. A. G. Schuur and Y. Q. Luo	Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming	Global Change Biology
2017	10.1016/j.jes.2016.10.005	Fernandez-Bayo, J. D., J. Toniato, B. A. Simmons and C. W. Simmons	Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer	Journal of Environmental Sciences
2017	10.1016/j.cub.2017.03.003	Floss, D. S., S. K. Gomez, H. J. Park, A. M. MacLean, L. M. Muller, K. K. Bhattarai, V. Levesque-Tremblay, I. E. Maldonado-Mendoza and M. J. Harrison	A transcriptional program for arbuscule degeneration during AM symbiosis is regulated by MYB1	Current Biology
2017	10.1111/nph.14279	Fochi, V., W. Chitarra, A. Kohler, S. Voyron, V. R. Singan, E. A. Lindquist, K. W. Barry, M. Girlanda, I. V. Grigoriev, F. Martin, R. Balestrini and S. Perotto	Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas	New Phytologist
2017	10.1111/1462-2920.13706	Freedman, A. J. E., B. Tan and J. R. Thompson	Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir	Environmental Microbiology
2017	10.1128/aem.03035-16	Fritts, R. K., B. LaSarre, A. M. Stoner, A. L. Posto and J. B. McKinlay	A Rhizobiales-specific unipolar polysaccharide adhesin contributes to Rhodopseudomonas palustris Biofilm formation across diverse photoheterotrophic conditions	Applied and Environmental Microbiology
2017	10.1021/jacs.6b10727	Fu, D., W. L. Yang and X. L. S. Xie	Label-free Imaging of Neurotransmitter Acetylcholine at Neuromuscular Junctions with Stimulated Raman Scattering	Journal of the American Chemical Society
2017	10.1086/692439	Fukami, T., M. Nakajima, C. Fortunel, P. V. A. Fine, C. Baraloto, S. E. Russo and K. G. Peay	Geographical variation in community divergence: Insights from tropical forest monodominance by ectomycorrhizal trees	American Naturalist
2017	10.1021/jacs.7b06560	Fukushima, T., S. Gupta, B. Rad, J. A. Cornejo, C. J. Petzold, L. J. G. Chan, R. A. Mizrahi, C. Y. Ralston and C. M. Ajo-Franklin	The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface	Journal of the American Chemical Society
2017	10.1039/c7lc00576h	Gach, P. C., K. Iwai, P. W. Kim, N. J. Hillson and A. K. Singh	Droplet microfluidics for synthetic biology	Lab Chip
2017	10.1038/ncomms15459	Gander, M. W., J. D. Vrana, W. E. Voje, J. M. Carothers and E. Klavins	Digital logic circuits in yeast with CRISPR-dCas9 NOR gates	Nature Communications
2017	10.1021/acs.analchem.7b00599	Gao, J., K. B. Louie, P. Steinke, B. P. Bowen, M. de Raad, R. N. Zuckermann, G. Siuzdak and T. R. Northen	Morphology-driven control of metabolite selectivity using nanostructure-initiator mass spectrometry	Analytical Chemistry
2017	10.3389/fpls.2017.01364	Gao, W., L. Long, X. Tian, F. Xu, J. Liu, P. K. Singh, J. R. Botella and C. Song	Genome Editing in Cotton with the CRISPR/Cas9 System	Frontiers in Plant Science
2017	10.1038/nbt.3718	Garst, A. D., M. C. Bassalo, G. Pines, S. A. Lynch, A. L. Halweg-Edwards, R. Liu, L. Liang, Z. Wang, R. Zeitoun, W. G. Alexander and R. T. Gill	Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering	Nature Biotechnology
2017	10.7717/peerj.4088	Gehan, M. A., N. Fahlgren, A. Abbasi, J. C. Berry, S. T. Callen, L. Chavez, A. N. Doust, M. J. Feldman, K. B. Gilbert, J. G. Hodge, J. S. Hoyer, A. Lin, S. X. Liu, C. Lizarraga, A. Lorence, M. Miller, E. Platon, M. Tessman and T. Sax	PlantCV v2: Image analysis software for high-throughput plant phenotyping	PeerJ
2017	10.1016/B978-0-323-35824-8.04001-9	Gilbert, M. E.	Brydson's Plastics Materials (Eighth Edition)	Brydson's Plastics Materials (Eighth Edition)
2017	10.1186/s13068-017-0971-1	Gilna, P., L. R. Lynd, D. Mohnen, M. F. Davis and B. H. Davison	Progress in understanding and overcoming biomass recalcitrance: a BioEnergy Science Center (BESC) perspective	Biotechnology for Biofuels
2017	10.1021/acsinfecdis.7b00003	Goins, C. M., S. Dajnowicz, S. Thanna, S. J. Sucheck, J. M. Parks and D. R. Ronning	Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives	ACS Infectious Diseases
2017	10.1186/s13059-017-1223-1	Goodman, D. B., G. Kuznetsov, M. J. Lajoie, B. W. Ahern, M. G. Napolitano, K. Y. Chen, C. P. Chen and G. M. Church	Millstone: software for multiplex microbial genome analysis and engineering	Genome Biology
2017	10.1111/nph.14758	Gou, J., C. Fu, S. Liu, C. Tang, S. Debnath, A. Flanagan, Y. Ge, Y. Tang, Q. Jiang, P. R. Larson, J. Wen and Z.-Y. Wang	The miR156-SPL4 module predominantly regulates aerial axillary bud formation and controls shoot architecture	New Phytologist
2017	10.1111/nph.14101	Grabowski, P. P., J. Evans, C. Daum, S. Deshpande, K. W. Barry, M. Kennedy, G. Ramstein, S. M. Kaeppler, C. R. Buell, Y. W. Jiang and M. D. Casler	Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data	New Phytologist
2017	10.1186/s13068-017-0757-5	Gunawan, C., S. Xue, S. Pattathil, L. da Costa Sousa, B. E. Dale and V. Balan	Comprehensive characterization of non-cellulosic recalcitrant cell wall carbohydrates in unhydrolyzed solids from AFEX-pretreated corn stover	Biotechnology for Biofuels
2017	10.1038/nmicrobiol.2017.87	Haitjema, C. H., S. P. Gilmore, J. K. Henske, K. V. Solomon, R. de Groot, A. Kuo, S. J. Mondo, A. A. Salamov, K. LaButti, Z. Y. Zhao, J. Chiniquy, K. Barry, H. M. Brewer, S. O. Purvine, A. T. Wright, M. Hainaut, B. Boxma, T. van Alen, J. H. P. Hackstein, B. Henrissat, S. E. Baker, I. V. Grigoriev and M. A. O'Malley	A parts list for fungal cellulosomes revealed by comparative genomics	Nature Microbiology
2017	10.1128/mSystems.00091-17	Hamilton, J. J., S. L. Garcia, B. S. Brown, B. O. Oyserman, F. Moya-Flores, S. Bertilsson, R. R. Malmstrom, K. T. Forest and K. D. McMahon	Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI	mSystems
2017	10.1186/s13068-017-0962-2	Harman-Ware, A. E., R. M. Happs, B. H. Davison and M. F. Davis	The effect of coumaryl alcohol incorporation on the structure and composition of lignin dehydrogenation polymers	Biotechnology for Biofuels
2017	10.1128/IAI.00601-16	Hasim, S., D. P. Allison, S. T. Retterer, A. Hopke, R. T. Wheeler, M. J. Doktycz and T. B. Reynolds	beta-(1,3)-Glucan Unmasking in Some Candida albicans Mutants Correlates with Increases in Cell Wall Surface Roughness and Decreases in Cell Wall Elasticity	Infection and Immunity
2017	10.1186/s13036-017-0048-5	Hays, S. G., L. L. W. Yan, P. A. Silver and D. C. Ducat	Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction	Journal of Biological Engineering
2017	10.1371/journal.pone.0180808	He H, W. R., Toutounchian JJ, Pagadala J, Steinle JJ, Baudry J, Miller DD, Yates CR	The quinic acid derivative KZ-41 prevents glucose-induced caspase-3 activation in retinal endothelial cells through an IGF-1 receptor dependent mechanism	PLOS ONE
2017	10.1016/j.bbrc.2017.05.131	He, H., J. Yan, X. Yu, Y. Liang, L. Fang, H. V. Scheller and A. Zhang	The NADPH-oxidase AtRbohI plays a positive role in drought-stress response in Arabidopsis thaliana	Biochemical and Biophysical Research Communications
2017	10.1016/j.ymben.2016.12.008	He, L., Y. Xiu, J. A. Jones, E. E. K. Baidoo, J. D. Keasling, Y. J. Tang and M. A. G. Koffas	Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions	Metabolic Engineering
2017	10.1007/7397_2016_17	He, X. and A. T. Groover	The Genomics of Wood Formation in Angiosperm Trees	Comparative and Evolutionary Genomics of Angiosperm Trees
2017	10.3389/fmicb.2017.01072	Heimerl, T., J. Flechsler, C. Pickl, V. Heinz, B. Salecker, J. Zweck, G. Wanner, S. Geimer, R. Y. Samson, S. D. Bell, H. Huber, R. Wirth, L. Wurch, M. Podar and R. Rachel	A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans	Frontiers in Microbiology
2017	10.1039/C6LC01182A	Heinemann, J., K. Deng, S. C. C. Shih, J. Gao, P. D. Adams, A. K. Singh and T. R. Northen	On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening	Lab on a Chip
2017	10.1093/infdis/jiw465	Henry, C. S., E. Rotman, W. W. Lathem, K. E. J. Tyo, A. R. Hauser and M. J. Mandel	Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1	The Journal of Infectious Diseases
2017	10.1186/s13068-017-0997-4	Henske, J. K., S. P. Gilmore, D. Knop, F. J. Cunningham, J. A. Sexton, C. R. Smallwood, V. Shutthanandan, J. E. Evans, M. K. Theodorou and M. A. O'Malley	Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus	Biotechnology for Biofuels
2017	10.1128/mBio.01739-16	Herivaux, A., T. Duge de Bernonville, C. Roux, M. Clastre, V. Courdavault, A. Gastebois, J. P. Bouchara, T. Y. James, J. P. Latge, F. Martin and N. Papon	The Identification of Phytohormone Receptor Homologs in Early Diverging Fungi Suggests a Role for Plant Sensing in Land Colonization by Fungi	mBio
2017	10.1016/j.algal.2017.01.010	Hildebrand, M., K. Manandhar-Shrestha and R. Abbriano	Effects of chrysolaminarin synthase knockdown in the diatom Thalassiosira pseudonana: Implications of reduced carbohydrate storage relative to green algae	Algal Research
2017	10.1186/s13068-017-0974-y	Himmel, M. E., C. A. Abbas, J. O. Baker, E. A. Bayer, Y. J. Bomble, R. Brunecky, X. Chen, C. Felby, T. Jeoh, R. Kumar, B. V. McCleary, B. I. Pletschke, M. P. Tucker, C. E. Wyman and S. R. Decker	Undefined cellulase formulations hinder scientific reproducibility	Biotechnology for Biofuels
2017	10.1128/aem.00223-17	Holmes, D. E., P. M. Shrestha, D. J. F. Walker, Y. Dang, K. P. Nevin, T. L. Woodard and D. R. Lovley	Metatranscriptomic evidence for direct interspecies electron transfer between Geobacter and Methanothrix species in methanogenic rice paddy soils	Applied and Environmental Microbiology
2017	10.1016/j.ymben.2017.06.011	Hon, S., D. G. Olson, E. K. Holwerda, A. A. Lanahan, S. J. L. Murphy, M. I. Maloney, T. Zheng, B. Papanek, A. M. Guss and L. R. Lynd	The ethanol pathway from Thermoanaerobacterium saccharolyticum improves ethanol production in Clostridium thermocellum	Metabolic Engineering
2017	10.1111/tpj.13743	Hooper, C. M., T. J. Stevens, A. Saukkonen, I. R. Castleden, P. Singh, G. W. Mann, B. Fabre, J. Ito, M. J. Deery, K. S. Lilley, C. J. Petzold, A. H. Millar, J. L. Heazlewood and H. T. Parsons	Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples	The Plant Journal
2017	10.1016/j.ejsobi.2017.04.003	Horton, D. J., M. W. Kershner and C. B. Blackwood	Suitability of PCR primers for characterizing invertebrate communities from soil and leaf litter targeting metazoan 18S ribosomal or cytochrorne oxidase I (COI) genes	European Journal of Soil Biology
2017	10.1111/nph.14421	Hossain, M. S., T. Kawakatsu, K. Do Kim, N. Zhang, C. T. Nguyen, S. M. Khan, J. M. Batek, T. Joshi, J. Schmutz, J. Grimwood, R. J. Schmitz, D. Xu, S. A. Jackson, J. R. Ecker and G. Stacey	Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs	New Phytologist
2017	10.1111/tpj.13582	Hsia, M. M., R. O'Malley, A. Cartwright, R. Nieu, S. P. Gordon, S. Kelly, T. G. Williams, D. F. Wood, Y. J. Zhao, J. Bragg, M. Jordan, M. Pauly, J. R. Ecker, Y. Gu and J. P. Vogel	Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection	Plant Journal
2017	10.1038/nmeth.4260	Huan, T., E. M. Forsberg, D. Rinehart, C. H. Johnson, J. Ivanisevic, H. P. Benton, M. Fang, A. Aisporna, B. Hilmers, F. L. Poole, M. P. Thorgersen, M. W. W. Adams, G. Krantz, M. W. Fields, P. D. Robbins, L. J. Niedernhofer, T. Ideker, E. L. Majumder, J. D. Wall, N. J. W. Rattray, R. Goodacre, L. L. Lairson and G. Siuzdak	Systems biology guided by XCMS Online metabolomics	Nature Methods
2017	10.1002/pld3.18	Huang, H., M. A. Gehan, S. E. Huss, S. Alvarez, C. Lizarraga, E. L. Gruebbling, J. Gierer, M. J. Naldrett, R. K. Bindbeutel, B. S. Evans, T. C. Mockler and D. A. Nusinow	Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots	Plant Direct
2017	10.1007/978-3-319-45105-3_3	Huang, P. and M. Feldman	Genetic Diversity and Geographic Distribution of North American Setaria viridis Populations	Genetics and Genomics of Setaria
2017	10.1038/nplants.2017.54	Huang, P., H. Jiang, C. Zhu, K. Barry, J. Jenkins, L. Sandor, J. Schmutz, M. S. Box, E. A. Kellogg and T. P. Brutnell	Sparse panicle1 is required for inflorescence development in Setaria viridis and maize	Nature Plants
2017	10.1021/acs.analchem.7b02555	Hurst, G. B., K. G. Asano, C. J. Doktycz, E. J. Consoli, W. L. Doktycz, C. M. Foster, J. L. Morrell-Falvey, R. F. Standaert and M. J. Doktycz	Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis	Analytical Chemistry
2017	10.1038/s41598-017-17049-y	Ievlev, A. V., A. Belianinov, S. Jesse, D. P. Allison, M. J. Doktycz, S. T. Retterer, S. V. Kalinin and O. S. Ovchinnikova	Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data	Scientific Reports
2017	10.1002/pca.2672	Jaini, R., P. Wang, N. Dudareva, C. Chapple and J. A. Morgan	Targeted metabolomics of the phenylpropanoid pathway in Arabidopsis thaliana using reversed phase liquid chromatography coupled with tandem mass spectrometry	Phytochemical Analysis
2017	10.1111/pce.12879	Jardine, K. J., A. B. Jardine, J. A. Holm, D. L. Lombardozzi, R. I. Negron-Juarez, S. T. Martin, H. R. Beller, B. O. Gimenez, N. Higuchi and J. Q. Chambers	Monoterpene 'thermometer' of tropical forest-atmosphere response to climate warming	Plant Cell & Environment
2017	10.3390/ijms18102045	Jardine, K. J., V. Fernandes de Souza, P. Oikawa, N. Higuchi, M. Bill, R. Porras, U. Niinemets and J. Q. Chambers	Integration of C(1) and C(2) Metabolism in Trees	International Journal of Molecular Sciences
2017	10.1016/j.ymben.2017.05.001	Jazmin, L. J., Y. Xu, Y. E. Cheah, A. O. Adebiyi, C. H. Johnson and J. D. Young	Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production	Metabolic Engineering
2017	10.3389/fmicb.2017.02618	Jenkins, S., T. L. Swenson, R. Lau, A. M. Rocha, A. Aaring, T. C. Hazen, R. Chakraborty and T. R. Northen	Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites	Frontiers in Microbiology
2017	10.1038/s41598-017-12901-7	Jensen, H. M., T. Eng, V. Chubukov, R. A. Herbert and A. Mukhopadhyay	Improving membrane protein expression and function using genomic edits	Scientific Reports
2017	10.1016/j.celrep.2017.07.062	Jensen, P. A., Z. Zhu and T. van Opijnen	Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria	Cell Reports
2017	10.3389/fmicb.2017.00040	Jewell, T. N. M., U. Karaoz, M. Bill, R. Chakraborty, E. L. Brodie, K. H. Williams and H. R. Beller	Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer	Frontiers in Microbiology
2017	10.3389/fpls.2017.00721	Jin, X. L., C. H. Shi, C. Y. Yu, T. Yamada and E. J. Sacks	Determination of leaf water content by visible and near-infrared spectrometry and multivariate calibration in Miscanthus	Frontiers in Plant Science
2017	10.1016/j.biortech.2017.05.047	Jin, X. L., X. L. Chen, C. H. Shi, M. Li, Y. J. Guan, C. Y. Yu, T. Yamada, E. J. Sacks and J. H. Peng	Determination of hemicellulose, cellulose and lignin content using visible and near infrared spectroscopy in Miscanthus sinensis	Bioresource Technology
2017	10.1371/journal.pone.0171360	Jin, X. L., X. L. Chen, L. Xiao, C. H. Shi, L. Chen, B. Yu, Z. L. Yi, J. H. Yoo, K. Heo, C. Y. Yu, T. Yamada, E. J. Sacks and J. H. Peng	Application of visible and near-infrared spectroscopy to classification of Miscanthus species	PLOS ONE
2017	10.1021/acs.jpcb.7b04519	Jing X, F. W., Baudry J, Serpersu EH	Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability Can We Draw a Line	Journal of Physical Chemistry B
2017	10.1201/9781315119496	John Dighton, J. F. W.	The Fungal Community Its Organization and Role in the Ecosystem	(Book)
2017	10.1186/s13068-017-0939-1	Johnson, C. R., R. J. Millwood, Y. Tang, J. Gou, R. W. Sykes, G. B. Turner, M. F. Davis, Y. Sang, Z.-Y. Wang and C. N. Stewart	Field-grown miR156 transgenic switchgrass reproduction, yield, global gene expression analysis, and bioconfinement	Biotechnology for Biofuels
2017	10.1002/pld3.26	Johnson, C. R., R. J. Millwood, Z.-Y. Wang and C. N. Stewart Jr	Light and temperature effects on miR156 transgenic switchgrass flowering: A simulated latitudinal study	Plant Direct
2017	10.1016/j.meteno.2017.05.002	Johnson, C. W., P. E. Abraham, J. G. Linger, P. Khanna, R. L. Hettich and G. T. Beckham	Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440	Metabolic Engineering Communications
2017	10.1007/978-1-4939-6658-5_7	Joshi, T., J. Wang, H. Zhang, S. Chen, S. Zeng, B. Xu and D. Xu	The evolution of soybean knowledge base (SoyKB)	Plant Genomics Databases
2017	10.1186/s12859-017-1761-2	Jun, S. R., I. Nookaew, L. Hauser and A. Gorin	Assessment of genome annotation using gene function similarity within the gene neighborhood	BMC Bioinformatics
2017	10.1128/AEM.01253-17	Justice, N. B., A. Sczesnak, T. C. Hazen and A. P. Arkin	Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing	Applied and Environmental Microbiology
2017	10.1038/nmeth.4285	Kalyaanamoorthy, S., B. Q. Minh, T. K. F. Wong, A. von Haeseler and L. S. Jermiin	ModelFinder: fast model selection for accurate phylogenetic estimates	Nat Methods
2017	10.1016/j.ymben.2017.03.010	Kang, A., C. W. Meadows, N. Canu, J. D. Keasling and T. S. Lee	High-throughput enzyme screening platform for the IPP-bypass mevalonate pathway for isopentenol production	Metabolic Engineering
2017	10.1186/s13068-017-0848-3	Kebrom, T. H., B. McKinley and J. E. Mullet	Dynamics of gene expression during development and expansion of vegetative stem internodes of bioenergy sorghum	Biotechnology for Biofuels
2017	10.1128/mBio.00857-17	Kerkhoven, E. J., Y. M. Kim, S. W. Wei, C. D. Nicora, T. L. Fillmore, S. O. Purvine, B. J. Webb-Robertson, R. D. Smith, S. E. Baker, T. O. Metz and J. Nielsen	Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica	mBio
2017	10.1016/j.jmbbm.2017.01.009	Khandaker, M. S. K., D. M. Dudek, E. P. Beers and D. A. Dillard	Expression, crosslinking, and developing modulus master curves of recombinant resilin	Journal of the Mechanical Behavior of Biomedical Materials
2017	10.1016/j.ymben.2017.11.004	Kim, E.-M., H. M. Woo, T. Tian, S. Yilmaz, P. Javidpour, J. D. Keasling and T. S. Lee	Autonomous control of metabolic state by a quorum sensing (QS)-mediated regulator for bisabolene production in engineered E. coli	Metabolic Engineering
2017	10.1038/ncomms14406	Kim, H., S.-T. Kim, J. Ryu, B.-C. Kang, J.-S. Kim and S.-G. Kim	CRISPR/Cpf1-mediated DNA-free plant genome editing	Nature Communications
2017	10.1039/C6GC02473D	Kim, K. H., B. A. Simmons and S. Singh	Catalytic transfer hydrogenolysis of ionic liquid processed biorefinery lignin to phenolic compounds	Green Chemistry
2017	10.1002/cssc.201601515	Kim, K. H., R. C. Brown, T. Daugaard, W. F. Tivol, M. Auer, B. Simmons and S. Singh	Strategy for Extending the Stability of Bio-oil-Derived Phenolic Oligomers by Mild Hydrotreatment with Ionic-Liquid-Stabilized Nanoparticles	ChemSusChem
2017	10.1021/acssuschemeng.6b03102	Kim, K. H., T. Dutta, E. D. Walter, N. G. Isern, J. R. Cort, B. A. Simmons and S. Singh	Chemoselective Methylation of Phenolic Hydroxyl Group Prevents Quinone Methide Formation and Repolymerization During Lignin Depolymerization	ACS Sustainable Chemistry & Engineering
2017	10.1186/s13068-017-0784-2	Kim, K. H., T. Dutta, J. Ralph, S. D. Mansfield, B. A. Simmons and S. Singh	Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar	Biotechnology for Biofuels
2017	10.1002/bit.26242	Kim, S.-K., D. Chung, M. E. Himmel, Y. J. Bomble and J. Westpheling	Engineering the N-terminal end of CelA results in improved performance and growth of Caldicellulosiruptor bescii on crystalline cellulose	Biotechnology and Bioengineering
2017	10.1002/bit.26366	Kim, S.-K., D. Chung, M. E. Himmel, Y. J. Bomble and J. Westpheling	In vivo synergistic activity of a CAZyme cassette from Acidothermus cellulolyticus significantly improves the cellulolytic activity of the C. bescii exoproteome	Biotechnology and Bioengineering
2017	10.1007/s10295-017-1982-4	Kim, S.-K., D. Chung, M. E. Himmel, Y. J. Bomble and J. Westpheling	Heterologous expression of a ?-d-glucosidase in Caldicellulosiruptor bescii has a surprisingly modest effect on the activity of the exoproteome and growth on crystalline cellulose	Journal of Industrial Microbiology and Biotechnology
2017	10.1186/s13068-017-0750-z	Kim, S.-K., J. Groom, D. Chung, J. Elkins and J. Westpheling	Expression of a heat-stable NADPH-dependent alcohol dehydrogenase from Thermoanaerobacter pseudethanolicus 39E in Clostridium thermocellum 1313 results in increased hydroxymethylfurfural resistance	Biotechnology for Biofuels
2017	10.1021/acs.est.6b04751	King, A. J., S. P. Preheim, K. L. Bailey, M. S. Robeson, T. Roy Chowdhury, B. R. Crable, R. A. Hurt, T. Mehlhorn, K. A. Lowe, T. J. Phelps, A. V. Palumbo, C. C. Brandt, S. D. Brown, M. Podar, P. Zhang, W. A. Lancaster, F. Poole, D. B. Watson, M. W. Fields, J.-M. Chandonia, E. J. Alm, J. Zhou, M. W. W. Adams, T. C. Hazen, A. P. Arkin and D. A. Elias	Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation	Environmental Science & Technology
2017	10.1073/pnas.1619263114	Kohler, A. C., M. J. L. Mills, P. D. Adams, B. A. Simmons and K. L. Sale	Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism	Proceedings of the National Academy of Sciences
2017	10.1186/s13068-017-0925-7	Kruer-Zerhusen, N., M. Alahuhta, V. V. Lunin, M. E. Himmel, Y. J. Bomble and D. B. Wilson	Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues	Biotechnology for Biofuels
2017	10.1186/s13059-017-1217-z	Kuznetsov, G., D. B. Goodman, G. T. Filsinger, M. Landon, N. Rohland, J. Aach, M. J. Lajoie and G. M. Church	Optimizing complex phenotypes through model-guided multiplex genome engineering	Genome Biology
2017	10.1007/978-1-4939-7136-7_23	Lakshmanan, V., P. Ray and K. D. Craven	Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes	Plant Stress Tolerance: Methods and Protocols
2017	10.1007/978-1-4939-7136-7_4	Lakshmanan, V., P. Ray and K. D. Craven	Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture	Plant Stress Tolerance: Methods and Protocols
2017	10.1007/978-1-4939-6533-5_17	Lao, J., A. M. Smith-Moritz, J. C. Mortimer and J. L. Heazlewood	Enrichment of the Plant Cytosolic Fraction	Isolation of Plant Organelles and Structures: Methods and Protocols
2017	10.1111/1758-2229.12523	Larkin, A. A. and A. C. Martiny	Microdiversity shapes the traits, niche space, and biogeography of microbial taxa	Environmental Microbiology Reports
2017	10.1038/ismej.2016.141	LaSarre, B., A. L. McCully, J. T. Lennon and J. B. McKinlay	Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients	ISME Journal
2017	10.1101/151704	Lee, J. Z., R. C. Everroad, U. Karaoz, A. M. Detweiler, J. Pett-Ridge, P. K. Weber, L. Prufert-Bebout and B. M. Bebout	Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat	bioRxiv
2017	10.1128/mSystems.00142-16	Levering, J., C. L. Dupont, A. E. Allen, B. O. Palsson and K. Zengler	Integrated regulatory and metabolic networks of the marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels	mSystems
2017	10.1105/tpc.17.00154	Li, G., R. Jain, M. Chern, N. T. Pham, J. A. Martin, T. Wei, W. S. Schackwitz, A. M. Lipzen, P. Q. Duong, K. C. Jones, L. Jiang, D. Ruan, D. Bauer, Y. Peng, K. W. Barry, J. Schmutz and P. C. Ronald	The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies	The Plant Cell
2017	10.1080/21690731.2017.1327006	Li, J., C. Zhang, P. Huang, E. Kuru, E. T. C. Forster-Benson, T. Li and G. M. Church	Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system	Translation
2017	10.1021/acssynbio.6b00342	Li, J., W. Haas, K. Jackson, E. Kuru, M. C. Jewett, Z. H. Fan, S. Gygi and G. M. Church	Cogenerating synthetic parts toward a self-replicating system	ACS Synthetic Biology
2017	10.1007/s12155-016-9798-z	Li, M., D. L. Williams, M. Heckwolf, N. de Leon, S. Kaeppler, R. W. Sykes and D. Hodge	Prediction of Cell Wall Properties and Response to Deconstruction Using Alkaline Pretreatment in Diverse Maize Genotypes Using Py-MBMS and NIR	BioEnergy Research
2017	10.1186/s13068-016-0695-7	Li, M., Y. Pu, C. G. Yoo, E. Gjersing, S. R. Decker, C. Doeppke, T. Shollenberger, T. J. Tschaplinski, N. L. Engle, R. W. Sykes, M. F. Davis, H. L. Baxter, M. Mazarei, C. Fu, R. A. Dixon, Z.-Y. Wang, C. Neal Stewart and A. J. Ragauskas	Study of traits and recalcitrance reduction of field-grown COMT down-regulated switchgrass	Biotechnology for Biofuels
2017	10.1002/slct.201700735	Li, M., Y. Pu, T. J. Tschaplinski and A. J. Ragauskas	31P?NMR Characterization of Tricin and Its Structurally Similar Flavonoids	ChemistrySelect
2017	10.1186/s13068-017-0736-x	Li, T. T., C. T. Li, K. Butler, S. G. Hays, M. T. Guarnieri, G. A. Oyler and M. J. Betenbaugh	Mimicking lichens: incorporation of yeast strains together with sucrose-secreting cyanobacteria improves survival, growth, ROS removal, and lipid production in a stable mutualistic co-culture production platform	Biotechnology for Biofuels
2017	10.1016/j.cell.2017.06.008	Li, W., Z. Zhu, M. Chern, J. Yin, C. Yang, L. Ran, M. Cheng, M. He, K. Wang, J. Wang, X. Zhou, X. Zhu, Z. Chen, J. Wang, W. Zhao, B. Ma, P. Qin, W. Chen, Y. Wang, J. Liu, W. Wang, X. Wu, P. Li, J. Wang, L. Zhu, S. Li and X. Chen	A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance	Cell
2017	10.1007/s10295-016-1864-1	Li, Z. J., K. J. Qiao, N. Liu and G. Stephanopoulos	Engineering Yarrowia lipolytica for poly-3-hydroxybutyrate production	Journal of Industrial Microbiology & Biotechnology
2017	10.1111/1462-2920.13605	Li, Z., Q. Yao, S. P. Dearth, M. R. Entler, H. F. Castro Gonzalez, J. K. Uehling, R. J. Vilgalys, G. B. Hurst, S. R. Campagna, J. L. Labbe and C. Pan	Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system	Environmental Microbiology
2017	10.1074/jbc.M117.777417	Li, Z., T. Mukherjee, K. Bowler, S. Namdari, Z. Snow, S. Prestridge, A. Carlton and M. Bar-Peled	A four-gene operon in Bacillus cereus produces two rare spore-decorating sugars	Journal of Biological Chemistry
2017	10.1038/s41467-017-01695-x	Lian, J. Z., M. HamediRad, S. M. Hu and H. M. Zhao	Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system	Nature Communications
2017	10.1016/j.tplants.2017.08.006	Libault, M., L. Pingault, P. Zogli and J. Schiefelbein	Plant Systems Biology at the Single-Cell Level	Trends in Plant Science
2017	10.3389/fpls.2017.01134	Lin, F., B. J. Williams, P. A. V. Thangella, A. Ladak, A. A. Schepmoes, H. J. Olivos, K. Zhao, S. J. Callister and L. E. Bartley	Proteomics coupled with metabolite and cell wall profiling reveal metabolic processes of a developing rice stem internode	Frontiers in Plant Science
2017	10.1038/hortres.2017.31	Liu, D. G., R. Mewalal, R. B. Hu, G. A. Tuskan and X. H. Yang	New technologies accelerate the exploration of non-coding RNAs in horticultural plants	Horticulture Research
2017	10.3389/fpls.2017.00982	Liu, S., C. Fu, J. Gou, L. Sun, D. Huhman, Y. Zhang and Z.-Y. Wang	Simultaneous Downregulation of MTHFR and COMT in Switchgrass Affects Plant Performance and Induces Lesion-Mimic Cell Death	Frontiers in Plant Science
2017	10.1103/PhysRevLett.119.048101	Liu, Z., J. Huang, M. Tyagi, H. O'Neill, Q. Zhang, E. Mamontov, N. Jain, Y. Wang, J. Zhang, J. C. Smith and L. Hong	Dynamical Transition of Collective Motions in Dry Proteins	Physical Review Letters
2017	10.1016/j.ymben.2016.10.018	Lo, J., D. G. Olson, S. J.-L. Murphy, L. Tian, S. Hon, A. Lanahan, A. M. Guss and L. R. Lynd	Engineering electron metabolism to increase ethanol production in Clostridium thermocellum	Metabolic Engineering
2017	10.1093/bioinformatics/btw706	Long, M. R. and J. L. Reed	Improving flux predictions by integrating data from multiple strains	Bioinformatics
2017	10.3390/metabo7040050	Lubbe, A., B. P. Bowen and T. Northen	Exometabolomic analysis of cross-feeding metabolites	Metabolites
2017	10.1002/1873-3468.12562	Lubner, J. M., K. L. Dodge-Kafka, C. R. Carlson, G. M. Church, M. F. Chou and D. Schwartz	Cushing's syndrome mutant PKA(L205R) exhibits altered substrate specificity	FEBS Letters
2017	10.1038/nbt.3976	Lynd, L. R.	The grand challenge of cellulosic biofuels	Nature Biotechnology
2017	10.1016/j.copbio.2017.03.008	Lynd, L. R., X. Liang, M. J. Biddy, A. Allee, H. Cai, T. Foust, M. E. Himmel, M. S. Laser, M. Wang and C. E. Wyman	Cellulosic ethanol: status and innovation	Current Opinion in Biotechnology
2017	10.1186/s13068-017-0934-6	Macaya-Sanz, D., J. G. Chen, U. C. Kalluri, W. Muchero, T. J. Tschaplinski, L. E. Gunter, S. J. Simon, A. K. Biswal, A. C. Bryan, R. Payyavula, M. Xie, Y. Yang, J. Zhang, D. Mohnen, G. A. Tuskan and S. P. DiFazio	Agronomic performance of Populus deltoides trees engineered for biofuel production	Biotechnology for Biofuels
2017	10.4236/ojic.2017.72003	Majumder, E. a. W., J.	Uranium Bio-Transformations: Chemical or Biological Processes?	Open Journal of Inorganic Chemistry
2017	10.1371/journal.pone.0184991	Maltz, M. R., K. K. Treseder and K. L. McGuire	Links between plant and fungal diversity in habitat fragments of coastal shrubland	PLOS ONE
2017	10.1038/s41598-017-08877-z	Marshall, C. W., D. E. Ross, K. M. Handley, P. B. Weisenhorn, J. N. Edirisinghe, C. S. Henry, J. A. Gilbert, H. D. May and R. S. Norman	Metabolic Reconstruction and Modeling Microbial Electrosynthesis	Scientific Reports
2017	10.1126/science.aad4501	Martin, F. M., S. Uroz and D. G. Barker	Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria	Science
2017	10.1016/j.sab.2017.10.008	Martin, M. Z., D. C. Glasgow, T. J. Tschaplinski, G. A. Tuskan, L. E. Gunter, N. L. Engle, A. M. Wymore and D. J. Weston	Correlating laser-induced breakdown spectroscopy with neutron activation analysis to determine the elemental concentration in the ionome of the Populus trichocarpa leaf	Spectrochimica Acta Part B: Atomic Spectroscopy
2017	10.1038/ncomms15892	Martinez-Hernandez, F., O. Fornas, M. L. Gomez, B. Bolduc, M. J. de la Cruz Pena, J. M. Martinez, J. Anton, J. M. Gasol, R. Rosselli, F. Rodriguez-Valera, M. B. Sullivan, S. G. Acinas and M. Martinez-Garcia	Single-virus genomics reveals hidden cosmopolitan and abundant viruses	Nature Communications
2017	10.1073/pnas.1708124114	McAndrew, R. P., N. Sathitsuksanoh, M. M. Mbughuni, R. A. Heins, J. H. Pereira, A. George, K. L. Sale, B. G. Fox, B. A. Simmons and P. D. Adams	Reply to Kiser: Dioxygen binding in NOV1 crystal structures	Proceedings of the National Academy of Sciences
2017	10.1105/tpc.16.00910	McCarthy, J. K., S. R. Smith, J. P. McCrow, M. Tan, H. Zheng, K. Beeri, R. Roth, C. Lichtle, U. Goodenough, C. P. Bowler, C. L. Dupont and A. E. Allen	Nitrate reductase knockout uncouples nitrate transport from nitrate assimilation and drives repartitioning of carbon flux in a model pennate diatom	Plant Cell
2017	10.1111/1462-2920.13847	McCully, A. L., B. LaSarre and J. B. McKinlay	Growth-independent cross-feeding modifies boundaries for coexistence in a bacterial mutualism	Environmental Microbiology
2017	10.1128/mBio.01620-17	McCully, A. L., B. LaSarre and J. B. McKinlay	Recipient-biased competition for an intracellularly generated cross-fed nutrient is required for coexistence of microbial mutualists	mBio
2017	10.1111/1462-2920.13678	McHugh, T. A., E. M. Morrissey, R. C. Mueller, L. V. Gallegos-Graves, C. R. Kuske and S. C. Reed	Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland	Environmental Microbiology
2017	10.1126/science.aan2874	Melillo, J. M., S. D. Frey, K. M. DeAngelis, W. J. Werner, M. J. Bernard, F. P. Bowles, G. Pold, M. A. Knorr and A. S. Grandy	Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world	Science
2017	10.1002/bit.26296	Mendez-Perez, D., J. Alonso-Gutierrez, Q. Hu, M. Molinas, E. E. K. Baidoo, G. Wang, L. J. G. Chan, P. D. Adams, C. J. Petzold, J. D. Keasling and T. S. Lee	Production of jet fuel precursor monoterpenoids from engineered Escherichia coli	Biotechnology and Bioengineering
2017	10.19080/RAPSCI.2017.01.555551	Meng, X. and A. J. Ragauskas	Pseudo-lignin Formation during Dilute Acid Pretreatment for Cellulosic Ethanol
2017	10.1021/acssuschemeng.7b01527	Meng, X., B. R. Evans, C. G. Yoo, Y. Pu, B. H. Davison and A. J. Ragauskas	Effect of in Vivo Deuteration on Structure of Switchgrass Lignin	ACS Sustainable Chemistry & Engineering
2017	10.1002/jcc.25054	Mills, M. J. L., K. L. Sale, B. A. Simmons and P. L. A. Popelier	Rhorix: An interface between quantum chemical topology and the 3D graphics program blender	Journal of Computational Chemistry
2017	10.3791/54771	Miquel Guennoc, C., C. Rose, F. Guinnet, I. Miquel, J. Labbe and A. Deveau	A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy	Journal of Visualized Experiments
2017	10.1021/acssuschemeng.7b01424	Mittal, A., R. Katahira, B. S. Donohoe, B. A. Black, S. Pattathil, J. M. Stringer and G. T. Beckham	Alkaline Peroxide Delignification of Corn Stover	ACS Sustainable Chemistry & Engineering
2017	10.1073/pnas.1620119114	Mizrachi, E., L. Verbeke, N. Christie, A. C. Fierro, S. D. Mansfield, M. F. Davis, E. Gjersing, G. A. Tuskan, M. Van Montagu, Y. Van de Peer, K. Marchal and A. A. Myburg	Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing	Proceedings of the National Academy of Sciences
2017	10.1016/j.jenvman.2016.09.060	Mohapatra, S., S. J. Dandapat and H. Thatoi	Physicochemical characterization, modelling and optimization of ultrasono-assisted acid pretreatment of two Pennisetum sp. using Taguchi and artificial neural networking for enhanced delignification	Journal of Environmental Management
2017	10.1111/1462-2920.13809	Mondav, R., C. K. McCalley, S. B. Hodgkins, S. Frolking, S. R. Saleska, V. I. Rich, J. P. Chanton and P. M. Crill	Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient	Environmental Microbiology
2017	10.1038/ng.3859	Mondo, S. J., R. O. Dannebaum, R. C. Kuo, K. B. Louie, A. J. Bewick, K. LaButti, S. Haridas, A. Kuo, A. Salamov, S. R. Ahrendt, R. Lau, B. P. Bowen, A. Lipzen, W. Sullivan, B. B. Andreopoulos, A. Clum, E. Lindquist, C. Daum, T. R. Northen, G. Kunde-Ramamoorthy, R. J. Schmitz, A. Gryganskyi, D. Culley, J. Magnuson, T. Y. James, M. A. O'Malley, J. E. Stajich, J. W. Spatafora, A. Visel and I. V. Grigoriev	Widespread adenine N6-methylation of active genes in fungi	Nature Genetics
2017	10.1021/acssynbio.7b00204	Morrell, W. C., G. W. Birkel, M. Forrer, T. Lopez, T. W. H. Backman, M. Dussault, C. J. Petzold, E. E. K. Baidoo, Z. Costello, D. Ando, J. Alonso-Gutierrez, K. W. George, A. Mukhopadhyay, I. Vaino, J. D. Keasling, P. D. Adams, N. J. Hillson and H. Garcia Martin	The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization	ACS Synthetic Biology
2017	10.1007/978-1-4939-6722-3_16	Mortimer, J. C.	Structural Analysis of Cell Wall Polysaccharides Using PACE	Xylem: Methods and Protocols
2017	10.1038/srep41569	Mueller, T. J., J. L. Ungerer, H. B. Pakrasi and C. D. Maranas	Identifying the metabolic differences of a fast-growth phenotype in Synechococcus UTEX 2973	Scientific Reports
2017	10.1093/molbev/msw238	Nagy, L. G., R. Riley, P. J. Bergmann, K. Krizsan, F. M. Martin, I. V. Grigoriev, D. Cullen and D. S. Hibbett	Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution	Molecular Biology and Evolution
2017	10.1128/mBio.01894-17	Nakayasu, E. S., M. C. Burnet, H. E. Walukiewicz, C. S. Wilkins, A. K. Shukla, S. Brooks, M. J. Plutz, B. D. Lee, B. Schilling, A. J. Wolfe, S. Muller, J. R. Kirby, C. V. Rao, J. R. Cort and S. H. Payne	Ancient regulatory role of lysine acetylation in central metabolism	mBio
2017	10.1111/mmi.13625	Nelson, C. E., A. Rogowski, C. Morland, J. A. Wilhide, H. J. Gilbert and J. G. Gardner	Systems analysis in Cellvibrio japonicus resolves predicted redundancy of beta-glucosidases and determines essential physiological functions	Molecular Microbiology
2017	10.1111/1462-2920.13959	Nelson, C. E., M. A. Attia, A. Rogowski, C. Morland, H. Brumer and J. G. Gardner	Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification	Environmental Microbiology
2017	10.1111/1462-2920.13878	Neumann, A. P., C. A. McCormick and G. Suen	Fibrobacter communities in the gastrointestinal tracts of diverse hindgut-fermenting herbivores are distinct from those of the rumen	Environmental Microbiology
2017	10.1016/j.rser.2016.11.253	Neupane, B. and J. Rubin	Implications of U.S. biofuels policy for sustainable transportation energy in Maine and the Northeast	Renewable and Sustainable Energy Reviews
2017	10.1021/acssuschemeng.7b02116	Neupane, B., N. V. S. N. M. Konda, S. Singh, B. A. Simmons and C. D. Scown	Life-Cycle Greenhouse Gas and Water Intensity of Cellulosic Biofuel Production Using Cholinium Lysinate Ionic Liquid Pretreatment	ACS Sustainable Chemistry & Engineering
2017	10.1073/pnas.1704652114	Nguyen, T. Y., C. M. Cai, R. Kumar and C. E. Wyman	Overcoming factors limiting high-solids fermentation of lignocellulosic biomass to ethanol	Proceedings of the National Academy of Sciences
2017	10.1128/genomeA.00610-17	Nicholls, C., A. Kump, S. Ford, R. Gonser and K. H. Cho	Draft Genome Sequence of Streptococcus pyogenes Strain M3KCL	Genome Announcements
2017	10.1002/jqs.2952	Nichols, J. E., D. M. Peteet, S. Frolking and J. Karavias	A probabilistic method of assessing carbon accumulation rate at Imnavait Creek Peatland, Arctic Long Term Ecological Research Station, Alaska	Journal of Quaternary Science
2017	10.1016/j.bpj.2016.11.1234	Nickels JD, C. S., Stanley C, Qian S, Cheng X, Myles DA, Standaert R, Elkins J, Katsaras J	Neutron Scattering to Study Membrane Systems From Model Membranes to Living Cells	Biophysical Journal
2017	10.1021/acs.jpclett.7b01877	Nickels, J. D., S. Chatterjee, B. Mostofian, C. B. Stanley, M. Ohl, P. Zolnierczuk, R. Schulz, D. A. A. Myles, R. F. Standaert, J. G. Elkins, X. Cheng and J. Katsaras	Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane	Journal of Physical Chemistry Letters
2017	10.1371/journal.pbio.2002214	Nickels, J. D., S. Chatterjee, C. B. Stanley, S. Qian, X. Cheng, D. A. A. Myles, R. F. Standaert, J. G. Elkins and J. Katsaras	The in vivo structure of biological membranes and evidence for lipid domains	PLOS Biology
2017	10.2134/agronj2016.05.0256	Obour, A. K., E. Obeng, Y. A. Mohammed, I. A. Ciampitti, T. P. Durrett, J. A. Aznar-Moreno and C. Chen	Camelina seed yield and fatty acids as influenced by genotype and environment	Agronomy Journal
2017	10.7554/eLife.31804	O'Connor, D. L., S. Elton, F. Ticchiarellin, M. M. Hsia, J. P. Vogel and O. Leyser	Cross-species functional diversity within the PIN auxin efflux protein family	eLife
2017	10.1038/nchembio.2453	Oslund, R. C., X. Y. Su, M. Haugbro, J. M. Kee, M. Esposito, Y. David, B. Y. Wang, E. Ge, D. H. Perlman, Y. B. Kang, T. W. Muir and J. D. Rabinowitz	Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate	Nature Chemical Biology
2017	10.1039/C6GC02637K	Papa, G., J. Kirby, N. V. S. N. Murthy Konda, K. Tran, S. Singh, J. D. Keasling, G. F. Peter and B. A. Simmons	Development of an integrated approach for ?-pinene recovery and sugar production from loblolly pine using ionic liquids	Green Chemistry
2017	10.1016/j.biortech.2017.05.167	Papa, G., T. Feldman, K. L. Sale, F. Adani, S. Singh and B. A. Simmons	Parametric study for the optimization of ionic liquid pretreatment of corn stover	Bioresource Technology
2017	10.1016/j.biortech.2017.05.001	Parisutham, V., S.-P. Chandran, A. Mukhopadhyay, S. K. Lee and J. D. Keasling	Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries	Bioresource Technology
2017	10.1186/s12284-017-0166-1	Park, C.-J., T. Wei, R. Sharma and P. C. Ronald	Overexpression of Rice Auxilin-Like Protein, XB21, Induces Necrotic Lesions, up-Regulates Endocytosis-Related Genes, and Confers Enhanced Resistance to Xanthomonas oryzae pv. oryzae	Rice
2017	10.1186/s13068-017-0972-0	Park, J.-J., C. G. Yoo, A. Flanagan, Y. Pu, S. Debnath, Y. Ge, A. J. Ragauskas and Z.-Y. Wang	Defined tetra-allelic gene disruption of the 4-coumarate:coenzyme A ligase 1 (Pv4CL1) gene by CRISPR/Cas9 in switchgrass results in lignin reduction and improved sugar release	Biotechnology for Biofuels
2017	10.1371/journal.pone.0179410	Park, J.-J., E. Dempewolf, W. Zhang and Z.-Y. Wang	RNA-guided transcriptional activation via CRISPR/dCas9 mimics overexpression phenotypes in Arabidopsis	PLOS ONE
2017	10.1038/s41564-017-0012-7	Parks, D. H., C. Rinke, M. Chuvochina, P. A. Chaumeil, B. J. Woodcroft, P. N. Evans, P. Hugenholtz and G. W. Tyson	Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life	Nature Microbiology
2017	10.1038/nmicrobiol.2017.45	Paul, B. G., D. Burstein, C. J. Castelle, S. Handa, D. Arambula, E. Czornyj, B. C. Thomas, P. Ghosh, J. F. Miller, J. F. Banfield and D. L. Valentine	Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea	Nature Microbiology
2017	10.1111/cbdd.13004	Pavlova, A., J. M. Parks, A. K. Oyelere and J. C. Gumbart	Toward the rational design of macrolide antibiotics to combat resistance	Chemical Biology & Drug Design
2017	10.1111/pbi.12733	Peng, A., S. Chen, T. Lei, L. Xu, Y. He, L. Wu, L. Yao and X. Zou	Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus	Plant Biotechnology Journal
2017	10.1186/s13068-017-0935-5	Peralta, A. G., S. Venkatachalam, S. C. Stone and S. Pattathil	Xylan epitope profiling: an enhanced approach to study organ development-dependent changes in xylan structure, biosynthesis, and deposition in plant cell walls	Biotechnology for Biofuels
2017	10.1039/c7cp04013j	Perticaroli, S., B. Mostofian, G. Ehlers, J. C. Neuefeind, S. O. Diallo, C. B. Stanley, L. Daemen, T. Egami, J. Katsaras, X. Cheng and J. D. Nickels	Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid	Physical Chemistry Chemical Physics
2017	10.1016/j.rhisph.2017.04.016	Pett-Ridge, J. and M. K. Firestone	Using stable isotopes to explore root-microbe-mineral interactions in soil	Rhizosphere
2017	10.1128/genomeA.01620-16	Pfaller, S., V. Tokarev, C. Kessler, C. McLimans, V. Gomez-Alvarez, J. Wright, D. King and R. Lamendella	Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169	Genome Announcements
2017	10.1128/mSphere.00038-17	Pomraning, K. R., E. L. Bredeweg and S. E. Baker	Regulation of nitrogen metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica	mSphere
2017	10.1186/s13068-016-0697-5	Poudel, S., R. J. Giannone, M. Rodriguez, B. Raman, M. Z. Martin, N. L. Engle, J. R. Mielenz, I. Nookaew, S. D. Brown, T. J. Tschaplinski, D. Ussery and R. L. Hettich	Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass	Biotechnology for Biofuels
2017	10.1128/aem.02987-16	Presley, G. N. and J. S. Schilling	Distinct growth and secretome strategies for two taxonomically divergent brown rot fungi	Applied and Environmental Microbiology
2017	10.1128/mSystems.00039-17	Price, M. N. and A. P. Arkin	PaperBLAST: Text Mining Papers for Information about Homologs	mSystems
2017	10.1111/nph.14609	Pruitt, R. N., A. Joe, W. Zhang, W. Feng, V. Stewart, B. Schwessinger, J. R. Dinneny and P. C. Ronald	A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone	New Phytologist
2017	10.1016/j.coisb.2017.01.008	Purdy, H. M. and J. L. Reed	Evaluating the capabilities of microbial chemical production using genome-scale metabolic models	Current Opinion in Systems Biology
2017	10.1038/nbt.3763	Qiao, K. J., T. M. Wasylenko, K. Zhou, P. Xu and G. Stephanopoulos	Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism	Nature Biotechnology
2017	10.3389/fmicb.2017.00158	Qin, Y., X. Pan, C. Kubicek, I. Druzhinina, K. Chenthamara, J. Labbe and Z. Yuan	Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth	Frontiers in Microbiology
2017	10.1371/journal.pone.0181943	Rahman, M. K. and M. S. Rahman	CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems	PLOS ONE
2017	10.3389/fpls.2017.00806	Rao, X. and R. A. Dixon	Brassinosteroid Mediated Cell Wall Remodeling in Grasses under Abiotic Stress	Frontiers in Plant Science
2017	10.1186/s13068-017-0954-2	Rao, X., H. Shen, S. Pattathil, M. G. Hahn, I. Gelineo-Albersheim, D. Mohnen, Y. Pu, A. J. Ragauskas, X. Chen, F. Chen and R. A. Dixon	Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells	Biotechnology for Biofuels
2017	10.1073/pnas.1701894114	Rautengarten, C., D. Birdseye, S. Pattathil, H. E. McFarlane, S. Saez-Aguayo, A. Orellana, S. Persson, M. G. Hahn, H. V. Scheller, J. L. Heazlewood and B. Ebert	The elaborate route for UDP-arabinose delivery into the Golgi of plants	Proceedings of the National Academy of Sciences
2017	10.1016/j.bbagen.2017.06.001	Rawle, R. A., T. Hamerly, B. P. Tripet, R. J. Giannone, L. Wurch, R. L. Hettich, M. Podar, V. Copie and B. Bothner	Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association	Biochimica et Biophysica Acta (BBA) - General Subjects
2017	10.17226/24751	Reed, J. L.	Genome-Scale Metabolic Modeling and Its Application to Microbial Communities	The Chemistry of Microbiomes: Proceedings of a Seminar Series
2017	10.1007/s00572-016-0758-4	Rineau, F., H. Lmalem, D. Ahren, F. Shah, T. Johansson, L. Coninx, J. Ruytinx, H. Nguyen, I. Grigoriev, A. Kuo, A. Kohler, E. Morin, J. Vangronsveld, F. Martin and J. V. Colpaert	Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes	Mycorrhiza
2017	10.1016/j.ymben.2017.03.011	Rivera, J. G. L., M. K. Theisen, P. W. Chen and J. C. Liao	Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites	Metabolic Engineering
2017	10.1016/j.coisb.2017.07.008	Rouached, H. and S. Y. Rhee	System-level understanding of plant mineral nutrition in the big data era	Current Opinion in Systems Biology
2017	10.7717/peerj.3817	Roux, S., J. B. Emerson, E. A. Eloe-Fadrosh and M. B. Sullivan	Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity	PeerJ
2017	10.1201/9781315119496	Ruytinx J., M. F.	Comparative and Functional Genomics of Ectomycorrhizal Symbiosis	The Fungal Community. Its Organization and Role in the Ecosystem, Fourth Edition
2017	10.1016/j.ymben.2017.04.002	Rydzak, T., D. Garcia, D. M. Stevenson, M. Sladek, D. M. Klingeman, E. K. Holwerda, D. Amador-Noguez, S. D. Brown and A. M. Guss	Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum	Metabolic Engineering
2017	10.1371/journal.pone.0178258	Sagawa, S., M. N. Price, A. M. Deutschbauer and A. P. Arkin	Validating regulatory predictions from diverse bacteria with mutant fitness data	PLOS ONE
2017	10.15252/msb.20167411	Sanchez, B. J., C. Zhang, A. Nilsson, P. J. Lahtvee, E. J. Kerkhoven and J. Nielsen	Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints	Molecular Systems Biology
2017	10.1186/s13068-017-0960-4	Sander, K., K. G. Asano, D. Bhandari, G. J. Van Berkel, S. D. Brown, B. Davison and T. J. Tschaplinski	Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum	Biotechnology for Biofuels
2017	10.1093/bioinformatics/btx207	Sastry, A., J. Monk, H. Tegel, M. Uhlen, B. O. Palsson, J. Rockberg and E. Brunk	Machine learning in computational biology to accelerate high-throughput protein expression	Bioinformatics
2017	10.1038/nplants.2017.24	Scheller, H. V.	Plant cell wall: Never too much acetate	Nature Plants
2017	10.1186/s13068-017-0965-z	Schuerg, T., J.-P. Prahl, R. Gabriel, S. Harth, F. Tachea, C.-S. Chen, M. Miller, F. Masson, Q. He, S. Brown, M. Mirshiaghi, L. Liang, L. M. Tom, D. Tanjore, N. Sun, T. R. Pray and S. W. Singer	Xylose induces cellulase production in Thermoascus aurantiacus	Biotechnology for Biofuels
2017	10.1007/978-3-319-45105-3_11	Sebastian, J. and J. R. Dinneny	Setaria viridis: A Model for Understanding Panicoid Grass Root Systems	Genetics and Genomics of Setaria
2017	10.1016/j.ymben.2017.09.008	Seppala, S., S. E. Wilken, D. Knop, K. V. Solomon and M. A. O'Malley	The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown	Metabolic Engineering
2017	10.1016/j.pbi.2017.05.006	Shakoor, N., S. Lee and T. C. Mockler	High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field	Current Opinion in Plant Biology
2017	10.1016/j.biocel.2017.06.016	Shaul, O.	How introns enhance gene expression	The International Journal of Biochemistry & Cell Biology
2017	10.1002/bit.26180	Shi, J., D. Wu, L. Zhang, B. A. Simmons, S. Singh, B. Yang and C. E. Wyman	Dynamic changes of substrate reactivity and enzyme adsorption on partially hydrolyzed cellulose	Biotechnology and Bioengineering
2017	10.3389/fmicb.2017.02185	Shi, S. B. and H. M. Zhao	Metabolic engineering of oleaginous yeasts for production of fuels and chemicals	Frontiers in Microbiology
2017	10.1073/pnas.1710798114	Shih, P. M., L. M. Ward and W. W. Fischer	Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi	Proceedings of the National Academy of Sciences
2017	10.1021/acs.jpcb.6b07884	Simakov, N., D. A. Leonard, J. C. Smith, T. Wymore and A. Szarecka	A Distal Disulfide Bridge in OXA-1 beta-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Omega Loop	Journal of Physical Chemistry B
2017	10.1007/s00253-017-8506-z	Sitepu, I. R., L. A. Garay, L. Enriquez, R. Fry, J. H. Butler, J. M. Lopez, A. Kanti, S. A. Faulina, A. J. Nugroho, B. A. Simmons, S. W. Singer, C. W. Simmons and K. Boundy-Mills	1-Ethyl-3-methylimidazolium tolerance and intracellular lipid accumulation of 38 oleaginous yeast species	Applied Microbiology and Biotechnology
2017	10.1128/mBio.00530-17	Skennerton, C. T., K. Chourey, R. Iyer, R. L. Hettich, G. W. Tyson and V. J. Orphan	Methane-fueled syntrophy through extracellular electron transfer: Uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea	mBio
2017	10.1038/s41598-017-15048-7	Smith MD, C. X., Petridis L, Mostofian B, Smith JC	Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose A Molecular Dynamics Analysis	Scientific Reports
2017	10.1016/j.bpj.2017.01.008	Smith, J. C.	Pickin' up Good Vibrations	Biophysical Journal
2017	10.1038/s41598-017-15048-7	Smith, M. D., X. Cheng, L. Petridis, B. Mostofian and J. C. Smith	Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis	Scientific Reports
2017	10.1021/acssynbio.6b00240	Soh, L. M. J., W. S. Mak, P. P. Lin, L. Mi, F. Y. H. Chen, R. Damoiseaux, J. B. Siegel and J. C. Liao	Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design	ACS Synthetic Biology
2017	10.1128/microbiolspec.FUNK-0053-2016	Spatafora, J. W., M. C. Aime, I. V. Grigoriev, F. Martin, J. E. Stajich and M. Blackwell	The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies	Microbiology Spectrum
2017	10.1111/gbi.12193	Stackhouse, B., M. C. Y. Lau, T. Vishnivetskaya, N. Burton, R. Wang, A. Southworth, L. Whyte and T. C. Onstott	Atmospheric CH4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature	Geobiology
2017	10.1128/genomeA.00617-17	Starkenburg, S. R., J. E. W. Polle, B. Hovde, H. E. Daligault, K. W. Davenport, A. Huang, P. Neofotis and Z. McKie-Krisberg	Draft nuclear genome, complete chloroplast genome, and complete mitochondrial genome for the biofuel/bioproduct feedstock species Scenedesmus obliquus strain DOE0152z	Genome Announcements
2017	10.1128/AEM.00696-17	Steven, B., C. Hesse, J. Soghigian, L. V. Gallegos-Graves and J. Dunbar	Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant	Applied and Environmental Microbiology
2017	10.1016/j.copbio.2017.02.016	Straub, C. T., B. M. Zeldes, G. J. Schut, M. W. W. Adams and R. M. Kelly	Extremely thermophilic energy metabolisms: biotechnological prospects	Current Opinion in Biotechnology
2017	10.21769/BioProtoc.2263	Stuart, R. K., X. Mayali, M. P. Thelen, J. Pett-Ridge and P. K. Weber	Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM)	Bio-protocol
2017	10.1021/acs.analchem.7b00396	Su, X. Y., W. Y. Lu and J. D. Rabinowitz	Metabolite spectral accuracy on orbitraps	Analytical Chemistry
2017	10.1186/s13068-017-0842-9	Sun, J., J. Shi, N. V. S. N. Murthy Konda, D. Campos, D. Liu, S. Nemser, J. Shamshina, T. Dutta, P. Berton, G. Gurau, R. D. Rogers, B. A. Simmons and S. Singh	Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation	Biotechnology for Biofuels
2017	10.1039/C7GC01179B	Sun, J., N. V. S. N. M. Konda, R. Parthasarathi, T. Dutta, M. Valiev, F. Xu, B. A. Simmons and S. Singh	One-pot integrated biofuel production using low-cost biocompatible protic ionic liquids	Green Chemistry
2017	10.1111/1462-2920.13765	Takemura, A. F., C. H. Corzett, F. Hussain, P. Arevalo, M. Datta, X. Yu, F. Le Roux and M. F. Polz	Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome	Environmental Microbiology
2017	10.1038/srep42839	Tanger, P., S. Klassen, J. P. Mojica, J. T. Lovell, B. T. Moyers, M. Baraoidan, M. E. B. Naredo, K. L. McNally, J. Poland, D. R. Bush, H. Leung, J. E. Leach and J. K. McKay	Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice	Scientific reports
2017	10.1128/microbiolspec.FUNK-0057-2016	Taylor, J. W., S. Branco, C. Gao, C. Hann-Soden, L. Montoya, I. Sylvain and P. Gladieux	Sources of fungal genetic variation and associating it with phenotypic diversity	Microbiology Spectrum
2017	10.1186/s13068-017-0937-3	Thomas, V. A., B. S. Donohoe, M. Li, Y. Pu, A. J. Ragauskas, R. Kumar, T. Y. Nguyen, C. M. Cai and C. E. Wyman	Adding tetrahydrofuran to dilute acid pretreatment provides new insights into substrate changes that greatly enhance biomass deconstruction by Clostridium thermocellum and fungal enzymes	Biotechnology for Biofuels
2017	10.1002/bit.26374	Thompson, R. A. and C. T. Trinh	Overflow metabolism and growth cessation in Clostridium thermocellum DSM1313 during high cellulose loading fermentations	Biotechnology and Bioengineering
2017	10.1128/AEM.03044-16	Thorgersen, M. P., W. A. Lancaster, L. Rajeev, X. Ge, B. J. Vaccaro, F. L. Poole, A. P. Arkin, A. Mukhopadhyay and M. W. W. Adams	A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium	Applied and Environmental Microbiology
2017	10.3389/fmicb.2017.01529	Thorgersen, M. P., W. A. Lancaster, X. Ge, G. M. Zane, K. M. Wetmore, B. J. Vaccaro, F. L. Poole, A. D. Younkin, A. M. Deutschbauer, A. P. Arkin, J. D. Wall and M. W. W. Adams	Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions	Frontiers in Microbiology
2017	10.1186/s13068-017-0961-3	Tian, L., S. J. Perot, D. Stevenson, T. Jacobson, A. A. Lanahan, D. Amador-Noguez, D. G. Olson and L. R. Lynd	Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol	Biotechnology for Biofuels
2017	10.1186/s12934-017-0783-9	Tian, L., S. J. Perot, S. Hon, J. Zhou, X. Liang, J. T. Bouvier, A. M. Guss, D. G. Olson and L. R. Lynd	Enhanced ethanol formation by Clostridium thermocellum via pyruvate decarboxylase	Microbial Cell Factories
2017	10.1007/978-3-319-31421-1_372-1	Tian, T. and T. S. Lee	Advanced Biodiesel and Biojet Fuels from Lignocellulosic Biomass	Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals
2017	10.1016/j.fuel.2017.04.051	To, T. Q., K. Shah, P. Tremain, B. A. Simmons, B. Moghtaderi and R. Atkin	Treatment of lignite and thermal coal with low cost amino acid based ionic liquid-water mixtures	Fuel
2017	https://journals-crea.4science.it/index.php/maydica/article/view/1578/1088	Todd, J., H. Sandhu, A. Hale, B. Glaz and J. P. Wang	Phenotypic evaluation of a diversity panel selected from the world collection of sugarcane (Saccharum spp) and related grasses	Maydica
2017	10.1002/ese3.144	Tolbert, A. and A. J. Ragauskas	Advances in understanding the surface chemistry of lignocellulosic biomass via time-of-flight secondary ion mass spectrometry	Energy Science & Engineering
2017	10.1002/cplu.201700138	Tolbert, A. K., C. G. Yoo and A. J. Ragauskas	Understanding the Changes to Biomass Surface Characteristics after Ammonia and Organosolv Pretreatments by Using Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS)	ChemPlusChem
2017	10.1021/acssuschemeng.6b01877	Tolbert, A. K., J. M. Young, S. Jung, D. Chung, A. Passian, J. Westpheling and A. J. Ragauskus	Surface Characterization of Populus during Caldicellulosiruptor bescii Growth by TOF-SIMS Analysis	ACS Sustainable Chemistry & Engineering
2017	10.1124/mol.116.105031	Toutounchian, J. J., J. Pagadala, D. D. Miller, J. Baudry, F. Park, E. Chaum, V. Morales-Tirado and C. R. Yates	Novel Small Molecule JP-153 Targets the Src-FAK-Paxillin Signaling Complex to Inhibit VEGF-Induced Retinal Angiogenesis	Molecular Pharmacology
2017	10.1038/nmeth.4343	Trigg, S. A., R. M. Garza, A. MacWilliams, J. R. Nery, A. Bartlett, R. Castanon, A. Goubil, J. Feeney, R. O'Malley, S. S. C. Huang, Z. Z. Zhang, M. Galli and J. R. Ecker	CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping	Nature Methods
2017	10.3389/fpls.2017.00335	Truong, S. K., R. F. McCormick and J. E. Mullet	Bioenergy sorghum crop model predicts vpd-limited transpiration traits enhance biomass yield in water-limited environments	Frontiers in Plant Science
2017	10.1016/j.soilbio.2016.12.017	Tu, Q. C., Z. L. He, L. Y. Wu, K. Xue, G. Xie, P. Chain, P. B. Reich, S. E. Hobbie and J. Z. Zhou	Metagenomic reconstruction of nitrogen cycling pathways in a CO2- enriched grassland ecosystem	Soil Biology & Biochemistry
2017	10.1016/j.aca.2017.09.023	Tuomivaara, S. T., P. Schliekelman, A. V. Nairn, K. W. Moremen and W. S. York	RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM)	Analytica Chimica Acta
2017	10.1371/journal.ppat.1006578	Uehling, J., A. Deveau and M. Paoletti	Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems	PLoS Pathogens
2017	10.1111/1462-2920.13669	Uehling, J., A. Gryganskyi, K. Hameed, T. Tschaplinski, P. K. Misztal, S. Wu, A. Desiro, N. Vande Pol, Z. Du, A. Zienkiewicz, K. Zienkiewicz, E. Morin, E. Tisserant, R. Splivallo, M. Hainaut, B. Henrissat, R. Ohm, A. Kuo, J. Yan, A. Lipzen, M. Nolan, K. LaButti, K. Barry, A. H. Goldstein, J. Labbe, C. Schadt, G. Tuskan, I. Grigoriev, F. Martin, R. Vilgalys and G. Bonito	Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens	Environmental Microbiology
2017	10.3389/fmicb.2017.01272	Utturkar, S. M., D. M. Klingeman, R. A. Hurt, Jr. and S. D. Brown	A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies	Frontiers in Microbiology
2017	10.1111/nph.14571	Valverde-Barrantes, O. J., G. T. Freschet, C. Roumet and C. B. Blackwood	A worldview of root traits: the influence of ancestry, growth form, climate and mycorrhizal association on the functional trait variation of fine-root tissues in seed plants	New Phytologist
2017	10.1128/AAC.01636-16	Vandavasi VG, L. P., Weiss KL, Parks JM, Cooper JB, Ginell SL, Coates L	Active-site protonation states in an acyl-enzyme intermediate of a class A B-lactamase with a monobactam substrate	Antimicrobial Agents and Chemotherapy
2017	10.1038/ncomms15128	Venturelli, O. S., M. Tei, S. Bauer, L. J. G. Chan, C. J. Petzold and A. P. Arkin	Programming mRNA decay to modulate synthetic circuit resource allocation	Nature Communications
2017	10.1186/s13068-017-0917-7	Verbeke, T. J., G. M. Garcia and J. G. Elkins	The effect of switchgrass loadings on feedstock solubilization and biofuel production by Clostridium thermocellum	Biotechnology for Biofuels
2017	10.1038/srep43355	Verbeke, T. J., R. J. Giannone, D. M. Klingeman, N. L. Engle, T. Rydzak, A. M. Guss, T. J. Tschaplinski, S. D. Brown, R. L. Hettich and J. G. Elkins	Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum	Scientific Reports
2017	10.3389/fpls.2017.01505	Verhertbruggen, Y., J. L. Walker, F. Guillon and H. V. Scheller	A Comparative Study of Sample Preparation for Staining and Immunodetection of Plant Cell Walls by Light Microscopy	Frontiers in Plant Science
2017	10.1002/wsbm.1391	Voit, E. O.	The best models of metabolism	WIREs Systems Biology and Medicine
2017	10.1016/j.bbagen.2016.06.015	Vural, D., X. Hu, B. Lindner, N. Jain, Y. Miao, X. Cheng, Z. Liu, L. Hong and J. C. Smith	Quasielastic neutron scattering in biology: Theory and applications	Biochimica et Biophysica Acta General Subjects
2017	10.1186/s12864-017-4158-8	Wai, C. M., J. S. Zhang, T. C. Jones, C. Nagai and R. Ming	Cell wall metabolism and hexose allocation contribute to biomass accumulation in high yielding extreme segregants of a Saccharum interspecific F2 population	BMC Genomics
2017	10.1111/tpj.13630	Wai, C. M., R. VanBuren, J. S. Zhang, L. X. Huang, W. J. Miao, P. P. Edger, W. C. Yim, H. D. Priest, B. C. Meyers, T. Mockler, J. A. C. Smith, J. C. Cushman and R. Ming	Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple	Plant Journal
2017	10.1186/s13068-017-0703-6	Walker, J. A., S. Pattathil, L. F. Bergeman, E. T. Beebe, K. Deng, M. Mirzai, T. R. Northen, M. G. Hahn and B. G. Fox	Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling	Biotechnology for Biofuels
2017	10.1002/bit.26287	Wan, N., D. M. DeLorenzo, L. He, L. You, C. M. Immethun, G. Wang, E. E. K. Baidoo, W. Hollinshead, J. D. Keasling, T. S. Moon and Y. J. Tang	Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence	Biotechnology and Bioengineering
2017	10.1016/j.tibtech.2016.12.010	Warth, B., N. Levin, D. Rinehart, J. Teijaro, H. P. Benton and G. Siuzdak	Metabolizing Data in the Cloud	Trends in Biotechnology
2017	10.1007/10_2016_46	Weighill, D. A. and D. Jacobson	Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology	Advances in Biochemical Engineering/Biotechnology
2017	doi:10.1107/S2053230X17004587	Welner, D. H., A. Y.-L. Tsai, A. M. DeGiovanni, H. V. Scheller and P. D. Adams	X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa	Acta Crystallographica Section F
2017	10.1371/journal.pone.0177591	Welner, D. H., D. Shin, G. P. Tomaleri, A. M. DeGiovanni, A. Y.-L. Tsai, H. M. Tran, S. F. Hansen, D. T. Green, H. V. Scheller and P. D. Adams	Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes	PLOS ONE
2017	10.1371/journal.pone.0176716	Wen, C. Q., L. Y. Wu, Y. J. Qin, J. D. Van Nostrand, D. L. Ning, B. Sun, K. Xue, F. F. Liu, Y. Deng, Y. T. Liang and J. Z. Zhou	Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform	PLOS ONE
2017	10.1038/nature24624	Whiteley, M., S. P. Diggle and E. P. Greenberg	Progress in and promise of bacterial quorum sensing research	Nature
2017	10.1186/s13068-017-0952-4	Wilbanks, B. and C. T. Trinh	Comprehensive characterization of toxicity of fermentative metabolites on microbial growth	Biotechnology for Biofuels
2017	10.1128/AEM.00444-17	Williams-Rhaesa, A. M., F. L. Poole, J. T. Dinsmore, G. L. Lipscomb, G. M. Rubinstein, I. M. Scott, J. M. Conway, L. L. Lee, P. A. Khatibi, R. M. Kelly and M. W. W. Adams	Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii	Applied and Environmental Microbiology
2017	10.1186/s13068-017-0918-6	Willis, J. D., J. N. Grant, M. Mazarei, L. M. Kline, C. S. Rempe, A. G. Collins, G. B. Turner, S. R. Decker, R. W. Sykes, M. F. Davis, N. Labbe, J. L. Jurat-Fuentes and C. N. Stewart	The TcEG1 beetle (Tribolium castaneum) cellulase produced in transgenic switchgrass is active at alkaline pH and auto-hydrolyzes biomass for increased cellobiose release	Biotechnology for Biofuels
2017	10.1128/AEM.02751-16	Wilson, C. M., D. M. Klingeman, C. Schlachter, M. H. Syed, C.-w. Wu, A. M. Guss and S. D. Brown	LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313	Applied and Environmental Microbiology
2017	10.1002/2016jg003600	Wilson, R. M., L. Fitzhugh, G. J. Whiting, S. Frolking, M. D. Harrison, N. Dimova, W. C. Burnett and J. P. Chanton	Greenhouse gas balance over thaw-freeze cycles in discontinuous zone permafrost	Journal of Geophysical Research-Biogeosciences
2017	10.1016/j.orggeochem.2017.06.011	Wilson, R. M., M. M. Tfaily, V. I. Rich, J. K. Keller, S. D. Bridgham, C. M. Zalman, L. Meredith, P. J. Hanson, M. Hines, L. Pfeifer-Meister, S. R. Saleska, P. Crill, W. T. Cooper, J. P. Chanton and J. E. Kostka	Hydrogenation of organic matter as a terminal electron sink sustains high CO2:CH4 production ratios during anaerobic decomposition	Organic Geochemistry
2017	10.1007/978-3-319-31421-1_219-1	Wong, J., L. Rios-Solis and J. D. Keasling	Microbial Production of Isoprenoids	Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals
2017	10.1128/genomeA.00300-17	Woo, H. L., K. M. DeAngelis, H. Teshima, K. Davenport, H. Daligault, T. Erkkila, L. Goodwin, W. Gu, C.-C. Lo, C. Munk, M. Scholz, Y. Xu, P. Chain, D. Bruce, C. Detter, R. Tapia, C. Han, B. A. Simmons and T. C. Hazen	High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp	Genome Announcements
2017	10.1038/s41598-017-02628-w	Wu, C.-w., T. Spike, D. M. Klingeman, M. Rodriguez, V. R. Bremer and S. D. Brown	Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85	Scientific Reports
2017	10.1038/ismej.2017.75	Wu, L. W., Y. F. Yang, S. P. Wang, H. W. Yue, Q. Y. Lin, Y. G. Hu, Z. L. He, J. D. Van Nostrand, L. Hale, X. Z. Li, J. A. Gilbert and J. Z. Zhou	Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling	ISME Journal
2017	10.1128/genomeA.00582-17	Wu, X., A. M. Deutschbauer, A. E. Kazakov, K. M. Wetmore, B. A. Cwick, R. M. Walker, P. S. Novichkov, A. P. Arkin and R. Chakraborty	Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center	Genome Announcements
2017	10.1007/978-3-319-56457-9_6	Wyman, C. E. and B. Yang	Combined Severity Factor for Predicting Sugar Recovery in Acid-Catalyzed Pretreatment Followed by Enzymatic Hydrolysis	Hydrothermal Processing in Biorefineries: Production of Bioethanol and High Added-Value Compounds of Second and Third Generation Biomass
2017	DOI 10.1007/978-1-4939-2493-6_521-3	Wyman, C. E., R. Kumar and C. M. Cai	Bioethanol from Lignocellulosic Biomass	Encyclopedia of Sustainability Science and Technology
2017	10.1016/j.soilbio.2017.04.011	Xia, M., A. F. Talhelm and K. S. Pregitzer	Chronic nitrogen deposition influences the chemical dynamics of leaf litter and fine roots during decomposition	Soil Biology and Biochemistry
2017	10.1126/scisignal.aaf5034	Xiao Z, R. D., Velazquez HA, Chin AL, Yates CR, Carrick JD, Baudry J, Smith JC, and Quarles LD	A Computationally Identified Compound Antagonizes Excess FGF-23 Signaling in Renal Tubules and a Mouse Model of Hypophosphatemia	Science Signaling
2017	10.1371/journal.pgen.1006737	Xiong, Y., V. W. Wu, A. Lubbe, L. Qin, S. Deng, M. Kennedy, D. Bauer, V. R. Singan, K. Barry, T. R. Northen, I. V. Grigoriev and N. L. Glass	A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism	PLOS Genetics
2017	10.1073/pnas.1703321114	Xu, J. Y., N. Liu, K. J. Qiao, S. Vogg and G. Stephanopoulos	Application of metabolic controls for the maximization of lipid production in semicontinuous fermentation	Proceedings of the National Academy of Sciences of the United States of America
2017	10.1002/bit.26285	Xu, P., K. J. Qiao and G. Stephanopoulos	Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica	Biotechnology and Bioengineering
2017	10.1186/s13068-017-0927-5	Yaegashi, J., J. Kirby, M. Ito, J. Sun, T. Dutta, M. Mirsiaghi, E. R. Sundstrom, A. Rodriguez, E. Baidoo, D. Tanjore, T. Pray, K. Sale, S. Singh, J. D. Keasling, B. A. Simmons, S. W. Singer, J. K. Magnuson, A. P. Arkin, J. M. Skerker and J. M. Gladden	Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts	Biotechnology for Biofuels
2017	10.1364/ol.42.000523	Yang, W. L., A. Li, Y. Z. Suo, F. K. Lu and X. S. Xie	Simultaneous two-color stimulated Raman scattering microscopy by adding a fiber amplifier to a 2 ps OPO-based SRS microscope	Optics Letters
2017	10.1186/s12864-017-3980-3	Yang, X. P., J. Song, Q. You, D. R. Paudel, J. S. Zhang and J. P. Wang	Mining sequence variations in representative polyploid sugarcane germplasm accessions	BMC Genomics
2017	10.1186/s13068-017-0760-x	Yang, Y., C. G. Yoo, H.-B. Guo, W. Rottmann, K. A. Winkeler, C. M. Collins, L. E. Gunter, S. S. Jawdy, X. Yang, H. Guo, Y. Pu, A. J. Ragauskas, G. A. Tuskan and J.-G. Chen	Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus	Biotechnology for Biofuels
2017	10.1128/AEM.03020-16	Yeager, C. M., L. V. Gallegos-Graves, J. Dunbar, C. N. Hesse, H. Daligault and C. R. Kuske	Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau	Applied and Environmental Microbiology
2017	10.1093/jxb/erx264	Yerramsetty, P., E. M. Agar, W. C. Yim, J. C. Cushman and J. O. Berry	An rbcL mRNA-binding protein is associated with C-3 to C-4 evolution and light-induced production of Rubisco in Flaveria	Journal of Experimental Botany
2017	10.7717/peerj.3486	Yim, W. C. and J. C. Cushman	Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments	PeerJ
2017	10.1039/C6GC03627A	Yoo, C. G., M. Li, X. Meng, Y. Pu and A. J. Ragauskas	Effects of organosolv and ammonia pretreatments on lignin properties and its inhibition for enzymatic hydrolysis	Green Chemistry
2017	10.1016/j.cogsc.2017.03.003	Yoo, C. G., Y. Pu and A. J. Ragauskas	Ionic liquids: Promising green solvents for lignocellulosic biomass utilization	Current Opinion in Green and Sustainable Chemistry
2017	10.1039/C7GC02219K	Yoo, C. G., Y. Yang, Y. Pu, X. Meng, W. Muchero, K. L. Yee, O. A. Thompson, M. Rodriguez, G. Bali, N. L. Engle, E. Lindquist, V. Singan, J. Schmutz, S. P. DiFazio, T. J. Tschaplinski, G. A. Tuskan, J.-G. Chen, B. Davison and A. J. Ragauskas	Insights of biomass recalcitrance in natural Populus trichocarpa variants for biomass conversion	Green Chemistry
2017	10.1007/s12155-016-9795-2	Yoon, S., S. Aucar, B. J. Hernlem, S. Edme, N. Palmer, G. Sarath, R. Mitchell, E. Blumwald and C. M. Tobias	Generation of octaploid switchgrass by seedling treatment with mitotic inhibitors	Bioenergy Research
2017	10.1371/journal.pone.0180527	Yordanov, Y. S., C. Ma, E. Yordanova, R. Meilan, S. H. Strauss and V. B. Busov	BIG LEAF is a regulator of organ size and adventitious root formation in poplar	PLOS ONE
2017	10.1039/9781782623946-00353	York, W. S., M. Allahyari and J. D. Hogan	CHAPTER 16 NMR Databases for Plant Cell Wall Biopolymers	NMR in Glycoscience and Glycotechnology
2017	10.1016/j.procbio.2016.11.002	Yu, C., D. R. Harrold, J. T. Claypool, B. A. Simmons, S. W. Singer, C. W. Simmons and J. S. VanderGheynst	Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition	Process Biochemistry
2017	10.1021/acs.energyfuels.7b01567	Yuan, X., L. He, S. Singh, B. A. Simmons and G. Cheng	Effect of Ionic Liquid Pretreatment on the Porosity of Pine: Insights from Small-Angle Neutron Scattering, Nitrogen Adsorption Analysis, and X-ray Diffraction	Energy & Fuels
2017	10.1021/acssuschemeng.7b00480	Yuan, X., S. Singh, B. A. Simmons and G. Cheng	Biomass Pretreatment Using Dilute Aqueous Ionic Liquid (IL) Solutions with Dynamically Varying IL Concentration and Its Impact on IL Recycling	ACS Sustainable Chemistry & Engineering
2017	10.1016/j.biortech.2017.02.014	Yuan, X., Y. Duan, L. He, S. Singh, B. Simmons and G. Cheng	Characterization of white poplar and eucalyptus after ionic liquid pretreatment as a function of biomass loading using X-ray diffraction and small angle neutron scattering	Bioresource Technology
2017	10.1016/j.cels.2017.08.003	Yurkovich, J. T., B. J. Yurkovich, A. Drager, B. O. Palsson and Z. A. King	A Padawan programmer's guide to developing software libraries	Cell Systems
2017	10.1074/jbc.M117.804914	Yurkovich, J. T., D. C. Zielinski, L. Yang, G. Paglia, O. Rolfsson, O. E. Sigurjonsson, J. T. Broddrick, A. Bordbar, K. Wichuk, S. Brynjolfsson, S. Palsson, S. Gudmundsson and B. O. Palsson	Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks	Journal of Biological Chemistry
2017	10.1371/journal.pcbi.1005424	Yurkovich, J. T., L. Yang and B. O. Palsson	Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells	Plos Computational Biology
2017	10.1109/CCTA.2017.8062584	Yurkovich, J. T., L. Yang, B. O. Palsson and Ieee	Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells	2017 IEEE Conference on Control Technology and Applications
2017	10.1021/acschembio.7b00714	Yuzawa, S., C. B. Bailey, T. Fujii, R. Jocic, J. F. Barajas, V. T. Benites, E. E. K. Baidoo, Y. Chen, C. J. Petzold, L. Katz and J. D. Keasling	Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase	ACS Chemical Biology
2017	10.1038/ja.2016.136	Yuzawa, S., J. D. Keasling and L. Katz	Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges	The Journal of Antibiotics
2017	10.1021/acssynbio.6b00376	Zeitoun, R. I., G. Pines, W. C. Grau and R. T. Gill	Quantitative tracking of combinatorially engineered populations with multiplexed binary assemblies	ACS Synthetic Biology
2017	10.1039/C6GC03379B	Zeng, J., M. J. L. Mills, B. A. Simmons, M. S. Kent and K. L. Sale	Understanding factors controlling depolymerization and polymerization in catalytic degradation of ?-ether linked model lignin compounds by versatile peroxidase	Green Chemistry
2017	10.1128/JB.00286-17	Zeng, L., E. Wooton, D. A. Stahl and P. J. Walian	Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough	Journal of Bacteriology
2017	10.1007/978-1-4939-6533-5_11	Zeng, W., B. Ebert, H. T. Parsons, C. Rautengarten, A. Bacic and J. L. Heazlewood	Enrichment of Golgi Membranes from Triticum aestivum (Wheat) Seedlings	Isolation of Plant Organelles and Structures: Methods and Protocols
2017	10.1186/s13068-017-0953-3	Zeng, Y., M. E. Himmel and S.-Y. Ding	Visualizing chemical functionality in plant cell walls	Biotechnology for Biofuels
2017	10.1016/j.fgb.2017.06.003	Zhang, J. W. and J. S. Schilling	Role of carbon source in the shift from oxidative to hydrolytic wood decomposition by Postia placenta	Fungal Genetics and Biology
2017	10.1021/acssynbio.6b00372	Zhang, J., J. F. Barajas, M. Burdu, G. Wang, E. E. Baidoo and J. D. Keasling	Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis	ACS Synthetic Biology
2017	10.1021/acssynbio.6b00136	Zhang, J., J. F. Barajas, M. Burdu, T. L. Ruegg, B. Dias and J. D. Keasling	Development of a Transcription Factor-Based Lactam Biosensor	ACS Synth Biol
2017	10.1021/acs.est.6b02980	Zhang, P., Z. He, J. D. Van Nostrand, Y. Qin, Y. Deng, L. Wu, Q. Tu, J. Wang, C. W. Schadt, M. W. Fields, T. C. Hazen, A. P. Arkin, D. A. Stahl and J. Zhou	Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer	Environmental Science & Technology
2017	10.1038/srep40712	Zhang, Q., S.-R. Jun, M. Leuze, D. Ussery and I. Nookaew	Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer	Scientific Reports
2017	10.1038/ismej.2016.180	Zhang, X. M., E. R. Johnston, L. H. Li, K. T. Konstantinidis and X. G. Han	Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe	ISME Journal
2017	10.1007/s00122-017-2876-6	Zhang, X. Y., O. Valdes-Lopez, C. Arellano, G. Stacey and P. Balint-Kurti	Genetic dissection of the maize (Zea mays L.) MAMP response	Theoretical and Applied Genetics
2017	10.1021/jacs.7b08012	Zhang, Z. Y., L. Chen, L. Liu, X. Y. Su and J. D. Rabinowitz	Chemical basis for deuterium labeling of fat and NADPH	Journal of the American Chemical Society
2017	10.1111/nph.14704	Zhao, C. S., T. Lasses, L. Bako, D. Y. Kong, B. Y. Zhao, B. Chanda, A. Bombarely, A. Cruz-Ramirez, B. Scheres, A. M. Brunner and E. P. Beers	XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED	New Phytologist
2017	10.1039/C7GC00944E	Zhao, W., L.-P. Xiao, G. Song, R.-C. Sun, L. He, S. Singh, B. A. Simmons and G. Cheng	From lignin subunits to aggregates: insights into lignin solubilization	Green Chemistry
2017	10.1128/JB.00542-16	Zheng, T., D. G. Olson, S. J. Murphy, X. Shao, L. Tian and L. R. Lynd	Both adhE and a Separate NADPH-Dependent Alcohol Dehydrogenase Gene, adhA, Are Necessary for High Ethanol Production in Thermoanaerobacterium saccharolyticum	Journal of Bacteriology
2017	10.1186/s13068-017-0940-8	Zheng, T., J. Cui, H. R. Bae, L. R. Lynd and D. G. Olson	Expression of adhA from different organisms in Clostridium thermocellum	Biotechnology for Biofuels
2017	10.1021/acs.est.7b02204	Zhou J, S. M., Cooper SJ, Cheng X, Smith JC, Parks JM	Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane	Environmental Science & Technology
2017	10.1128/mBio.01780-17	Zhou, A., R. Lau, R. Baran, J. Ma, F. von Netzer, W. Shi, D. Gorman-Lewis, M. L. Kempher, Z. He, Y. Qin, Z. Shi, G. M. Zane, L. Wu, B. P. Bowen, T. R. Northen, K. L. Hillesland, D. A. Stahl, J. D. Wall, A. P. Arkin and J. Zhou	Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris	mBio
2017	10.1128/mmbr.00002-17	Zhou, J. Z. and D. L. Ning	Stochastic community assembly: does it matter in microbial ecology?	Microbiology and Molecular Biology Reviews
2017	10.1007/s10295-016-1896-6	Zhou, J., X. Shao, D. G. Olson, S. J.-L. Murphy, L. Tian and L. R. Lynd	Determining the roles of the three alcohol dehydrogenases (AdhA, AdhB and AdhE) in Thermoanaerobacter ethanolicus during ethanol formation	Journal of Industrial Microbiology and Biotechnology
2017	10.3389/fpls.2017.01562	Zhu, C., J. Yang and C. Shyu	Setaria comes of age: Meeting Report on the Second International Setaria Genetics Conference	Frontiers in Plant Science
2017	10.1016/j.plantsci.2017.07.008	Zogli, P. and M. Libault	Plant response to biotic stress: Is there a common epigenetic response during plant-pathogenic and symbiotic interactions?	Plant Science
2017	10.1111/1751-7915.12855	Zuniga, C., L. Zaramela and K. Zengler	Elucidation of complexity and prediction of interactions in microbial communities	Microbial Biotechnology
2017	10.1128/AEM.00969-17	Zurawski, J. V., P. A. Khatibi, H. O. Akinosho, C. T. Straub, S. H. Compton, J. M. Conway, L. L. Lee, A. J. Ragauskas, B. H. Davison, M. W. W. Adams and R. M. Kelly	Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii	Applied and Environmental Microbiology
2016	10.1038/ncomms11706	Abdel-Ghany, S. E., M. Hamilton, J. L. Jacobi, P. Ngam, N. Devitt, F. Schilkey, A. Ben-Hur and A. S. N. Reddy	A survey of the sorghum transcriptome using single-molecule long reads	Nature Communications
2016	10.1038/nplants.2016.178	Abraham, P. E., H. F. Yin, A. M. Borland, D. Weighill, S. D. Lim, H. C. De Paoli, N. Engle, P. C. Jones, R. Agh, D. J. Weston, S. D. Wullschleger, T. Tschaplinski, D. Jacobson, J. C. Cushman, R. L. Hettich, G. A. Tuskan and X. H. Yang	Transcript, protein and metabolite temporal dynamics in the CAM plant Agave	Nature Plants
2016	10.1107/S2052252516010514	Aggarwal M, K. A., Velazquez H, Zoeuml S, Smith J, and McKenna R	Neutron Structure of Human Carbonic Anhydrase II in Complex with Methazolamide Mapping the Solvent and H-Bonding Patterns of an Effective Clinical Drug	IUCrJ
2016	10.3389/fenrg.2016.00036	Al Abdallah, Q., B. T. Nixon and J. R. Fortwendel	The enzymatic conversion of major algal and cyanobacterial carbohydrates to bioethanol	Frontiers in Energy Research
2016	10.1021/acs.jpcb.6b02839	Arbelo-Lopez HD, S. N., Smith JC, Lopez-Garriga J, and Wymore T	Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme	Journal of Physical Chemistry B
2016	10.1007/s10681-016-1672-8	Arro, J., J. W. Park, C. M. Wai, R. VanBuren, Y. B. Pan, C. Nagai, J. da Silva and R. Ming	Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.)	Euphytica
2016	10.1089/3dp.2016.0027	Bader, C., W. G. Patrick, D. Kolb, S. G. Hays, S. Keating, S. Sharma, D. Dikovsky, B. Belocon, J. C. Weaver, P. A. Silver and N. Oxman	Grown, printed, and biologically augmented: An additively manufactured microfluidic wearable, functionally templated for synthetic microbes	3D Printing and Additive Manufacturing
2016	10.1016/j.biochi.2015.06.009	Bansal, S. and T. P. Durrett	Camelina sativa: An ideal platform for the metabolic engineering and field production of industrial lipids	Biochimie
2016	10.1016/j.copbio.2016.03.016	Bassalo, M. C., R. Liu and R. T. Gill	Directed evolution and synthetic biology applications to microbial systems	Current Opinion in Biotechnology
2016	10.1007/s11101-015-9426-0	Berim, A. and D. R. Gang	Methoxylated flavones: occurrence, importance, biosynthesis	Phytochemistry Reviews
2016	10.1186/s13068-016-0660-5	Bhagia, S., H. Li, X. Gao, R. Kumar and C. E. Wyman	Flowthrough pretreatment with very dilute acid provides insights into high lignin contribution to biomass recalcitrance	Biotechnology for Biofuels
2016	10.3389/fmicb.2016.00491	Bible, A. N., S. J. Fletcher, D. A. Pelletier, C. W. Schadt, S. S. Jawdy, D. J. Weston, N. L. Engle, T. Tschaplinski, R. Masyuko, S. Polisetti, P. W. Bohn, T. A. Coutinho, M. J. Doktycz and J. L. Morrell-Falvey	A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization	Frontiers in Microbiology
2016	10.1080/15592324.2015.1117721	Bihmidine, S., B. T. Julius, I. Dweikat and D. M. Braun	Tonoplast Sugar Transporters (SbTSTs) putatively control sucrose accumulation in sweet sorghum stems	Plant Signaling & Behavior
2016	10.3389/fmicb.2016.01221	Bird, J. T., B. J. Baker, A. J. Probst, M. Podar and K. G. Lloyd	Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales	Frontiers in Microbiology
2016	10.1039/c6mt00063k	Blaby-Haas, C. E., M. Castruita, S. T. Fitz-Gibbon, J. Kropat and S. S. Merchant	Ni induces the CRR1-dependent regulon revealing overlap and distinction between hypoxia and Cu deficiency responses in Chlamydomonas reinhardtii	Metallomics
2016	10.1016/j.funeco.2016.04.007	Bonito, G., K. Hameed, R. Ventura, J. Krishnan, C. W. Schadt and R. Vilgalys	Isolating a functionally relevant guild of fungi from the root microbiome of Populus	Fungal Ecology
2016	10.1016/j.pbi.2016.04.001	Borland, A. M., H. B. Guo, X. H. Yang and J. C. Cushman	Orchestration of carbohydrate processing for crassulacean acid metabolism	Current Opinion in Plant Biology
2016	10.1016/j.soilbio.2016.02.008	Bracho, R., S. Natali, E. Pegoraro, K. G. Crummer, C. Schadel, G. Celis, L. Hale, L. Y. Wu, H. Q. Yin, J. M. Tiedje, K. T. Konstantinidis, Y. Q. Luo, J. Z. Zhou and E. A. G. Schuur	Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations	Soil Biology & Biochemistry
2016	10.1073/pnas.1613446113	Broddrick, J. T., B. E. Rubin, D. G. Welkie, N. Du, N. Mih, S. Diamond, J. J. Lee, S. S. Golden and B. O. Palsson	Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis	Proceedings of the National Academy of Sciences of the United States of America
2016	10.1021/acs.analchem.6b02479	Broeckling, C. D., A. Ganna, M. Layer, K. Brown, B. Sutton, E. Ingelsson, G. Peers and J. E. Prenni	Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction	Analytical Chemistry
2016	10.1038/nbt.3704	Brown, C. T., M. R. Olm, B. C. Thomas and J. F. Banfield	Measurement of bacterial replication rates in microbial communities	Nature Biotechnology
2016	10.1021/acssynbio.6b00115	Brown, M. E., A. Mukhopadhyay and J. D. Keasling	Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol	ACS Synthetic Biology
2016	10.1038/ncomms10613	Burstein, D., C. L. Sun, C. T. Brown, I. Sharon, K. Anantharaman, A. J. Probst, B. C. Thomas and J. F. Banfield	Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems	Nature Communications
2016	10.1016/j.algal.2016.10.008	Caballero, M. A., D. Jallet, L. B. Shi, C. Rithner, Y. Zhang and G. Peers	Quantification of chrysolaminarin from the model diatom Phaeodactylum tricornutum	Algal Research-Biomass Biofuels and Bioproducts
2016	10.3732/apps.1600031	Carlson, C. H. and L. B. Smart	Electrical capacitance as a predictor of root dry weight in shrub willow (Salix; Salicaceae) parents and progeny(1)	Applications in Plant Sciences
2016	10.1039/c6mb00237d	Chaiboonchoe, A., L. Ghamsari, B. Dohai, P. Ng, B. Khraiwesh, A. Jaiswal, K. Jijakli, J. Koussa, D. R. Nelson, H. Cai, X. P. Yang, R. L. Chang, J. Papin, H. Y. Yu, S. Balaji and K. Salehi-Ashtiani	Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation	Molecular BioSystems
2016	10.3389/fmicb.2016.01874	Chase, A. B., P. Arevalo, M. F. Polz, R. Berlemont and J. B. H. Martiny	Evidence for ecological flexibility in the cosmopolitan genus Curtobacterium	Frontiers in Microbiology
2016	10.1093/femsle/fnw020	Chen, C.-T. and J. C. Liao	Frontiers in microbial 1-butanol and isobutanol production	FEMS Microbiology Letters
2016	10.3389/fpls.2016.01143	Chiang, C. P., W. C. Yim, Y. H. Sun, M. Ohnishi, T. Mimura, J. C. Cushman and H. E. Yen	Identification of ice plant (Mesembryanthemum crystallinum L.) MicroRNAs using RNA-Seq and their putative roles in high salinity responses in seedlings	Frontiers in Plant Science
2016	10.1021/acs.jpcb.6b02057	Clark, A. K., J. H. Wilder, A. W. Grayson, Q. R. Johnson, R. J. Lindsay, R. B. Nellas, E. J. Fernandez and T. Shen	The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor	Journal of Physical Chemistry B
2016	10.1186/s13029-016-0057-7	Clark, L. V. and E. J. Sacks	TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data	Source Code for Biology and Medicine
2016	10.1093/aob/mcw137	Clark, L. V., E. Dzyubenko, N. Dzyubenko, L. Bagmet, A. Sabitov, P. Chebukin, D. A. Johnson, J. B. Kjeldsen, K. K. Petersen, U. Jorgensen, J. H. Yoo, K. Heo, C. Y. Yu, H. Zhao, X. L. Jin, J. H. Peng, T. Yamada and E. J. Sacks	Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia	Annals of Botany
2016	10.3389/fpls.2016.00716	Collier, R., J. Bragg, B. T. Hernandez, J. P. Vogel and R. Thilmony	Use of Agrobacterium rhizogenes Strain 18r12v and Paromomycin Selection for Transformation of Brachypodium distachyon and Brachypodium sylvaticum	Frontiers in Plant Science
2016	10.1038/ncomms10373	Couradeau, E., U. Karaoz, H. C. Lim, U. Nunes da Rocha, T. Northen, E. Brodie and F. Garcia-Pichel	Bacteria increase arid-land soil surface temperature through the production of sunscreens	Nature Communications
2016	10.1007/7397_2016_33	Cronk, Q. C. and A. T. Groover	Introduction: Comparative Genomics of Angiosperm Trees: A New Era of Tree Biology	Plant Genetics and Genomics: Crops and Models
2016	10.1371/journal.pone.0154043	Cui, J. Y., N. M. Good, B. Hu, J. Yang, Q. W. Wang, M. Sadilek and S. Yang	Metabolomics revealed an association of metabolite changes and defective growth in Methylobacterium extorquens AM1 overexpressing ecm during growth on methanol	PLOS ONE
2016	10.1186/s13007-016-0116-8	Czarnecki, O., A. C. Bryan, S. S. Jawdy, X. H. Yang, Z. M. Cheng, J. G. Chen and G. A. Tuskan	Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana	Plant Methods
2016	10.1093/femsle/fnw004	Dash, S., C. Y. Ng and C. D. Maranas	Metabolic modeling of clostridia: current developments and applications	FEMS Microbiology Letters
2016	10.1002/ecy.1513	de Carvalho, T. S., E. D. Jesus, J. Barlow, T. A. Gardner, I. C. Soares, J. M. Tiedje and F. M. D. Moreira	Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria	Ecology
2016	10.1016/j.algal.2016.02.019	de-Bashan, L. E., X. Mayali, B. M. Bebout, P. K. Weber, A. M. Detweiler, J.-P. Hernandez, L. Prufert-Bebout and Y. Bashan	Establishment of stable synthetic mutualism without co-evolution between microalgae and bacteria demonstrated by mutual transfer of metabolites (NanoSIMS isotopic imaging) and persistent physical association (Fluorescent in situ hybridization)	Algal Research
2016	10.1038/ismej.2015.145	Dekas, A. E., S. A. Connon, G. L. Chadwick, E. Trembath-Reichert and V. J. Orphan	Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses	ISME Journal
2016	10.1038/ncomms11152	DeLoache, W. C., Z. N. Russ and J. E. Dueber	Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways	Nature Communications
2016	10.1111/gcb.13098	Deng, Y., Z. L. He, J. B. Xiong, H. Yu, M. Y. Xu, S. E. Hobbie, P. B. Reich, C. W. Schadt, A. Kent, E. Pendall, M. Wallenstein and J. Z. Zhou	Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities	Global Change Biology
2016	10.3852/14-293	Deshpande, V., Q. Wang, P. Greenfield, M. Charleston, A. Porras-Alfaro, C. R. Kuske, J. R. Cole, D. J. Midgley and T. D. Nai	Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences	Mycologia
2016	10.1093/femsec/fiw107	Deveau, A., H. Gross, B. Palin, S. Mehnaz, M. Schnepf, P. Leblond, P. C. Dorrestein and B. Aigle	Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron-limited conditions	FEMS Microbiology Ecology
2016	10.3589/fmicb.2016.00880	Diner, R. E., S. M. Schwenck, J. P. McCrow, H. Zheng and A. E. Allen	Genetic manipulation of competition for nitrate between heterotrophic bacteria and diatoms	Frontiers in Microbiology
2016	10.3389/fbioe.2016.00065	Diner, R. E., V. A. Bielinski, C. L. Dupont, A. E. Allen and P. D. Weyman	Refinement of the diatom episome maintenance sequence and improvement of conjugation-based DNA delivery methods	Frontiers in Bioengineering and Biotechnology
2016	10.1371/journal.pone.0161837	Douglas, S. M., L. M. Chubiz, W. R. Harcombe, F. M. Ytreberg and C. J. Marx	Parallel mutations result in a wide range of cooperation and community consequences in a two-species bacterial consortium	PLOS ONE
2016	10.1016/j.pbi.2016.04.006	Ellsworth, P. Z. and A. B. Cousins	Carbon isotopes and water use efficiency in C4 plants	Current Opinion in Plant Biology
2016	10.1016/j.bmc.2016.07.064	Evangelista, W., R. L. Weir, S. R. Ellingson, J. B. Harris, K. Kapoor, J. C. Smith and J. Baudry	Ensemble-based docking: From hit discovery to metabolism and toxicity predictions	Bioorganic & Medicinal Chemistry
2016	10.1186/s40793-016-0174-6	Everroad, R. C., R. K. Stuart, B. M. Bebout, A. M. Detweiler, J. Z. Lee, D. Woebken, L. Prufert-Bebout and J. Pett-Ridge	Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria	Standards in Genomic Sciences
2016	10.1105/tpc.16.00186	Fang, L., T. Ishikawa, E. A. Rennie, G. M. Murawska, J. Lao, J. Yan, A. Y.-L. Tsai, E. E. K. Baidoo, J. Xu, J. D. Keasling, T. Demura, M. Kawai-Yamada, H. V. Scheller and J. C. Mortimer	Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis	The Plant Cell
2016	10.1534/g3.116.030510	Felderhoff, T. J., L. M. McIntyre, A. Saballos and W. Vermerris	Using genotyping by sequencing to map two novel anthracnose resistance loci in Sorghum bicolor	G3-Genes Genomes Genetics
2016	10.1016/j.soilbio.2016.06.003	Feng, W. T., Z. Shi, J. Jiang, J. Y. Xia, J. Y. Liang, J. Z. Zhou and Y. Q. Luo	Methodological uncertainty in estimating carbon turnover times of soil fractions	Soil Biology & Biochemistry
2016	10.1105/tpc.16.00182	Feng, W., H. Lindner, N. E. Robbins and J. R. Dinneny	Growing Out of Stress: The Role of cell- and organ-scale growth control in plant water-stress responses	Plant Cell
2016	10.1016/j.apenergy.2016.05.100	Field, J. L., P. Tanger, S. J. Shackley and S. M. Haefele	Agricultural residue gasification for low-cost, low-carbon decentralized power: An empirical case study in Cambodia	Applied Energy
2016	10.1002/pro.3050	Filippova, E. V., Z. Wawrzak, J. Ruan, S. Pshenychnyi, R. M. Schultz, A. J. Wolfe and W. F. Anderson	Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli	Protein Science
2016	10.1007/7397_2015_9	Franke, K. R. and P. J. Green	The microRNAs of Brachypodium	Genetics and Genomics of Brachypodium
2016	10.1016/j.algal.2016.06.020	Gallina, A. A., M. Layer, Z. A. King, J. Levering, B. O. Palsson, K. Zengler and G. Peers	A Phaeodactylum tricornutum literature database for interactive annotation of content	Algal Research-Biomass Biofuels and Bioproducts
2016	10.1021/acs.jafc.6b04273	Gao, R. L., F. C. Lu, Y. M. Zhu, M. G. Hahn and J. Ralph	Flexible method for conjugation of phenolic lignin model compounds to carrier proteins	Journal of Agricultural and Food Chemistry
2016	10.1007/s11274-016-2068-6	Gardner, J. G.	Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus	World Journal of Microbiology & Biotechnology
2016	10.1186/s12870-015-0696-x	Gelli, M., S. E. Mitchell, K. Liu, T. E. Clemente, D. P. Weeks, C. Zhang, D. R. Holding and I. M. Dweikat	Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum	BMC Plant Biology
2016	10.1007/s00248-016-0746-4	Geng, H., K. L. Sale, M. B. Tran-Gyamfi, T. W. Lane and E. T. Yu	Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures	Microbial Ecology
2016	10.3389/fmicb.2016.01155	Geng, H., M. B. Tran-Gyamfi, T. W. Lane, K. L. Sale and E. T. Yu	Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds	Frontiers in Microbiology
2016	10.1002/anie.201509989	Gerlits O, W. T., Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, and Kovalevsky A	Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site	Angewandte Chemie
2016	10.1104/pp.15.01977	Gidda, S. K., S. Park, M. Pyc, O. Yurchenko, Y. Q. Cai, P. Wu, D. W. Andrews, K. D. Chapman, J. M. Dyer and R. T. Mullen	Lipid Droplet-Associated Proteins (LDAPs) Are required for the dynamic regulation of neutral lipid compartmentation in plant cells	Plant Physiology
2016	10.1186/s12864-016-3286-x	Gregory, A. C., S. A. Solonenko, J. C. Ignacio-Espinoza, K. LaButti, A. Copeland, S. Sudek, A. Maitland, L. Chittick, F. dos Santos, J. S. Weitz, A. Z. Worden, T. Woyke and M. B. Sullivan	Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer	BMC Genomics
2016	10.1128/aem.02772-15	Guo, J. R., J. R. Cole, Q. P. Zhang, C. T. Brown and J. M. Tiedje	Microbial community analysis with ribosomal gene fragments from shotgun metagenomes	Applied and Environmental Microbiology
2016	10.1126/science.aaf2786	Hackett, S. R., V. R. T. Zanotelli, W. X. Xu, J. Goya, J. O. Park, D. H. Perlman, P. A. Gibney, D. Botstein, J. D. Storey and J. D. Rabinowitz	Systems-level analysis of mechanisms regulating yeast metabolic flux	Science
2016	10.1016/j.soilbio.2016.04.010	Hall, S. J., W. L. Silver, V. I. Timokhin and K. E. Hammel	Iron addition to soil specifically stabilized lignin	Soil Biology and Biochemistry
2016	10.1016/B978-0-444-63475-7.00009-1	Halweg-Edwards, A., M. Bassalo, J. Winkler and R. Gill	Biotechnological strategies for advanced biofuel production: enhancing tolerance phenotypes through genome-scale modifications	Biotechnology for Biofuel Production and Optimization
2016	10.1111/evo.12973	Harcombe, W. R., A. Betts, J. W. Shapiro and C. J. Marx	Adding biotic complexity alters the metabolic benefits of mutualism	Evolution
2016	10.1016/j.pbi.2016.03.019	Hartwell, J., L. V. Dever and S. F. Boxall	Emerging model systems for functional genomics analysis of Crassulacean acid metabolism	Current Opinion in Plant Biology
2016	10.1038/ncomms12860	Hehemann, J.-H., P. Arevalo, M. S. Datta, X. Yu, C. H. Corzett, A. Henschel, S. P. Preheim, S. Timberlake, E. J. Alm and M. F. Polz	Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes	Nature Communications
2016	10.7717/peerj.2606	Henning, J. A., D. J. Weston, D. A. Pelletier, C. M. Timm, S. S. Jawdy and A. T. Classen	Root bacterial endophytes alter plant phenotype, but not physiology	PeerJ
2016	10.1016/j.gca.2016.05.015	Hodgkins, S. B., M. M. Tfaily, D. C. Podgorski, C. K. McCalley, S. R. Saleska, P. M. Crill, V. I. Rich, J. P. Chanton and W. T. Cooper	Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland	Geochimica Et Cosmochimica Acta
2016	10.1186/s13068-016-0630-y	Hollinshead, W. D., S. Rodriguez, H. G. Martin, G. Wang, E. E. K. Baidoo, K. L. Sale, J. D. Keasling, A. Mukhopadhyay and Y. J. Tang	Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using ?pfk mutants	Biotechnology for Biofuels
2016	10.1002/bit.25702	Hollinshead, W. D., W. R. Henson, M. Abernathy, T. S. Moon and Y. J. J. Tang	Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel C-13-metabolite fingerprinting	Biotechnology and Bioengineering
2016	10.1126/sciadv.1600886	Hong L, J. N., Cheng X, Bernal A, Tyagi M, and Smith JC	Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering	Science Advances
2016	10.1016/j.pbi.2016.03.013	Hopkinson, B. M., C. L. Dupont and Y. Matsuda	The physiology and genetics of CO2 concentrating mechanisms in model diatoms	Current Opinion in Plant Biology
2016	10.1371/journal.pone.0159715	Houtman, C. J., P. Kitin, J. C. D. Houtman, K. E. Hammel and C. G. Hunt	Acridine Orange indicates early oxidation of wood cell walls by fungi	PLOS ONE
2016	10.1007/7397_2015_16	Hsia, M. M. and J. P. Vogel	Transformation and T-DNA Mutagenesis	Genetics and Genomics of Brachypodium
2016	10.1038/nphys3553	Hu X, H. L., Smith MD, Neusius T, Cheng X, and Smith JC	The Dynamics of Single Protein Molecules is Non-Equilibrium and Self-Similar over Thirteen Decades in Time	Nature Physics
2016	10.3389/fpls.2016.01493	Hu, H., X. Gu, L. J. Xue, P. S. Swamy, S. A. Harding and C. J. Tsai	Tubulin C-terminal post-translational modifications do not occur in wood forming tissue of Populus	Frontiers in Plant Science
2016	10.1128/mBio.01669-15	Hu, P., L. Tom, A. Singh, B. C. Thomas, B. J. Baker, Y. M. Piceno, G. L. Andersen and J. F. Banfield	Genome-resolved metagenomic analysis reveals roles for candidate phyla and other microbial community members in biogeochemical transformations in oil reservoirs	mBio
2016	10.1073/pnas.1516867113	Hu, P., S. Chakraborty, A. Kumar, B. Woolston, H. J. Liu, D. Emerson and G. Stephanopoulos	Integrated bioprocess for conversion of gaseous substrates to liquids	Proceedings of the National Academy of Sciences of the United States of America
2016	10.1016/j.pbi.2016.03.014	Huang, P. and T. P. Brutnell	A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis	Current Opinion in Plant Biology
2016	10.1016/B978-0-444-63475-7.00001-7	Immethun, C. M., W. R. Henson, X. Wang, D. R. Nielsen and T. S. Moon	Engineering Central Metabolism for Production of Higher Alcohol-based Biofuels	Biotechnology for Biofuel Production and Optimization
2016	10.1002/bit.25863	Irani, Z. A., E. J. Kerkhoven, S. A. Shojaosadati and J. Nielsen	Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins	Biotechnology and Bioengineering
2016	10.1016/j.algal.2016.05.014	Jallet, D., M. A. Caballero, A. A. Gallina, M. Youngblood and G. Peers	Photosynthetic physiology and biomass partitioning in the model diatom Phaeodactylum tricornutum grown in a sinusoidal light regime	Algal Research-Biomass Biofuels and Bioproducts
2016	10.1128/mBio.01208-16	James, K. L., L. A. Rios-Hernandez, N. Q. Wofford, H. Mouttaki, J. R. Sieber, C. S. Sheik, H. H. Nguyen, Y. N. Yang, Y. M. Xie, J. Erde, L. Rohlin, E. A. Karr, J. A. Loo, R. R. O. Loo, G. B. Hurst, R. P. Gunsalus, L. I. Szweda and M. J. McInerney	Pyrophosphate-Dependent ATP formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a new twist on ATP formation	mBio
2016	10.1016/j.molp.2015.12.020	Jia, Q. D. and F. Chen	Catalytic functions of the isoprenyl diphosphate synthase superfamily in plants: A growing repertoire	Molecular Plant
2016	10.1002/prot.25031	Johnson, Q. R., R. J. Lindsay, R. B. Nellas and T. Shen	Pressure-induced conformational switch of an interfacial protein	Proteins
2016	10.1128/mBio.02214-15	Johnson, T. A., R. D. Stedtfeld, Q. Wang, J. R. Cole, S. A. Hashsham, T. Looft, Y. G. Zhu and J. M. Tiedje	Clusters of antibiotic resistance genes enriched together stay together in swine agriculture	mBio
2016	10.3389/fmicb.2016.00579	Johnston, E. R., L. M. Rodriguez-R, C. W. Luo, M. M. Yuan, L. Y. Wu, Z. L. He, E. A. G. Schuur, Y. Q. Luo, J. M. Tiedje, J. Z. Zhou and K. T. Konstantinidis	Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem	Frontiers in Microbiology
2016	10.1093/femsle/fnw063	Jones, A. J., K. P. Venkataramanan and T. Papoutsakis	Overexpression of two stress-responsive, small, non-coding RNAs, 6S and tmRNA, imparts butanol tolerance in Clostridium acetobutylicum	FEMS Microbiology Letters
2016	10.1128/AEM.02612-15	Jun, S. R., T. M. Wassenaar, I. Nookaew, L. Hauser, V. Wanchai, M. Land, C. M. Timm, T. Y. Lu, C. W. Schadt, M. J. Doktycz, D. A. Pelletier and D. W. Ussery	Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis	Applied and Environmental Microbiology
2016	10.3389/fpls.2016.01455	Kalluri, U. C., R. S. Payyavula, J. L. Labbe, N. Engle, G. Bali, S. S. Jawdy, R. W. Sykes, M. Davis, A. Ragauskas, G. A. Tuskan and T. J. Tschaplinski	Down-Regulation of KORRIGAN-Like Endo-beta-1,4-Glucanase Genes Impacts Carbon Partitioning, Mycorrhizal Colonization and Biomass Production in Populus	Frontiers in Plant Science
2016	10.1021/acs.jcim.5b00596	Kapoor, K., N. McGill, C. B. Peterson, H. V. Meyers, M. N. Blackburn and J. Baudry	Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex	Journal of Chemical Information and Modeling
2016	10.1126/sciadv.1600393	Karlen, S. D., C. C. Zhang, M. L. Peck, R. A. Smith, D. Padmakshan, K. E. Helmich, H. C. A. Free, S. Lee, B. G. Smith, F. C. Lu, J. C. Sedbrook, R. Sibout, J. H. Grabber, T. M. Runge, K. S. Mysore, P. J. Harris, L. E. Bartley and J. Ralph	Monolignol ferulate conjugates are naturally incorporated into plant lignins	Science Advances
2016	10.1104/pp.16.00014	Kebrom, T. H. and J. E. Mullet	Transcriptome profiling of tiller buds provides new insights into PhyB regulation of tillering and indeterminate growth in Sorghum	Plant Physiology
2016	10.1038/ismej.2015.265	Kent, A. G., C. L. Dupont, S. Yooseph and A. C. Martiny	Global biogeography of Prochlorococcus genome diversity in the surface ocean	ISME Journal
2016	10.1038/npjsba.2016.5	Kerkhoven, E. J., K. R. Pomraning, S. E. Baker and J. Nielsen	Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica	npj Systems Biology and Applications
2016	10.1016/j.jmbbm.2016.01.017	Khandaker, M. S. K., D. M. Dudek, E. P. Beers, D. A. Dillard and D. R. Bevan	Molecular modeling of the elastomeric properties of repeating units and building blocks of resilin, a disordered elastic protein	Journal of the Mechanical Behavior of Biomedical Materials
2016	10.1038/ncomms13806	Khodayari, A. and C. D. Maranas	A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains	Nature Communications
2016	10.1016/j.plaphy.2016.04.020	Kim, J., Y. M. Liu, X. Z. Zhang, B. Y. Zhao and K. L. Childs	Analysis of salt-induced physiological and proline changes in 46 switchgrass (Panicum virgatum) lines indicates multiple response modes	Plant Physiology and Biochemistry
2016	10.1093/nar/gkv1049	King, Z. A., J. Lu, A. Drager, P. Miller, S. Federowicz, J. A. Lerman, A. Ebrahim, B. O. Palsson and N. E. Lewis	BiGG Models: A platform for integrating, standardizing and sharing genome-scale models	Nucleic Acids Research
2016	10.1016/j.ymben.2016.10.017	Kirby, J., K. L. Dietzel, G. Wichmann, R. Chan, E. Antipov, N. Moss, E. E. K. Baidoo, P. Jackson, S. P. Gaucher, S. Gottlieb, J. LaBarge, T. Mahatdejkul, K. M. Hawkins, S. Muley, J. D. Newman, P. Liu, J. D. Keasling and L. Zhao	Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae	Metabolic Engineering
2016	10.1111/nph.13993	Kostka, J. E., D. J. Weston, J. B. Glass, E. A. Lilleskov, A. J. Shaw and M. R. Turetsky	The Sphagnum microbiome: new insights from an ancient plant lineage	New Phytologist
2016	10.1093/femsyr/fow041	Kurtzman, C. P., C. J. Robnett and M. Blackwell	Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov	FEMS Yeast Research
2016	10.1099/mgen.0.000099	La Reau, A. J., J. P. Meier-Kolthoff and G. Suen	Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association	Microbial Genomics
2016	10.1016/j.jmb.2015.09.003	Lajoie, M. J., D. Soll and G. M. Church	Overcoming challenges in engineering the genetic code	Journal of Molecular Biology
2016	10.1111/tpj.13315	Lan, W., J. Rencoret, F. C. Lu, S. D. Karlen, B. G. Smith, P. J. Harris, J. C. del Rio and J. Ralph	Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny	Plant Journal
2016	10.1186/s40168-016-0162-5	Lan, Y. M., G. Rosen and R. Hershberg	Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains	Microbiome
2016	10.1093/nar/gkw436	Lee, D. F., J. Lu, S. Chang, J. J. Loparo and X. L. S. Xie	Mapping DNA polymerase errors by single-molecule sequencing	Nucleic Acids Research
2016	10.1186/s12859-016-0887-y	Leung, E., A. Huang, E. Cadag, A. Montana, J. L. Soliman and C. L. E. Zhou	Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations	BMC Bioinformatics
2016	10.1371/journal.pone.0155038	Levering, J., J. Broddrick, C. L. Dupont, G. Peers, K. Beeri, J. Mayers, A. A. Gallina, A. E. Allen, B. O. Palsson and K. Zengler	Genome-Scale model reveals metabolic basis of biomass partitioning in a model diatom	PLOS ONE
2016	10.5194/bg-13-2689-2016	Liang, J. Y., X. Qi, L. Souza and Y. Q. Luo	Processes regulating progressive nitrogen limitation under elevated carbon dioxide: a meta-analysis	Biogeosciences
2016	10.1038/nrmicro.2016.32	Liao, J. C., L. Mi, S. Pontrelli and S. Luo	Fuelling the future: microbial engineering for the production of sustainable biofuels	Nature Reviews Microbiology
2016	10.1111/pbi.12566	Lin, J., M. Mazarei, N. Zhao, C. N. Hatcher, W. A. Wuddineh, M. Rudis, T. J. Tschaplinski, V. R. Pantalone, P. R. Arelli, T. Hewezi, F. Chen and C. N. Stewart, Jr.	Transgenic soybean overexpressing GmSAMT1 exhibits resistance to multiple-HG types of soybean cyst nematode Heterodera glycines	Plant Biotechnology Journal
2016	10.1002/bip.22924	Lindsay RJ, J. Q., Evangelista W, Nellas RB, and Shen T	DMSO enhanced conformational switch of an interfacial enzyme	Biopolymers
2016	10.1016/j.pbi.2016.01.007	Liu, D. G., R. B. Hu, K. J. Palla, G. A. Tuskan and X. H. Yang	Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research	Current Opinion in Plant Biology
2016	10.1111/pbi.12453	Liu, F. S., Q. R. Zhao, N. Mano, Z. Ahmed, F. Nitschke, Y. Q. Cai, K. D. Chapman, M. Steup, I. J. Tetlow and M. J. Emes	Modification of starch metabolism in transgenic Arabidopsis thaliana increases plant biomass and triples oilseed production	Plant Biotechnology Journal
2016	10.1016/j.ymben.2016.06.006	Liu, N., K. J. Qiao and G. Stephanopoulos	13C Metabolic flux analysis of acetate conversion to lipids by Yarrowia lipolytica	Metabolic Engineering
2016	10.1111/gcbb.12275	Liu, S. Y., L. V. Clark, K. Swaminathan, J. M. Gifford, J. A. Juvik and E. J. Sacks	High-density genetic map of Miscanthussinensis reveals inheritance of zebra stripe	Global Change Biology Bioenergy
2016	10.3389/fmolb.2016.00070	Liu, Y. M., J. M. Miao, S. Traore, D. Y. Kong, Y. Liu, X. Z. Zhang, Z. L. Nimchu, Z. R. Liu and B. Y. Zhao	SacB-SacR gene cassette as the negative selection marker to suppress Agrobacterium overgrowth in Agrobacterium-mediated plant transformation	Frontiers in Molecular Biosciences
2016	10.1016/j.tim.2016.04.006	Long, P. E., K. H. Williams, S. S. Hubbard and J. F. Banfield	Microbial metagenomics reveals climate-relevant subsurface biogeochemical processes	Trends in Microbiology
2016	10.1104/pp.16.00545	Lovell, J. T., E. V. Shakirov, S. Schwartz, D. B. Lowry, M. J. Aspinwall, S. H. Taylor, J. Bonnette, J. D. Palacio-Mejia, C. V. Hawkes, P. A. Fay and T. E. Juenger	Promises and challenges of eco-physiological genomics in the field: Tests of drought responses in switchgrass	Plant Physiology
2016	10.1101/gr.198135.115	Lovell, J. T., S. Schwartz, D. B. Lowry, E. V. Shakirov, J. E. Bonnette, X. Y. Weng, M. Wang, J. Johnson, A. Sreedasyam, C. Plott, J. Jenkins, J. Schmutz and T. E. Juenger	Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass	Genome Research
2016	10.1007/s11104-015-2640-0	Lowman, S., S. Kim-Dura, C. S. Mei and J. Nowak	Strategies for enhancement of switchgrass (Panicum virgatum L.) performance under limited nitrogen supply based on utilization of N-fixing bacterial endophytes	Plant and Soil
2016	10.1007/978-3-319-46326-1_5	Lubbe, A. and T. Northen	Exometabolomics for Linking Soil Carbon Dynamics to Microbial Communities	Microbial Metabolomics: Applications in Clinical, Environmental, and Industrial Microbiology
2016	10.1002/2015gb005239	Luo, Y. Q., A. Ahlstrom, S. D. Allison, N. H. Batjes, V. Brovkin, N. Carvalhais, A. Chappell, P. Ciais, E. A. Davidson, A. C. Finzi, K. Georgiou, B. Guenet, O. Hararuk, J. W. Harden, Y. J. He, F. Hopkins, L. F. Jiang, C. Koven, R. B. Jackson, C. D. Jones, M. J. Lara, J. Y. Liang, A. D. McGuire, W. Parton, C. H. Peng, J. T. Randerson, A. Salazar, C. A. Sierra, M. J. Smith, H. Q. Tian, K. E. O. Todd-Brown, M. Torn, K. J. van Groenigen, Y. P. Wang, T. O. West, Y. X. Wei, W. R. Wieder, J. Y. Xia, X. Xu, X. F. Xu and T. Zhou	Toward more realistic projections of soil carbon dynamics by Earth system models	Global Biogeochemical Cycles
2016	10.1002/jcc.23982	Lv, C., E. W. Aitchison, D. Wu, L. Zheng, X. Cheng and W. Yang	Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling	Journal of Computational Chemistry
2016	10.1016/j.cels.2016.06.009	Ma, N. J. and F. J. Isaacs	Genomic recoding broadly obstructs the propagation of horizontally transferred genetic elements	Cell Systems
2016	10.1146/annurev-earth-060614-105126	Mackelprang, R., S. R. Saleska, C. S. Jacobsen, J. K. Jansson and N. Ta?	Permafrost meta-omics and climate change	Annual Review of Earth and Planetary Sciences
2016	10.3389/fmicb.2016.00563	Marlow, J. J., C. T. Skennerton, Z. Li, K. Chourey, R. L. Hettich, C. Pan and V. J. Orphan	Proteomic stable isotope probing reveals biosynthesis dynamics of slow growing methane based microbial communities	Frontiers in Microbiology
2016	10.1038/nrmicro.2016.149	Martin, F., A. Kohler, C. Murat, C. Veneault-Fourrey and D. S. Hibbett	Unearthing the roots of ectomycorrhizal symbioses	Nature Reviews Microbiology
2016	10.1111/1758-2229.12352	Mayali, X., B. Stewart, S. Mabery and P. K. Weber	Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms	Environmental Microbiology Reports
2016	10.1073/pnas.1608917113	McAndrew, R. P., N. Sathitsuksanoh, M. M. Mbughuni, R. A. Heins, J. H. Pereira, A. George, K. L. Sale, B. G. Fox, B. A. Simmons and P. D. Adams	Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase	Proceedings of the National Academy of Sciences of the United States of America
2016	10.1021/acs.analchem.5b03887	McCloskey, D., J. D. Young, S. B. Xu, B. O. Palsson and A. M. Feist	MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications	Analytical Chemistry
2016	10.1021/acs.analchem.5b04914	McCloskey, D., J. D. Young, S. B. Xu, B. O. Palsson and A. M. Feist	Modeling method for increased precision and scope of directly measurable fluxes at a genome-scale	Analytical Chemistry
2016	10.1016/j.ijhydene.2016.01.003	McCully, A. L. and J. B. McKinlay	Disrupting Calvin cycle phosphoribulokinase activity in Rhodopseudomonas palustris increases the H-2 yield and specific production rate proportionately	International Journal of Hydrogen Energy
2016	10.1007/s13361-016-1476-z	Meyer, J. G., A. K. D'Souza, D. J. Sorensen, M. J. Rardin, A. J. Wolfe, B. W. Gibson and B. Schilling	Quantification of lysine acetylation and succinylation stoichiometry in proteins using mass spectrometric data-independent acquisitions (SWATH)	Journal of the American Society for Mass Spectrometry
2016	10.1002/prot.24996	Miao, Y., J. Baudry, J. C. Smith and J. A. McCammon	General trends of dihedral conformational transitions in a globular protein	Proteins
2016	10.1534/g3.116.032763	Milano, E. R., D. B. Lowry and T. E. Juenger	The genetic basis of upland/lowland ecotype divergence in switchgrass (Panicum virgatum)	G3-Genes Genomes Genetics
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2016	10.3389/fmicb.2016.00238	Mosier, A. C., C. S. Miller, K. R. Frischkorn, R. A. Ohm, Z. Li, K. LaButti, A. Lapidus, A. Lipzen, C. Chen, J. Johnson, E. A. Lindquist, C. L. Pan, R. L. Hettich, I. V. Grigoriev, S. W. Singer and J. F. Banfield	Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage	Frontiers in Microbiology
2016	10.1021/jacs.6b03285	Mostofian, B., C. M. Cai, M. D. Smith, L. Petridis, X. Cheng, C. E. Wyman and J. C. Smith	Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications	Journal of the American Chemical Society
2016	10.1016/j.copbio.2016.06.007	Musat, N., F. Musat, P. K. Weber and J. Pett-Ridge	Tracking microbial interactions with NanoSIMS	Current Opinion in Biotechnology
2016	10.1073/pnas.1605856113	Napolitano, M. G., M. Landon, C. J. Gregg, M. J. Lajoie, L. Govindarajan, J. A. Mosberg, G. Kuznetsov, D. B. Goodman, O. Vargas-Rodriguez, F. J. Isaacs, D. Soll and G. M. Church	Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli	Proceedings of the National Academy of Sciences of the United States of America
2016	10.1016/j.mimet.2016.09.013	Nelson, C. E., N. R. Beri and J. G. Gardner	Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates	Journal of Microbiological Methods
2016	10.1155/2016/4182071	Nourbakhsh-Rey, M. and M. Libault	Decipher the molecular response of plant single cell types to environmental stresses	Biomed Research International
2016	10.1890/15-0882.1	Nuccio, E. E., J. Anderson-Furgeson, K. Y. Estera, J. Pett-Ridge, P. de Valpine, E. L. Brodie and M. K. Firestone	Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass	Ecology
2016	10.1093/nar/gkw900	Orellana, L. H., L. M. Rodriguez-R and K. T. Konstantinidis	ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores	Nucleic Acids Research
2016	10.1126/science.aaf3639	Ostrov, N., M. Landon, M. Guell, G. Kuznetsov, J. Teramoto, N. Cervantes, M. Zhou, K. Singh, M. G. Napolitano, M. Moosburner, E. Shrock, B. W. Pruitt, N. Conway, D. B. Goodman, C. L. Gardner, G. Tyree, A. Gonzales, B. L. Wanner, J. E. Norville, M. J. Lajoie and G. M. Church	Design, synthesis, and testing toward a 57-codon genome	Science
2016	10.3389/fmicb.2016.00191	Otwell, A. E., S. J. Callister, E. M. Zink, R. D. Smith and R. E. Richardson	Comparative proteomic analysis of Desulfotomaculum reducens MI-1: Insights into the metabolic versatility of a gram-positive sulfate- and metal-reducing bacterium	Frontiers in Microbiology
2016	10.1038/nchembio.2077	Park, J. O., S. A. Rubin, Y. F. Xu, D. Amador-Noguez, J. Fan, T. Shlomi and J. D. Rabinowitz	Metabolite concentrations, fluxes and free energies imply efficient enzyme usage	Nature Chemical Biology
2016	10.1146/annurev-ecolsys-121415-032100	Peay, K. G.	The Mutualistic niche: Mycorrhizal symbiosis and community dynamics	Annual Review of Ecology, Evolution, and Systematics
2016	10.1016/j.coche.2016.09.003	Peng, X. F., S. P. Gilmore and M. A. O'Malley	Microbial communities for bioprocessing: lessons learned from nature	Current Opinion in Chemical Engineering
2016	10.3389/fmicb.2016.01894	Penton, C. R., C. Y. Yang, L. Y. Wu, Q. Wang, J. Zhang, F. F. Liu, Y. J. Qin, Y. Deng, C. L. Hemme, T. L. Zheng, E. A. G. Schuur, J. Tiedje and J. Z. Zhou	NifH-harboring bacterial community composition across an Alaskan permafrost thaw gradient	Frontiers in Microbiology
2016	10.3389/fmicb.2016.00824	Penton, C. R., V. S. R. Gupta, J. L. Yu and J. M. Tiedje	Size Matters: Assessing optimum soil sample size for fungal and bacterial community structure analyses using high throughput sequencing of rRNA gene amplicons	Frontiers in Microbiology
2016	10.3389/fmicb.2016.00703	Pepe-Ranney, C., A. N. Campbell, C. N. Koechli, S. Berthrong and D. H. Buckley	Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil	Frontiers in Microbiology
2016	10.1038/ismej.2015.106	Pepe-Ranney, C., C. Koechli, R. Potrafka, C. Andam, E. Eggleston, F. Garcia-Pichel and D. H. Buckley	Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation	ISME Journal
2016	10.1002/bit.25717	Pereira, B., H. R. Zhang, M. De Mey, C. G. Lim, Z. J. Li and G. Stephanopoulos	Engineering a novel biosynthetic pathway in Escherichia coli for production of renewable ethylene glycol	Biotechnology and Bioengineering
2016	10.1021/jacs.6b08845	Perticaroli S, E. G., Stanley C, Mamontov E, O'Neill H, Zhang Q, Cheng X, Myles DA, Katsaras J, Nickels JD	Description of Hydration Water in Protein GFP Solution	Journal of the American Chemical Society
2016	10.1038/ncomms12662	Peter, M., A. Kohler, R. A. Ohm, A. Kuo, J. Krutzmann, E. Morin, M. Arend, K. W. Barry, M. Binder, C. Choi, A. Clum, A. Copeland, N. Grisel, S. Haridas, T. Kipfer, K. LaButti, E. Lindquist, A. Lipzen, R. Maire, B. Meier, S. Mihaltcheva, V. Molinier, C. Murat, S. Poggeler, C. A. Quandt, C. Sperisen, A. Tritt, E. Tisserant, P. W. Crous, B. Henrissat, U. Nehls, S. Egli, J. W. Spatafora, I. V. Grigoriev and F. M. Martin	Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum	Nature Communications
2016	10.1186/s12918-016-0298-8	Petereit, J., S. Smith, F. C. Harris and K. A. Schlauch	petal: Co-expression network modelling in R	BMC Systems Biology
2016	10.1186/s12864-016-3219-8	Peterson, J. R., S. Thor, L. Kohler, P. R. A. Kohler, W. W. Metcalf and Z. Luthey-Schulten	Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans	BMC Genomics
2016	10.1073/pnas.1601926113	Pfleger, B. F.	Microbes paired for biological gas-to-liquids (Bio-GTL) process	Proceedings of the National Academy of Sciences
2016	10.1210/en.2015-2010	Pi, M., K. Kapoor, R. Ye, S. K. Nishimoto, J. C. Smith, J. Baudry and L. D. Quarles	Evidence for Osteocalcin Binding and Activation of GPRC6A in beta-Cells	Endocrinology
2016	10.1101%2Fcshperspect.a024018	Polka, J. K., S. G. Hays and P. A. Silver	Building spatial synthetic biology with compartments, scaffolds, and communities	Cold Spring Harbor Perspectives in Biology
2016	10.1186/s12864-016-2471-2	Pomraning, K. R., Y. M. Kim, C. D. Nicora, R. K. Chu, E. L. Bredeweg, S. O. Purvine, D. H. Hu, T. O. Metz and S. E. Baker	Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica	BMC Genomics
2016	10.1007/s00285-016-0990-8	Rasmussen, M., A. Hastings, M. J. Smith, F. B. Agusto, B. M. Chen-Charpentier, F. M. Hoffman, J. Jiang, K. E. O. Todd-Brown, Y. Wang, Y. P. Wang and Y. Q. Luo	Transit times and mean ages for nonautonomous and autonomous compartmental systems	Journal of Mathematical Biology
2016	10.1038/ismej.2016.83	Raveh-Sadka, T., B. Firek, I. Sharon, R. Baker, C. T. Brown, B. C. Thomas, M. J. Morowitz and J. F. Banfield	Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants	ISME Journal
2016	10.1186/s12870-016-0753-0	Ribeiro, C. L., C. M. Silva, D. R. Drost, E. Novaes, C. R. D. B. Novaes, C. Dervinis and M. Kirst	Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus	BMC Plant Biology
2016	10.7717/peerj.2486	Rinke, C., S. Low, B. Woodcroft, J. B. Raina, A. Skarshewski, X. Y. H. Le, M. K. Butler, R. Stocker, J. Seymour, G. W. Tyson and P. Hugenholtz	Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics	PeerJ
2016	10.7287/peerj.preprints.1900v1	Rodriguez-R, L. M. and K. T. Konstantinidis	The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes	PeerJ Preprints
2016	10.1021/acs.jpcb.6b00789	Sangha, A. K., L. Petridis, X. Cheng and J. C. Smith	Relative Binding Affinities of Monolignols to Horseradish Peroxidase	Journal of Physical Chemistry B
2016	10.1128/mBio.01101-16	Schaefer, A. L., Y. Oda, B. G. Coutinho, D. A. Pelletier, J. Weiburg, V. Venturi, E. P. Greenberg and C. S. Harwood	A LuxR Homolog in a Cottonwood Tree Endophyte That Activates Gene Expression in Response to a Plant Signal or Specific Peptides	mBio
2016	10.1126/science.aad7154	Scheller, S., H. Yu, G. L. Chadwick, S. E. McGlynn and V. J. Orphan	Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction	Science
2016	10.1071/fp15244	Schneebeli, K., U. Mathesius, A. B. Zwart, J. N. Bragg, J. P. Vogel and M. Watt	Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8	Functional Plant Biology
2016	10.1111/jipb.12375	Scully, E. D., T. Gries, D. L. Funnell-Harris, Z. Xin, F. A. Kovacs, W. Vermerris and S. E. Sattler	Characterization of novel Brown midrib 6 mutations affecting lignin biosynthesis in sorghum	Journal of Integrative Plant Biology
2016	10.1186/s12934-016-0611-7	Seppala, S., K. V. Solomon, S. P. Gilmore, J. K. Henske and M. A. O'Malley	Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters	Microbial Cell Factories
2016	10.1126/science.aaf6159	Shaw, A. J., F. H. Lam, M. Hamilton, A. Consiglio, K. MacEwen, E. E. Brevnova, E. Greenhagen, W. G. LaTouf, C. R. South, H. van Dijken and G. Stephanopoulos	Metabolic engineering of microbial competitive advantage for industrial fermentation processes	Science
2016	10.1111/ele.12630	Shi, S. J., E. E. Nuccio, Z. J. Shi, Z. L. He, J. Z. Zhou and M. K. Firestone	The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages	Ecology Letters
2016	10.1007/s00425-016-2507-5	Sillo, F., J. U. Fangel, B. Henrissat, A. Faccio, P. Bonfante, F. Martin, W. G. Willats and R. Balestrini	Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray	Planta
2016	10.1007/s00253-016-7376-0	Silverman, A. M., K. J. Qiao, P. Xu and G. Stephanopoulos	Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica	Applied Microbiology and Biotechnology
2016	10.1128/aem.02730-15	Simmons, M. P., S. Sudek, A. Monier, A. J. Limardo, V. Jimenez, C. R. Perle, V. A. Elrod, J. T. Pennington and A. Z. Worden	Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the Eastern North Pacific Ocean	Applied and Environmental Microbiology
2016	10.1038/ismej.2016.55	Skennerton, C. T., M. F. Haroon, A. Briegel, J. Shi, G. J. Jensen, G. W. Tyson and V. J. Orphan	Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps	ISME Journal
2016	10.1039/C5GC01952D	Smith M, M. B., Cheng X, Petridis L, Cai C, Wyman C, and Smith J	Cosolvent Pretreatment in Cellulosic Biofuel Production Effect of Tetrahydrofuran-Water on Lignin Structure and Dynamics	Green Chemistry
2016	10.1021/acs.jpcb.5b09770	Smith, M. D., B. Mostofian, L. Petridis, X. Cheng and J. C. Smith	Molecular Driving Forces behind the Tetrahydrofuran-Water Miscibility Gap	Journal of Physical Chemistry B
2016	10.1039/c5cp07088k	Smith, M. D., L. Petridis, X. Cheng, B. Mostofian and J. C. Smith	Enhanced sampling simulation analysis of the structure of lignin in the THF-water miscibility gap	Physical Chemistry Chemical Physics
2016	10.1111/nph.13843	Smith, S. R., C. Gle, R. M. Abbriano, J. C. Traller, A. Davis, E. Trentacoste, M. Vernet, A. E. Allen and M. Hildebrand	Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana	New Phytologist
2016	10.1371/journal.pgen.1006490	Smith, S. R., J. T. F. Gillard, A. B. Kustka, J. P. McCrow, J. H. Badger, H. Zheng, A. M. New, C. L. Dupont, T. Obata, A. R. Fernie and A. E. Allen	Transcriptional orchestration of the global cellular response of a model pennate diatom to Diel Light Cycling under iron limitation	PLOS Genetics
2016	10.1126/science.aad1431	Solomon, K. V., C. H. Haitjema, J. K. Henske, S. P. Gilmore, D. Borges-Rivera, A. Lipzen, H. M. Brewer, S. O. Purvine, A. T. Wright, M. K. Theodorou, I. V. Grigoriev, A. Regev, D. A. Thompson and M. A. O'Malley	Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes	Science
2016	10.1016/j.anaerobe.2015.11.008	Solomon, K. V., J. K. Henske, M. K. Theodorou and M. A. O'Malley	Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi	Anaerobe
2016	10.1021/acssuschemeng.6b00245	Springer, S. D., J. He, M. Chui, R. D. Little, M. Foston and A. Butler	Peroxidative oxidation of lignin and a lignin model compound by a manganese SALEN derivative	ACS Sustainable Chemistry & Engineering
2016	10.1128/mBio.00650-16	Stuart, R. K., X. Mayali, A. A. Boaro, A. Zemla, R. C. Everroad, D. Nilson, P. K. Weber, M. Lipton, B. M. Bebout, J. Pett-Ridge and M. P. Thelen	Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm	mBio
2016	10.1038/ismej.2015.180	Stuart, R. K., X. Mayali, J. Z. Lee, R. Craig Everroad, M. Hwang, B. M. Bebout, P. K. Weber, J. Pett-Ridge and M. P. Thelen	Cyanobacterial reuse of extracellular organic carbon in microbial mats	ISME Journal
2016	10.1039/C6GC02258H	Sun, J., T. Dutta, R. Parthasarathi, K. H. Kim, N. Tolic, R. K. Chu, N. G. Isern, J. R. Cort, B. A. Simmons and S. Singh	Rapid room temperature solubilization and depolymerization of polymeric lignin at high loadings	Green Chemistry
2016	10.1128/AEM.00611-16	Tai, V., K. J. Carpenter, P. K. Weber, C. A. Nalepa, S. J. Perlman and P. J. Keeling	Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches	Applied and Environmental Microbiology
2016	10.15376/biores.11.1.Tang	Tang, Y. T., J. N. Rosenberg, P. Bohutskyi, G. Yu, M. J. Betenbaugh and F. Wang	Microalgae as a feedstock for biofuel precursors and value-added products: Green fuels and golden opportunities	BioResources
2016	10.3390/app6110343	Tang, Y., Y. Zhang, J. N. Rosenberg, M. J. Betenbaugh and F. Wang	Optimization of One-Step In Situ Transesterification Method for Accurate Quantification of EPA in Nannochloropsis gaditana	Applied Sciences-Basel
2016	10.1038/nmeth.3696	Taylor, N. D., A. S. Garruss, R. Moretti, S. Chan, M. A. Arbing, D. Cascio, J. K. Rogers, F. J. Isaacs, S. Kosuri, D. Baker, S. Fields, G. M. Church and S. Raman	Engineering an allosteric transcription factor to respond to new ligands	Nature Methods
2016	10.1371/journal.pcbi.1004800	Theisen, M. K., J. G. L. Rivera and J. C. Liao	Stability of ensemble models predicts productivity of enzymatic systems	PloS Computational Biology
2016	10.3389/fpls.2016.00497	Timm, C. M., D. A. Pelletier, S. S. Jawdy, L. E. Gunter, J. A. Henning, N. Engle, J. Aufrecht, E. Gee, I. Nookaew, Z. Yang, T. Y. Lu, T. J. Tschaplinski, M. J. Doktycz, G. A. Tuskan and D. J. Weston	Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System	Frontiers in Plant Science
2016	10.1186/s13068-016-0670-3	Traller, J. C., S. J. Cokus, D. A. Lopez, O. Gaidarenko, S. R. Smith, J. P. McCrow, S. D. Gallaher, S. Podell, M. Thompson, O. Cook, M. Morselli, A. Jaroszewicz, E. E. Allen, A. E. Allen, S. S. Merchant, M. Pellegrini and M. Hildebrand	Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype	Biotechnology for Biofuels
2016	10.7717/peerj.1913	Trembath-Reichert, E., D. H. Case and V. J. Orphan	Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments	PeerJ
2016	10.1209/0295-5075/116/18007	Trizac E, a. S. T.	Bending stiff charged polymers The electrostatic persistence length	Europhysics Letters
2016	10.1007/s00248-015-0659-7	Tu, Q. C., X. S. Zhou, Z. L. He, K. Xue, L. Y. Wu, P. Reich, S. Hobbie and J. Z. Zhou	The Diversity and co-occurrence patterns of N2-fixing communities in a CO2-enriched grassland ecosystem	Microbial Ecology
2016	10.3835/plantgenome2015.08.0074	Tyler, L., S. J. Lee, N. D. Young, G. A. DeIulio, E. Benavente, M. Reagon, J. Sysopha, R. M. Baldini, A. Troia, S. P. Hazen and A. L. Caicedo	Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas	Plant Genome
2016	10.1128/AEM.01285-16	Utturkar, S. M., W. N. Cude, M. S. Robeson, Jr., Z. K. Yang, D. M. Klingeman, M. L. Land, S. L. Allman, T. Y. Lu, S. D. Brown, C. W. Schadt, M. Podar, M. J. Doktycz and D. A. Pelletier	Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis	Applied and Environmental Microbiology
2016	10.3389/fpls.2016.00517	Valdes-Lopez, O., J. Batek, N. Gomez-Hernandez, C. T. Nguyen, M. C. Isidra-Arellano, N. Zhang, T. Joshi, D. Xu, K. K. Hixson, K. K. Weitz, J. T. Aldrich, L. Pasa-Tolic and G. Stacey	Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles	Frontiers in Plant Science
2016	10.1186/s12864-016-2585-6	van Baren, M. J., C. Bachy, E. N. Reistetter, S. O. Purvine, J. Grimwood, S. Sudek, H. Yu, C. Poirier, T. J. Deerinck, A. Kuo, I. V. Grigoriev, C.-H. Wong, R. D. Smith, S. J. Callister, C.-L. Wei, J. Schmutz and A. Z. Worden	Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants	BMC Genomics
2016	10.1007/978-1-4939-3369-3_11	Van Nostrand, J. D., H. Yin, L. Wu, T. Yuan and J. Zhou	Hybridization of environmental microbial community nucleic acids by GeoChip	Microbial Environmental Genomics (MEG)
2016	10.1104/pp.15.01356	Vandavasi, V. G., D. K. Putnam, Q. Zhang, L. Petridis, W. T. Heller, B. T. Nixon, C. H. Haigler, U. Kalluri, L. Coates, P. Langan, J. C. Smith, J. Meiler and H. O'Neill	A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers	Plant Physiology
2016	10.1038/nmicrobiol.2016.170	Vanwonterghem, I., P. N. Evans, D. H. Parks, P. D. Jensen, B. J. Woodcroft, P. Hugenholtz and G. W. Tyson	Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota	Nature Microbiology
2016	10.1021/acschembio.6b00324	Villareal, V. A., D. Fu, D. A. Costello, X. S. Xie and P. L. Yang	Hepatitis C virus selectively alters the intracellular localization of desmosterol	ACS Chemical Biology
2016	10.1021/acs.accounts.6b00204	Walden DM, O. O., Johnston RC, and Cheong PHY	Computational Insights into the Central Role of Nonbonding Interactions in Modern Covalent Organocatalysis	Accounts of Chemical Research
2016	10.1186/s12918-016-0369-x	Walsh, J. R., M. L. Schaeffer, P. Zhang, S. Y. Rhee, J. A. Dickerson and T. Z. Sen	The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize	BMC Systems Biology
2016	10.1371/journal.pone.0155839	Waltman, P. H., J. Guo, E. N. Reistetter, S. Purvine, C. K. Ansong, M. J. van Baren, C.-H. Wong, C.-L. Wei, R. D. Smith, S. J. Callister, J. M. Stuart and A. Z. Worden	Identifying aspects of the post-transcriptional program governing the proteome of the green alga Micromonas pusilla	PLOS ONE
2016	10.1007/s11104-016-2897-y	Wang, M. M., S. P. Wang, L. W. Wu, D. P. Xu, Q. Y. Lin, Y. G. Hu, X. Z. Li, J. Z. Zhou and Y. F. Yang	Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils	Plant and Soil
2016	10.1016/j.talanta.2016.01.062	Wang, M., P. Z. Ellsworth, J. Zhou, A. B. Cousins and S. Sankaran	Evaluation of water-use efficiency in foxtail millet (Setaria italica) using visible-near infrared and thermal spectral sensing techniques	Talanta
2016	10.7717/peerj.2507	Wei, T., T. C. Chen, Y. T. Ho and P. C. Ronald	Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae	PeerJ
2016	10.1093/bioinformatics/btw241	Woodcroft, B. J., J. A. Boyd and G. W. Tyson	OrfM: a fast open reading frame predictor for metagenomic data	Bioinformatics
2016	10.1038/ismej.2016.53	Wrighton, K. C., C. J. Castelle, V. A. Varaljay, S. Satagopan, C. T. Brown, M. J. Wilkins, B. C. Thomas, I. Sharon, K. H. Williams, F. R. Tabita and J. F. Banfield	RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria	ISME Journal
2016	10.1128/mSystems.00120-16	Wu, Y.-W., B. Higgins, C. Yu, A. P. Reddy, S. Ceballos, L. D. Joh, B. A. Simmons, S. W. Singer and J. S. VanderGheynst	Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis	mSystems
2016	10.1038/ncomms12115	Wurch, L., R. J. Giannone, B. S. Belisle, C. Swift, S. Utturkar, R. L. Hettich, A. L. Reysenbach and M. Podar	Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment	Nature Communications
2016	10.1073/pnas.1607295113	Xu, P., K. J. Qiao, W. S. Ahn and G. Stephanopoulos	Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals	Proceedings of the National Academy of Sciences of the United States of America
2016	10.1016/j.geoderma.2015.08.038	Xu, X., Z. Shi, D. J. Li, A. Rey, H. H. Ruan, J. M. Craine, J. Y. Liang, J. Z. Zhou and Y. Q. Luo	Soil properties control decomposition of soil organic carbon: Results from data-assimilation analysis	Geoderma
2016	10.1111/gcb.13192	Xu, X., Z. Shi, X. C. Chen, Y. Lin, S. L. Niu, L. F. Jiang, R. S. Luo and Y. Q. Luo	Unchanged carbon balance driven by equivalent responses of production and respiration to climate change in a mixed-grass prairie	Global Change Biology
2016	10.3389/fmicb.2016.00668	Xue, K., J. P. Xie, A. F. Zhou, F. F. Liu, D. J. Li, L. Y. Wu, Y. Deng, Z. L. He, J. D. Van Nostrand, Y. Q. Luo and J. Z. Zhou	Warming alters expressions of microbial functional genes important to ecosystem functioning	Frontiers in Microbiology
2016	10.1038/nclimate2940	Xue, K., M. M. Yuan, Z. J. Shi, Y. J. Qin, Y. Deng, L. Cheng, L. Y. Wu, Z. L. He, J. D. Van Nostrand, R. Bracho, S. Natali, E. A. G. Schuur, C. W. Luo, K. T. Konstantinidis, Q. Wang, J. R. Cole, J. M. Tiedje, Y. Q. Luo and J. Z. Zhou	Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming	Nature Climate Change
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2016	10.1016/j.bioelechem.2015.08.003	Zacharoff, L., C. H. Chan and D. R. Bond	Reduction of low potential electron acceptors requires the CbcL inner membrane cytochrome of Geobacter sulfurreducens	Bioelectrochemistry
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2015	10.1021/mp500392q	Abil, Z., X. Xiong and H. Zhao	Synthetic biology for therapeutic applications	Molecular Pharmaceutics
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2015	10.1105/tpc.15.00373	Anderson, N. A., Y. Tobimatsu, P. N. Ciesielski, E. Ximenes, J. Ralph, B. S. Donohoe, M. Ladisch and C. Chapple	Manipulation of guaiacyl and syringyl monomer biosynthesis in an arabidopsis cinnamyl alcohol dehydrogenase mutant results in atypical lignin biosynthesis and modified cell wall structure	Plant Cell
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