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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

Research Publications [Beta: 02/2020]

This bibliography contains publications from research funded by the Genomic Science Program. Most publications are from FY 2019 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 ( to get your publications added.

Related Publications from Users of BER-Funded Facilities and Resources


Author NameYearTitleJournalDOI
Bader, C., Patrick, W. G., Kolb, D., Hays, S. G., Keating, S., Sharma, S., Dikovsky, D., Belocon, B., Weaver, J. C., Silver, P. A. and Oxman, N. 2016 Grown, Printed, and Biologically Augmented: An Additively Manufactured Microfluidic Wearable, Functionally Templated for Synthetic Microbes 3D Printing and Additive Manufacturing 10.1089/3dp.2016.0027
Chen, X., Hu, X. H., Shen, X. J. and Rosen, G. 2010 Probabilistic Topic Modeling for Genomic Data Interpretation 2010 IEEE International Conference on Bioinformatics and Biomedicine 10.1109/BIBM.2010.5706554
Yurkovich, J. T., Yang, L., Palsson, B. O. and Ieee 2017 Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells 2017 IEEE Conference on Control Technology and Applications 10.1109/CCTA.2017.8062584
Kim, C., Yin, P., Soto, C. X., Blaby, I. K. and Yoo, S. 2018 Multimodal biological analysis using NLP and expression profile 2018 New York Scientific Data Summit (NYSDS) 10.1109/NYSDS.2018.8538944
Mirts, E. N., Bhagi-Damodaran, A. and Lu, Y. 2019 Understanding and Modulating Metalloenzymes with Unnatural Amino Acids, Non-Native Metal Ions, and Non-Native Metallocofactors Accounts of Chemical Research 10.1021/acs.accounts.9b00011
Walden DM, Ogba OM, Johnston RC, and Cheong PHY 2016 Computational Insights into the Central Role of Nonbonding Interactions in Modern Covalent Organocatalysis Accounts of Chemical Research 10.1021/acs.accounts.6b00204
Das, L., Li, M., Stevens, J., Li, W. Q., Pu, Y. Q., Ragauskas, A. J. and Shi, J. 2018 Characterization and Catalytic Transfer Hydrogenolysis of Deep Eutectic Solvent Extracted Sorghum Lignin to Phenolic Compounds ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b01763
Dajnowicz S, Parks JM, Hu X, Johnston RC, Kovalevsky AY, Mueser TC 2018 Hyperconjugation promotes catalysis in a pyridoxal 5’-phosphate-dependent enzyme ACS Catalysis 10.1021/acscatal.8b01911
Fasan, R., Kan, S. B. J. and Zhao, H. M. 2019 A Continuing Career in Biocatalysis: Frances H. Arnold ACS Catalysis 10.1021/acscatal.9b02737
Langan PS, Vandavasi VG, Cooper SJ, Weiss KL, Ginell SL, Parks JM, Coates L 2018 Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis ACS Catalysis 10.1021/acscatal.7b04114
Baran, R., Lau, R., Bowen, B. P., Diamond, S., Jose, N., Garcia-Pichel, F. and Northen, T. R. 2017 Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D2O) Stable Isotope Probing ACS Chemical Biology 10.1021/acschembio.6b00890
Erbilgin, O., Rubel, O., Louie, K. B., Trinh, M., Raad, M., Wildish, T., Udwary, D., Hoover, C., Deutsch, S., Northen, T. R. and Bowen, B. P. 2019 MAGI: A Method for Metabolite Annotation and Gene Integration ACS Chemical Biology 10.1021/acschembio.8b01107
Fischer, C. R., Bowen, B. P., Pan, C. L., Northen, T. R. and Banfield, J. F. 2013 Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific ACS Chemical Biology 10.1021/cb400210q
Garcia, D. C., Cheng, X., Land, M. L., Standaert, R. F., Morrell-Falvey, J. L. and Doktycz, M. J. 2019 Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways ACS Chemical Biology 10.1021/acschembio.9b00725
Throckmorton, K., Vinnik, V., Chowdhury, R., Cook, T., Cheyrette, M. G., Maranas, C., Pfleger, B. and Thomas, M. G. 2019 Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code ACS Chemical Biology 10.1021/acschembio.9b00532
Villareal, V. A., Fu, D., Costello, D. A., Xie, X. S. and Yang, P. L. 2016 Hepatitis C Virus Selectively Alters the Intracellular Localization of Desmosterol ACS Chemical Biology 10.1021/acschembio.6b00324
Xu, Y. F., Lu, W. Y., Chen, J. C., Johnson, S. A., Gibney, P. A., Thomas, D. G., Brown, G., May, A. L., Campagna, S. R., Yakunin, A. F., Botstein, D. and Rabinowitz, J. D. 2018 Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase ACS Chemical Biology 10.1021/acschembio.8b00804
Abdali N, Parks JM, Haynes KM, Chaney JL, Green AT, Wolloscheck D, Walker JK, Rybenkov VV, Baudry J, Smith JC, Zgurskaya HI 2017 Reviving antibiotics: Efflux pump inhibitors that interact with AcrA, a membrane fusion protein of the AcrAB-TolC multidrug efflux pump ACS Infectious Diseases 10.1021/acsinfecdis.6b00167
Cooper SJ, Krishnamoorthy G, Wolloscheck D, Walker JK, Rybenkov VV, Parks JM, Zgurskaya HI 2018 Molecular Properties that Define the Activities of Antibiotics in Escherichia coli and Pseudomonas aeruginosa ACS Infectious Diseases 10.1021/acsinfecdis.8b00036
Goins, C. M., Dajnowicz, S., Thanna, S., Sucheck, S. J., Parks, J. M. and Ronning, D. R. 2017 Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives ACS Infectious Diseases 10.1021/acsinfecdis.7b00003
Ando, D. and Ralph, J. 2019 Method to Regioselectively Iodine-Tag Free-Phenolic Aromatic End-Groups in Lignin for H-1-C-13-HSQC NMR Analysis ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.9b04981
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. 2019 Glycosylation is vital for industrial performance of hyperactive cellulases ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b05049
Garedew, M., Young-Farhat, D., Jackson, J. E. and Saffron, C. M. 2019 Electrocatalytic Upgrading of Phenolic Compounds Observed after Lignin Pyrolysis ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.9b00019
Liu, X. R., Li, Y. D., Ewulonu, C. M., Ralph, J., Xu, F., Zhang, Q. L., Wu, M. and Huang, Y. 2019 Mild Alkaline Pretreatment for Isolation of Native-Like Lignin and Lignin-Containing Cellulose Nanofibers (LCNF) from Crop Waste ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.9b02800
Meng, X., Parikh, A., Seemala, B., Kumar, R., Cai, C.M., Ragauskas, A.J. 2018 Chemical transformations of poplar lignin during Cosolvent enhanced lignocellulosic fractionation process ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b01028
Shen, W., Collings, C., Li, M. Y., Markovicz, J., Ralph, J., Mansfield, S. D. and Ding, S. Y. 2019 Imaging Changes in Cell Walls of Engineered Poplar by Stimulated Raman Scattering and Atomic Force Microscopy ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.9b01166
Springer, S. D., He, J., Chui, M., Little, R. D., Foston, M. and Butler, A. 2016 Peroxidative Oxidation of Lignin and a Lignin Model Compound by a Manganese SALEN Derivative ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.6b00245
Stone, M. L., Anderson, E. M., Meek, K. M., Reed, M., Katahira, R., Chen, F., Dixon, R. A., Beckham, G. T. and Roman-Leshkoy, Y. 2018 Reductive Catalytic Fractionation of C-Lignin ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b02741
Vermaas, J.V., Dellon, L., Broadbelt, L.J., Beckham, G.T., and Crowley, M.F. 2018 Automated transformation of lignin topologies into atomic structures with LigninBuilder ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b05665
Villegas Calvo, M., Colombo, B., Corno, L., Eisele, G., Cosentino, C., Papa, G., Adani, F. 2018 Bioconversion of Giant Cane for Integrated Production of Biohydrogen, Carboxylic Acids, and Polyhydroxyalkanoates (PHAs) in a Multistage Biorefinery Approach ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b03794
Wang, S., Cheng, G., Dong, J., Tian, T., Lee, T. S., Mukhopadhyay, A., Singer, S. W. 2018 Tolerance Characterization and Isoprenol Production of Adapted Escherichia coli in the Presence of Ionic Liquids ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b05144
Wu, L., Gokhale, A., Goulas, K. A., Myers, J. E., Dean Toste, F., and Scown, C. D. 2018 Hybrid Biological–Chemical Approach Offers Flexibility and Reduces the Carbon Footprint of Biobased Plastics, Rubbers, and Fuels ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.8b03158
Yoo, C.G., Dumitrache, A., Muchero, W., Natzke, J., Akinosho, H., Li, M., Sykes, R.W., Brown, S.D., Davison, B.H., Tuskan, G.A., Pu, Y., Ragauskas, A.J. 2018 Significance of lignin S/G ratio in biomass recalcitrance of Populus trichocarpa variants for bioethanol production ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.7b03586
Yun-Yan Wang, Mi Li, Charles E. Wyman, Charles M. Cai, Arthur J. Ragauskas 2018 Fast Fractionation of Technical Lignins by Organic Cosolvents ACS Sustainable Chemistry & Engineering 10.1021/acssuschemeng.7b04546
DeLorenzo, D. M., Henson, W. R. and Moon, T. S. 2017 Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630 ACS Synthetic Biology 10.1021/acssynbio.7b00192
DeLorenzo, D. M. and Moon, T. S. 2019 Construction of Genetic Logic Gates Based on the T7 RNA Polymerase Expression System in Rhodococcus opacus PD630 ACS Synthetic Biology 10.1021/acssynbio.9b00213
DeLorenzo, D. M., Rottinghaus, A. G., Henson, W. R. and Moon, T. S. 2018 Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630 ACS Synthetic Biology 10.1021/acssynbio.7b00416
DiCarlo, J. E., Conley, A. J., Penttila, M., Jantti, J., Wang, H. H. and Church, G. M. 2013 Yeast Oligo-Mediated Genome Engineering (YOGE) ACS Synthetic Biology 10.1021/sb400117c
Gilmore, S. P., Lankiewicz, T. S., Wilken, S., Brown, J. L., Sexton, J. A., Henske, J. K., Theodorou, M. K., Valentine, D. L. and O'Malley, M. A. 2019 Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation ACS Synthetic Biology 10.1021/acssynbio.9b00271
Goyal, G., Costello, Z., Gutierrez, J. A., Kang, A., Lee, T. S., Martin, H. G., and Hillson, N. J. 2018 Parallel Integration and Chromosomal Expansion of Metabolic Pathways ACS Synthetic Biology 10.1021/acssynbio.8b00243
HamediRad, M., Weisberg, S., Chao, R., Lian, J. Z. and Zhao, H. M. 2019 Highly Efficient Single-Pot Scarless Golden Gate Assembly ACS Synthetic Biology 10.1021/acssynbio.8b00480
Lee, M. E., DeLoache, W. C., Cervantes, B. and Dueber, J. E. 2015 A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly ACS Synthetic Biology 10.1021/sb500366v
Li, J., Haas, W., Jackson, K., Kuru, E., Jewett, M. C., Fan, Z. H., Gygi, S. and Church, G. M. 2017 Cogenerating Synthetic Parts toward a Self-Replicating System ACS Synthetic Biology 10.1021/acssynbio.6b00342
Liu, F., Mao, J. W., Lu, T. and Hua, Q. 2019 Synthetic, Context-Dependent Microbial Consortium of Predator and Prey ACS Synthetic Biology 10.1021/acssynbio.9b00110
Liu, Y., Landick, R. and Raman, S. 2019 A Regulatory NADH/NAD plus Redox Biosensor for Bacteria ACS Synthetic Biology 10.1021/acssynbio.8b00485
Lobs, A. K., Schwartz, C., Thorwall, S. and Wheeldon, I. 2018 Highly Multiplexed CRISPRi Repression of Respiratory Functions Enhances Mitochondrial Localized Ethyl Acetate Biosynthesis in Kluyveromyces marxianus ACS Synthetic Biology 10.1021/acssynbio.8b00331
Stark, J. C., Huang, A., Hsu, K. J., Dubner, R. S., Forbrook, J., Marshalla, S., Rodriguez, F., Washington, M., Rzimicky, G. A., Nguyen, P. Q., Hasselbacher, B., Jabri, R., Kamran, R., Koralewski, V., Wightkin, W., Martinez, T. and Jewett, M. C. 2019 BioBits Health: Classroom Activities Exploring Engineering, Biology, and Human Health with Fluorescent Readouts ACS Synthetic Biology 10.1021/acssynbio.8b00381
Sun, L., Kwak, S. and Jin, Y. S. 2019 Vitamin A Production by Engineered Saccharomyces cerevisiae from Xylose via Two-Phase in Situ Extraction ACS Synthetic Biology 10.1021/acssynbio.9b00217
Tian, T., Kang, J. W., Kang, A., and Lee, T. S. 2019 Redirecting metabolic flux via combinatorial multiplex CRISPRi-mediated repression for isopentenol production in Escherichia coli ACS Synthetic Biology 10.1021/acssynbio.8b00429
Wang, L. and Maranas, C. D. 2018 MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes ACS Synthetic Biology 10.1021/acssynbio.7b00296
Wiegand, D. J., Lee, H. H., Ostrov, N. and Church, G. M. 2018 Establishing a Cell-Free Vibrio natriegens Expression System ACS Synthetic Biology 10.1021/acssynbio.8b00222
Rao, X., and Dixon, R.A. 2019 Co-expression networks for plant biology: why and how Acta Biochimica et Biophysica Sinica 10.1093/abbs/gmz080
Bellesia G, Asztalos A, Shen T, Langan P, Redondo A, and Gnanakaran S 2010 In Silico Studies of Crystalline Cellulose and Its Degradation by Enzymes Acta Crystallographica Section D Biological Crystallography 10.1107/S0907444910029483
Ellinghaus, T. L., Pereira, J. h., McAndrew, R. P., Welner, D. h., DeGiovanni, A. M., Guenther, J. M., Adams, P. D. 2018 Engineering glycoside hydrolase stability by the introduction of zinc binding Acta Crystallographica Section D Structural Biology 10.1107/S2059798318006678
Chan, S., Giuroiu, I., Chernishof, I., Sawaya, M. R., Chiang, J., Gunsalus, R. P., Arbing, M. A. and Perry, L. J. 2010 Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans Acta Crystallographica Section F-Structural Biology Communications 10.1107/s1744309109055158
Paul, C., Filippidou, S., Jamil, I., Kooli, W., House, G. L., Estoppey, A., Hayoz, M., Junier, T., Palmieri, F., Wunderlin, T., Lehmann, A., Bindschedler, S., Vennemann, T., Chain, P. S. G. and Junier, P. 2019 Bacterial spores, from ecology to biotechnology Advanced Applied Microbiology 10.1016/bs.aambs.2018.10.002
Aufrecht, Jayde A., Timm, Collin M., Bible, Amber, Morrell-Falvey, Jennifer L., Pelletier, Dale A., Doktycz, Mitchel J. and Retterer, Scott T. 2018 Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat Advanced Biosystems 10.1002/adbi.201800048
Palmieri, F., Estoppey, A., House, G. L., Lohberger, A., Bindschedler, S., Chain, P. S. G. and Junier, P. 2019 Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions Advances in Applied Microbiology 10.1016/bs.aambs.2018.10.001
Weighill, D. A. and Jacobson, D. 2017 Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology Advances in Biochemical Engineering/Biotechnology 10.1007/10_2016_46
Abraha, M., Hamilton, S. K., Chen, J. Q. and Robertson, G. P. 2018 Ecosystem carbon exchange on conversion of Conservation Reserve Program grasslands to annual and perennial cropping systems Agricultural and Forest Meteorology 10.1016/j.agrformet.2018.02.016
Anand, M., Miao, R. Q. and Khanna, M. 2019 Adopting bioenergy crops: Does farmers' attitude toward loss matter? Agricultural Economics 10.1111/agec.12501
Hussain, M. Z., Hamilton, S. K., Bhardwaj, A. K., Basso, B., Thelen, K. D. and Robertson, G. P. 2019 Evapotranspiration and water use efficiency of continuous maize and maize and soybean in rotation in the upper Midwest US Agricultural Water Management 10.1016/j.agwat.2019.02.049
Stenjem, R. S., Thompson, A. M., Karthikeyan, K. G., Lepore, B. J., Kendall, A. D. and Hyndman, D. W. 2019 Quantity and quality of water percolating below the root zone of three biofuel feedstock crop systems Agricultural Water Management 10.1016/j.agwat.2019.04.008
Abernathy, M. H., Zhang, Y. C., Hollinshead, W. D., Wang, G., Baidoo, E. E. K., Liu, T. G. and Tang, Y. J. J. 2018 Comparative studies of glycolytic pathways and channeling under in vitro and in vivo modes AIChE Journal 10.1002/aic.16367
Conway, J.M., Crosby, J.R., Hren, A.P., Southerland, R.T., Lee, L.L., Lunin, V.V., Alahuhta, P., Himmel, M.E., Bomble, Y.J., Adams, M.W.W., Kelly, R.M. 2018 Novel multi-domain, multi-functional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species AIChE Journal 10.1002/aic.16354
Henske, J. K., Gilmore, S. P., Haitjema, C. H., Solomon, K. V. and O'Malley, M. A. 2018 Biomass-degrading enzymes are catabolite repressed in anaerobic gut fungi AIChE Journal 10.1002/aic.16395
Kong, L. X. and Maravelias, C. T. 2019 From graphical to model-based distillation column design: A McCabe-Thiele-inspired mathematical programming approach AIChE Journal 10.1002/aic.16731
Ralston, M. T. and Papoutsakis, E. T. 2018 RNAseq-based transcriptome assembly of Clostridium acetobutylicum for functional genome annotation and discovery AIChE Journal 10.1002/aic.16396
Wang, Y. J., Yu, X. W. and Zhao, H. M. 2019 Biosystems design by directed evolution AIChE Journal 10.1002/aic.16716
H, Guo 2012 Narrowing the Gap in Understanding Protein Structure and Function through Computer Simulations AIP Conference Proceedings 10.1063/1.4730658
de-Bashan, Luz E., Mayali, Xavier, Bebout, Brad M., Weber, Peter K., Detweiler, Angela M., Hernandez, Juan-Pablo, Prufert-Bebout, Leslie and Bashan, Yoav 2016 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 10.1016/j.algal.2016.02.019
Fisher, Carolyn L., Ward, Christopher S., Lane, Pamela D., Kimbrel, Jeffrey A., Sale, Kenneth L., Stuart, Rhona K., Mayali, Xavier and Lane, Todd W. 2019 Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis Algal Research 10.1016/j.algal.2019.101500
Kimbrel, Jeffrey A., Samo, Ty J., Ward, Christopher, Nilson, Daniel, Thelen, Michael P., Siccardi, Anthony, Zimba, Paul, Lane, Todd W. and Mayali, Xavier 2019 Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere Algal Research 10.1016/j.algal.2019.101489
Caballero, M. A., Jallet, D., Shi, L. B., Rithner, C., Zhang, Y. and Peers, G. 2016 Quantification of chrysolaminarin from the model diatom Phaeodactylum tricornutum Algal Research-Biomass Biofuels and Bioproducts 10.1016/j.algal.2016.10.008
Gaidarenko, O., Sathoff, C., Staub, K., Huesemann, M. H., Vernet, M. and Hildebrand, M. 2019 Timing is everything: Diel metabolic and physiological changes in the diatom Cyclotella cryptica grown in simulated outdoor conditions Algal Research-Biomass Biofuels and Bioproducts 10.1016/j.algal.2019.101598
Gallina, A. A., Layer, M., King, Z. A., Levering, J., Palsson, B. O., Zengler, K. and Peers, G. 2016 A Phaeodactylum tricornutum literature database for interactive annotation of content Algal Research-Biomass Biofuels and Bioproducts 10.1016/j.algal.2016.06.020
Jallet, D., Caballero, M. A., Gallina, A. A., Youngblood, M. and Peers, G. 2016 Photosynthetic physiology and biomass partitioning in the model diatom Phaeodactylum tricornutum grown in a sinusoidal light regime Algal Research-Biomass Biofuels and Bioproducts 10.1016/j.algal.2016.05.014
Henning, J. A., Weston, D. J., Pelletier, D. A., Timm, C. M., Jawdy, S. S. and Classen, A. T. 2019 Relatively rare root endophytic bacteria drive plant resource allocation patterns and tissue nutrient concentration in unpredictable ways American Journal of Botany 10.1002/ajb2.1373
Fukami, T., Nakajima, M., Fortunel, C., Fine, P. V. A., Baraloto, C., Russo, S. E. and Peay, K. G. 2017 Geographical Variation in Community Divergence: Insights from Tropical Forest Monodominance by Ectomycorrhizal Trees American Naturalist 10.1086/692439
Solomon, K. V., Henske, J. K., Theodorou, M. K. and O'Malley, M. A. 2016 Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi Anaerobe 10.1016/j.anaerobe.2015.11.008
Sheflin, A. M., Kirkwood, J. S., Wolfe, L. M., Jahn, C. E., Broeckling, C. D., Schachtman, D. P. and Prenni, J. E. 2019 High-throughput quantitative analysis of phytohormones in sorghum leaf and root tissue by ultra-performance liquid chromatography-mass spectrometry Analytical and Bioanalytical Chemistry 10.1007/s00216-019-01658-9
Tfaily, M. M., Hodgkins, S., Podgorski, D. C., Chanton, J. P. and Cooper, W. T. 2012 Comparison of dialysis and solid-phase extraction for isolation and concentration of dissolved organic matter prior to Fourier transform ion cyclotron resonance mass spectrometry Analytical and Bioanalytical Chemistry 10.1007/s00216-012-6120-6
Broeckling, C. D., Ganna, A., Layer, M., Brown, K., Sutton, B., Ingelsson, E., Peers, G. and Prenni, J. E. 2016 Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction Analytical Chemistry 10.1021/acs.analchem.6b02479
Domingo-Almenara, X., Montenegro-Burke, J. R., Guijas, C., Majumder, E. L., Benton, H. P. and Siuzdak, G. 2019 Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics Analytical Chemistry 10.1021/acs.analchem.8b03126
Duncombe, T. A., Raad, M., Bowen, B. P., Singh, A. K., and Northen, T. R. 2018 Insulator Nanostructure Desorption Ionization Mass Spectrometry Analytical Chemistry 10.1021/acs.analchem.8b01989
Gao, J., Louie, K. B., Steinke, P., Bowen, B. P., de Raad, M., Zuckermann, R. N., Siuzdak, G. and Northen, T. R. 2017 Morphology-Driven Control of Metabolite Selectivity Using Nanostructure-Initiator Mass Spectrometry Analytical Chemistry 10.1021/acs.analchem.7b00599
Gates, Sean D., Condit, Richard C., Moussatche, Nissin, Stewart, Benjamin J., Malkin, Alexander J. and Weber, Peter K. 2018 High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM Analytical Chemistry 10.1021/acs.analchem.7b02786
Giannone, R. J., Wurch, L. L., Podar, M. and Hettich, R. L. 2015 Rescuing Those Left Behind: Recovering and Characterizing Underdigested Membrane and Hydrophobic Proteins To Enhance Proteome Measurement Depth Analytical Chemistry 10.1021/acs.analchem.5b01187
Hebert, A. S., Prasad, S., Belford, M. W., Bailey, D. J., McAlister, G. C., Abbatiello, S. E., Huguet, R., Wouters, E. R., Dunyach, J. J., Brademan, D. R., Westphall, M. S. and Coon, J. J. 2018 Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer Analytical Chemistry 10.1021/acs.analchem.8b02233
Hurst, G. B., Asano, K. G., Doktycz, C. J., Consoli, E. J., Doktycz, W. L., Foster, C. M., Morrell-Falvey, J. L., Standaert, R. F. and Doktycz, M. J. 2017 Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis Analytical Chemistry 10.1021/acs.analchem.7b02555
Li, Z., Chu, L. Q., Sweedler, J. V. and Bohn, P. W. 2010 Spatial Correlation of Confocal Raman Scattering and Secondary Ion Mass Spectrometric Molecular Images of Lignocellulosic Materials Analytical Chemistry 10.1021/ac100026r
McCloskey, D., Young, J. D., Xu, S. B., Palsson, B. O. and Feist, A. M. 2016 Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale Analytical Chemistry 10.1021/acs.analchem.5b04914
McCloskey, D., Young, J. D., Xu, S. B., Palsson, B. O. and Feist, A. M. 2016 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 10.1021/acs.analchem.5b03887
Su, X. Y., Lu, W. Y. and Rabinowitz, J. D. 2017 Metabolite Spectral Accuracy on Orbitraps Analytical Chemistry 10.1021/acs.analchem.7b00396
Trujillo, E. A., Hebert, A. S., Brademan, D. R. and Coon, J. J. 2019 Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics Analytical Chemistry 10.1021/acs.analchem.9b02979
Veličković, Dušan, Chu, Rosalie K., Carrell, Alyssa A., Thomas, Mathew, Paša-Tolić, Ljiljana, Weston, David J. and Anderton, Christopher R. 2018 Multimodal MSI in Conjunction with Broad Coverage Spatially Resolved MS2 Increases Confidence in Both Molecular Identification and Localization Analytical Chemistry 10.1021/acs.analchem.7b04319
Victor, T., Delpratt, N., Cseke, S. B., Miller, L. M. and Cseke, L. J. 2017 Imaging Nutrient Distribution in the Rhizosphere Using FTIR Imaging Analytical Chemistry 10.1021/acs.analchem.6b04376
Villalobos Solis, M. I., Giannone, R. J., Hettich, R. L. and Abraham, P. E. 2019 Exploiting the Dynamic Relationship between Peptide Separation Quality and Peptide Coisolation in a Multiple-Peptide Matches-per-Spectrum Approach Offers a Strategy To Optimize Bottom-Up Proteomics Throughput and Depth Analytical Chemistry 10.1021/acs.analchem.9b00819
Wang, L., Xing, X., Chen, L., Yang, L. F., Su, X. Y., Rabitz, H., Lu, W. Y. and Rabinowitz, J. D. 2019 Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics Analytical Chemistry 10.1021/acs.analchem.8b03132
Wang, Y. F., Kora, G., Bowen, B. P. and Pan, C. L. 2014 MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics Analytical Chemistry 10.1021/ac5014783
Xu, Y. F., Lu, W. Y. and Rabinowitz, J. D. 2015 Avoiding Misannotation of In-Source Fragmentation Products as Cellular Metabolites in Liquid Chromatography-Mass Spectrometry-Based Metabolomics Analytical Chemistry 10.1021/ac504118y
Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, and Kovalevsky A 2016 Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site Angewandte Chemie 10.1002/anie.201509989
McLain SE, Soper AK, Daidone I, Smith JC, and Watts A 2008 Charge-Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution Angewandte Chemie 10.1002/anie.200802679
Wang X, Yang T, Cheng X, and Shen Q 2013 Enantioselective Electrophilic Trifluoromethylthiolation of β-Ketoesters: A Case of Reactivity and Selectivity Bias for Organocatalysis Angewandte Chemie 10.1002/anie.201305075
Saar, B. G., Zeng, Y. N., Freudiger, C. W., Liu, Y. S., Himmel, M. E., Xie, X. S. and Ding, S. Y. 2010 Label-Free, Real-Time Monitoring of Biomass Processing with Stimulated Raman Scattering Microscopy Angewandte Chemie-International Edition 10.1002/anie.201000900
Stadlmeier, M., Bogena, J., Wallner, M., Wuhr, M. and Carell, T. 2018 A Sulfoxide-Based Isobaric Labelling Reagent for Accurate Quantitative Mass Spectrometry Angewandte Chemie-International Edition 10.1002/anie.201708867
Carlson, C. H., Gouker, F. E., Crowell, C. R., Evans, L., DiFazio, S. P., Smart, C. D. and Smart, L. B. 2019 Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.) Annals of Botany 10.1093/aob/mcz047
Clark, L. V., Dzyubenko, E., Dzyubenko, N., Bagmet, L., Sabitov, A., Chebukin, P., Johnson, D. A., Kjeldsen, J. B., Petersen, K. K., Jorgensen, U., Yoo, J. H., Heo, K., Yu, C. Y., Zhao, H., Jin, X. L., Peng, J. H., Yamada, T. and Sacks, E. J. 2016 Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia Annals of Botany 10.1093/aob/mcw137
Clark, L. V., Jin, X. L., Petersen, K. K., Anzoua, K. G., Bagmet, L., Chebukin, P., Deuter, M., Dzyubenko, E., Dzyubenko, N., Heo, K., Johnson, D. A., Jorgensen, U., Kjeldsen, J. B., Nagano, H., Peng, J. H., Sabitov, A., Yamada, T., Yoo, J. H., Yu, C. Y., Long, S. P. and Sacks, E. J. 2019 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 10.1093/aob/mcy161
Costa, R. M. F., Lee, S. J., Allison, G. G., Hazen, S. P., Winters, A. and Bosch, M. 2014 Genotype, development and tissue-derived variation of cell-wall properties in the lignocellulosic energy crop Miscanthus Annals of Botany 10.1093/aob/mcu054
Tschaplinski, T. J., Abraham, P. E., Jawdy, S. S., Gunter, L. E., Martin, M. Z., Engle, N. L., Yang, X. and Tuskan, G. A. 2019 The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides Annals of Botany 10.1093/aob/mcz002
Blaby-Haas, C. E. and Merchant, S. S. 2019 Comparative and Functional Algal Genomics Annu Review of Plant Biology 10.1146/annurev-arplant-050718-095841
Retterer, S. T., Morrell-Falvey, J. L. and Doktycz, M. J. 2018 Nano-Enabled Approaches to Chemical Imaging in Biosystems Annual Review of Analytical Chemistry 10.1146/annurev-anchem-061417-125635
Smith JC, Tan P, Petridis L, Hong L 2018 Dynamic Neutron Scattering by Biological Systems Annual Review of Biophysics 10.1146/annurev-biophys-070317-033358
Vandavasi VG, Langan PS, Weiss KL, Parks JM, Cooper JB, Ginell SL, Coates L 2017 Active-site protonation states in an acyl-enzyme intermediate of a class A B-lactamase with a monobactam substrate Antimicrobial Agents and Chemotherapy 10.1128/AAC.01636-16
Motaung, Thabiso E., Albertyn, Jacobus, Kock, Johan L. F., Lee, Ching-Fu, Suh, Sung-Oui, Blackwell, Meredith and Pohl, Carolina H. 2013 Trichosporon vanderwaltii sp. nov., an asexual basidiomycetous yeast isolated from soil and beetles Antonie van Leeuwenhoek 10.1007/s10482-012-9811-2
Daloglu, M. U., Ray, A., Collazo, M. J., Brown, C., Tseng, D., Chocarro-Ruiz, B., Lechuga, L. M., Cascio, D. and Ozcan, A. 2019 Low-cost and portable UV holographic microscope for high-contrast protein crystal imaging APL Photonics 10.1063/1.5080158
Carlson, C. H. and Smart, L. B. 2016 Electrical capacitance as a predictor of root dry weight in shrub willow (Salix; Salicaceae) parents and progeny(1) Applications in Plant Sciences 10.3732/apps.1600031
Al-Hinai, M. A., Fast, A. G. and Papoutsakis, E. T. 2012 Novel System for Efficient Isolation of Clostridium Double-Crossover Allelic Exchange Mutants Enabling Markerless Chromosomal Gene Deletions and DNA Integration Applied and Environmental Microbiology 10.1128/aem.02214-12
Allam, A. B., Reyes, L., Assad-Garcia, N., Glass, J. I. and Brown, M. B. 2010 Enhancement of Targeted Homologous Recombination in Mycoplasma mycoides subsp. capri by Inclusion of Heterologous recA Applied and Environmental Microbiology 10.1128/aem.00056-10
Amador-Noguez, D., Brasg, I. A., Feng, X. J., Roquet, N. and Rabinowitz, J. D. 2011 Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum Applied and Environmental Microbiology 10.1128/aem.05374-11
Andrews-Pfannkoch, C., Fadrosh, D. W., Thorpe, J. and Williamson, S. J. 2010 Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages Applied and Environmental Microbiology 10.1128/aem.00204-10
Aristilde, L., Lewis, I. A., Park, J. O. and Rabinowitz, J. D. 2015 Hierarchy in Pentose Sugar Metabolism in Clostridium acetobutylicum Applied and Environmental Microbiology 10.1128/aem.03199-14
Carrieri, D., Ananyev, G., Lenz, O., Bryant, D. A. and Dismukes, G. C. 2011 Contribution of a Sodium Ion Gradient to Energy Conservation during Fermentation in the Cyanobacterium Arthrospira (Spirulina) maxima CS-328 Applied and Environmental Microbiology 10.1128/aem.00612-11
Chan, C. H., Levar, C. E., Zacharoff, L., Badalamenti, J. P. and Bond, D. R. 2015 Scarless Genome Editing and Stable Inducible Expression Vectors for Geobacter sulfurreducens Applied and Environmental Microbiology 10.1128/aem.01967-15
Christensen, D. G., Orr, J. S., Rao, C. V. and Wolfe, A. J. 2017 Increasing Growth Yield and Decreasing Acetylation in Escherichia coli by Optimizing the Carbon-to-Magnesium Ratio in Peptide-Based Media Applied and Environmental Microbiology 10.1128/aem.03034-16
Embree, M., Qiu, Y., Shieu, W. D., Nagarajan, H., O'Neil, R., Lovley, D. and Zengler, K. 2014 The Iron Stimulon and Fur Regulon of Geobacter sulfurreducens and Their Role in Energy Metabolism Applied and Environmental Microbiology 10.1128/aem.03916-13
Fritts, R. K., LaSarre, B., Stoner, A. M., Posto, A. L. and McKinlay, J. B. 2017 A Rhizobiales-Specific Unipolar Polysaccharide Adhesin Contributes to Rhodopseudomonas palustris Biofilm Formation across Diverse Photoheterotrophic Conditions Applied and Environmental Microbiology 10.1128/aem.03035-16
Gladden, J. M., Allgaier, M., Miller, C. S., Hazen, T. C., VanderGheynst, J. S., Hugenholtz, P., Simmons, B. A. and Singer, S. W. 2011 Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass Applied and Environmental Microbiology 10.1128/aem.00032-11
Gottel, N. R., Castro, H. F., Kerley, M., Yang, Z., Pelletier, D. A., Podar, M., Karpinets, T., Uberbacher, E., Tuskan, G. A., Vilgalys, R., Doktycz, M. J. and Schadt, C. W. 2011 Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types Applied and Environmental Microbiology 10.1128/AEM.05255-11
Govindaraju, A., McKinlay, J. B. and LaSarre, B. 2019 Phototrophic Lactate Utilization by Rhodopseudomonas palustris Is Stimulated by Coutilization with Additional Substrates Applied and Environmental Microbiology 10.1128/aem.00048-19
Guo, J. R., Cole, J. R., Zhang, Q. P., Brown, C. T. and Tiedje, J. M. 2016 Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes Applied and Environmental Microbiology 10.1128/aem.02772-15
Holmes, D. E., Shrestha, P. M., Walker, D. J. F., Dang, Y., Nevin, K. P., Woodard, T. L. and Lovley, D. R. 2017 Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils Applied and Environmental Microbiology 10.1128/aem.00223-17
Jones, A. J., Fast, A. G., Clupper, M. and Papoutsakis, E. T. 2018 Small and Low but Potent: the Complex Regulatory Role of the Small RNA SolB in Solventogenesis in Clostridium acetobutylicum Applied and Environmental Microbiology 10.1128/aem.00597-18
Jun, S. R., Wassenaar, T. M., Nookaew, I., Hauser, L., Wanchai, V., Land, M., Timm, C. M., Lu, T. Y., Schadt, C. W., Doktycz, M. J., Pelletier, D. A. and Ussery, D. W. 2016 Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis Applied and Environmental Microbiology 10.1128/AEM.02612-15
Justice, N. B., Pan, C., Mueller, R., Spaulding, S. E., Shah, V., Sun, C. L., Yelton, A. P., Miller, C. S., Thomas, B. C., Shah, M., VerBerkmoes, N., Hettich, R. and Banfield, J. F. 2012 Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities Applied and Environmental Microbiology 10.1128/aem.01938-12
Kontur, W. S., Ziegelhoffer, E. C., Spero, M. A., Imam, S., Noguera, D. R. and Donohue, T. J. 2011 Pathways Involved in Reductant Distribution during Photobiological H-2 Production by Rhodobacter sphaeroides Applied and Environmental Microbiology 10.1128/aem.05273-11
Luo, C. W., Rodriguez-R, L. M., Johnston, E. R., Wu, L. Y., Cheng, L., Xue, K., Tu, Q. C., Deng, Y., He, Z. L., Shi, J. Z., Yuan, M. M., Sherry, R. A., Li, D. J., Luo, Y. Q., Schuur, E. A. G., Chain, P., Tiedje, J. M., Zhou, J. Z. and Konstantinidis, K. T. 2014 Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics Applied and Environmental Microbiology 10.1128/aem.03712-13
McCully, A. L., Behringer, M. G., Gliessman, J. R., Pilipenko, E. V., Mazny, J. L., Lynch, M., Drummond, D. A. and McKinlay, J. B. 2018 An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris Applied and Environmental Microbiology 10.1128/aem.00404-18
McGlynn, S. E., Chadwick, G. L., O'Neill, A., Mackey, M., Thor, A., Deerinck, T. J., Ellisman, M. H. and Orphan, V. J. 2018 Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy Applied and Environmental Microbiology 10.1128/aem.00399-18
Papp, K., Hungate, B. A. and Schwartz, E. 2018 Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H-2 O-18 Applied and Environmental Microbiology 10.1128/aem.02441-17
Penton, C. R., St Louis, D., Cole, J. R., Luo, Y. Q., Wu, L. Y., Schuur, E. A. G., Zhou, J. Z. and Tiedje, J. M. 2013 Fungal Diversity in Permafrost and Tallgrass Prairie Soils under Experimental Warming Conditions Applied and Environmental Microbiology 10.1128/aem.01702-13
Presley, G. N., Panisko, E., Purvine, S. O. and Schilling, J. S. 2018 Coupling Secretomics with Enzyme Activities To Compare the Temporal Processes of Wood Metabolism among White and Brown Rot Fungi Applied and Environmental Microbiology 10.1128/aem.00159-18
Presley, G. N. and Schilling, J. S. 2017 Distinct Growth and Secretome Strategies for Two Taxonomically Divergent Brown Rot Fungi Applied and Environmental Microbiology 10.1128/aem.02987-16
Rodriguez-R, L. M., Castro, J. C., Kyrpides, N. C., Cole, J. R., Tiedje, J. M. and Konstantinidis, K. T. 2018 How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity? Applied and Environmental Microbiology 10.1128/aem.00014-18
Rotaru, A. E., Shrestha, P. M., Liu, F., Markovaite, B., Chen, S., Nevin, K. P. and Lovley, D. R. 2014 Direct Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri Applied and Environmental Microbiology 10.1128/aem.00895-14
Rotaru, A. E., Shrestha, P. M., Liu, F. H., Ueki, T., Nevin, K., Summers, Z. M. and Lovley, D. R. 2012 Interspecies Electron Transfer via Hydrogen and Formate Rather than Direct Electrical Connections in Cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens Applied and Environmental Microbiology 10.1128/aem.01946-12
Schaefer, A. L., Lappala, C. R., Morlen, R. P., Pelletier, D. A., Lu, T. Y., Lankford, P. K., Harwood, C. S. and Greenberg, E. P. 2013 LuxR- and luxI-type quorum-sensing circuits are prevalent in members of the Populus deltoides microbiome Applied and Environmental Microbiology 10.1128/AEM.01417-13
Smercina, D. N., Evans, S. E., Friesen, M. L. and Tiemann, L. K. 2019 To Fix or Not To Fix: Controls on Free-Living Nitrogen Fixation in the Rhizosphere Applied and Environmental Microbiology 10.1128/aem.02546-18
Smith SD, Bridou R, Johs A, Parks JM, Elias DA, Hurt Jr RA, Brown SD, Podar M, and Wall JD 2015 Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation Applied and Environmental Microbiology 10.1128/AEM.00217-15
Streett, H. E., Kalis, K. M. and Papoutsakis, E. T. 2019 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 10.1128/aem.00622-19
Tai, Vera, Carpenter, Kevin J., Weber, Peter K., Nalepa, Christine A., Perlman, Steve J. and Keeling, Patrick J. 2016 Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches Applied and Environmental Microbiology 10.1128/AEM.00611-16
Thorgersen, M. P., Ge, X., Poole, F. L., 2nd, Price, M. N., Arkin, A. P. and Adams, M. W. W. 2019 Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation Applied and Environmental Microbiology 10.1128/AEM.00896-19
Tu, Q. C., Yuan, M. T., He, Z. L., Deng, Y., Xue, K., Wu, L. Y., Hobbie, S. E., Reich, P. B. and Zhou, J. Z. 2015 Fungal Communities Respond to Long-Term CO2 Elevation by Community Reassembly Applied and Environmental Microbiology 10.1128/aem.04040-14
Utturkar, S. M., Cude, W. N., Robeson, M. S., Jr., Yang, Z. K., Klingeman, D. M., Land, M. L., Allman, S. L., Lu, T. Y., Brown, S. D., Schadt, C. W., Podar, M., Doktycz, M. J. and Pelletier, D. A. 2016 Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis Applied and Environmental Microbiology 10.1128/AEM.01285-16
Wang, H., He, Z. L., Lu, Z. M., Zhou, J. Z., Van Nostrand, J. D., Xu, X. H. and Zhang, Z. J. 2012 Genetic Linkage of Soil Carbon Pools and Microbial Functions in Subtropical Freshwater Wetlands in Response to Experimental Warming Applied and Environmental Microbiology 10.1128/aem.01602-12
Wang, J., Van Nostrand, J. D., Wu, L. Y., He, Z. L., Li, G. H. and Zhou, J. Z. 2011 Microarray-Based Evaluation of Whole-Community Genome DNA Amplification Methods Applied and Environmental Microbiology 10.1128/aem.01834-10
Yilmaz, L. S., Parnerkar, S. and Noguera, D. R. 2011 mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models for In Silico Evaluation of Oligonucleotide Probes for Fluorescence In Situ Hybridization Applied and Environmental Microbiology 10.1128/aem.01733-10
Zhang, B. Z., Penton, C. R., Xue, C., Wang, Q., Zheng, T. L. and Tiedje, J. M. 2015 Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH Applied and Environmental Microbiology 10.1128/aem.00111-15
Li L, Jiang X, Guan H, Wang P, and Guo H 2010 Three Alginate Lyases from Marine Bacterium Pseudomonas fluorescens HZJ216: Purification and Characterization Applied Biochemistry and Biotechnology 10.1007/s12010-010-9136-4
Qiu, H. F., Geng, A., Zhu, D. C., Le, Y. L., Wu, J., Chow, N. W., Wu, J. H. D. and Sun, J. Z. 2015 Purification and Characterization of a Hemocyanin (Hemo1) with Potential Lignin-Modification Activities from the Wood-Feeding Termite, Coptotermes formosanus Shiraki Applied Biochemistry and Biotechnology 10.1007/s12010-014-1326-z
Fasahati, P., Liu, J. J., Ohlrogge, J. B. and Saffron, C. M. 2019 Process design and economics for production of advanced biofuels from genetically modified lipid-producing sorghum Applied Energy 10.1016/j.apenergy.2019.01.143
Ng, R. T. L., Fasahati, P., Huang, K. F. and Maravelias, C. T. 2019 Utilizing stillage in the biorefinery: Economic, technological and energetic analysis Applied Energy 10.1016/j.apenergy.2019.03.020
Baker, S. E. 2018 Protein hyperproduction in fungi by design Applied Microbiology and Biotechnology 10.1007/s00253-018-9265-1
Berim, A. and Gang, D. R. 2018 Production of methoxylated flavonoids in yeast using ring A hydroxylases and flavonoid O-methyltransferases from sweet basil Applied Microbiology and Biotechnology 10.1007/s00253-018-9043-0
Newcomb, M., Millen, J., Chen, C. Y. and Wu, J. H. D. 2011 Co-transcription of the celC gene cluster in Clostridium thermocellum Applied Microbiology and Biotechnology 10.1007/s00253-011-3121-x
Silverman, A. M., Qiao, K. J., Xu, P. and Stephanopoulos, G. 2016 Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica Applied Microbiology and Biotechnology 10.1007/s00253-016-7376-0
Tang, Y., Zhang, Y., Rosenberg, J. N., Betenbaugh, M. J. and Wang, F. 2016 Optimization of One-Step In Situ Transesterification Method for Accurate Quantification of EPA in Nannochloropsis gaditana Applied Sciences-Basel 10.3390/app6110343
Davison BH, Parks JM, Davis MF, and Donohoe BS 2013 Plant Cell Walls Basics of Structure, Chemistry, Accessibility and the Influence on Conversion Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals 10.1002/9780470975831
Hamerly, T., Tripet, B., Wurch, L., Hettich, R. L., Podar, M., Bothner, B. and Copie, V. 2015 Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR Archaea-an International Microbiological Journal 10.1155/2015/472726
Rohlin, L., Leon, D. R., Kim, U., Loo, J. A., Loo, R. R. O. and Gunsalus, R. P. 2012 Identification of the Major Expressed S-Layer and Cell Surface-Layer-Related Proteins in the Model Methanogenic Archaea: Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2A Archaea-an International Microbiological Journal 10.1155/2012/873589
Le RK, Harris BJ, Iwuchukwu IJ, Bruce BD, Cheng X, Qian S, Heller WT, O'Neill H, and Frymier PD 2014 Analysis of the Solution Structure of Thermosynechococcus elongatus Photosystem I in n-Dodecyl- -D-Maltoside Using Small-Angle Neutron Scattering and Molecular Dynamics Simulation Archives of Biochemistry and Biophysics 10.1016/
Jardine, Kolby J., Jardine, Angela B., Souza, Vinicius F., Carneiro, Vilany, Ceron, Joao V., Gimenez, Bruno O., Soares, Cilene P., Durgante, Flavia M., Higuchi, Niro, Manzi, Antonio O., Gonçalves, José F. C., Garcia, Sabrina, Martin, Scot T., Zorzanelli, Raquel F., Piva, Luani R. and Chambers, Jeff Q. 2016 Methanol and isoprene emissions from the fast growing tropical pioneer species Vismia guianensis (Aubl.) Pers. (Hypericaceae) in the central Amazon forest Atmospheric Chemistry and Physics 10.5194/acp-16-6441-2016
Stuart, Rhona K., Mayali, Xavier, Thelen, Michael P., Pett-Ridge, Jennifer and Weber, Peter K. 2017 Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM) Bio-protocol 10.21769/BioProtoc.2263
Ozseyhan, M. E., Li, P. C., Na, G., Li, Z. J., Wang, C. L. and Lu, C. F. 2018 Improved fatty acid profiles in seeds of Camelina sativa by artificial microRNA mediated FATB gene suppression Biochemical and Biophysical Research Communications 10.1016/j.bbrc.2018.06.051
Henske, J. K., Springer, S. D., O'Malley, M. A. and Butler, A. 2018 Substrate-based differential expression analysis reveals control of biomass degrading enzymes in Pycnoporus cinnabarinus Biochemical Engineering Journal 10.1016/j.bej.2017.11.015
Chapman, K. D., Aziz, M., Dyer, J. M. and Mullen, R. T. 2019 Mechanisms of lipid droplet biogenesis Biochemical Journal 10.1042/bcj20180021
Cho, S. H., Du, J., Sines, I., Poosarla, V. G., Vepachedu, V., Kafle, K., Park, Y. B., Kim, S. H., Kumar, M. and Nixon, B. T. 2015 In vitro synthesis of cellulose microfibrils by a membrane protein from protoplasts of the non-vascular plant Physcomitrella patens Biochemical Journal 10.1042/bj20141391
Hartman, K. and Tringe, S. G. 2019 Interactions between plants and soil shaping the root microbiome under abiotic stress Biochemical Journal 10.1042/bcj20180615
Wang, L., Ng, C. Y., Dash, S. and Maranas, C. D. 2018 Exploring the combinatorial space of complete pathways to chemicals Biochemical Society Transactions 10.1042/Bst20170272
Becker V, Sengupta D, Ketteler R, Ullmann MG, Smith JC, and Klingmu ller U 2008 Packing Density of the Erythropoietin Receptor Transmembrane Domain Correlates with Amplification of Biological Responses Biochemistry 10.1021/bi801425e
Budin, I. and Keasling, J. D. 2019 Synthetic Biology for Fundamental Biochemical Discovery Biochemistry 10.1021/acs.biochem.8b00915
Chen, Q., Luan, Z. J., Cheng, X. and Xu, J. H. 2015 Molecular dynamics investigation of the substrate binding mechanism in carboxylesterase Biochemistry 10.1021/bi5015612
Guo, H., Wlodawer, A., Nakayama, T., Xu, Q. and Guo, H. 2006 Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase Biochemistry 10.1021/bi060461i
Hu, X., Norris, A. L., Baudry, J. and Serpersu, E. H. 2011 Coenzyme A binding to the aminoglycoside acetyltransferase (3)-IIIb increases conformational sampling of antibiotic binding site Biochemistry 10.1021/bi201008f
Imhof, P., Fischer, S. and Smith, J. C. 2009 Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis Biochemistry 10.1021/bi900585m
Johnson, Q. R., Nellas, R. B. and Shen, T. 2012 Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa Biochemistry 10.1021/bi300557y
Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, and Shen T 2015 Mapping Allostery through Computational Glycine Scanning and Correlation Analysis of Residue–Residue Contacts Biochemistry 10.1021/bi501152d
Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, and Baudry J 2016 Highly Dynamic Anion–Quadrupole Networks in Proteins Biochemistry 10.1021/acs.biochem.6b00624
Li, T., Choi, W. G., Wallace, I. S., Baudry, J. and Roberts, D. M. 2011 Arabidopsis thaliana NIP7;1: an anther-specific boric acid transporter of the aquaporin superfamily regulated by an unusual tyrosine in helix 2 of the transport pore Biochemistry 10.1021/bi2004476
Lian P, Guo H, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, and Guo H 2014 X-ray Structure of a Hg2+ Complex of Mercuric Reductase MerA and Quantum Mechanical/Molecular Mechanical Study of Hg2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs Biochemistry 10.1021/bi500608u
Mitchell, J. M., Clasman, J. R., June, C. M., Kaitany, K. C., LaFleur, J. R., Taracila, M. A., Klinger, N. V., Bonomo, R. A., Wymore, T., Szarecka, A., Powers, R. A. and Leonard, D. A. 2015 Structural basis of activity against aztreonam and extended spectrum cephalosporins for two carbapenem-hydrolyzing class D beta-lactamases from Acinetobacter baumannii Biochemistry 10.1021/bi501547k
Nellas, R. B., Johnson, Q. R. and Shen, T. 2013 Solvent-induced alpha- to 3(10)-helix transition of an amphiphilic peptide Biochemistry 10.1021/bi400537z
Philip, V., Harris, J., Adams, R., Nguyen, D., Spiers, J., Baudry, J., Howell, E. E. and Hinde, R. J. 2011 A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-pi pairs Biochemistry 10.1021/bi200066k
Satagopan, S., North, J. A., Arbing, M. A., Varaljay, V. A., Haines, S. N., Wildenthal, J. A., Byerly, K. M., Shin, A. and Tabita, F. R. 2019 Structural Perturbations of Rhodopseudomonas palustris Form II RuBisCO Mutant Enzymes That Affect CO2 Fixation Biochemistry 10.1021/acs.biochem.9b00617
Schwarzl SM, Smith JC, and Fischer S 2006 Insights into the Chemomechanical Coupling of the Myosin Motor from Simulation of its ATP Hydrolysis Mechanism Biochemistry 10.1021/bi052433q
Shen, Y. Q., Bonnot, F., Imsand, E. M., RoseFigura, J. M., Sjolander, K. and Klinman, J. P. 2012 Distribution and Properties of the Genes Encoding the Biosynthesis of the Bacterial Cofactor, Pyrroloquinoline Quinone Biochemistry 10.1021/bi201763d
Urtecho, G., Tripp, A. D., Insigne, K. D., Kim, H. and Kosuri, S. 2019 Systematic Dissection of Sequence Elements Controlling sigma 70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli Biochemistry 10.1021/acs.biochem.7b01069
Xu, Q., Guo, H. B., Wlodawer, A., Nakayama, T. and Guo, H. 2007 The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As Biochemistry 10.1021/bi061737p
Yao, J., Guo, H., Chaiprasongsuk, M., Zhao, N., Chen, F., Yang, X. and Guo, H. 2015 Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes Biochemistry 10.1021/acs.biochem.5b00638
Yao, J., Nellas, R. B., Glover, M. M. and Shen, T. 2011 Stability and sugar recognition ability of ricin-like carbohydrate binding domains Biochemistry 10.1021/bi102021p
Sengupta, D., Smith, J. C. and Ullmann, G. M. 2008 Partitioning of amino-acid analogues in a five-slab membrane model Biochim Biophys Acta 10.1016/j.bbamem.2008.06.014
Kumar, S. V., Taylor, G., Hasim, S., Collier, C. P., Farmer, A. T., Campagna, S. R., Bible, A. N., Doktycz, M. J. and Morrell-Falvey, J. 2019 Loss of carotenoids from membranes of Pantoea sp. YR343 results in altered lipid composition and changes in membrane biophysical properties Biochim Biophys Acta Biomembr 10.1016/j.bbamem.2019.05.009
Vural, D., Hu, X., Lindner, B., Jain, N., Miao, Y., Cheng, X., Liu, Z., Hong, L. and Smith, J. C. 2017 Quasielastic neutron scattering in biology: Theory and applications Biochimica et Biophysica Acta General Subjects 10.1016/j.bbagen.2016.06.015
Nagarajan, V. K., Jones, C. I., Newbury, S. F. and Green, P. J. 2013 XRN 5 ' -> 3 ' exoribonucleases: Structure, mechanisms and functions Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms 10.1016/j.bbagrm.2013.03.005
Rawle, R. A., Hamerly, T., Tripet, B. P., Giannone, R. J., Wurch, L., Hettich, R. L., Podar, M., Copie, V. and Bothner, B. 2017 Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association Biochimica Et Biophysica Acta-General Subjects 10.1016/j.bbagen.2017.06.001
Chen, X. J., Parelkar, S. S., Henchey, E., Schneider, S. and Emrick, T. 2012 PolyMPC-Doxorubicin Prodrugs Bioconjugate Chemistry 10.1021/bc200667s
Zacharoff, L., Chan, C. H. and Bond, D. R. 2016 Reduction of low potential electron acceptors requires the CbcL inner membrane cytochrome of Geobacter sulfurreducens Bioelectrochemistry 10.1016/j.bioelechem.2015.08.003
Kar, S., Weng, T. Y., Nakashima, T., Villanueva-Morales, A., Stewart, J. R., Sacks, E. J., Terajima, Y. and Yamada, T. 2019 Field Performance of Saccharum x Miscanthus Intergeneric Hybrids (Miscanes) Under Cool Climatic Conditions of Northern Japan Bioenergy Research 10.1007/s12155-019-10066-x
Kim, H., Ralph, J. and Akiyama, T. 2008 Solution-state 2D NMR of Ball-milled Plant Cell Wall Gels in DMSO-d(6) Bioenergy Research 10.1007/s12155-008-9004-z
Taylor, M., Tornqvist, C. E., Zhao, X. W., Doerge, R. W., Casler, M. D. and Jiang, Y. W. 2019 Identification of Quantitative Trait Loci for Plant Height, Crown Diameter, and Plant Biomass in a Pseudo-F-2 Population of Switchgrass Bioenergy Research 10.1007/s12155-019-09978-5
Tejera, M., Boersma, N., Vanloocke, A., Archontoulis, S., Dixon, P., Miguez, F. and Heaton, E. 2019 Multi-year and Multi-site Establishment of the Perennial Biomass Crop Miscanthus x giganteus Using a Staggered Start Design to Elucidate N Response Bioenergy Research 10.1007/s12155-019-09985-6
Yilmaz, L. S., Kontur, W. S., Sanders, A. P., Sohmen, U., Donohue, T. J. and Noguera, D. R. 2010 Electron Partitioning During Light-and Nutrient-Powered Hydrogen Production by Rhodobacter sphaeroides Bioenergy Research 10.1007/s12155-009-9072-8
Yoon, S., Aucar, S., Hernlem, B. J., Edme, S., Palmer, N., Sarath, G., Mitchell, R., Blumwald, E. and Tobias, C. M. 2017 Generation of Octaploid Switchgrass by Seedling Treatment with Mitotic Inhibitors Bioenergy Research 10.1007/s12155-016-9795-2
Zeng, Y. N., Saar, B. G., Friedrich, M. G., Chen, F., Liu, Y. S., Dixon, R. A., Himmel, M. E., Xie, X. S. and Ding, S. Y. 2010 Imaging Lignin-Downregulated Alfalfa Using Coherent Anti-Stokes Raman Scattering Microscopy Bioenergy Research 10.1007/s12155-010-9079-1
Krantz, G. P., Lucas, K., Wunderlich, E. L., Hoang, L. T., Avci, R., Siuzdak, G. and Fields, M. W. 2019 Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm Biofouling 10.1080/08927014.2019.1646731
Cheng, M. H., Huang, H. B., Dien, B. S. and Singh, V. 2019 The costs of sugar production from different feedstocks and processing technologies Biofuels Bioproducts & Biorefining-Biofpr 10.1002/bbb.1976
Kim, S., Zhang, X. S., Dale, B. E., Reddy, A. D., Jones, C. D. and Izaurralde, R. C. 2018 EISA (Energy Independence and Security Act) compliant ethanol fuel from corn stover in a depot-based decentralized system Biofuels Bioproducts & Biorefining-Biofpr 10.1002/bbb.1899
Hodgkins, S. B., Chanton, J. P., Langford, L. C., McCalley, C. K., Saleska, S. R., Rich, V. I., Crill, P. M. and Cooper, W. T. 2015 Soil incubations reproduce field methane dynamics in a subarctic wetland Biogeochemistry 10.1007/s10533-015-0142-z
Treseder, Kathleen K., Balser, Teri C., Bradford, Mark A., Brodie, Eoin L., Dubinsky, Eric A., Eviner, Valerie T., Hofmockel, Kirsten S., Lennon, Jay T., Levine, Uri Y., MacGregor, Barbara J., Pett-Ridge, Jennifer and Waldrop, Mark P. 2012 Integrating microbial ecology into ecosystem models: challenges and priorities Biogeochemistry 10.1007/s10533-011-9636-5
von Haden, A. C., Kucharik, C. J., Jackson, R. D. and Marin-Spiotta, E. 2019 Litter quantity, litter chemistry, and soil texture control changes in soil organic carbon fractions under bioenergy cropping systems of the North Central US Biogeochemistry 10.1007/s10533-019-00564-7
Deng, J., Li, C., Frolking, S., Zhang, Y., Backstrand, K. and Crill, P. 2014 Assessing effects of permafrost thaw on C fluxes based on multiyear modeling across a permafrost thaw gradient at Stordalen, Sweden Biogeosciences 10.5194/bg-11-4753-2014
Jose, Nicholas A., Lau, Rebecca, Swenson, Tami L., Klitgord, Niels, Garcia-Pichel, Ferran, Bowen, Benjamin P., Baran, Richard and Northen, Trent R. 2018 Flux balance modeling to predict bacterial survival during pulsed-activity events Biogeosciences 10.5194/bg-15-2219-2018
Liang, J. Y., Qi, X., Souza, L. and Luo, Y. Q. 2016 Processes regulating progressive nitrogen limitation under elevated carbon dioxide: a meta-analysis Biogeosciences 10.5194/bg-13-2689-2016
Pold, G., Sistla, S. A. and DeAngelis, K. M. 2019 Metabolic tradeoffs and heterogeneity in microbial responses to temperature determine the fate of litter carbon in simulations of a warmer world Biogeosciences 10.5194/bg-16-4875-2019
Banf, M., Zhao, K. M. and Rhee, S. Y. 2019 METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters Bioinformatics 10.1093/bioinformatics/btz021
Chan, S.H.J., Wang, L., Dash, S., and Maranas, C.D. 2018 Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints Bioinformatics 10.1093/bioinformatics/bty446
Chan, S. H. J., Wang, L., Dash, S. and Maranas, C. D. 2018 Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints Bioinformatics 10.1093/bioinformatics/bty446
Chen, C. P. J. and Zhang, Z. W. 2018 iPat: intelligent prediction and association tool for genomic research Bioinformatics 10.1093/bioinformatics/bty015
Goren, E., Liu, P., Wang, C. and Wang, C. 2018 BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates Bioinformatics 10.1093/bioinformatics/bty227
Hyatt, D., LoCascio, P. F., Hauser, L. J. and Uberbacher, E. C. 2012 Gene and translation initiation site prediction in metagenomic sequences Bioinformatics 10.1093/bioinformatics/bts429
Long, M. R. and Reed, J. L. 2017 Improving flux predictions by integrating data from multiple strains Bioinformatics 10.1093/bioinformatics/btw706
Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, and Lindahl E 2013 GROMACS 4 5 A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit Bioinformatics 10.1093/bioinformatics/btt055
Rosen, G. L., Reichenberger, E. R. and Rosenfeld, A. M. 2011 NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads Bioinformatics 10.1093/bioinformatics/btq619
Sastry, A., Monk, J., Tegel, H., Uhlen, M., Palsson, B. O., Rockberg, J. and Brunk, E. 2017 Machine learning in computational biology to accelerate high-throughput protein expression Bioinformatics 10.1093/bioinformatics/btx207
Tian, M. Y. and Reed, J. L. 2018 Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis Bioinformatics 10.1093/bioinformatics/bty445
Utturkar, S. M., Klingeman, D. M., Land, M. L., Schadt, C. W., Doktycz, M. J., Pelletier, D. A. and Brown, S. D. 2014 Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences Bioinformatics 10.1093/bioinformatics/btu391
Wang, Y., Ahn, T. H., Li, Z. and Pan, C. 2013 Sipros/ProRata: a versatile informatics system for quantitative community proteomics Bioinformatics 10.1093/bioinformatics/btt329
Young, J. D. 2014 INCA: a computational platform for isotopically non-stationary metabolic flux analysis Bioinformatics 10.1093/bioinformatics/btu015
Haan, N. L. and Landis, D. A. 2019 Grassland disturbance increases monarch butterfly oviposition and decreases arthropod predator abundance Biological Conservation 10.1016/j.biocon.2019.03.007
Helms, J. A., Ijelu, S. E. and Haddad, N. M. 2019 Range expansion in an introduced social parasite-host species pair Biological Invasions 10.1007/s10530-019-02011-y
Xue, C., Hao, Y. W., Pu, X. W., Penton, C. R., Wang, Q., Zhao, M. X., Zhang, B. Z., Ran, W., Huang, Q. W., Shen, Q. R. and Tiedje, J. M. 2019 Effect of LSU and ITS genetic markers and reference databases on analyses of fungal communities Biology and Fertility of Soils 10.1007/s00374-018-1331-4
Podar, M., Makarova, K. S., Graham, D. E., Wolf, Y. I., Koonin, E. V. and Reysenbach, A. L. 2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Biology Direct 10.1186/1745-6150-8-9
Glass, D. C., Moritsugu, K., Cheng, X. and Smith, J. C. 2012 REACH coarse-grained simulation of a cellulose fiber Biomacromolecules 10.1021/bm300460f
Hansen, R. R., Hinestrosa, J. P., Shubert, K. R., Morrell-Falvey, J. L., Pelletier, D. A., Messman, J. M., Kilbey, S. M., 2nd, Lokitz, B. S. and Retterer, S. T. 2013 Lectin-functionalized poly(glycidyl methacrylate)-block-poly(vinyldimethyl azlactone) surface scaffolds for high avidity microbial capture Biomacromolecules 10.1021/bm4011358
Lindner, B., Petridis, L., Schulz, R. and Smith, J. C. 2013 Solvent-driven preferential association of lignin with regions of crystalline cellulose in molecular dynamics simulation Biomacromolecules 10.1021/bm400442n
McRae, S., Chen, X. J., Kratz, K., Samanta, D., Henchey, E., Schneider, S. and Emrick, T. 2012 Pentafluorophenyl Ester-Functionalized Phosphorylcholine Polymers: Preparation of Linear, Two-Arm, and Grafted Polymer-Protein Conjugates Biomacromolecules 10.1021/bm3004836
Petridis, L., O'Neill, H. M., Johnsen, M., Fan, B., Schulz, R., Mamontov, E., Maranas, J., Langan, P. and Smith, J. C. 2014 Hydration control of the mechanical and dynamical properties of cellulose Biomacromolecules 10.1021/bm5011849
Wang, B. X., Seiler, J. R. and Mei, C. S. 2015 Burkholderia phytofirmans strain PsJN advanced development and altered leaf level physiology of switchgrass Biomass & Bioenergy 10.1016/j.biombioe.2015.10.029
Dulys-Nusbaum, E., Klammer, S. S. H. and Swinton, S. M. 2019 How willing are different types of landowner to supply hardwood timber residues for bioenergy? Biomass and Bioenergy 10.1016/j.biombioe.2019.01.026
Graham, B. J. and Raines, R. T. 2019 Efficient metal-free conversion of glucose to 5-hydroxymethylfurfural using a boronic acid Biomass Conversion and Biorefinery 10.1007/s13399-018-0346-2
Nourbakhsh-Rey, M. and Libault, M. 2016 Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses Biomed Research International 10.1155/2016/4182071
Cao, M., Zhou, W., Breidt, F. J. and Peers, G. 2019 Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis Biometrics 10.1111/biom.13144
Lian, M., Collier, C. P., Doktycz, M. J. and Retterer, S. T. 2012 Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator Biomicrofluidics 10.1063/1.4765337
Timm, C. M., Hansen, R. R., Doktycz, M. J., Retterer, S. T. and Pelletier, D. A. 2015 Microstencils to generate defined, multi-species patterns of bacteria Biomicrofluidics 10.1063/1.4935938
Evangelista, W., Weir, R. L., Ellingson, S. R., Harris, J. B., Kapoor, K., Smith, J. C. and Baudry, J. 2016 Ensemble-based docking: From hit discovery to metabolism and toxicity predictions Bioorganic & Medicinal Chemistry 10.1016/j.bmc.2016.07.064
Sharma H, Sanchez TW, Neamati N, Detorio M, Schinazi RF, Cheng X, and Buolamwini JK 2013 Synthesis, docking, and biological studies of phenanthrene β-diketo acids as novel HIV-1 integrase inhibitors Bioorganic & Medicinal Chemistry Letters 10.1016/j.bmcl.2013.09.009
Perticaroli S, Ehlers G, Stanley C, Mamontov E, O'Neill H, Zhang Q, Cheng X, Myles DA, Katsaras J, Nickels JD 2017 Description of Hydration Water in Protein (GFP) Solution Biophyical Journal 10.1016/j.bpj.2016.11.111
Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC 2018 Ensemble Docking in Drug Discovery Biophysical Journal 10.1016/j.bpj.2018.02.038
Cheng, X., Ivanov, I., Wang, H., Sine, S. M. and McCammon, J. A. 2009 Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor Biophysical Journal 10.1016/j.bpj.2009.03.018
Daidone I, Di Nola A, and Smith JC 2011 Molecular Origin of Gerstmann-Sträussler-Scheinker Syndrome Insight from Computer Simulation of an Amyloidogenic Prion Peptide Biophysical Journal 10.1016/j.bpj.2011.04.053
Daidone I, Iacobucci C, McLain SE, and Smith JC 2012 Alteration of Water Structure by Peptide Clusters Revealed by Neutron Scattering in the Small-Angle Region (below 1 Å−1) Biophysical Journal 10.1016/j.bpj.2012.08.010
Erler, J., Zhang, R., Petridis, L., Cheng, X., Smith, J. C. and Langowski, J. 2014 The role of histone tails in the nucleosome: a computational study Biophysical Journal 10.1016/j.bpj.2014.10.065
Fritsch, S., Ivanov, I., Wang, H. and Cheng, X. 2011 Ion selectivity mechanism in a bacterial pentameric ligand-gated ion channel Biophysical Journal 10.1016/j.bpj.2010.11.077
GhattyVenkataKrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, and Cheng X 2013 Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity Biophysical Journal 10.1016/j.bpj.2012.12.052
Hong, L., Sharp, M. A., Poblete, S., Biehl, R., Zamponi, M., Szekely, N., Appavou, M. S., Winkler, R. G., Nauss, R. E., Johs, A., Parks, J. M., Yi, Z., Cheng, X., Liang, L., Ohl, M., Miller, S. M., Richter, D., Gompper, G. and Smith, J. C. 2014 Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase Biophysical Journal 10.1016/j.bpj.2014.06.013
Khadka, N. K., Cheng, X., Ho, C. S., Katsaras, J. and Pan, J. 2015 Interactions of the anticancer drug tamoxifen with lipid membranes Biophysical Journal 10.1016/j.bpj.2015.04.010
Lopez, M., Kurkal-Siebert, V., Dunn, R. V., Tehei, M., Finney, J. L., Smith, J. C. and Daniel, R. M. 2010 Activity and dynamics of an enzyme, pig liver esterase, in near-anhydrous conditions Biophysical Journal 10.1016/j.bpj.2010.07.066
Meinhold L, Clement D, Tehei M, Daniel R, Finney JL, and Smith JC 2008 Protein Dynamics and Stability The Distribution of Atomic Fluctuations in Thermophilic and Mesophilic Dihydrofolate Reductase Derived Using Elastic Incoherent Neutron Scattering Biophysical Journal 10.1529/biophysj.107.121418
Miao, Y. and Baudry, J. 2011 Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process Biophysical Journal 10.1016/j.bpj.2011.08.020
Miao, Y., Yi, Z., Cantrell, C., Glass, D. C., Baudry, J., Jain, N. and Smith, J. C. 2012 Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation Biophysical Journal 10.1016/j.bpj.2012.10.013
Moritsugu, K., Kurkal-Siebert, V. and Smith, J. C. 2009 REACH coarse-grained normal mode analysis of protein dimer interaction dynamics Biophysical Journal 10.1016/j.bpj.2009.05.015
Moritsugu, K. and Smith, J. C. 2007 Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian Biophysical Journal 10.1529/biophysj.107.111898
Moritsugu K, and Smith JC 2008 REACH Coarse-Grained Biomolecular Simulation Transferability between Different Protein Structural Classes Biophysical Journal 10.1529/biophysj.108.131714
Nickels, J. D., O'Neill, H., Hong, L., Tyagi, M., Ehlers, G., Weiss, K. L., Zhang, Q., Yi, Z., Mamontov, E., Smith, J. C. and Sokolov, A. P. 2012 Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP Biophysical Journal 10.1016/j.bpj.2012.08.046
Nickels JD, Chatterjee S, Stanley C, Qian S, Cheng X, Myles DA, Standaert R, Elkins J, Katsaras J 2017 Neutron Scattering to Study Membrane Systems From Model Membranes to Living Cells Biophysical Journal 10.1016/j.bpj.2016.11.1234
Schulz, R., Krishnan, M., Daidone, I. and Smith, J. C. 2009 Instantaneous normal modes and the protein glass transition Biophysical Journal 10.1016/j.bpj.2008.10.007
Smith, J. C. 2017 Pickin' up Good Vibrations Biophysical Journal 10.1016/j.bpj.2017.01.008
Smolin N, Biehl R, Kneller GR, Richter D, and Smith JC 2012 Functional Domain Motions in Proteins on the 1–100 ns Timescale: Comparison of Neutron Spin-Echo Spectroscopy of Phosphoglycerate Kinase with Molecular-Dynamics Simulation Biophysical Journal 10.1016/j.bpj.2012.01.002
Tehei M, Smith JC, Monk C, Ollivier J, Öttl M, Kurkal V, Finney JL, and Daniel RM 2006 Dynamics of Immobilized and Native Escherichia coli Dihydrofolate Reductase by Quasieleastic Neutron Scattering Biophysical Journal 10.1529/biophysj.105.062182
Topham, C. M. and Smith, J. C. 2007 Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form Biophysical Journal 10.1529/biophysj.105.079723
Tran, L. M., Rizk, M. L. and Liao, J. C. 2008 Ensemble Modeling of Metabolic Networks Biophysical Journal 10.1529/biophysj.108.135442
Ulmschneider JP, Smith JC, Ulmschneider MB, Ulrich AS, and Strandberg E 2012 Reorientation and Dimerization of the Membrane-Bound Antimicrobial PeptidePGLa from Microsecond All-Atom MD Simulations Biophysical Journal 10.1016/j.bpj.2012.06.040
Ulmschneider, M. B., Smith, J. C. and Ulmschneider, J. P. 2010 Peptide partitioning properties from direct insertion studies Biophysical Journal 10.1016/j.bpj.2010.03.043
Voltz, K., Trylska, J., Calimet, N., Smith, J. C. and Langowski, J. 2012 Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study Biophysical Journal 10.1016/j.bpj.2011.11.4028
Vural D, Smith JC, Glyde HR 2018 Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins Biophysical Journal 10.1016/j.bpj.2018.02.024
Lindner B, Petridis L, Langan P, and Smith JC 2015 Determination of Cellulose Crystallinity from Powder Diffraction Patterns Biopolymers 10.1002/bip.22555
Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, and Shen T 2016 DMSO enhanced conformational switch of an interfacial enzyme Biopolymers 10.1002/bip.22924
Burrows, E. H., Chaplen, F. W. R. and Ely, R. L. 2011 Effects of selected electron transport chain inhibitors on 24-h hydrogen production by Synechocystis sp PCC 6803 Bioresource Technology 10.1016/j.biortech.2010.10.042
Cheng, M. H., Dien, B. S., Lee, D. K. and Singh, V. 2019 Sugar production from bioenergy sorghum by using pilot scale continuous hydrothermal pretreatment combined with disk refining Bioresource Technology 10.1016/j.biortech.2019.121663
Chu, L. Q., Masyuko, R., Sweedler, J. V. and Bohn, P. W. 2010 Base-induced delignification of miscanthus x giganteus studied by three-dimensional confocal raman imaging Bioresource Technology 10.1016/j.biortech.2009.10.096
Jin, X. L., Chen, X. L., Shi, C. H., Li, M., Guan, Y. J., Yu, C. Y., Yamada, T., Sacks, E. J. and Peng, J. H. 2017 Determination of hemicellulose, cellulose and lignin content using visible and near infrared spectroscopy in Miscanthus sinensis Bioresource Technology 10.1016/j.biortech.2017.05.047
Kellock, M., Maaheimo, H., Marjamaa, K., Rahikainen, J., Zhang, H., Holopainen-Mantila, U., Ralph, J., Tamminen, T., Felby, C. and Kruus, K. 2019 Effect of hydrothermal pretreatment severity on lignin inhibition in enzymatic hydrolysis Bioresource Technology 10.1016/j.biortech.2019.02.051
Li, Z., Bohn, P. W. and Sweedler, J. V. 2010 Comparison of sample pre-treatments for laser desorption ionization and secondary ion mass spectrometry imaging of Miscanthus x giganteus Bioresource Technology 10.1016/j.biortech.2010.01.136
Lu, K., Hao, N., Meng, X., Luo, Z., Tuskan, G. A. and Ragauskas, A. J. 2019 Investigating the correlation of biomass recalcitrance with pyrolysis oil using poplar as the feedstock Bioresource Technology 10.1016/j.biortech.2019.121589
Meng, X., Parikh, A., Seemala, B., Kumar, R., Pu, Y., Wyman, C. E., Cai, C. M. and Ragauskas, A. J. 2019 Characterization of fractional cuts of co-solvent enhanced lignocellulosic fractionation lignin isolated by sequential precipitation Bioresource Technology 10.1016/j.biortech.2018.09.130
Mokomele, T., Sousa, L. D., Balan, V., van Rensburg, E., Dale, B. E. and Gorgens, J. F. 2019 Incorporating anaerobic co-digestion of steam exploded or ammonia fiber expansion pretreated sugarcane residues with manure into a sugarcane-based bioenergy-livestock nexus Bioresource Technology 10.1016/j.biortech.2018.10.049
Wang, H., Pu, Y., Ragauskas, A.J., Yang, B. 2018 From lignin to valuable products-strategies, challenges, and prospects Bioresource Technology 10.1016/j.biortech.2018.09.072
Wang, Z. Q., Dien, B. S., Rausch, K. D., Tumbleson, M. E. and Singh, V. 2019 Improving ethanol yields with deacetylated and two-stage pretreated corn stover and sugarcane bagasse by blending commercial xylose-fermenting and wild type Saccharomyces yeast Bioresource Technology 10.1016/j.biortech.2019.02.123
Yao, L., Yang, H., Yoo, C.G., Pu, Y., Meng, X., Muchero, W., Tuskan, G.A., Tschaplinski, T.J., and Ragauskas, A.J. 2018 Understanding the influences of different pretreatments on recalcitrance of Populus natural variants Bioresource Technology 10.1016/j.biortech.2018.05.057
Tang, Y. T., Rosenberg, J. N., Bohutskyi, P., Yu, G., Betenbaugh, M. J. and Wang, F. 2016 Microalgae as a Feedstock for Biofuel Precursors and Value-Added Products: Green Fuels and Golden Opportunities Bioresources 10.15376/biores.11.1.Tang
Griesemer, Marc, Kimbrel, Jeffrey, Zhou, Carol, Navid, Ali and D’haeseleer, Patrik 2018 Combining multiple functional annotation tools increases coverage of metabolic annotation bioRxiv 10.1101/160887
Lee, Jackson Z., Everroad, R. Craig, Karaoz, Ulas, Detweiler, Angela M., Pett-Ridge, Jennifer, Weber, Peter K., Prufert-Bebout, Leslie and Bebout, Brad M. 2017 Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat bioRxiv 10.1101/151704
Marotz, C., Sharma, A., Humphrey, G., Gottel, N., Daum, C., Gilbert, J. A., Eloe-Fadrosh, E. and Knight, R. 2019 Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary Biotechniques 10.2144/btn-2018-0192
Freed, E., Fenster, J., Smolinski, S. L., Walker, J., Henard, C. A., Gill, R. and Eckert, C. A. 2018 Building a genome engineering toolbox in nonmodel prokaryotic microbes Biotechnol Bioeng 10.1002/bit.26727
Tarasava, K., Oh, E. J., Eckert, C. A. and Gill, R. T. 2018 CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes Biotechnol Journal 10.1002/biot.201700586
Garcia, S. and Trinh, C. T. 2019 Modular design: Implementing proven engineering principles in biotechnology Biotechnology Advances 10.1016/j.biotechadv.2019.06.002
Kwak, S., Jo, J. H., Yun, E. J., Jin, Y. S. and Seo, J. H. 2019 Production of biofuels and chemicals from xylose using native and engineered yeast strains Biotechnology Advances 10.1016/j.biotechadv.2018.12.003
Oyetunde, T., Bao, F. S., Chen, J. W., Martin, H. G., and Tang, Y. J. 2018 Leveraging knowledge engineering and machine learning for microbial bio-manufacturing Biotechnology Advances 10.1016/j.biotechadv.2018.04.008
Bergenholm, D., Gossing, M., Wei, Y. J., Siewers, V. and Nielsen, J. 2018 Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids Biotechnology and Bioengineering 10.1002/bit.26518
Emerson, D. F., Woolston, B. M., Liu, N., Donnelly, M., Currie, D. H. and Stephanopoulos, G. 2019 Enhancinghydrogen-dependent growth of and carbon dioxide fixation by Clostridium ljungdahlii through nitrate supplementation Biotechnology and Bioengineering 10.1002/bit.26847
Henske, J. K., Wilken, S. E., Solomon, K. V., Smallwood, C. R., Shutthanandan, V., Evans, J. E., Theodorou, M. K. and O'Malley, M. A. 2018 Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose Biotechnology and Bioengineering 10.1002/bit.26515
Hollinshead, W. D., Henson, W. R., Abernathy, M., Moon, T. S. and Tang, Y. J. J. 2016 Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel C-13-metabolite fingerprinting Biotechnology and Bioengineering 10.1002/bit.25702
Irani, Z. A., Kerkhoven, E. J., Shojaosadati, S. A. and Nielsen, J. 2016 Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins Biotechnology and Bioengineering 10.1002/bit.25863
Kim, Y., Kreke, T., Ko, J. K. and Ladisch, M. R. 2015 Hydrolysis-Determining Substrate Characteristics in Liquid Hot Water Pretreated Hardwood Biotechnology and Bioengineering 10.1002/bit.25465
Ko, J. K., Kim, Y., Ximenes, E. and Ladisch, M. R. 2015 Effect of Liquid Hot Water Pretreatment Severity on Properties of Hardwood Lignin and Enzymatic Hydrolysis of Cellulose Biotechnology and Bioengineering 10.1002/bit.25349
Ko, J. K., Ximenes, E., Kim, Y. and Ladisch, M. R. 2015 Adsorption of Enzyme Onto Lignins of Liquid Hot Water Pretreated Hardwoods Biotechnology and Bioengineering 10.1002/bit.25359
Lane, S., Zhang, Y. F., Yun, E. J., Ziolkowski, L., Zhang, G. C., Jin, Y. S. and Avalos, J. L. 2019 Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae Biotechnology and Bioengineering 10.1002/bit.27202
McTaggart, T. L., Bever, D., Bassett, S. and Da Silva, N. A. 2019 Synthesis of polyketides from low cost substrates by the thermotolerant yeast Kluyveromyces marxianus Biotechnology and Bioengineering 10.1002/bit.26976
Noor-Mohammadi, S., Pourmir, A. and Johannes, T. W. 2012 Method to assemble and integrate biochemical pathways into the chloroplast genome of Chlamydomonas reinhardtii Biotechnology and Bioengineering 10.1002/bit.24569
Pereira, B., Zhang, H. R., De Mey, M., Lim, C. G., Li, Z. J. and Stephanopoulos, G. 2016 Engineering a Novel Biosynthetic Pathway in Escherichia coli for Production of Renewable Ethylene Glycol Biotechnology and Bioengineering 10.1002/bit.25717
Schultz, J. C., Cao, M. F. and Zhao, H. M. 2019 Development of a CRISPR/Cas9 system for high efficiency multiplexed gene deletion in Rhodosporidium toruloides Biotechnology and Bioengineering 10.1002/bit.27001
Wu, W. Z., Long, M. R., Zhang, X. L., Reed, J. L. and Maravelias, C. T. 2018 A framework for the identification of promising bio-based chemicals Biotechnology and Bioengineering 10.1002/bit.26779
Xu, P., Qiao, K. J. and Stephanopoulos, G. 2017 Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica Biotechnology and Bioengineering 10.1002/bit.26285
Yang, D., Moran-Mirabal, J. M., Parlange, J. Y. and Walker, L. P. 2013 Investigation of the Porous Structure of Cellulosic Substrates Through Confocal Laser Scanning Microscopy Biotechnology and Bioengineering 10.1002/bit.24958
Zeng, M. J., Ximenes, E., Ladisch, M. R., Mosier, N. S., Vermerris, W., Huang, C. P. and Sherman, D. M. 2012 Tissue-specific biomass recalcitrance in corn stover pretreated with liquid hot-water: Enzymatic hydrolysis (part 1) Biotechnology and Bioengineering 10.1002/bit.23337
Zeng, M. J., Ximenes, E., Ladisch, M. R., Mosier, N. S., Vermerris, W., Huang, C. P. and Sherman, D. M. 2012 Tissue-specific biomass recalcitrance in corn stover pretreated with liquid hot-water: SEM imaging (part 2) Biotechnology and Bioengineering 10.1002/bit.23335
Anthony, W. E., Carr, R. R., DeLorenzo, D. M., Campbell, T. P., Shang, Z. Y., Foston, M., Moon, T. S. and Dantas, G. 2019 Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds Biotechnology for Biofuels 10.1186/s13068-019-1535-3
Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, and Gnanakaran S 2012 A Coarse-Grained Model for Synergistic Action of Multiple Enzymes on Cellulose Biotechnology for Biofuels 10.1186/1754-6834-5-55
Attia, M. A., Nelson, C. E., Offen, W. A., Jain, N., Davies, G. J., Gardner, J. G. and Brumer, H. 2018 In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions Biotechnology for Biofuels 10.1186/s13068-018-1039-6
Bai, W. Q., Geng, W. T., Wang, S. J. and Zhang, F. Z. 2019 Biosynthesis, regulation, and engineering of microbially produced branched biofuels Biotechnology for Biofuels 10.1186/s13068-019-1424-9
Bhagia, S., Wyman, C.E., and Kumar, R. 2019 Impacts of cellulase deactivation at the moving air-liquid interface on cellulose conversions at low enzyme loadings BioTechnology for Biofuels 10.1186/s13068-019-1439-2
Bhalla, A., Cai, C.M., Xu, F., Singh, S., Bansal, N., Phongpreecha, T., Dutta, T., Foster, C.E., Kumar, R., Simmons, B., Singh, S., Wyman, C.E., Hegg, E.L., and Hodge, D.B. 2019 Performance of three delignifying pretreatments on hardwoods: hydrolysis yields Biotechnology for Biofuels 10.1186/s13068-019-1546-0
Bhalla, A., Cai, C. M., Xu, F., Singh, S. K., Bansal, N., Phongpreecha, T., Dutta, T., Foster, C. E., Kumar, R., Simmons, B. A., Singh, S., Wyman, C. E., Hegg, E. L. and Hodge, D. B. 2019 Performance of three delignifying pretreatments on hardwoods: hydrolysis yields, comprehensive mass balances, and lignin properties Biotechnology for Biofuels 10.1186/s13068-019-1546-0
Bhalla, A., Fasahati, P., Particka, C. A., Assad, A. E., Stoklosa, R. J., Bansal, N., Semaan, R., Saffron, C. M., Hodge, D. B. and Hegg, E. L. 2018 Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline-oxidative pretreatment of hybrid poplar Biotechnology for Biofuels 10.1186/s13068-018-1124-x
Biswal, A.K., Atmodjo, M.A., Pattathil, S., Amos, R.A., Yang, X., Winkeler, K., Collins, C., Mohanty, S.S., Ryno, D., Tan, L., Gelineo-Albersheim, I., Hunt, K., Sykes, R.W., Turner, G.B., Ziebell, A., Davis, M.F., Decker, S.R., Hahn, M.G., Mohnen, D. 2018 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 10.1186/s13068-017-1002-y
Bredeweg, E. L., Pomraning, K. R., Dai, Z. Y., Nielsen, J., Kerkhoven, E. J. and Baker, S. E. 2017 A molecular genetic toolbox for Yarrowia lipolytica Biotechnology for Biofuels 10.1186/s13068-016-0687-7
Brunecky, R., Chung, D., Sarai, N. S., Hengge, N., Russell, J. F., Young, J., Mittal, A., Pason, P., Vander Wall, T., Michener, W., Shollenberger, T., Westpheling, J., Himmel, M. E. and Bomble, Y. J. 2018 High activity CAZyme cassette for improving biomass degradation in thermophiles Biotechnology for Biofuels 10.1186/s13068-018-1014-2
da Costa, R. M. F., Pattathil, S., Avci, U., Winters, A., Hahn, M. G. and Bosch, M. 2019 Desirable plant cell wall traits for higher-quality miscanthus lignocellulosic biomass Biotechnology for Biofuels 10.1186/s13068-019-1426-7
Dash, S., Khodayari, A., Zhou, J., Holwerda, E. K., Olson, D. G., Lynd, L. R. and Maranas, C. D. 2017 Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations Biotechnology for Biofuels 10.1186/s13068-017-0792-2
Dash, S., Mueller, T. J., Venkataramanan, K. P., Papoutsakis, E. T. and Maranas, C. D. 2014 Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model Biotechnology for Biofuels 10.1186/s13068-014-0144-4
Du, Z. Y., Alvaro, J., Hyden, B., Zienkiewicz, K., Benning, N., Zienkiewicz, A., Bonito, G. and Benning, C. 2018 Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata Biotechnology for Biofuels 10.1186/s13068-018-1172-2
Ghosh, S., Holwerda, E. K., Worthen, R. S., Lynd, L. R. and Epps, B. P. 2018 Rheological properties of corn stover slurries during fermentation by Clostridium thermocellum Biotechnology for Biofuels 10.1186/s13068-018-1248-z
Henske, J. K., Gilmore, S. P., Knop, D., Cunningham, F. J., Sexton, J. A., Smallwood, C. R., Shutthanandan, V., Evans, J. E., Theodorou, M. K. and O'Malley, M. A. 2017 Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus Biotechnology for Biofuels 10.1186/s13068-017-0997-4
Henson, W. R., Hsu, F. F., Dantas, G., Moon, T. S. and Foston, M. 2018 Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion Biotechnology for Biofuels 10.1186/s13068-018-1337-z
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. 2019 Multiple levers for overcoming the recalcitrance of lignocellulosic biomass Biotechnology for Biofuels 10.1186/s13068-019-1353-7
Hon, S., Holwerda, E.K., Worthen, R.S., Maloney, M.I., Tian, L., Cui, J., Lin, P.L., Lynd, L.R., Olson, D.G. 2018 Expressing the thermoanaerobacterium saccharolticum pforA in engineereed Clostridium thermocellum improves ethanol production Biotechnology for Biofuels 10.1186/s13068-018-1245-2
Jagtap, S. S., Bedekar, A. A., Liu, J. J., Jin, Y. S. and Rao, C. V. 2019 Production of galactitol from galactose by the oleaginous yeast Rhodosporidium toruloides IFO0880 Biotechnology for Biofuels 10.1186/s13068-019-1586-5
Kahn, A., Morais, S., Galanopoulou, A. P., Chung, D., Sarai, N. S., Hengge, N., Hatzinikolaou, D. G., Himmel, M. E., Bomble, Y. J. and Bayer, E. A. 2019 Creation of a functional hyperthermostable designer cellulosome Biotechnology for Biofuels 10.1186/s13068-019-1386-y
Kebrom, T. H., McKinley, B. and Mullet, J. E. 2017 Dynamics of gene expression during development and expansion of vegetative stem internodes of bioenergy sorghum Biotechnology for Biofuels 10.1186/s13068-017-0848-3
Kim, S., Lowman, S., Hou, G. C., Nowak, J., Flinn, B. and Mei, C. S. 2012 Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN Biotechnology for Biofuels 10.1186/1754-6834-5-37
Kothari, N., Holwerda, E.K., Cai, C.M., Kumar, R., and Wyman, C.E. 2019 Biomass augmentation through thermochemical pretreatments greatly enhances digestion of switchgrass by Clostridium thermocellum Biotechnology for Biofuels 10.1186/s13068-018-1216-7
Li, T. T., Li, C. T., Butler, K., Hays, S. G., Guarnieri, M. T., Oyler, G. A. and Betenbaugh, M. J. 2017 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 10.1186/s13068-017-0736-x
Li, W., Amos, K., Li, M., Pu, Y., Debolt, S., Ragauskas, A. J. and Shi, J. 2018 Fractionation and characterization of lignin streams from unique high-lignin content endocarp feedstocks Biotechnology for Biofuels 10.1186/s13068-018-1305-7
Li, X., Ximenes, E., Kim, Y., Slininger, M., Meilan, R., Ladisch, M. and Chapple, C. 2010 Lignin monomer composition affects Arabidopsis cell-wall degradability after liquid hot water pretreatment Biotechnology for Biofuels 10.1186/1754-6834-3-27
Liu, C.-L., Tian, T., Alonso-Gutierrez, J., Garabedian, B., Wang, S., Baidoo, E. E. K., Lee, T. S. 2018 Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli Biotechnology for Biofuels 10.1186/s13068-018-1272-z
Meadows, C. W., Mingardon, F., Garabedian, B. M., Baidoo, E. E. K., Benites, V. T., Rodrigues, A. V., Lee, T. S. 2018 Discovery of novel geranylgeranyl reductases and characterization of their substrate promiscuity Biotechnology for Biofuels 10.1186/s13068-018-1342-2
Milano, E. R., Payne, C. E., Wolfrum, E., Lovell, J., Jenkins, J., Schmutz, J. and Juenger, T. E. 2018 Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii Biotechnology for Biofuels 10.1186/s13068-018-1033-z
Na, G., Aryal, N., Fatihi, A., Kang, J. L. and Lu, C. F. 2018 Seed-specific suppression of ADP-glucose pyrophosphorylase in Camelina sativa increases seed size and weight Biotechnology for Biofuels 10.1186/s13068-018-1334-2
Neumann, A. P., Weimer, P. J. and Suen, G. 2018 A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates Biotechnology for Biofuels 10.1186/s13068-018-1290-x
Ohlsson, J. A., Hallingback, H. R., Jebrane, M., Harman-Ware, A. E., Shollenberger, T., Decker, S. R., Sandgren, M. and Ronnberg-Wastljung, A. C. 2019 Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population Biotechnology for Biofuels 10.1186/s13068-019-1479-7
Patri, A. S., McAlister, L., Cai, C. M., Kumar, R. and Wyman, C. E. 2019 CELF significantly reduces milling requirements and improves soaking effectiveness for maximum sugar recovery of Alamo switchgrass over dilute sulfuric acid pretreatment Biotechnology for Biofuels 10.1186/s13068-019-1515-7
Poudel, S., Giannone, R. J., Basen, M., Nookaew, I., Poole, F. L., 2nd, Kelly, R. M., Adams, M. W. W. and Hettich, R. L. 2018 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 10.1186/s13068-018-1076-1
Russell, J., Kim, S-K., Duma, J., Nothaft, H., Himmel, M.E., Bomble, Y.J., Szymanski, C.M., Westpheling, J. 2018 Deletion of a single glycosyltransferase in Caldicelulosiruptor bescii eliminates protein glycosylation and growth on crystalline cellulose Biotechnology for Biofuels 10.1186/s13068-018-1266-x
Scarborough, M. J., Lynch, G., Dickson, M., McGee, M., Donohue, T. J. and Noguera, D. R. 2018 Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production Biotechnology for Biofuels 10.1186/s13068-018-1193-x
Song, B., Li, B. Y., Wang, X. Y., Shen, W., Park, S. J., Collings, C., Feng, A. R., Smith, S. J., Walton, J. D. and Ding, S. Y. 2018 Real-time imaging reveals that lytic polysaccharide monooxygenase promotes cellulase activity by increasing cellulose accessibility Biotechnology for Biofuels 10.1186/s13068-018-1023-1
Tian, L., Conway, P. M., Cervenka, N. D., Cui, J., Maloney, M., Olson, D. G. and Lynd, L. R. 2019 Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose Biotechnology for Biofuels 10.1186/s13068-019-1524-6
Tibocha-Bonilla, J. D., Zuniga, C., Godoy-Silva, R. D. and Zengler, K. 2018 Advances in metabolic modeling of oleaginous microalgae Biotechnology for Biofuels 10.1186/s13068-018-1244-3
Traller, J. C., Cokus, S. J., Lopez, D. A., Gaidarenko, O., Smith, S. R., McCrow, J. P., Gallaher, S. D., Podell, S., Thompson, M., Cook, O., Morselli, M., Jaroszewicz, A., Allen, E. E., Allen, A. E., Merchant, S. S., Pellegrini, M. and Hildebrand, M. 2016 Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype Biotechnology for Biofuels 10.1186/s13068-016-0670-3
Tschaplinski TJ, Standaert RF, Engle NL, Martin MZ, Sangha AK, Parks JM, Smith JC, Samuel R, Pu Y, Ragauskas AJ, Hamilton CY, Fu C, Wang ZY, Davison BH, Dixon RA, and Mielenz JR 2012 Down-Regulation of the Caffeic Acid O-Methyltransferase Gene in Switchgrass Reveals a Novel Monolignol Analog Biotechnology for Biofuels 10.1186/1754-6834-5-71
Venkataramanan, K. P., Min, L., Hou, S. Y., Jones, S. W., Ralston, M. T., Lee, K. H. and Papoutsakis, E. T. 2015 Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum Biotechnology for Biofuels 10.1186/s13068-015-0260-9
Vermaas JV, Petridis L, Qi X, Schulz R, Lindner B, and Smith JC 2015 Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction Biotechnology for Biofuels 10.1186/s13068-015-0379-8
Wu, W. Z. and Maravelias, C. T. 2018 Synthesis and techno-economic assessment of microbial-based processes for terpenes production Biotechnology for Biofuels 10.1186/s13068-018-1285-7
Xiao, Y., He, X. J., Ojeda-Lassalle, Y., Poovaiah, C. and Coleman, H. D. 2018 Expression of a hyperthermophilic endoglucanase in hybrid poplar modifies the plant cell wall and enhances digestibility Biotechnology for Biofuels 10.1186/s13068-018-1224-7
Xie, H., Engle, N.L., Venketachalam, S., Yoo, C.G., Barros, J., Lecoultre, M., Howard, N., Li, G., Sun, L., Srivastava, A.C., Pattathil, S., Pu, Y., Hahn, M.G., Ragauskas, A.J., Nelson, R.S., Dixon, R.A., Tschaplinski, T.J., Blancaflor, E.B., and Tang, Y. 2019 Combining loss of function of FOLYLPOLYGLUTAMATE SYNTHETASE1 and CAFFEOYL-COA 3-O-METHYLTRANSFERASE1 for lignin reduction and improved saccharification efficiency in Arabidopsis thaliana Biotechnology for Biofuels 10.1186/s13068-019-1446-3
Yan, J., Aznar, A., Chalvin, C., Birdseye, D. S., Baidoo, E. E. K., Eudes, A., Scheller, H. V. 2018 Increased drought tolerance in plants engineered for low lignin and low xylan content Biotechnology for Biofuels 10.1186/s13068-018-1196-7
Yang, S. H., Vera, J. M., Grass, J., Savvakis, G., Moskvin, O. V., Yang, Y. F., McIlwain, S. J., Lyu, Y. C., Zinonos, I., Hebert, A. S., Coon, J. J., Bates, D. M., Sato, T. K., Brown, S. D., Himmel, M. E., Zhang, M., Landick, R., Pappas, K. M. and Zhang, Y. P. 2018 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 10.1186/s13068-018-1116-x
Zhang, Y. F., Lane, S., Chen, J. M., Hammer, S. K., Luttinger, J., Yang, L. F., Jin, Y. S. and Avalos, J. L. 2019 Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in Saccharomyces cerevisiae Biotechnology for Biofuels 10.1186/s13068-019-1560-2
Kim, J., Tremaine, M., Grass, J. A., Purdy, H. M., Landick, R., Kiley, P. J. and Reed, J. L. 2019 Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose-Derived Sugars Biotechnology Journal 10.1002/biot.201800441
Kwak, S., Yun, E. J., Lane, S., Oh, E. J., Kim, K. H. and Jin, Y. S. 2019 Redirection of the Glycolytic Flux Enhances Isoprenoid Production in Saccharomyces cerevisiae Biotechnology Journal 10.1002/biot.201900173
Lian, J. Z., HamediRad, M. and Zhao, H. M. 2018 Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System Biotechnology Journal 10.1002/biot.201700601
Schmidt, B. J., Lin-Schmidt, X., Chamberlin, A., Salehi-Ashtiani, K. and Papin, J. A. 2010 Metabolic systems analysis to advance algal biotechnology Biotechnology Journal 10.1002/biot.201000129
Vu, T. T., Hill, E. A., Kucek, L. A., Konopka, A. E., Beliaev, A. S. and Reed, J. L. 2013 Computational evaluation of Synechococcus sp PCC 7002 metabolism for chemical production Biotechnology Journal 10.1002/biot.201200315
Wasylenko, T. M. and Stephanopoulos, G. 2013 Kinetic isotope effects significantly influence intracellular metabolite C-13 labeling patterns and flux determination Biotechnology Journal 10.1002/biot.201200276
You, L., Berla, B., He, L., Pakrasi, H. B. and Tang, Y. J. 2014 C-13-MFA delineates the photomixotrophic metabolism of Synechocystis sp PCC 6803 under light-and carbon-sufficient conditions Biotechnology Journal 10.1002/biot.201300477
Zhang, H. R. and Stephanopoulos, G. 2016 Co-culture engineering for microbial biosynthesis of 3-amino-benzoic acid in Escherichia coli Biotechnology Journal 10.1002/biot.201600013
Noor-Mohammadi, S., Pourmir, A. and Johannes, T. W. 2014 Method for assembling and expressing multiple genes in the nucleus of microalgae Biotechnology Letters 10.1007/s10529-013-1378-0
Sake, C. L., Metcalf, A. J. and Boyle, N. R. 2019 The challenge and potential of photosynthesis: unique considerations for metabolic flux measurements in photosynthetic microorganisms Biotechnology Letters 10.1007/s10529-018-2622-4
Rizk, M. L., Laguna, R., Smith, K. M., Tabita, F. R. and Liao, J. C. 2011 Redox Homeostasis Phenotypes in RubisCO-Deficient Rhodobacter sphaeroides via Ensemble Modeling Biotechnology Progress 10.1002/btpr.506
Bare, J. C., Koide, T., Reiss, D. J., Tenenbaum, D. and Baliga, N. S. 2010 Integration and visualization of systems biology data in context of the genome BMC Bioinformatics 10.1186/1471-2105-11-382
Deng, Y., Jiang, Y. H., Yang, Y. F., He, Z. L., Luo, F. and Zhou, J. Z. 2012 Molecular ecological network analyses BMC Bioinformatics 10.1186/1471-2105-13-113
Jun, S. R., Nookaew, I., Hauser, L. and Gorin, A. 2017 Assessment of genome annotation using gene function similarity within the gene neighborhood BMC Bioinformatics 10.1186/s12859-017-1761-2
Leung, Elo, Huang, Amy, Cadag, Eithon, Montana, Aldrin, Soliman, Jan Lorenz and Zhou, Carol L. Ecale 2016 Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations BMC Bioinformatics 10.1186/s12859-016-0887-y
Navid, Ali, Jiao, Yongqin, Wong, Sergio Ernesto and Pett-Ridge, Jennifer 2019 System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris BMC Bioinformatics 10.1186/s12859-019-2844-z
Yok, N. G. and Rosen, G. L. 2011 Combining gene prediction methods to improve metagenomic gene annotation BMC Bioinformatics 10.1186/1471-2105-12-20
Opulente, D. A., Rollinson, E. J., Bernick-Roehr, C., Hulfachor, A. B., Rokas, A., Kurtzman, C. P. and Hittinger, C. T. 2018 Factors driving metabolic diversity in the budding yeast subphylum BMC Biology 10.1186/s12915-018-0498-3
Chirico G, Gansen A, Leuba SH, Olins AL, Olins DE, Smith JC, Tóth K 2018 Jörg Langowski his scientific legacy and the future it promises BMC Biophysics 10.1186/s13628-018-0045-1
Li, G., Jones, K. C., Eudes, A., Pidatala, V. R., Sun, J., Xu, F., Ronald, P. C. 2018 Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification BMC Biotechnology 10.1186/s12896-018-0464-8
Panchy, N. L., Azodi, C. B., Winship, E. F., O'Malley, R. C. and Shiu, S. H. 2019 Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication BMC Evolutionary Biology 10.1186/s12862-019-1398-z
Zhang, X. C., Wang, Z., Zhang, X. Y., Le, M. H., Sun, J. G., Xu, D., Cheng, J. L. and Stacey, G. 2012 Evolutionary dynamics of protein domain architecture in plants BMC Evolutionary Biology 10.1186/1471-2148-12-6
Armaleo, D., Muller, O., Lutzoni, F., Andresson, O. S., Blanc, G., Bode, H. B., Collart, F. R., Dal Grande, F., Dietrich, F., Grigoriev, I. V., Joneson, S., Kuo, A., Larsen, P. E., Logsdon, J. M., Lopez, D., Martin, F., May, S. P., McDonald, T. R., Merchant, S. S., Miao, V., Morin, E., Oono, R., Pellegrini, M., Rubinstein, N., Sanchez-Puerta, M. V., Savelkoul, E., Schmitt, I., Slot, J. C., Soanes, D., Szovenyi, P., Talbot, N. J., Veneault-Fourrey, C. and Xavier, B. B. 2019 The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata BMC Genomics 10.1186/s12864-019-5629-x
Barling, A., Swaminathan, K., Mitros, T., James, B. T., Morris, J., Ngamboma, O., Hall, M. C., Kirkpatrick, J., Alabady, M., Spence, A. K., Hudson, M. E., Rokhsar, D. S. and Moose, S. P. 2013 A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes BMC Genomics 10.1186/1471-2164-14-864
Bowen, B. P., Fischer, C. R., Baran, R., Banfield, J. F. and Northen, T. 2011 Improved genome annotation through untargeted detection of pathway-specific metabolites BMC Genomics 10.1186/1471-2164-12-s1-s6
Chen, Y. F., Qin, N., Guo, J., Qian, G. R., Fang, D. Q., Shi, D., Xu, M., Yang, F. L., He, Z. L., Van Nostrand, J. D., Yuan, T., Deng, Y., Zhou, J. Z. and Li, L. J. 2014 Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis BMC Genomics 10.1186/1471-2164-15-753
Christopherson, M. R., Dawson, J. A., Stevenson, D. M., Cunningham, A. C., Bramhacharya, S., Weimer, P. J., Kendziorski, C. and Suen, G. 2014 Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis BMC Genomics 10.1186/1471-2164-15-1066
Daguerre, Y., Levati, E., Ruytinx, J., Tisserant, E., Morin, E., Kohler, A., Montanini, B., Ottonello, S., Brun, A., Veneault-Fourrey, C. and Martin, F. 2017 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 10.1186/s12864-017-4114-7
Franke, K. R., Schmidt, S. A., Park, S., Jeong, D. H., Accerbi, M. and Green, P. J. 2018 Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops BMC Genomics 10.1186/s12864-018-4911-7
Ghamsari, L., Balaji, S., Shen, Y., Yang, X. P., Balcha, D., Fan, C. Y., Hao, T., Yu, H. Y., Papin, J. A. and Salehi-Ashtiani, K. 2011 Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii BMC Genomics 10.1186/1471-2164-12-s1-s4
Gilmore, S. P., Henske, J. K., Sexton, J. A., Solomon, K. V., Seppala, S., Yoo, J. I., Huyett, L. M., Pressman, A., Cogan, J. Z., Kivenson, V., Peng, X. F., Tan, Y. P., Valentine, D. L. and O'Malley, M. A. 2017 Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Bmc Genomics 10.1186/s12864-017-4036-4
Griesemer, Marc, Kimbrel, Jeffrey A., Zhou, Carol E., Navid, Ali and D’haeseleer, Patrik 2018 Combining multiple functional annotation tools increases coverage of metabolic annotation BMC Genomics 10.1186/s12864-018-5221-9
Joshi, T., Patil, K., Fitzpatrick, M. R., Franklin, L. D., Yao, Q. M., Cook, J. R., Wang, Z., Libault, M., Brechenmacher, L., Valliyodan, B., Wu, X. L., Cheng, J. L., Stacey, G., Nguyen, H. T. and Xu, D. 2012 Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics BMC Genomics 10.1186/1471-2164-13-s1-s15
Justice, N. B., Norman, A., Brown, C. T., Singh, A., Thomas, B. C. and Banfield, J. F. 2014 Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms BMC Genomics 10.1186/1471-2164-15-1107
Khosravi, C., Battaglia, E., Kun, R. S., Dalhuijsen, S., Visser, J., Aguilar-Pontes, M. V., Zhou, M., Heyman, H. M., Kim, Y. M., Ronald, S. E. B. and de Vries, R. P. 2018 Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans BMC Genomics 10.1186/s12864-018-4609-x
Kolbe, A. R., Studer, A. J., Cornejo, O. E. and Cousins, A. B. 2019 Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO2 BMC Genomics 10.1186/s12864-019-5522-7
Ma, F. Y., Fuqua, B. K., Hasin, Y., Yukhtman, C., Vulpe, C. D., Lusis, A. J. and Pellegrini, M. 2019 A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods BMC Genomics 10.1186/s12864-018-5393-3
Nguyen, N. D., Blaby, I. K. and Wang, D. 2019 ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks BMC Genomics 10.1186/s12864-019-6329-2
Patyshakuliyeva, A., Jurak, E., Kohler, A., Baker, A., Battaglia, E., de Bruijn, W., Burton, K. S., Challen, M. P., Coutinho, P. M., Eastwood, D. C., Gruben, B. S., Makela, M. R., Martin, F., Nadal, M., van den Brink, J., Wiebenga, A., Zhou, M., Henrissat, B., Kabel, M., Gruppen, H. and de Vries, R. P. 2013 Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus BMC Genomics 10.1186/1471-2164-14-663
Pechanova, O., Hsu, C. Y., Adams, J. P., Pechan, T., Vandervelde, L., Drnevich, J., Jawdy, S., Adeli, A., Suttle, J. C., Lawrence, A. M., Tschaplinski, T. J., Seguin, A. and Yuceer, C. 2010 Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar BMC Genomics 10.1186/1471-2164-11-674
Peterson, J. R., Thor, S., Kohler, L., Kohler, P. R. A., Metcalf, W. W. and Luthey-Schulten, Z. 2016 Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans BMC Genomics 10.1186/s12864-016-3219-8
Pomraning, K. R., Kim, Y. M., Nicora, C. D., Chu, R. K., Bredeweg, E. L., Purvine, S. O., Hu, D. H., Metz, T. O. and Baker, S. E. 2016 Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica BMC Genomics 10.1186/s12864-016-2471-2
Roske, K., Foecking, M. F., Yooseph, S., Glass, J. I., Calcutt, M. J. and Wise, K. S. 2010 A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes BMC Genomics 10.1186/1471-2164-11-430
Shrestha, R. P., Tesson, B., Norden-Krichmar, T., Federowicz, S., Hildebrand, M. and Allen, A. E. 2012 Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana BMC Genomics 10.1186/1471-2164-13-499
Tyler, L., Bragg, J. N., Wu, J. J., Yang, X. H., Tuskan, G. A. and Vogel, J. P. 2010 Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon BMC Genomics 10.1186/1471-2164-11-600
Ullah, F., Hamilton, M., Reddy, A. S. N. and Ben-Hur, A. 2018 Exploring the relationship between intron retention and chromatin accessibility in plants BMC Genomics 10.1186/s12864-017-4393-z
Vining, K. J., Pomraning, K. R., Wilhelm, L. J., Priest, H. D., Pellegrini, M., Mockler, T. C., Freitag, M. and Strauss, S. H. 2012 Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression BMC Genomics 10.1186/1471-2164-13-27
Wai, C. M., Zhang, J. S., Jones, T. C., Nagai, C. and Ming, R. 2017 Cell wall metabolism and hexose allocation contribute to biomass accumulation in high yielding extreme segregants of a Saccharum interspecific F2 population BMC Genomics 10.1186/s12864-017-4158-8
Yang, X. P., Song, J., You, Q., Paudel, D. R., Zhang, J. S. and Wang, J. P. 2017 Mining sequence variations in representative polyploid sugarcane germplasm accessions BMC Genomics 10.1186/s12864-017-3980-3
Yang, Y., Labbe, J., Muchero, W., Yang, X., Jawdy, S. S., Kennedy, M., Johnson, J., Sreedasyam, A., Schmutz, J., Tuskan, G. A. and Chen, J. G. 2016 Genome-wide analysis of lectin receptor-like kinases in Populus BMC Genomics 10.1186/s12864-016-3026-2
Yin, H. F., Guo, H. B., Weston, D. J., Borland, A. M., Ranjan, P., Abraham, P. E., Jawdy, S. S., Wachira, J., Tuskan, G. A., Tschaplinski, T. J., Wullschleger, S. D., Guo, H., Hettich, R. L., Gross, S. M., Wang, Z., Visel, A. and Yang, X. H. 2018 Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave BMC Genomics 10.1186/s12864-018-4964-7
Zhang, J. S., Sharma, A., Yu, Q. Y., Wang, J. P., Li, L. T., Zhu, L., Zhang, X. T., Chen, Y. Q. and Ming, R. 2016 Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum BMC Genomics 10.1186/s12864-016-2817-9
Zhu, M. Z., Deng, X., Joshi, T., Xu, D., Stacey, G. and Cheng, J. L. 2012 Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells BMC Genomics 10.1186/1471-2164-13-437
Kosina, S. M., Greiner, A. M., Lau, R. K., Jenkins, S., Baran, R., Bowen, B. P. and Northen, T. R. 2018 Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes BMC Microbiology 10.1186/s12866-018-1256-y
Wu, L. Y., Wen, C. Q., Qin, Y. J., Yin, H. Q., Tu, Q. C., Van Nostrand, J. D., Yuan, T., Yuan, M. T., Deng, Y. and Zhou, J. Z. 2015 Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis BMC Microbiology 10.1186/s12866-015-0450-4
Xu, M. Y., He, Z. L., Deng, Y., Wu, L. Y., van Nostrand, J. D., Hobbie, S. E., Reich, P. B. and Zhou, J. Z. 2013 Elevated CO2 influences microbial carbon and nitrogen cycling BMC Microbiology 10.1186/1471-2180-13-124
Bihmidine, S., Baker, R. F., Hoffner, C. and Braun, D. M. 2015 Sucrose accumulation in sweet sorghum stems occurs by apoplasmic phloem unloading and does not involve differential Sucrose transporter expression BMC Plant Biology 10.1186/s12870-015-0572-8
Mazaheri, M., Heckwolf, M., Vaillancourt, B., Gage, J. L., Burdo, B., Heckwolf, S., Barry, K., Lipzen, A., Ribeiro, C. B., Kono, T. J. Y., Kaeppler, H. F., Spalding, E. P., Hirsch, C. N., Buell, C. R., de Leon, N. and Kaeppler, S. M. 2019 Genome-wide association analysis of stalk biomass and anatomical traits in maize BMC Plant Biology 10.1186/s12870-019-1653-x
Qi, P., Gimode, D., Saha, D., Schroder, S., Chakraborty, D., Wang, X. W., Dida, M. M., Malmberg, R. L. and Devos, K. M. 2018 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 10.1186/s12870-018-1316-3
Stonebloom, S. h., and Scheller, H. V. 2019 Transcriptome analysis of rubber biosynthesis in guayule (Parthenium argentatum gray) BMC Plant Biology 10.1186/s12870-019-1653-x
Yurchenko, O. P., Park, S., Ilut, D. C., Inmon, J. J., Millhollon, J. C., Liechty, Z., Page, J. T., Jenks, M. A., Chapman, K. D., Udall, J. A., Gore, M. A. and Dyer, J. M. 2014 Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium BMC Plant Biology 10.1186/s12870-014-0312-5
Jun, S. R., Robeson, M. S., Hauser, L. J., Schadt, C. W. and Gorin, A. A. 2015 PanFP: pangenome-based functional profiles for microbial communities BMC Research Notes 10.1186/s13104-015-1462-8
Facciotti, M. T., Pang, W. L., Lo, F. Y., Whitehead, K., Koide, T., Masumura, K., Pan, M., Kaur, A., Larsen, D. J., Reiss, D. J., Hoang, L., Kalisiak, E., Northen, T., Trauger, S. A., Siuzdak, G. and Baliga, N. S. 2010 Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis BMC Systems Biology 10.1186/1752-0509-4-64
Imam, S., Yilmaz, S., Sohmen, U., Gorzalski, A. S., Reed, J. L., Noguera, D. R. and Donohue, T. J. 2011 iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network BMC Systems Biology 10.1186/1752-0509-5-116
Mueller, T. J., Berla, B. M., Pakrasi, H. B. and Maranas, C. D. 2013 Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow BMC Systems Biology 10.1186/1752-0509-7-142
Navid, Ali and Almaas, Eivind 2012 Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach BMC Systems Biology 10.1186/1752-0509-6-150
Plaisier, C. L., Lo, F. Y., Ashworth, J., Brooks, A. N., Beer, K. D., Kaur, A., Pan, M., Reiss, D. J., Facciotti, M. T. and Baliga, N. S. 2014 Evolution of context dependent regulation by expansion of feast/famine regulatory proteins BMC Systems Biology 10.1186/s12918-014-0122-2
Wang, Q. H., Venkataramanan, K. P., Huang, H. Z., Papoutsakis, E. T. and Wu, C. H. 2013 Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress BMC Systems Biology 10.1186/1752-0509-7-120
John Dighton, James F. White 2017 The Fungal Community Its Organization and Role in the Ecosystem (Book) 10.1201/9781315119496
Bare, J. C. and Baliga, N. S. 2014 Architecture for interoperable software in biology Briefings in Bioinformatics 10.1093/bib/bbs074
Sjolander, K., Datta, R. S., Shen, Y. Q. and Shoffner, G. M. 2011 Ortholog identification in the presence of domain architecture rearrangement Briefings in Bioinformatics 10.1093/bib/bbr036
Chu Y, Li G, and Guo H 2013 QM/MM MD and Free Energy Simulations of the Methylation Reactions Catalyzed by Protein Arginine Methyltransferase PRMT3 Canadian Journal of Chemistry 10.1139/cjc-2012-0483
Kerio, S., Daniels, H. A., Gomez-Gallego, M., Tabima, J. F., Lenz, R. R., Sondreli, K. L., Grunwald, N. J., Williams, N., McDougal, R. and LeBoldus, J. M. 2019 From genomes to forest management - tackling invasive Phytophthora species in the era of genomics Canadian Journal of Plant Pathology 10.1080/07060661.2019.1626910
Sowinski, E. E., Gilbert, S., Lam, E. and Carpita, N. C. 2019 Linkage structure of cell-wall polysaccharides from three duckweed species Carbohydrate Polymers 10.1016/j.carbpol.2019.115119
Nguyen, Hang Ngoc, Chaves-Lopez, Clemencia, Oliveira, Rodrigo Cardoso, Paparella, Antonello and Rodrigues, Debora F. 2019 Cellular and metabolic approaches to investigate the effects of graphene and graphene oxide in the fungi Aspergillus flavus and Aspergillus niger Carbon 10.1016/j.carbon.2018.10.099
Barbieri, E. M., Muir, P., Akhuetie-Oni, B. O., Yellman, C. M. and Isaacs, F. J. 2017 Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes Cell 10.1016/j.cell.2017.10.034
Jang, C., Chen, L. and Rabinowitz, J. D. 2018 Metabolomics and Isotope Tracing Cell 10.1016/j.cell.2018.03.055
Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., Assad-Garcia, N., Glass, J. I. and Covert, M. W. 2012 A Whole-Cell Computational Model Predicts Phenotype from Genotype Cell 10.1016/j.cell.2012.05.044
Kominek, J., Doering, D. T., Opulente, D. A., Shen, X. X., Zhou, X. F., DeVirgilio, J., Hulfachor, A. B., Groenewald, M., McGee, M. A., Karlen, S. D., Kurtzman, C. P., Rokas, A. and Hittinger, C. T. 2019 Eukaryotic Acquisition of a Bacterial Operon Cell 10.1016/j.cell.2019.01.034
Shen, X. X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., Boudouris, J. T., Schneider, R. M., Langdon, Q. K., Ohkuma, M., Endoh, R., Takashima, M., Manabe, R., Cadez, N., Libkind, D., Rosa, C. A., DeVirgilio, J., Hulfachor, A. B., Groenewald, M., Kurtzman, C. P., Hittinger, C. T. and Rokas, A. 2018 Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum Cell 10.1016/j.cell.2018.10.023
Efferth, T., Schwarzl, S. M., Smith, J. and Osieka, R. 2006 Role of glucose-6-phosphate dehydrogenase for oxidative stress and apoptosis Cell Death and Differentiation 10.1038/sj.cdd.4401807
Levy, A., Conway, J. M., Dangl, J. L. and Woyke, T. 2018 Elucidating Bacterial Gene Functions in the Plant Microbiome Cell Host & Microbe 10.1016/j.chom.2018.09.005
Drigo, R. A. E., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T., Bushong, E., Phan, S., Orphan, V., Lechene, C., Ellisman, M. H. and Hetzer, M. W. 2019 Age Mosaicism across Multiple Scales in Adult Tissues Cell Metabolism 10.1016/j.cmet.2019.05.010
Cano, M., Holland, S. C., Artier, J., Burnap, R. L., Ghirardi, M., Morgan, J. A. and Yu, J. P. 2018 Glycogen Synthesis and Metabolite Overflow Contribute to Energy Balancing in Cyanobacteria Cell Reports 10.1016/j.celrep.2018.03.083
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Leiby, N., Mehta, P., Marx, C. J. and Segre, D. 2014 Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics Cell Reports 10.1016/j.celrep.2014.03.070
Ma, N. J. and Isaacs, F. J. 2016 Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements Cell Systems 10.1016/j.cels.2016.06.009
Yurkovich, J. T., Yurkovich, B. J., Drager, A., Palsson, B. O. and King, Z. A. 2017 A Padawan Programmer's Guide to Developing Software Libraries Cell Systems 10.1016/j.cels.2017.08.003
Alekozai E, GhattyVenkataKrishna PK, Uberbacher EC, Crowley MF, Smith JC, and Cheng X 2014 Simulation Analysis of the Cellulase Cel7A Carbohydrate Binding Module on the Surface of the Cellulose Iβ Cellulose 10.1007/s10570-013-0026-0
Lian P, Guo HB, Smith JC, Wei DQ, and Guo H 2014 Catalytic Mechanism and Origin of High Activity of Cellulase TmCel12A at High Temperature A Quantum Mechanical/Molecular Mechanical Study Cellulose 10.1007/s10570-013-0011-7
Mostofian B, Smith JC, and Cheng X 2014 Simulation of a Cellulose Fiber in Ionic Liquid Suggests a Synergistic Approach to Dissolution Cellulose 10.1007/s10570-013-0018-0
Pingali SV, O'Neill HM, Nishiyama Y, He L, Melnichenko YB, Urban V, Petridis L, Davison B, and Langan P 2014 Morphological Changes in the Cellulose and Lignin Components of Biomass Occur at Different Stages during Steam Pretreatment Cellulose 10.1007/s10570-013-0162-6
Sawada D, Nishiyama Y, Petridis L, Parthasarathi R, Gnanakaran S, Forsyth VT, Wada M, and Langan P 2013 Structure and Dynamics of a Complex of Cellulose with EDA Insights into the Action of Amines on Cellulose Cellulose 10.1007/s10570-013-9974-7
Yang H, Wang T, Oehme D, Petridis L, Hong M, Kubicki JD 2018 Structural factors affecting 13C NMR chemical shifts of cellulose a computational study Cellulose 10.1007/s10570-017-1549-6
Muchero, Wellington, Labbé, Jessy, Ranjan, Priya, DiFazio, Stephen and Tuskan, Gerald A. 2014 Genome Resequencing in Populus: Revealing Large-Scale Genome Variation and Implications on Specialized-Trait Genomics Challenges and Opportunities for the World's Forests in the 21st Century. 10.1007/978-94-007-7076-8_25
Chatterjee, A., Lajoie, M. J., Xiao, H., Church, G. M. and Schultz, P. G. 2014 A Bacterial Strain with a Unique Quadruplet Codon Specifying Non-native Amino Acids ChemBioChem 10.1002/cbic.201402104
Pappireddi, N., Martin, L. and Wuhr, M. 2019 A Review on Quantitative Multiplexed Proteomics ChemBioChem 10.1002/cbic.201800650
Pelot, K. A., Hagelthorn, D. M., Hong, Y. J., Tantillo, D. J. and Zerbe, P. 2019 Diterpene Synthase-Catalyzed Biosynthesis of Distinct Clerodane Stereoisomers ChemBioChem 10.1002/cbic.201800580
Ruprecht, C., Dallabermardina, P., Smith, P.J, Urbanowicz, B.R., Pfrengle, F. 2018 Analyzing Xyloglucan Endotransglycosylases by Incorporating Synthetic Oligosaccharides into Plant Cell Walls ChemBioChem 10.1002/cbic.201700638
Stadlmeier, M., Runtsch, L. S., Streshnev, F., Wuhr, M. and Carell, T. 2019 A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry ChemBioChem 10.1002/cbic.201900611
Pavlova, A., Parks, J. M., Oyelere, A. K. and Gumbart, J. C. 2017 Toward the rational design of macrolide antibiotics to combat resistance Chemical Biology & Drug Design 10.1111/cbdd.13004
Velazquez, H. A., Riccardi, D., Xiao, Z., Quarles, L. D., Yates, C. R., Baudry, J. and Smith, J. C. 2018 Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23 Chemical Biology & Drug Design 10.1111/cbdd.13110
Nagy, G., Velickovic, D., Chu, R. K., Carrell, A. A., Weston, D. J., Ibrahim, Y. M., Anderton, C. R. and Smith, R. D. 2019 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 10.1039/c8cc07482h
Tobimatsu, Y., Van de Wouwer, D., Allen, E., Kumpf, R., Vanholme, B., Boerjan, W. and Ralph, J. 2014 A click chemistry strategy for visualization of plant cell wall lignification Chemical Communications 10.1039/c4cc04692g
Ramapriya, G. M., Won, W. Y. and Maravelias, C. T. 2018 A superstructure optimization approach for process synthesis under complex reaction networks Chemical Engineering Research & Design 10.1016/j.cherd.2018.07.015
Qian P, Zhao N, Chen F, and Guo H 2015 Understanding Substrate Specificity of Related Plant Methylesterases MESs from Computational Investigations Chemical Journal of Chinese Universities 10.7503/cjcu20150674
Esposito, E. X., Stouch, T. R., Wymore, T. and Madura, J. D. 2014 Exploring the physicochemical properties of oxime-reactivation therapeutics for cyclosarin, sarin, tabun, and VX inactivated acetylcholinesterase Chemical Research in Toxicology 10.1021/tx400350b
Cheng, X. L. and Smith, J. C. 2019 Biological Membrane Organization and Cellular Signaling Chemical Reviews 10.1021/acs.chemrev.8b00439
Song, Y., Mobley, J. K., Motagamwala, A. H., Isaacs, M., Dumesic, J. A., Ralph, J., Lee, A. F., Wilson, K. and Crocker, M. 2018 Gold-catalyzed conversion of lignin to low molecular weight aromatics Chemical Science 10.1039/c8sc03208d
de Hatten X, Cournia Z, Huc I, Smith JC, and Metzler-Nolte N 2007 Force-Field Development and Molecular Dynamics Simulations of Ferrocene-Peptide Conjugates as a Scaffold for Hydrogenase Mimics Chemistry - A European Journal 10.1002/chem.200700358
Xu Q, Chu Y, Guo HB, Smith JC, and Guo H 2009 Energy Triplets for Writing Epigenetic Marks Insights from QM/MM Free Energy Simulations of Protein Lysine Methyltransferases Chemistry - A European Journal 10.1002/chem.200902297
Yao J, Wlodawer A, and Guo H 2013 Understanding the Autocatalytic Process of Pro-kumamolisin Activation from Molecular Dynamics and Quantum Mechanical/Molecular Mechanical QM/MM Free-Energy Simulations Chemistry - A European Journal 10.1002/chem.201301310
Nickels, J. D., Smith, J. C. and Cheng, X. 2015 Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes Chemistry and Physics of Lipids 10.1016/j.chemphyslip.2015.07.012
Reed, J. L. 2017 Genome-Scale Metabolic Modeling and Its Application to Microbial Communities The Chemistry of Microbiomes: Proceedings of a Seminar Series 10.17226/24751
Jung, S., Trajano, H. L., Yoo, C. G., Foston, M. B., Hu, F., Tolbert, A. K., Wyman, C. E. and Ragauskas, A. J. 2018 Topochemical Understanding of Lignin Distribution During Hydrothermal Flowthrough Pretreatment ChemistrySelect 10.1002/slct.201801837
Min, W., Lu, S., Holtom, G. R. and Xie, X. S. 2009 Triple-Resonance Coherent Anti-Stokes Raman Scattering Microspectroscopy ChemPhysChem 10.1002/cphc.200800502
Bond, D. R., Strycharz-Glaven, S. M., Tender, L. M. and Torres, C. I. 2012 On Electron Transport through Geobacter Biofilms ChemSusChem 10.1002/cssc.201100748
Gao, R. L., Li, Y. D., Kim, H., Mobley, J. K. and Ralph, J. 2018 Selective Oxidation of Lignin Model Compounds ChemSusChem 10.1002/cssc.201800598
Jiang, H. J., Imberti, S., Simmons, B. A., Atkin, R., and Warr, G. 2018 Structural Design of Ionic Liquids for Optimizing Aromatic Dissolution ChemSusChem 10.1002/cssc.201802016
Klinger, G. E., Zhou, Y. T., Hao, P. C., Robbins, J., Aquilina, J. M., Jackson, J. E. and Hegg, E. L. 2019 Biomimetic Reductive Cleavage of Keto Aryl Ether Bonds by Small-Molecule Thiols ChemSuschem 10.1002/cssc.201901742
Liu, Y. and Bond, D. R. 2012 Long-Distance Electron Transfer by G. sulfurreducens Biofilms Results in Accumulation of Reduced c-Type Cytochromes ChemSusChem 10.1002/cssc.201100734
Regner, M., Bartuce, A., Padmakshan, D., Ralph, J. and Karlen, S. D. 2018 Reductive Cleavage Method for Quantitation of Monolignols and Low-Abundance Monolignol Conjugates ChemSusChem 10.1002/cssc.201800617
Blaby, Ian K. and Blaby-Haas, Crysten E. 2017 Genomics and Functional Genomics in Chlamydomonas reinhardtii Chlamydomonas: Molecular Genetics and Physiology 10.1007/978-3-319-66365-4_1
Gallagher-Jones, M., Ophus, C., Bustillo, K. C., Boyer, D. R., Panova, O., Glynn, C., Zee, C. T., Ciston, J., Mancia, K. C., Minor, A. M. and Rodriguez, J. A. 2019 Nanoscale mosaicity revealed in peptide microcrystals by scanning electron nanodiffraction Communications Biology 10.1038/s42003-018-0263-8
Li, M., Yoo, C. G., Pu, Y., Biswal, A. K., Tolbert, A. K., Mohnen, D. and Ragauskas, A. J. 2019 Downregulation of pectin biosynthesis gene GAUT4 leads to reduced ferulate and lignin-carbohydrate cross-linking in switchgrass Communications Biology 10.1038/s42003-018-0265-6
Roth, M. S., Westcott, D. J., Iwai, M. and Niyogi, K. K. 2019 Hexokinase is necessary for glucose-mediated photosynthesis repression and lipid accumulation in a green alga Communications Biology 10.1038/s42003-019-0577-1
Xu, Z., Cai, W. and Cheng, X. 2011 Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model Communications in Computational Physics 10.4208/cicp.160410.200910a
Zhang B, Lu B, Cheng X, Huang J, Pitsianis N, Sun X, and McCammon A 2013 Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver Communications in Computational Physics 10.4208/cicp.210711.111111s
Garbarine, E., DePasquale, J., Gadia, V., Polikar, R. and Rosen, G. 2011 Information-theoretic approaches to SVM feature selection for metagenome read classification Computational Biology and Chemistry 10.1016/j.compbiolchem.2011.04.007
Topham, C. M. and Smith, J. C. 2015 Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues Computational Biology and Chemistry 10.1016/j.compbiolchem.2014.11.007
Petridis L, Xu J, Crowley M, Smith JC, and Cheng X 2011 Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes Computational Modeling in Lignocellulosic Biofuel Production 10.1021/bk-2010-1052.ch003
Saharay M, Guo HB, Smith JC, and Guo H 2011 QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates Computational Modeling in Lignocellulosic Biofuel Production 10.1021/bk-2010-1052.ch007
Lindner B, and Smith JC 2012 Sassena - X-ray and Neutron Scattering Calculations from Molecular Dynamics Trajectories using Massively Parallel Computers Computer Physics Communications 10.1016/j.cpc.2012.02.010
Lu B, Cheng X, Huang J, and McCammon JA 2010 AFMPB An Adaptive Fast Multipole Poisson–Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems Computer Physics Communications 10.1016/j.cpc.2010.02.015
Moritsugu K, and Smith JC 2009 REACH A Program for Coarse-Grained Biomolecular Simulation Computer Physics Communications 10.1016/j.cpc.2009.01.007
Ellingson S, and Baudry J 2014 High-Throughput Virtual Molecular Docking with AutoDockCloud Concurrency and Computation Practice and Experience 10.1002/cpe.2926
Ellingson SR, Dakshanamurthy S, Brown M, Smith JC, and Baudry J 2014 Accelerating Virtual High-Throughput Ligand Docking Screening One Million Compounds Using a Petascale Supercomputer Concurrency and Computation Practice and Experience 10.1002/cpe.3070
Chen, H., Stout, M. J., Qian, Q. and Chen, F. 2012 Genetic, Molecular and Genomic Basis of Rice Defense against Insects Critical Reviews in Plant Sciences 10.1080/07352689.2011.616052
Yin, H. F., Chen, C. J., Yang, J., Weston, D. J., Chen, J. G., Muchero, W., Ye, N., Tschaplinski, T. J., Wullschleger, S. D., Cheng, Z. M., Tuskan, G. A. and Yang, X. H. 2014 Functional Genomics of Drought Tolerance in Bioenergy Crops Critical Reviews in Plant Sciences 10.1080/07352689.2014.870417
Zhao, N., Wang, G. D., Norris, A., Chen, X. L. and Chen, F. 2013 Studying Plant Secondary Metabolism in the Age of Genomics Critical Reviews in Plant Sciences 10.1080/07352689.2013.789648
Qian, J. Y., Jia, G. Q., Zhi, H., Li, W., Wang, Y. F., Li, H. Q., Shang, Z. L., Doust, A. N. and Diao, X. M. 2012 Sensitivity to Gibberellin of Dwarf Foxtail Millet Varieties Crop Science 10.2135/cropsci2011.04.0192
Chang, K. Y., Riley, W. J., Crill, P. M., Grant, R. F., Rich, V. I. and Saleska, S. R. 2019 Large carbon cycle sensitivities to climate across a permafrost thaw gradient in subarctic Sweden Cryosphere 10.5194/tc-13-647-2019
Gao, Y. B., Xi, F. H., Zhang, H. X., Liu, X. Q., Wang, H. Y., Zhao, L. Z., Reddy, A. S. N. and Gu, L. F. 2019 Single-Molecule Real-Time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity Current Bioinformatics 10.2174/1574893614666190204151746
Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., Taylor, R. C., Williams, K. H. and Banfield, J. F. 2015 Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling Current Biology 10.1016/j.cub.2015.01.014
Floss, D. S., Gomez, S. K., Park, H. J., MacLean, A. M., Muller, L. M., Bhattarai, K. K., Levesque-Tremblay, V., Maldonado-Mendoza, I. E. and Harrison, M. J. 2017 A Transcriptional Program for Arbuscule Degeneration during AM Symbiosis Is Regulated by MYB1 Current Biology 10.1016/j.cub.2017.03.003
Krassowski, T., Kominek, J., Shen, X. X., Opulente, D. A., Zhou, X. F., Rokas, A., Hittinger, C. T. and Wolfe, K. H. 2019 Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution Current Biology 10.1016/j.cub.2019.06.056
Morrissey, J., Sutak, R., Paz-Yepes, J., Tanaka, A., Moustafa, A., Veluchamy, A., Thomas, Y., Botebol, H., Bouget, F. Y., McQuaid, J. B., Tirichine, L., Allen, A. E., Lesuisse, E. and Bowler, C. 2015 A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake Current Biology 10.1016/j.cub.2014.12.004
Nagel, D. H. and Kay, S. A. 2012 Complexity in the Wiring and Regulation of Plant Circadian Networks Current Biology 10.1016/j.cub.2012.07.025
Plett, J. M., Kemppainen, M., Kale, S. D., Kohler, A., Legue, V., Brun, A., Tyler, B. M., Pardo, A. G. and Martin, F. 2011 A secreted effector protein of Laccaria bicolor is required for symbiosis development Current Biology 10.1016/j.cub.2011.05.033
Labbe, J., Murat, C., Morin, E., Le Tacon, F. and Martin, F. 2011 Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers Current Genetics 10.1007/s00294-010-0328-9
Sardi, M. and Gasch, A. P. 2018 Genetic background effects in quantitative genetics: gene-by-system interactions Current Genetics 10.1007/s00294-018-0835-7
Allen, D. K. and Young, J. D. 2019 Tracing metabolic flux through time and space with isotope labeling experiments Current Opinion in Biotechnology 10.1016/j.copbio.2019.11.003
Ashworth, J., Wurtmann, E. J. and Baliga, N. S. 2012 Reverse engineering systems models of regulation: discovery, prediction and mechanisms Current Opinion in Biotechnology 10.1016/j.copbio.2011.12.005
Barros, J., Temple, S., Dixon, R.A. 2018 Development and commercialization of reduced lignin alfalfa Current Opinion in Biotechnology 10.1016/j.copbio.2018.09.003
Bevan, M. W., Garvin, D. F. and Vogel, J. P. 2010 Brachypodium distachyon genomics for sustainable food and fuel production Current Opinion in Biotechnology 10.1016/j.copbio.2010.03.006
Boock, J. T., Gupta, A. and Prather, K. L. J. 2015 Screening and modular design for metabolic pathway optimization Current Opinion in Biotechnology 10.1016/j.copbio.2015.08.013
Cardenas, E. and Tiedje, J. M. 2008 New tools for discovering and characterizing microbial diversity Current Opinion in Biotechnology 10.1016/j.copbio.2008.10.010
Cheah, Y. E. and Young, J. D. 2018 Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice Current Opinion in Biotechnology 10.1016/j.copbio.2018.02.013
Chowdhury, A., Khodayari, A. and Maranas, C. D. 2015 Improving prediction fidelity of cellular metabolism with kinetic descriptions Current Opinion in Biotechnology 10.1016/j.copbio.2015.08.011
Hays, S. G., Patrick, W. G., Ziesack, M., Oxman, N. and Silver, P. A. 2015 Better together: engineering and application of microbial symbioses Current Opinion in Biotechnology 10.1016/j.copbio.2015.08.008
Hoynes-O'Connor, A. and Moon, T. S. 2015 Programmable genetic circuits for pathway engineering Current Opinion in Biotechnology 10.1016/j.copbio.2015.08.007
Kontur, W. S., Noguera, D. R. and Donohue, T. J. 2012 Maximizing reductant flow into microbial H-2 production Current Opinion in Biotechnology 10.1016/j.copbio.2011.10.003
Levering, J., Broddrick, J. and Zengler, K. 2015 Engineering of oleaginous organisms for lipid production Current Opinion in Biotechnology 10.1016/j.copbio.2015.08.001
Long, M. R., Ong, W. K. and Reed, J. L. 2015 Computational methods in metabolic engineering for strain design Current Opinion in Biotechnology 10.1016/j.copbio.2014.12.019
Mahon, E. L. and Mansfield, S. D. 2019 Tailor-made trees: engineering lignin for ease of processing and tomorrow's bioeconomy Current Opinion in Biotechnology 10.1016/j.copbio.2018.10.014
McAtee, A. G., Jazmin, L. J. and Young, J. D. 2015 Application of isotope labeling experiments and C-13 flux analysis to enable rational pathway engineering Current Opinion in Biotechnology 10.1016/j.copbio.2015.08.004
McInerney, M. J., Sieber, J. R. and Gunsalus, R. P. 2009 Syntrophy in anaerobic global carbon cycles Current Opinion in Biotechnology 10.1016/j.copbio.2009.10.001
Montague, M. G., Lartigue, C. and Vashee, S. 2012 Synthetic genomics: potential and limitations Current Opinion in Biotechnology 10.1016/j.copbio.2012.01.014
Musat, Niculina, Musat, Florin, Weber, Peter Kilian and Pett-Ridge, Jennifer 2016 Tracking microbial interactions with NanoSIMS Current Opinion in Biotechnology 10.1016/j.copbio.2016.06.007
Perkins, M., Smith, R. A. and Samuels, L. 2019 The transport of monomers during lignification in plants: anything goes but how? Current Opinion in Biotechnology 10.1016/j.copbio.2018.09.011
Ralph, J., Lapierre, C. and Boerjan, W. 2019 Lignin structure and its engineering Current Opinion in Biotechnology 10.1016/j.copbio.2019.02.019
Tuskan, G. A., Muchero, W., Tschaplinski, T. J. and Ragauskas, A. J. 2019 Population-level approaches reveal novel aspects of lignin biosynthesis, content, composition and structure Current Opinion in Biotechnology 10.1016/j.copbio.2019.02.017
Vanholme, R., De Meester, B., Ralph, J. and Boerjan, W. 2019 Lignin biosynthesis and its integration into metabolism Current Opinion in Biotechnology 10.1016/j.copbio.2019.02.018
Wang, P., Dudareva, N., Morgan, J. A. and Chapple, C. 2015 Genetic manipulation of lignocellulosic biomass for bioenergy Current Opinion in Chemical Biology 10.1016/j.cbpa.2015.08.006
Bundy, B. C., Hunt, J. P., Jewett, M. C., Swartz, J. R., Wood, D. W., Frey, D. D. and Rao, G. 2018 Cell-free biomanufacturing Current Opinion in Chemical Engineering 10.1016/j.coche.2018.10.003
Peng, X. F., Gilmore, S. P. and O'Malley, M. A. 2016 Microbial communities for bioprocessing: lessons learned from nature Current Opinion in Chemical Engineering 10.1016/j.coche.2016.09.003
Allen, A. E., Allen, L. Z. and McCrow, J. P. 2013 Lineage specific gene family enrichment at the microscale in marine systems Current Opinion in Microbiology 10.1016/j.mib.2013.10.001
Teixeira, Pjpl, Colaianni, N. R., Fitzpatrick, C. R. and Dangl, J. L. 2019 Beyond pathogens: microbiota interactions with the plant immune system Current Opinion in Microbiology 10.1016/j.mib.2019.08.003
Blaby-Haas, C. E. and Merchant, S. S. 2017 Regulating cellular trace metal economy in algae Current Opinion in Plant Biology 10.1016/j.pbi.2017.06.005
Borland, A. M., Guo, H. B., Yang, X. H. and Cushman, J. C. 2016 Orchestration of carbohydrate processing for crassulacean acid metabolism Current Opinion in Plant Biology 10.1016/j.pbi.2016.04.001
Gehan, M. A., Greenham, K., Mockler, T. C. and McClung, C. R. 2015 Transcriptional networks - crops, clocks, and abiotic stress Current Opinion in Plant Biology 10.1016/j.pbi.2015.01.004
Hartwell, J., Dever, L. V. and Boxall, S. F. 2016 Emerging model systems for functional genomics analysis of Crassulacean acid metabolism Current Opinion in Plant Biology 10.1016/j.pbi.2016.03.019
Hopkinson, B. M., Dupont, C. L. and Matsuda, Y. 2016 The physiology and genetics of CO2 concentrating mechanisms in model diatoms Current Opinion in Plant Biology 10.1016/j.pbi.2016.03.013
Juenger, T. E. 2013 Natural variation and genetic constraints on drought tolerance Current Opinion in Plant Biology 10.1016/j.pbi.2013.02.001
Liu, D. G., Hu, R. B., Palla, K. J., Tuskan, G. A. and Yang, X. H. 2016 Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research Current Opinion in Plant Biology 10.1016/j.pbi.2016.01.007
Muller, L. M. and Harrison, M. J. 2019 Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis Current Opinion in Plant Biology 10.1016/j.pbi.2019.05.004
Plett, J. M. and Martin, F. 2015 Reconsidering mutualistic plant-fungal interactions through the lens of effector biology Current Opinion in Plant Biology 10.1016/j.pbi.2015.06.001
Shakoor, N., Lee, S. and Mockler, T. C. 2017 High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field Current Opinion in Plant Biology 10.1016/j.pbi.2017.05.006
Veneault-Fourrey, C. and Martin, F. 2011 Mutualistic interactions on a knife-edge between saprotrophy and pathogenesis Current Opinion in Plant Biology 10.1016/j.pbi.2011.03.022
Cannon, K. A., Ochoa, J. M. and Yeates, T. O. 2019 High-symmetry protein assemblies: patterns and emerging applications Current Opinion in Structural Biology 10.1016/
Kelley, B. R., Ellis, J. C., Hyatt, D., Jacobson, D. and Johnson, J. 2018 Isolation and Whole-Genome Sequencing of Environmental Campylobacter Current Protocols in Microbiology 10.1002/cpmc.64
Karpinets, T. V., Romine, M. F., Schmoyer, D. D., Kora, G. H., Syed, M. H., Leuze, M. R., Serres, M. H., Park, B. H., Samatova, N. F. and Uberbacher, E. C. 2010 Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions Database 10.1093/database/baq012
Nag, A., Karpinets, T. V., Chang, C. H. and Bar-Peled, M. 2012 Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa Database 10.1093/database/bas013
Yilin, L., Huayou, C., Robert, Z., David, W. J. H. and Weilan, S. 2013 Thermostable DNA Ligase-Mediated PCR Production of Circular Plasmid (PPCP) and Its Application in Directed Evolution via In situ Error-Prone PCR DNA Research 10.1093/dnares/dst016
Smith JC, Krishnan M, Smolin N, and Petridis L 2011 Integration of Neutron Scattering with Computer Simulation to Study the Structure and Dynamics of Biological Systems Dynamics of Biological Macromolecules by Neutron Scattering 10.2174/97816080521961110101
Abraha, M., Gelfand, I., Hamilton, S. K., Chen, J. Q. and Robertson, G. P. 2018 Legacy effects of land use on soil nitrous oxide emissions in annual crop and perennial grassland ecosystems Ecological Applications 10.1002/eap.1745
Martin, Francis and Kohler, Annegret 2013 The Mycorrhizal Symbiosis Genomics The Ecological Genomics of Fungi 10.1002/9781118735893.ch8
Murat, Claude, Payen, Thibaut, Petitpierre, Denis and Labbé, Jessy 2013 Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay Fungi THe Ecological Genomics of Fungi 10.1002/9781118735893.ch2
Cheng, Yiwei, Bouskill, Nicholas J. and Brodie, Eoin L. 2019 Model exploration of interactions between algal functional diversity and productivity in chemostats to represent open ponds systems across climate gradients Ecological Modelling 10.1016/j.ecolmodel.2019.05.007
Duhamel, M., Wan, J., Bogar, L. M., Segnitz, R. M., Duncritts, N. C. and Peay, K. G. 2019 Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance Ecological Monographs 10.1002/ecm.1367
de Carvalho, T. S., Jesus, E. D., Barlow, J., Gardner, T. A., Soares, I. C., Tiedje, J. M. and Moreira, F. M. D. 2016 Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria Ecology 10.1002/ecy.1513
Nuccio, E. E., Anderson-Furgeson, J., Estera, K. Y., Pett-Ridge, J., de Valpine, P., Brodie, E. L. and Firestone, M. K. 2016 Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass Ecology 10.1890/15-0882.1
Papp, K., Hungate, B. A. and Schwartz, E. 2020 Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP Ecology 10.1002/ecy.2887
Zeglin, L. H., Bottomley, P. J., Jumpponen, A., Rice, C. W., Arango, M., Lindsley, A., McGowan, A., Mfombep, P. and Myrold, D. D. 2013 Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales Ecology 10.1890/12-2018.1
Escalas, A., Hale, L., Voordeckers, J. W., Yang, Y. F., Firestone, M. K., Alvarez-Cohen, L. and Zhou, J. Z. 2019 Microbial functional diversity: From concepts to applications Ecology and Evolution 10.1002/ece3.5670
Kim, T., Bartel, S. and Gratton, C. 2019 Grassland harvesting alters ant community trophic structure: An isotopic study in tallgrass prairies Ecology and Evolution 10.1002/ece3.5523
Shi, S. J., Nuccio, E. E., Shi, Z. J., He, Z. L., Zhou, J. Z. and Firestone, M. K. 2016 The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages Ecology Letters 10.1111/ele.12630
Chen, M. S., Parton, W. J., Hartman, M. D., Del Grosso, S., Smith, W. K., Knapp, A. K., Lutz, S., Derner, J., Tucker, C. J., Ojima, D. S., Volesky, J. D., Stephenson, M. B., Schacht, W. H. and Gao, W. 2019 Assessing precipitation, evapotranspiration, and NDVI as controls of US Great Plains plant production Ecosphere 10.1002/ecs2.2889
Koch, B. J., McHugh, T. A., Hayer, M., Schwartz, E., Blazewicz, S. J., Dijkstra, P., van Gestel, N., Marks, J. C., Mau, R. L., Morrissey, E. M., Pett-Ridge, J. and Hungate, B. A. 2018 Estimating taxon-specific population dynamics in diverse microbial communities Ecosphere 10.1002/ecs2.2090
Rogers, Timothy J., Leppanen, Christy, Brown, Veronica, Fordyce, James A., LeBude, Anthony, Ranney, Thomas, Simberloff, Daniel and Cregger, Melissa A. 2018 Exploring variation in phyllosphere microbial communities across four hemlock species Ecosphere 10.1002/ecs2.2524
Niu, S. L., Sherry, R. A., Zhou, X. H. and Luo, Y. Q. 2013 Ecosystem Carbon Fluxes in Response to Warming and Clipping in a Tallgrass Prairie Ecosystems 10.1007/s10021-013-9661-4
Shcherbak, I. and Robertson, G. P. 2019 Nitrous Oxide (N2O) Emissions from Subsurface Soils of Agricultural Ecosystems Ecosystems 10.1007/s10021-019-00363-z
Martin, Francis and Bonito, Gregory 2012 Ten Years of Genomics for Ectomycorrhizal Fungi: What Have We Achieved and Where Are We Heading? Edible Ectomycorrhizal Mushrooms 10.1007/978-3-642-33823-6_21
Plett, Jonathan M. and Martin, Francis 2011 Mutualistic Effectors: Architects of Symbiosis Effectors in Plant-Microbe Interactions 10.1002/9781119949138.ch12
Bernstein, D. B., Dewhirst, F. E. and Segre, D. 2019 Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome ELife 10.7554/eLife.39733
Di Rienzi, S. C., Sharon, I., Wrighton, K. C., Koren, O., Hug, L. A., Thomas, B. C., Goodrich, J. K., Bell, J. T., Spector, T. D., Banfield, J. F. and Ley, R. E. 2013 The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria ELife 10.7554/eLife.01102
Du, Z. Y., Zienkiewicz, K., Vande Pol, N., Ostrom, N. E., Benning, C. and Bonito, G. M. 2019 Algal-fungal symbiosis leads to photosynthetic mycelium ELife 10.7554/eLife.47815
Feng, J., Jester, B. W., Tinberg, C. E., Mandell, D. J., Antunes, M. S., Chari, R., Morey, K. J., Rios, X., Medford, J. I., Church, G. M., Fields, S. and Baker, D. 2015 A general strategy to construct small molecule biosensors in eukaryotes ELife 10.7554/eLife.10606
O'Connor, D. L., Elton, S., Ticchiarellin, F., Hsia, M. M., Vogel, J. P. and Leyser, O. 2017 Cross-species functional diversity within the PIN auxin efflux protein family ELife 10.7554/eLife.31804
Raveh-Sadka, T., Thomas, B. C., Singh, A., Firek, B., Brooks, B., Castelle, C. J., Sharon, I., Baker, R., Good, M., Morowitz, M. J. and Banfield, J. F. 2015 Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development ELife 10.7554/eLife.05477
Rellan-Alvarez, R., Lobet, G., Lindner, H., Pradier, P. L., Sebastian, J., Yee, M. C., Geng, Y., Trontin, C., LaRue, T., Schrager-Lavelle, A., Haney, C. H., Nieu, R., Maloof, J., Vogel, J. P. and Dinneny, J. R. 2015 GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems ELife 10.7554/eLife.07597
Tye, B. W., Commins, N., Ryazanova, L. V., Wuhr, M., Springer, M., Pincue, D. and Churchman, L. S. 2019 Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness ELife 10.7554/eLife.43002
Lee, M. H., Jeon, H. S., Kim, S. H., Chung, J. H., Roppolo, D., Lee, H. J., Cho, H. J., Tobimatsu, Y., Ralph, J. and Park, O. K. 2019 Lignin-based barrier restricts pathogens to the infection site and confers resistance in plants The EMBO Journal 10.15252/embj.2019101948
Glynn, C. and Rodriguez, J. A. 2019 Data-driven challenges and opportunities in crystallography Emerging Topics in Life Sciences 10.1042/etls20180177
Parks JM, Imhof P, and Smith JC 2010 Understanding Enzyme Catalysis Using Computer Simulation Encyclopedia of Catalysis 10.1002/0471227617.eoc217
Pi, M., Kapoor, K., Ye, R., Nishimoto, S. K., Smith, J. C., Baudry, J. and Quarles, L. D. 2016 Evidence for Osteocalcin Binding and Activation of GPRC6A in beta-Cells Endocrinology 10.1210/en.2015-2010
Baral, N. R., Kavvada, O., Mendez-Perez, D., Mukhopadhyay, A., Lee, T. S., Simmons, B. A., and Scown, C. D. 2019 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 10.1039/c8ee03266a
Jayakody, L. N., Johnson, C. W., Whitham, J. M., Giannone, R. J., Black, B. A., Cleveland, N. S., Klingeman, D. M., Michener, W. E., Olstad, J. L., Vardon, D. R., Brown, R. C., Brown, S. D., Hettich, R. L., Guss, A. M. and Beckham, G. T. 2018 Thermochemical wastewater valorization via enhanced microbial toxicity tolerance Energy & Environmental Science 10.1039/c8ee00460a
Liu, F. H., Rotaru, A. E., Shrestha, P. M., Malvankar, N. S., Nevin, K. P. and Lovley, D. R. 2012 Promoting direct interspecies electron transfer with activated carbon Energy & Environmental Science 10.1039/c2ee22459c
Lovley, D. R. 2011 Live wires: direct extracellular electron exchange for bioenergy and the bioremediation of energy-related contamination Energy & Environmental Science 10.1039/c1ee02229f
Motagamwala, A. H., Huang, K. F., Maravelias, C. T. and Dumesic, J. A. 2019 Solvent system for effective near-term production of hydroxymethylfurfural (HMF) with potential for long-term process improvement Energy & Environmental Science 10.1039/c9ee00447e
Rotaru, A. E., Shrestha, P. M., Liu, F. H., Shrestha, M., Shrestha, D., Embree, M., Zengler, K., Wardman, C., Nevin, K. P. and Lovley, D. R. 2014 A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane Energy & Environmental Science 10.1039/c3ee42189a
Harman-Ware, A.E., Ferrell III, J.R. 2018 Methods and challenges in the determination of molecular weight metrics of bio-oils Energy and Fuels 10.1021/acs.energyfuels.8b02113
Tompsett, G. A., Boock, J. T., DiSpirito, C., Stolz, E., Knutson, D. R., Rivard, A. G., Overdevest, M. R., Conlon, C. N., Prather, K. L. J., Thompson, J. R. and Timko, M. T. 2018 Extraction Rate and Energy Efficiency of Supercritical Carbon Dioxide Recovery of Higher Alcohols from Dilute Aqueous Solution Energy Technology 10.1002/ente.201700626
Guo, H. B., Ma, Y., Tuskan, G. A., Qin, H., Yang, X. H. and Guo, H. 2019 A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon's Information Theory Entropy 10.3390/e21060591
Baral, N. R., Quiroz-Arita, C., AND Bradley, T. h. 2018 Probabilistic Lifecycle Assessment of Butanol Production from Corn Stover Using Different Pretreatment Methods Environ Science & Technology 10.1021/acs.est.8b05176
Caro-Quintero, A. and Konstantinidis, K. T. 2012 Bacterial species may exist, metagenomics reveal Environmental Microbiology 10.1111/j.1462-2920.2011.02668.x
Dekas, A. E., Chadwick, G. L., Bowles, M. W., Joye, S. B. and Orphan, V. J. 2014 Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea Environmental Microbiology 10.1111/1462-2920.12247
Dekas, A. E., Fike, D. A., Chadwick, G. L., Green-Saxena, A., Fortney, J., Connon, S. A., Dawson, K. S. and Orphan, V. J. 2018 Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading Environmental Microbiology 10.1111/1462-2920.14342
Dore, J., Kohler, A., Dubost, A., Hundley, H., Singan, V., Peng, Y., Kuo, A., Grigoriev, I. V., Martin, F., Marmeisse, R. and Gay, G. 2017 The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation Environmental Microbiology 10.1111/1462-2920.13670
Freedman, A. J. E., Tan, B. and Thompson, J. R. 2017 Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir Environmental Microbiology 10.1111/1462-2920.13706
Glass, J. B., Yu, H., Steele, J. A., Dawson, K. S., Sun, S. L., Chourey, K., Pan, C. L., Hettich, R. L. and Orphan, V. J. 2014 Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments Environmental Microbiology 10.1111/1462-2920.12314
Hacquard, S., Tisserant, E., Brun, A., Legue, V., Martin, F. and Kohler, A. 2013 Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments Environmental Microbiology 10.1111/1462-2920.12080
He, X. J., Chadwick, G., Kempes, C., Shi, Y. M., McGlynn, S., Orphan, V. and Meile, C. 2019 Microbial interactions in the anaerobic oxidation of methane: model simulations constrained by process rates and activity patterns Environmental Microbiology 10.1111/1462-2920.14507
Hodkinson, B. P., Gottel, N. R., Schadt, C. W. and Lutzoni, F. 2012 Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome Environmental Microbiology 10.1111/j.1462-2920.2011.02560.x
Justice, N. B., Li, Z., Wang, Y. F., Spaudling, S. E., Mosier, A. C., Hettich, R. L., Pan, C. L. and Banfield, J. F. 2014 N-15- and H-2 proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity Environmental Microbiology 10.1111/1462-2920.12488
Li, Z., Yao, Q., Dearth, S. P., Entler, M. R., Castro Gonzalez, H. F., Uehling, J. K., Vilgalys, R. J., Hurst, G. B., Campagna, S. R., Labbe, J. L. and Pan, C. 2017 Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system Environmental Microbiology 10.1111/1462-2920.13605
Liu, F. H., Rotaru, A. E., Shrestha, P. M., Malvankar, N. S., Nevin, K. P. and Lovley, D. R. 2015 Magnetite compensates for the lack of a pilin-associated c-type cytochrome in extracellular electron exchange Environmental Microbiology 10.1111/1462-2920.12485
Liu, S. S., Wang, F., Xue, K., Sun, B., Zhang, Y. G., He, Z. L., Van Nostrand, J. D., Zhou, J. Z. and Yang, Y. F. 2015 The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry Environmental Microbiology 10.1111/1462-2920.12398
McCully, A. L., LaSarre, B. and McKinlay, J. B. 2017 Growth-independent cross-feeding modifies boundaries for coexistence in a bacterial mutualism Environmental Microbiology 10.1111/1462-2920.13847
Mondav, R., McCalley, C. K., Hodgkins, S. B., Frolking, S., Saleska, S. R., Rich, V. I., Chanton, J. P. and Crill, P. M. 2017 Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient Environmental Microbiology 10.1111/1462-2920.13809
Morrissey, E. M., Mau, R. L., Schwartz, E., Koch, B. J., Hayer, M. and Hungate, B. A. 2018 Taxonomic patterns in the nitrogen assimilation of soil prokaryotes Environmental Microbiology 10.1111/1462-2920.14051
Mueller, R. S., Dill, B. D., Pan, C. L., Belnap, C. P., Thomas, B. C., VerBerkmoes, N. C., Hettich, R. L. and Banfield, J. F. 2011 Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community Environmental Microbiology 10.1111/j.1462-2920.2011.02486.x
Nelson, C. E., Attia, M. A., Rogowski, A., Morland, C., Brumer, H. and Gardner, J. G. 2017 Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification Environmental Microbiology 10.1111/1462-2920.13959
Neumann, A. P., McCormick, C. A. and Suen, G. 2017 Fibrobacter communities in the gastrointestinal tracts of diverse hindgut-fermenting herbivores are distinct from those of the rumen Environmental Microbiology 10.1111/1462-2920.13878
Nuccio, Erin E., Hodge, Angela, Pett-Ridge, Jennifer, Herman, Donald J., Weber, Peter K. and Firestone, Mary K. 2013 An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition Environmental Microbiology 10.1111/1462-2920.12081
Pellegrin, C., Daguerre, Y., Ruytinx, J., Guinet, F., Kemppainen, M., Frey, N. F. D., Puech-Pages, V., Hecker, A., Pardo, A. G., Martin, F. M. and Veneault-Fourrey, C. 2019 Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis Environmental Microbiology 10.1111/1462-2920.14727
Quandt, C. A., Kohler, A., Hesse, C. N., Sharpton, T. J., Martin, F. and Spatafora, J. W. 2015 Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome Environmental Microbiology 10.1111/1462-2920.12840
Samo, Ty J., Kimbrel, Jeffrey A., Nilson, Daniel J., Pett-Ridge, Jennifer, Weber, Peter K. and Mayali, Xavier 2018 Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions Environmental Microbiology 10.1111/1462-2920.14357
Shakya, M., Quince, C., Campbell, J. H., Yang, Z. K., Schadt, C. W. and Podar, M. 2013 Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities Environmental Microbiology 10.1111/1462-2920.12086
Sieber, J. R., Sims, D. R., Han, C., Kim, E., Lykidis, A., Lapidus, A. L., McDonnald, E., Rohlin, L., Culley, D. E., Gunsalus, R. and McInerney, M. J. 2010 The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production Environmental Microbiology 10.1111/j.1462-2920.2010.02237.x
Uehling, J., Gryganskyi, A., Hameed, K., Tschaplinski, T., Misztal, P. K., Wu, S., Desiro, A., Vande Pol, N., Du, Z., Zienkiewicz, A., Zienkiewicz, K., Morin, E., Tisserant, E., Splivallo, R., Hainaut, M., Henrissat, B., Ohm, R., Kuo, A., Yan, J., Lipzen, A., Nolan, M., LaButti, K., Barry, K., Goldstein, A. H., Labbe, J., Schadt, C., Tuskan, G., Grigoriev, I., Martin, F., Vilgalys, R. and Bonito, G. 2017 Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens Environmental Microbiology 10.1111/1462-2920.13669
Whitman, T., Neurath, R., Perera, A., Chu-Jacoby, I., Ning, D. L., Zhou, J. Z., Nico, P., Pett-Ridge, J. and Firestone, M. 2018 Microbial community assembly differs across minerals in a rhizosphere microcosm Environmental Microbiology 10.1111/1462-2920.14366
Zimmerman, A. E., Bachy, C., Ma, X. F., Roux, S., Jang, H. B., Sullivan, M. B., Waldbauer, J. R. and Worden, A. Z. 2019 Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies Environmental Microbiology 10.1111/1462-2920.14608
Ma, Y. F., Allen, L. Z. and Palenik, B. 2014 Diversity and genome dynamics of marine cyanophages using metagenomic analyses Environmental Microbiology Reports 10.1111/1758-2229.12160
Mayali, Xavier, Stewart, Benjamin, Mabery, Shalini and Weber, Peter K. 2016 Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms Environmental Microbiology Reports 10.1111/1758-2229.12352
Pannu, M. W., Meinhardt, K. A., Bertagnolli, A., Fransen, S. C., Stahl, D. A. and Strand, S. E. 2019 Nitrous oxide emissions associated with ammonia-oxidizing bacteria abundance in fields of switchgrass with and without intercropped alfalfa Environmental Microbiology Reports 10.1111/1758-2229.12790
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., 2019 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 10.1111/1758-2229.12757
Singer, E., Bonnette, J., Kenaley, S. C., Woyke, T. and Juenger, T. E. 2019 Plant compartment and genetic variation drive microbiome composition in switchgrass roots Environmental Microbiology Reports 10.1111/1758-2229.12727
Sirois, S. H. and Buckley, D. H. 2019 Factors governing extracellular DNA degradation dynamics in soil Environmental Microbiology Reports 10.1111/1758-2229.12725
Youngblut, N. D. and Buckley, D. H. 2014 Intra-genomic variation in G plus C content and its implications for DNA stable isotope probing Environmental Microbiology Reports 10.1111/1758-2229.12201
Yang, Q. C., Zhang, X. S., Almendinger, J. E., Huang, M. Y., Chen, X. Y., Leng, G. Y., Zhou, Y. Y., Zhao, K. G., Asrar, G. R. and Li, X. 2019 Climate change will pose challenges to water quality management in the St. Croix River basin Environmental Pollution 10.1016/j.envpol.2019.04.129
Sangha A, Petridis L, Smith JC, Ziebell A, and Parks JM 2012 Molecular Simulation as a Tool for Studying Lignin Environmental Progress & Sustainable Energy 10.1002/ep.10628
Abraha, M., Gelfand, I., Hamilton, S. K., Chen, J. Q. and Robertson, G. P. 2019 Carbon debt of field-scale conservation reserve program grasslands converted to annual and perennial bioenergy crops Environmental Research Letters 10.1088/1748-9326/aafc10
Huang, W. J., Hammel, K. E., Hao, J. L., Thompson, A., Timokhin, V. I. and Hall, S. J. 2019 Enrichment of Lignin-Derived Carbon in Mineral-Associated Soil Organic Matter Environmental Science & Technology 10.1021/acs.est.9b01834
Kim, S., Dale, B. E., Zhang, X. S., Jones, C. D., Reddy, A. D. and Izaurralde, R. C. 2019 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 10.1021/acs.est.8b02808
Yeung, L. Y., Haslun, J. A., Ostrom, N. E., Sun, T., Young, E. D., van Kessel, Mahj, Lucker, S. and Jetten, M. S. M. 2019 In Situ Quantification of Biological N-2 Production Using Naturally Occurring (NN)-N-15-N-15 Environmental Science & Technology 10.1021/acs.est.9b00812
Zhou, A. F., He, Z. L., Qin, Y. J., Lu, Z. M., Deng, Y., Tu, Q. C., Hemme, C. L., Van Nostrand, J. D., Wu, L. Y., Hazen, T. C., Arkin, A. P. and Zhou, J. Z. 2013 StressChip as a High-Throughput Tool for Assessing Microbial Community Responses to Environmental Stresses Environmental Science & Technology 10.1021/es4018656
Zhou J, Smith MD, Cooper SJ, Cheng X, Smith JC, Parks JM 2017 Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane Environmental Science & Technology 10.1021/acs.est.7b02204
Chen H, Johnston RC, Mann BF, Chu RK, Tolic N, Parks JM, Gu B 2017 Identification of Mercury and Dissolved Organic Matter Complexes Using Ultrahigh Resolution Mass Spectrometry Environmental Science & Technology Letters 10.1021/acs.estlett.6b00460
Lin H, Hurt Jr RA, Johs A, Parks JM, Morrell-Falvey JL, Liang L, Elias DA, and Gu B 2014 Unexpected Effects of Gene Deletion on Interactions of Mercury with the Methylation-Deficient Mutant ΔhgcAB Environmental Science & Technology Letters 10.1021/ez500107r
Vandehey, Nicholas T., Northen, Trent R., Brodie, Eoin L. and O’Neil, James P. 2014 Noninvasive Mapping of Photosynthetic Heterogeneity in Biological Soil Crusts by Positron Emission Tomography: Carbon Fixation Environmental Science & Technology Letters 10.1021/ez500209c
Satchwell, A. J., Scown, C. D., Smith, S. J., Amirebrahimi, J., Jin, L., Kirchstetter, T. W., Preble, C. V. 2018 Accelerating the Deployment of Anaerobic Digestion to Meet Zero Waste Goals Environmental Science & Technolology 10.1021/acs.est.8b04481
Kanzler, C. R., Lian, P., Trainer, E. L., Yang, X., Govind, N., Parks, J. M. and Graham, A. M. 2018 Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions Environmental Science: Processes & Impacts 10.1039/c7em00533d
Harris, J. B., Eldridge, M. L., Sayler, G., Menn, F. M., Layton, A. C. and Baudry, J. 2014 A computational approach predicting CYP450 metabolism and estrogenic activity of an endocrine disrupting compound (PCB-30) Environmental Toxicolology and Chemistry 10.1002/etc.2595
Kim, Y., Ximenes, E., Mosier, N. S. and Ladisch, M. R. 2011 Soluble inhibitors/deactivators of cellulase enzymes from lignocellulosic biomass Enzyme and Microbial Technology 10.1016/j.enzmictec.2011.01.007
Ximenes, E., Kim, Y., Mosier, N., Dien, B. and Ladisch, M. 2010 Inhibition of cellulases by phenols Enzyme and Microbial Technology 10.1016/j.enzmictec.2009.11.001
Ximenes, E., Kim, Y., Mosier, N., Dien, B. and Ladisch, M. 2011 Deactivation of cellulases by phenols Enzyme and Microbial Technology 10.1016/j.enzmictec.2010.09.006
Fu, K., Bonora, G. and Pellegrini, M. 2019 Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues Epigenetics 10.1080/15592294.2019.1666649
Goodenough, U., Blaby, I., Casero, D., Gallaher, S. D., Goodson, C., Johnson, S., Lee, J. H., Merchant, S. S., Pellegrini, M., Roth, R., Rusch, J., Singh, M., Umen, J. G., Weiss, T. L. and Wulan, T. 2014 The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii Eukaryotic Cell 10.1128/ec.00013-14
Lee, J. H., Heuser, J. E., Roth, R. and Goodenough, U. 2015 Eisosome Ultrastructure and Evolution in Fungi, Microalgae, and Lichens Eukaryotic Cell 10.1128/ec.00106-15
Pomraning, K. R., Smith, K. M. and Freitag, M. 2011 Bulk Segregant Analysis Followed by High-Throughput Sequencing Reveals the Neurospora Cell Cycle Gene, ndc-1, To Be Allelic with the Gene for Ornithine Decarboxylase, spe-1 Eukaryotic Cell 10.1128/ec.00016-11
Arro, J., Park, J. W., Wai, C. M., VanBuren, R., Pan, Y. B., Nagai, C., da Silva, J. and Ming, R. 2016 Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.) Euphytica 10.1007/s10681-016-1672-8
Felderhoff, T. J., Olmstead, J. W. and Vermerris, W. 2017 A cost-benefit analysis to select the most effective method for positional cloning: genotyping by sequencing versus allele-specific PCR Euphytica 10.1007/s10681-017-2068-0
Zhu, F., Wai, C. M., Zhang, J. S., Jones, T. C., Nagai, C. and Ming, R. 2018 Differential expression of hormone related genes between extreme segregants of a Saccharum interspecific F2 population Euphytica 10.1007/s10681-018-2137-z
Miao, Y., Hong, L., Yi, Z. and Smith, J. C. 2013 Zaccai neutron resilience and site-specific hydration dynamics in a globular protein Eur Physical Journal E Soft Matter and Biological Physics 10.1140/epje/i2013-13072-5
Horton, D. J., Kershner, M. W. and Blackwood, C. B. 2017 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 10.1016/j.ejsobi.2017.04.003
Guber, A. K., Kravchenko, A. N., Razavi, B. S., Blagodatskaya, E. and Kuzyakov, Y. 2019 Calibration of 2-D soil zymography for correct analysis of enzyme distribution European Journal of Soil Science 10.1111/ejss.12744
Biswas M, Wocjan T, Langowski J, and Smith JC 2012 DNA Bending Potentials for Loop-Mediated Nucleosome Repositioning Europhysics Letters 10.1209/0295-5075/97/38004
Trizac E, and Shen T 2016 Bending stiff charged polymers The electrostatic persistence length Europhysics Letters 10.1209/0295-5075/116/18007
Harcombe, W. R., Betts, A., Shapiro, J. W. and Marx, C. J. 2016 Adding biotic complexity alters the metabolic benefits of mutualism Evolution 10.1111/evo.12973
Mortimer, J. C. 2018 Plant synthetic biology could drive a revolution in biofuels and medicine Experimental Biology and Medicine 10.1177/1535370218793890
Mohr, B. P., Retterer, S. T. and Doktycz, M. J. 2016 While-you-wait proteins? Producing biomolecules at the point of need Expert Review of Proteomics 10.1080/14789450.2016.1209415
Mohnen, D., Amos, R.A., Biswal, A.K., Engle, K.A., Ryno, Mohanty, S.S., and Atmodjo, Melani A. 2019 A new model for the biochemistry of pectin synthesis: GAUTs synthesize diverse HG glycans in structurally and functionally distinct plant cell wall polymers FASEB Journal 10.1038/s41598-018-37979-5
GhattyVenkataKrishna PK, Uberbacher EC, and Cheng X 2013 Effect of the amyloid β hairpin’s structure on the handedness of helices formed by its aggregates FEBS Letters 10.1016/j.febslet.2013.06.050
Lubner, J. M., Dodge-Kafka, K. L., Carlson, C. R., Church, G. M., Chou, M. F. and Schwartz, D. 2017 Cushing's syndrome mutant PKA(L205R) exhibits altered substrate specificity FEBS Letters 10.1002/1873-3468.12562
Zahran M, Berezniak T, Imhof P, and Smith JC 2011 Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease FEBS Letters 10.1016/j.febslet.2011.07.036
Altshuler, I., Ronholm, J., Layton, A., Onstott, T. C., Greer, C. W. and Whyte, L. G. 2019 Denitrifiers, nitrogen-fixing bacteria and N2O soil gas flux in high Arctic ice-wedge polygon cryosols FEMS Microbiology Ecology 10.1093/femsec/fiz049
Deveau, A., Gross, H., Palin, B., Mehnaz, S., Schnepf, M., Leblond, P., Dorrestein, P. C. and Aigle, B. 2016 Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron-limited conditions FEMS Microbiology Ecology 10.1093/femsec/fiw107
Mayali, Xavier and Weber, Peter K. 2018 Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community FEMS Microbiology Ecology 10.1093/femsec/fiy047
Miquel Guennoc, C., Rose, C., Labbe, J. and Deveau, A. 2018 Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls? FEMS Microbiology Ecology 10.1093/femsec/fiy093
Stedtfeld, R. D., Guo, X. P., Stedtfeld, T. M., Sheng, H. J., Williams, M. R., Hauschild, K., Gunturu, S., Tift, L., Wang, F., Howes, A., Chai, B. L., Yin, D. Q., Cole, J. R., Tiedje, J. M. and Hashsham, S. A. 2018 Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements FEMS Microbiology Ecology 10.1093/femsec/fiy130
Vishnivetskaya, T. A., Layton, A. C., Lau, M. C. Y., Chauhan, A., Cheng, K. R. R., Meyers, A. J., Murphy, J. R., Rogers, A. W., Saarunya, G. S., Williams, D. E., Pfiffner, S. M., Biggerstaff, J. P., Stackhouse, B. T., Phelps, T. J., Whyte, L., Sayler, G. S. and Onstott, T. C. 2014 Commercial DNA extraction kits impact observed microbial community composition in permafrost samples FEMS Microbiology Ecology 10.1111/1574-6941.12219
Xavier, Mayali, Peter K, Weber and Jennifer, Pett-Ridge 2013 Taxon-specific C/N relative use efficiency for amino acids in an estuarine community FEMS Microbiology Ecology 10.1111/j.1574-6941.12000.x
Dash, S., Ng, C. Y. and Maranas, C. D. 2016 Metabolic modeling of clostridia: current developments and applications FEMS Microbiology Letters 10.1093/femsle/fnw004
Edwards, A. N., Siuti, P., Bible, A. N., Alexandre, G., Retterer, S. T., Doktycz, M. J. and Morrell-Falvey, J. L. 2011 Characterization of cell surface and extracellular matrix remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy FEMS Microbiology Letters 10.1111/j.1574-6968.2010.02156.x
Jones, A. J., Venkataramanan, K. P. and Papoutsakis, T. 2016 Overexpression of two stress-responsive, small, non-coding RNAs, 6S and tmRNA, imparts butanol tolerance in Clostridium acetobutylicum FEMS Microbiology Letters 10.1093/femsle/fnw063
Pacheco, A. R. and Segre, D. 2019 A multidimensional perspective on microbial interactions FEMS Microbiology Letters 10.1093/femsle/fnz125
Deveau, A., Bonito, G., Uehling, J., Paoletti, M., Becker, M., Bindschedler, S., Hacquard, S., Herve, V., Labbe, J., Lastovetsky, O. A., Mieszkin, S., Millet, L. J., Vajna, B., Junier, P., Bonfante, P., Krom, B. P., Olsson, S., van Elsas, J. D. and Wick, L. Y. 2018 Bacterial-fungal interactions: ecology, mechanisms and challenges FEMS Microbiology Reviews 10.1093/femsre/fuy008
Gossing, M., Smialowska, A. and Nielsen, J. 2018 Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae FEMS Yeast Research 10.1093/femsyr/foy096
Kurtzman, Cletus P., Robnett, Christie J. and Blackwell, Meredith 2016 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 10.1093/femsyr/fow041
Opulente, D. A., Langdon, Q. K., Buh, K. V., Haase, M. A. B., Sylvester, K., Moriarty, R. V., Jarzyna, M., Considine, S. L., Schneider, R. M. and Hittinger, C. T. 2019 Pathogenic budding yeasts isolated outside of clinical settings FEMS Yeast Research 10.1093/femsyr/foz032
Garcia, Sabrina, Jardine, Kolby, Souza, Vinicius, Souza, Rodrigo, Duvoisin Junior, Sergio and Gonçalves, José 2019 Reassimilation of Leaf Internal CO2 Contributes to Isoprene Emission in the Neotropical Species Inga edulis Mart Forests 10.3390/f10060472
Kapuscinski, Kevin L., Farrell, John M., Stehman, Stephen V., Boyer, Gregory L., Fernando, Danilo D., Teece, Mark A. and Tschaplinski, Timothy J. 2014 Selective herbivory by an invasive cyprinid, the ruddScardinius erythrophthalmus Freshwater Biology 10.1111/fwb.12433
Noirot-Gros, M. F., Shinde, S., Larsen, P. E., Zerbs, S., Korajczyk, P. J., Kemner, K. M. and Noirot, P. H. 2018 Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation Front Microbiology 10.3389/fmicb.2018.00853
Wei, H., Yang, Y. F., Himmel, M. E., Tucker, M. P., Ding, S. Y., Yang, S. H. and Arora, R. 2019 Identification and Characterization of Five Cold Stress-Related Rhododendron Dehydrin Genes: Spotlight on a FSK-Type Dehydrin With Multiple F-Segments Frontiers in Bioengineering and Biotechnology 10.3389/fbioe.2019.00030
Wilson, R. M., Neumann, R. B., Crossen, K. B., Raab, N. M., Hodgkins, S. B., Saleska, S. R., Bolduc, B., Woodcroft, B., Tyson, G. W., Chanton, J. P. and Rich, V. I. 2019 Microbial Community Analyses Inform Geochemical Reaction Network Models for Predicting Pathways of Greenhouse Gas Production Frontiers in Earth Science 10.3389/feart.2019.00059
Haan, N. L. and Landis, D. A. 2019 The Importance of Shifting Disturbance Regimes in Monarch Butterfly Decline and Recovery Frontiers in Ecology and Evolution 10.3389/fevo.2019.00191
Veen, G. F., Wubs, E. R. J., Bardgett, R. D., Barrios, E., Bradford, M. A., Carvalho, S., De Deyn, G. B., de Vries, F. T., Giller, K. E., Kleijn, D., Landis, D. A., Rossing, W. A. H., Schrama, M., Six, J., Struik, P. C., van Gils, S., Wiskerke, J. S. C., van der Putten, W. H. and Vet, L. E. M. 2019 Applying the Aboveground-Belowground Interaction Concept in Agriculture: Spatio-Temporal Scales Matter Frontiers in Ecology and Evolution 10.3389/fevo.2019.00300
Avci, U., Zhou, X. L., Pattathil, S., Sousa, L. D., Hahn, M. G., Dale, B., Xu, Y. and Balan, V. 2019 Effects of Extractive Ammonia Pretreatment on the Ultrastructure and Glycan Composition of Corn Stover Frontiers in Energy Research 10.3389/fenrg.2019.00085
Decker, S. R., Harman-Ware, A. E., Happs, R. M., Wolfrum, E. J., Tuskan, G. A., Kainer, D., Oguntimein, G. B., Rodriguez, M., Weighill, D., Jones, P. and Jacobson, D. 2018 High Throughput Screening Technologies in Biomass Characterization Frontiers in Energy Research 10.3389/fenrg.2018.00120
Ragauskas, A.J., and Yoo, C.G. 2018 Editorial: Advancements in biomass recalcitrance: The use of lignin for the production of fuels and chemicals Frontiers in Energy Research 10.3389/fenrg.2018.00118
Weighill, D., Sykes, R., Zhao, N., Martin, M., DiFazio, S., Tschaplinski, T., Tuskan, G.A, Jacobson, D., Macaya Sanz, D., Sreedasyam, A., Schmutz, J., Muchero, W., Ranjan, P., Shah, M., Jones, P. 2018 Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery Frontiers in Energy Research 10.3389/fenrg.2018.00030
Williams, D. L., Ong, R. G., Mullet, J. E. and Hodge, D. B. 2019 Integration of Pretreatment With Simultaneous Counter-Current Extraction of Energy Sorghum for High-Titer Mixed Sugar Production Frontiers in Energy Research 10.3389/fenrg.2018.00133
Couradeau, Estelle, Felde, Vincent J. M. N. L., Parkinson, Dilworth, Uteau, Daniel, Rochet, Alexis, Cuellar, Charlene, Winegar, Geoffrey, Peth, Stephan, Northen, Trent R. and Garcia-Pichel, Ferran 2018 In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation Frontiers in Environmental Science 10.3389/fenvs.2018.00065
Guo, J. R., Quensen, J. F., Sun, Y. N., Wang, Q., Brown, C. T., Cole, J. R. and Tedje, J. M. 2019 Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes Frontiers in Genetics 10.3389/fgene.2019.00957
Weighill, D., Jones, P., Bleker, C., Ranjan, P., Shah, M., Zhao, N., Martin, M., DiFazio, S., Macaya-Sanz, D., Schmutz, J., Sreedasyam, A., Tschaplinski, T., Tuskan, G. and Jacobson, D. 2019 Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships Frontiers in Genetics 10.3389/fgene.2019.00417
Weighill, D., Macaya-Sanz, D., DiFazio, S. P., Joubert, W., Shah, M., Schmutz, J., Sreedasyam, A., Tuskan, G. and Jacobson, D. 2019 Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation Frontiers in Genetics 10.3389/fgene.2019.00487
Weighill, D., Tschaplinski, T. J., Tuskan, G. A. and Jacobson, D. 2019 Data Integration in Poplar: 'Omics Layers and Integration Strategies Frontiers in Genetics 10.3389/fgene.2019.00874
Zhao, L. Z., Zhang, H. X., Kohnen, M. V., Prasad, Kvsk, Gu, L. F. and Reddy, A. S. N. 2019 Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing Frontiers in Genetics 10.3389/fgene.2019.00253
Bertrand, E. M. and Allen, A. E. 2012 Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton Frontiers in Microbiology 10.3389/fmicb.2012.00375
Bible, A. N., Fletcher, S. J., Pelletier, D. A., Schadt, C. W., Jawdy, S. S., Weston, D. J., Engle, N. L., Tschaplinski, T., Masyuko, R., Polisetti, S., Bohn, P. W., Coutinho, T. A., Doktycz, M. J. and Morrell-Falvey, J. L. 2016 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 10.3389/fmicb.2016.00491
Bird, J. T., Baker, B. J., Probst, A. J., Podar, M. and Lloyd, K. G. 2016 Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales Frontiers in Microbiology 10.3389/fmicb.2016.01221
Bonito, G., Benucci, G. M. N., Hameed, K., Weighill, D., Jones, P., Chen, K. H., Jacobson, D., Schadt, C. and Vilgalys, R. 2019 Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype Frontiers in Microbiology 10.3389/fmicb.2019.00481
Chevrette, M. G., Carlos-Shanley, C., Louie, K. B., Bowen, B. P., Northen, T. R. and Currie, C. R. 2019 Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces Frontiers in Microbiology 10.3389/fmicb.2019.02170
de Freitas Pereira, M., Veneault-Fourrey, C., Vion, P., Guinet, F., Morin, E., Barry, K. W., Lipzen, A., Singan, V., Pfister, S., Na, H., Kennedy, M., Egli, S., Grigoriev, I., Martin, F., Kohler, A. and Peter, M. 2018 Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum Frontiers in Microbiology 10.3389/fmicb.2018.00141
Diner, R. E., Schwenck, S. M., McCrow, J. P., Zheng, H. and Allen, A. E. 2016 Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms Frontiers in Microbiology 10.3589/fmicb.2016.00880
Edwards, J. E., Forster, R. J., Callaghan, T. M., Dollhofer, V., Dagar, S. S., Cheng, Y. F., Chang, J., Kittelmann, S., Fliegerova, K., Puniya, A. K., Henske, J. K., Gilmore, S. P., O'Malley, M. A., Griffith, G. W. and Smidt, H. 2017 PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities Frontiers in Microbiology 10.3389/fmicb.2017.01657
Felczak, M. M., Jacobson, T. B., Ong, W. K., Amador-Noguez, D. and TerAvest, M. A. 2019 Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4 Frontiers in Microbiology 10.3389/fmicb.2019.02270
Fish, J. A., Chai, B. L., Wang, Q., Sun, Y. N., Brown, C. T., Tiedje, J. M. and Cole, J. R. 2013 FunGene: the functional gene pipeline and repository Frontiers in Microbiology 10.3389/fmicb.2013.00291
Freedman, A. J. E., Peet, K. C., Boock, J. T., Penn, K., Prather, K. L. J. and Thompson, J. R. 2018 Isolation, Development, and Genomic Analysis of Bacillus megaterium SR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide Frontiers in Microbiology 10.3389/fmicb.2018.02152
Geng, Haifeng, Tran-Gyamfi, Mary B., Lane, Todd W., Sale, Kenneth L. and Yu, Eizadora T. 2016 Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds Frontiers in Microbiology 10.3389/fmicb.2016.01155
Gómez-Consarnau, Laura, Needham, David M., Weber, Peter K., Fuhrman, Jed A. and Mayali, Xavier 2019 Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria Frontiers in Microbiology 10.3389/fmicb.2019.01204
Guo, X., Zhou, X. S., Hale, L., Yuan, M. T., Feng, J. J., Ning, D. L., Shi, Z., Qin, Y. J., Liu, F. F., Wu, L. Y., He, Z. L., Van Nostrand, J. D., Liu, X. D., Luo, Y. Q., Tiedje, J. M. and Zhou, J. Z. 2018 Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass Frontiers in Microbiology 10.3389/fmicb.2018.00954
Hasim, Sahar, Allison, David P., Mendez, Berlin, Farmer, Abigail T., Pelletier, Dale A., Retterer, Scott T., Campagna, Shawn R., Reynolds, Todd B. and Doktycz, Mitchel J. 2018 Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope Frontiers in Microbiology 10.3389/fmicb.2018.00219
Heimerl, T., Flechsler, J., Pickl, C., Heinz, V., Salecker, B., Zweck, J., Wanner, G., Geimer, S., Samson, R. Y., Bell, S. D., Huber, H., Wirth, R., Wurch, L., Podar, M. and Rachel, R. 2017 A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans Frontiers in Microbiology 10.3389/fmicb.2017.01072
Johnston, E. R., Rodriguez-R, L. M., Luo, C. W., Yuan, M. M., Wu, L. Y., He, Z. L., Schuur, E. A. G., Luo, Y. Q., Tiedje, J. M., Zhou, J. Z. and Konstantinidis, K. T. 2016 Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem Frontiers in Microbiology 10.3389/fmicb.2016.00579
Kuo, A., Kohler, A., Martin, F. M. and Grigoriev, I. V. 2014 Expanding genomics of mycorrhizal symbiosis Frontiers in Microbiology 10.3389/fmicb.2014.00582
Lal, P. B., Wells, F. M., Lyu, Y. C., Ghosh, I. N., Landick, R. and Kiley, P. J. 2019 A Markerless Method for Genome Engineering in Zymomonas mobilis ZM4 Frontiers in Microbiology 10.3389/fmicb.2019.02216
Lee, Jackson, Burow, Luke, Woebken, Dagmar, Everroad, R, Kubo, Michael, Spormann, Alfred, Weber, Peter, Pett-Ridge, Jennifer, Bebout, Brad and Hoehler, Tori 2014 Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats Frontiers in Microbiology 10.3389/fmicb.2014.00061
Leon, D. R., Ytterberg, A. J., Boontheung, P., Kim, U., Loo, J. A., Gunsalus, R. P. and Loo, R. R. O. 2015 Mining proteonnic data to expose protein modifications in Methanosarcina mazei strain Go1 Frontiers in Microbiology 10.3389/fmicb.2015.00149
Li, Z., Yao, Q., Guo, X., Crits-Christoph, A., Mayes, M. A., Iv, W. J. H., Lebeis, S. L., Banfield, J. F., Hurst, G. B., Hettich, R. L. and Pan, C. 2019 Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using (13)CO2 and (13)C-Methanol Frontiers in Microbiology 10.3389/fmicb.2019.02706
Lohberger, A., Spangenberg, J. E., Ventura, Y., Bindschedler, S., Verrecchia, E. P., Bshary, R. and Junier, P. 2019 Effect of Organic Carbon and Nitrogen on the Interactions of Morchella spp. and Bacteria Dispersing on Their Mycelium Frontiers in Microbiology 10.3389/fmicb.2019.00124
Marlow, J. J., Skennerton, C. T., Li, Z., Chourey, K., Hettich, R. L., Pan, C. and Orphan, V. J. 2016 Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities Frontiers in Microbiology 10.3389/fmicb.2016.00563
Matsen, J. B., Yang, S., Stein, L. Y., Beck, D. and Kalyuzhnaya, M. G. 2013 Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study Frontiers in Microbiology 10.3389/fmicb.2013.00040
McGlynn, S. E., Boyd, E. S., Peters, J. W. and Orphan, V. J. 2013 Classifying the metal dependence of uncharacterized nitrogenases Frontiers in Microbiology 10.3389/fmicb.2012.00419
Mewalal, R., Yin, H., Hu, R., Jawdy, S., Vion, P., Tuskan, G. A., Le Tacon, F., Labbe, J. L. and Yang, X. 2019 Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis Frontiers in Microbiology 10.3389/fmicb.2019.00515
Mosier, A. C., Miller, C. S., Frischkorn, K. R., Ohm, R. A., Li, Z., LaButti, K., Lapidus, A., Lipzen, A., Chen, C., Johnson, J., Lindquist, E. A., Pan, C. L., Hettich, R. L., Grigoriev, I. V., Singer, S. W. and Banfield, J. F. 2016 Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage Frontiers in Microbiology 10.3389/fmicb.2016.00238
Nunes da Rocha, U., Cadillo-Quiroz, H., Karaoz, U., Rajeev, L., Klitgord, N., Dunn, S., Truong, V., Buenrostro, M., Bowen, B. P., Garcia-Pichel, F., Mukhopadhyay, A., Northen, T. R. and Brodie, E. L. 2015 Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust Frontiers in Microbiology 10.3389/fmicb.2015.00277
Pellegrin, C., Morin, E., Martin, F. M. and Veneault-Fourrey, C. 2015 Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins Frontiers in Microbiology 10.3389/fmicb.2015.01278
Penton, C. R., Gupta, V. S. R., Yu, J. L. and Tiedje, J. M. 2016 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 10.3389/fmicb.2016.00824
Penton, C. R., Johnson, T. A., Quensen, J. F., Iwai, S., Cole, J. R. and Tiedje, J. M. 2013 Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter Frontiers in Microbiology 10.3389/fmicb.2013.00279
Penton, C. R., Louis, D. S., Pham, A., Cole, J. R., Wu, L. Y., Luo, Y. Q., Schuur, E. A. G., Zhou, J. Z. and Tiedje, J. M. 2015 Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils Frontiers in Microbiology 10.3389/fmicb.2015.00746
Penton, C. R., Yang, C. Y., Wu, L. Y., Wang, Q., Zhang, J., Liu, F. F., Qin, Y. J., Deng, Y., Hemme, C. L., Zheng, T. L., Schuur, E. A. G., Tiedje, J. and Zhou, J. Z. 2016 NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient Frontiers in Microbiology 10.3389/fmicb.2016.01894
Pepe-Ranney, C., Campbell, A. N., Koechli, C. N., Berthrong, S. and Buckley, D. H. 2016 Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil Frontiers in Microbiology 10.3389/fmicb.2016.00703
Porcar, M., Louie, K. B., Kosina, S. M., Van Goethem, M. W., Bowen, B. P., Tanner, K. and Northen, T. R. 2018 Microbial Ecology on Solar Panels in Berkeley, CA, United States Frontiers in Microbiology 10.3389/fmicb.2018.03043
Poudel, S., Giannone, R. J., Farmer, A. T., Campagna, S. R., Bible, A. N., Morrell-Falvey, J. L., Elkins, J. G. and Hettich, R. L. 2019 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 10.3389/fmicb.2019.02594
Purwantini, E., Torto-Alalibo, T., Lomax, J., Setubal, J. C., Tyler, B. M. and Mukhopadhyay, B. 2014 Genetic resources for methane production from biomass described with the Gene Ontology Frontiers in Microbiology 10.3389/fmicb.2014.00634
Qin, Y., Pan, X., Kubicek, C., Druzhinina, I., Chenthamara, K., Labbe, J. and Yuan, Z. 2017 Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth Frontiers in Microbiology 10.3389/fmicb.2017.00158
Shi, S. B. and Zhao, H. M. 2017 Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals Frontiers in Microbiology 10.3389/fmicb.2017.02185
Singer, E., Bonnette, J., Woyke, T. and Juenger, T. E. 2019 Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species Frontiers in Microbiology 10.3389/fmicb.2019.02181
Tatli, M., Hebert, A. S., Coon, J. J. and Amador-Noguez, D. 2019 Genome Wide Phosphoproteome Analysis of Zymomonas mobilis Under Anaerobic, Aerobic, and N-2-Fixing Conditions Frontiers in Microbiology 10.3389/fmicb.2019.01986
Timm, C. M., Campbell, A. G., Utturkar, S. M., Jun, S. R., Parales, R. E., Tan, W. A., Robeson, M. S., Lu, T. Y., Jawdy, S., Brown, S. D., Ussery, D. W., Schadt, C. W., Tuskan, G. A., Doktycz, M. J., Weston, D. J. and Pelletier, D. A. 2015 Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment Frontiers in Microbiology 10.3389/fmicb.2015.01118
Torto-Alalibo, T., Purwantini, E., Lomax, J., Setubal, J. C., Mukhopadhyay, B. and Tyler, B. M. 2014 Genetic resources for advanced biofuel production described with the Gene Ontology Frontiers in Microbiology 10.3389/fmicb.2014.00528
Uehling, J. K., Entler, M. R., Meredith, H. R., Millet, L. J., Timm, C. M., Aufrecht, J. A., Bonito, G. M., Engle, N. L., Labbe, J. L., Doktycz, M. J., Retterer, S. T., Spatafora, J. W., Stajich, J. E., Tschaplinski, T. J. and Vilgalys, R. J. 2019 Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange Frontiers in Microbiology 10.3389/fmicb.2019.02163
Utturkar, S. M., Klingeman, D. M., Hurt, R. A., Jr. and Brown, S. D. 2017 A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies Frontiers in Microbiology 10.3389/fmicb.2017.01272
Vuono, D. C., Read, R. W., Hemp, J., Sullivan, B. W., Arnone, J. A., 3rd, Neveux, I., Blank, R. R., Loney, E., Miceli, D., Winkler, M. H., Chakraborty, R., Stahl, D. A. and Grzymski, J. J. 2019 Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium Frontiers in Microbiology 10.3389/fmicb.2019.00003
Xue, K., Xie, J. P., Zhou, A. F., Liu, F. F., Li, D. J., Wu, L. Y., Deng, Y., He, Z. L., Van Nostrand, J. D., Luo, Y. Q. and Zhou, J. Z. 2016 Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning Frontiers in Microbiology 10.3389/fmicb.2016.00668
Yang, S., Matsen, J. B., Konopka, M., Green-Saxena, A., Clubb, J., Sadilek, M., Orphan, V. J., Beck, D. and Kalyuzhnaya, M. G. 2013 Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study Frontiers in Microbiology 10.3389/fmicb.2013.00070
Youngblut, N. D., Barnett, S. E. and Buckley, D. H. 2018 SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments Frontiers in Microbiology 10.3389/fmicb.2018.00570
Yu, H., Susanti, D., McGlynn, S. E., Skennerton, C. T., Chourey, K., Iyer, R., Scheller, S., Tavormina, P. L., Hettich, R. L., Mukhopadhyay, B. and Orphan, V. J. 2018 Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea Frontiers in Microbiology 10.3389/fmicb.2018.02917
Zhang, Y. P., Vera, J. M., Xie, D., Serate, J., Pohlmann, E., Russell, J. D., Hebert, A. S., Coon, J. J., Sato, T. K. and Landick, R. 2019 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 10.3389/fmicb.2019.02596
Demerdash, O., Shrestha, U. R., Petridis, L., Smith, J. C., Mitchell, J. C. and Ramanathan, A. 2019 Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins Frontiers in Molecular Biosciences 10.3389/fmolb.2019.00064
Liu, Y. M., Miao, J. M., Traore, S., Kong, D. Y., Liu, Y., Zhang, X. Z., Nimchu, Z. L., Liu, Z. R. and Zhao, B. Y. 2016 SacB-SacR Gene Cassette As the Negative Selection Marker to Suppress Agrobacterium Overgrowth in Agrobacterium-Mediated Plant Transformation Frontiers in Molecular Biosciences 10.3389/fmolb.2016.00070
Amin, A. B., Rathnayake, K. N., Yim, W. C., Garcia, T. M., Wone, B., Cushman, J. C. and Wone, B. W. M. 2019 Crassulacean Acid Metabolism Abiotic Stress-Responsive Transcription Factors: a Potential Genetic Engineering Approach for Improving Crop Tolerance to Abiotic Stress Frontiers in Plant Science 10.3389/fpls.2019.00129
Amos, R.A., and Mohnen, D. 2019 Critical review of plant cell wall matrix polysaccharide glycosyltransferase activities verified by heterologous protein expression Frontiers in Plant Science 10.3389/fpls.2019.00915
Badmi, R., Payyavula, R.S., Bali, G., Guo, H-B., Jawdy, S.S., Gunter, L., Yang, X., Winkeler, K., Collins, C., Rottmann, W.H., Yee, K., Rodriguez Jr., M., Sykes, R., Decker, S.R., Davis, M.F., Ragauskas, A.J., Tuskan, G., and Kalluri, U.C. 2018 A new calmodulin-binding protein expresses in the context of secondary cell wall biosynthesis and impacts biomass properties in Populus Frontiers in Plant Science 10.3389/fpls.2018.01669
Bewg, W.P., Ci, D., and Tsai, C-J. 2018 Genome editing in trees: from multiple repair pathways to long-term stability Frontiers in Plant Science 10.3389/fpls.2018.01732
Bihmidine, S., Hunter, C. T., Johns, C. E., Koch, K. E. and Braun, D. M. 2013 Regulation of assimilate import into sink organs: update on molecular drivers of sink strength Frontiers in Plant Science 10.3389/fpls.2013.00177
Busov, V. B. 2018 Manipulation of Growth and Architectural Characteristics in Trees for Increased Woody Biomass Production Frontiers in Plant Science 10.3389/fpls.2018.01505
Chaudhary, S., Khokhar, W., Jabre, I., Reddy, A. S. N., Byrne, L. J., Wilson, C. M. and Syed, N. H. 2019 Alternative Splicing and Protein Diversity: Plants Versus Animals Frontiers in Plant Science 10.3389/fpls.2019.00708
Chiang, C. P., Yim, W. C., Sun, Y. H., Ohnishi, M., Mimura, T., Cushman, J. C. and Yen, H. E. 2016 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 10.3339/fpls.2016.01143
Collier, R., Bragg, J., Hernandez, B. T., Vogel, J. P. and Thilmony, R. 2016 Use of Agrobacterium rhizogenes Strain 18r12v and Paromomycin Selection for Transformation of Brachypodium distachyon and Brachypodium sylvaticum Frontiers in Plant Science 10.3389/fpls.2016.00716
Conde, D., Perales, M., Sreedasyam, A., Tuskan, G.A., Lloret, A., Badenes, M.L., Gonzalez-Melendi, P., Rios, G., and Allona, I., 2019 Engineering tree seasonal cycles of growth through chromatin modification Frontiers in Plant Science 10.3389/fpls.2019.00412
Filichkin, S. A., Hamilton, M., Dharmawardhana, P. D., Singh, S. K., Sullivan, C., Ben-Hur, A., Reddy, A. S. N. and Jaiswal, P. 2018 Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching Frontiers in Plant Science 10.3389/fpls.2018.00005
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, 2019 Finding new cell wall regulatory genes in Populus trichocarpa using multiple lines of evidence Frontiers in Plant Science 10.3389/fpls.2019.01249
Hu, H., Gu, X., Xue, L. J., Swamy, P. S., Harding, S. A. and Tsai, C. J. 2016 Tubulin C-terminal Post-translational Modifications Do Not Occur in Wood Forming Tissue of Populus Frontiers in Plant Science 10.3389/fpls.2016.01493
Jin, X. L., Shi, C. H., Yu, C. Y., Yamada, T. and Sacks, E. J. 2017 Determination of Leaf Water Content by Visible and Near-Infrared Spectrometry and Multivariate Calibration in Miscanthus Frontiers in Plant Science 10.3389/fpls.2017.00721
Jones, P., Garcia, B. J., Furches, A., Tuskan, G. A. and Jacobson, D. 2019 Plant Host-Associated Mechanisms for Microbial Selection Frontiers in Plant Science 10.3389/fpls.2019.00862
Kalluri, U. C., Payyavula, R. S., Labbe, J. L., Engle, N., Bali, G., Jawdy, S. S., Sykes, R. W., Davis, M., Ragauskas, A., Tuskan, G. A. and Tschaplinski, T. J. 2016 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 10.3389/fpls.2016.01455
Karunanithi, P. S. and Zerbe, P. 2019 Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity Frontiers in Plant Science 10.3389/fpls.2019.01166
Khasanova, A., Lovell, J. T., Bonnette, J., Weng, X. Y., Jenkins, J., Yoshinaga, Y., Schmutz, J. and Juenger, T. E. 2019 The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass Frontiers in Plant Science 10.3389/fpls.2019.00366
Khokhar, W., Hassan, M. A., Reddy, A. S. N., Chaudhary, S., Jabre, I., Byrne, L. J. and Syed, N. H. 2019 Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana Frontiers in Plant Science 10.3389/fpls.2019.01160
Labbe, J. L., Weston, D. J., Dunkirk, N., Pelletier, D. A. and Tuskan, G. A. 2014 Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus Frontiers in Plant Science 10.3389/fpls.2014.00579
Lakusta, A. M., Kwon, M., Kwon, E. G., Stonebloom, S., Scheller, H. V. and Ro, D. K. 2019 Molecular Studies of the Protein Complexes Involving Cis-Prenyltransferase in Guayule (Parthenium argentatum), an Alternative Rubber-Producing Plant Frontiers in Plant Science 10.3389/fpls.2019.00165
Li, J. T., Shi, Y. Y., Veeranampalayam-Sivakumar, A. N. and Schachtman, D. P. 2018 Elucidating Sorghum Biomass, Nitrogen and Chlorophyll Contents With Spectral and Morphological Traits Derived From Unmanned Aircraft System Frontiers in Plant Science 10.3389/fpls.2018.01406
Lim, S. D., Lee, S., Choi, W. G., Yim, W. C. and Cushman, J. C. 2019 Laying the Foundation for Crassulacean Acid Metabolism (CAM) Biodesign: Expression of the C-4 Metabolism Cycle Genes of CAM in Arabidopsis Frontiers in Plant Science 10.3389/fpls.2019.00101
Liu, W., Xiang, Y., Zhang, X., Han, G., Sun, X., Sheng, Y., Zhang, A. 2019 Over-Expression of a Maize N-Acetylglutamate Kinase Gene (ZmNAGK) Improves Drought Tolerance in Tobacco Frontiers in Plant Science 10.3389/fpls.2018.01902
Moseley, R.C., Mewalal, R., Motta, F., Haase, S., Tuskan, G.A., and Yang, X. 2018 Conservation and diversification of circadian rhythmicity between a model crassulacean acid metabolism plant Kalanchoe fedtschenkoi and a model C3 photosynthesis plant Arabidopsis thaliana Frontiers in Plant Science 10.3389/fpls.2018.01757
Moseley, R. C., Tuskan, G. A. and Yang, X. 2019 Comparative Genomics Analysis Provides New Insight Into Molecular Basis of Stomatal Movement in Kalanchoe fedtschenkoi Frontiers in Plant Science 10.3389/fpls.2019.00292
Moseley, R. C., Tuskan, G. A. and Yang, X. H. 2019 Comparative Genomics Analysis Provides New Insight Into Molecular Basis of Stomatal Movement in Kalanchoe fedtschenkoi Frontiers in Plant Science 10.3389/fpls.2019.00292
Olins, J. R., Lin, L., Lee, S. J., Trabucco, G. M., MacKinnon, K. J. M. and Hazen, S. P. 2018 Secondary Wall Regulating NACs Differentially Bind at the Promoter at a CELLULOSE SYNTHASE A4 Cis-eQTL Frontiers in Plant Science 10.3389/fpls.2018.01895
Pendleton, A. L., Smith, K. E., Feau, N., Martin, F. M., Grigoriev, I. V., Hamelin, R., Nelson, C. D., Burleigh, J. G. and Davis, J. M. 2014 Duplications and losses in gene families of rust pathogens highlight putative effectors Frontiers in Plant Science 10.3389/fpls.2014.00299
Peng, D., Gu, X., Xue, L. J., Leebens-Mack, J. H. and Tsai, C. J. 2014 Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots Frontiers in Plant Science 10.3389/fpls.2014.00615
Rao, X., Dixon, R.A. 2018 Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses Frontiers in Plant Science 10.3389/fpls.2018.00399
Taylor, M., Tornqvist, C. E., Zhao, X. W., Grabowski, P., Doerge, R., Ma, J. X., Volenec, J., Evans, J., Ramstein, G. P., Sanciangco, M. D., Buell, C. R., Casler, M. D. and Jiang, Y. W. 2018 Genome-Wide Association Study in Pseudo-F-2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates Frontiers in Plant Science 10.3389/fpls.2018.01250
Timm, C. M., Pelletier, D. A., Jawdy, S. S., Gunter, L. E., Henning, J. A., Engle, N., Aufrecht, J., Gee, E., Nookaew, I., Yang, Z., Lu, T. Y., Tschaplinski, T. J., Doktycz, M. J., Tuskan, G. A. and Weston, D. J. 2016 Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System Frontiers in Plant Science 10.3389/fpls.2016.00497
Truong, S. K., McCormick, R. F. and Mullet, J. E. 2017 Bioenergy Sorghum Crop Model Predicts VPD-Limited Transpiration Traits Enhance Biomass Yield in Water-Limited Environments Frontiers in Plant Science 10.3389/fpls.2017.00335
Tuskan, G. A., Groover, A. T., Schmutz, J., DiFazio, S. P., Myburg, A., Grattapaglia, D., Smart, L. B., Yin, T., Aury, J. M., Kremer, A., Leroy, T., Le Provost, G., Plomion, C., Carlson, J. E., Randall, J., Westbrook, J., Grimwood, J., Muchero, W., Jacobson, D. and Michener, J. K. 2018 Hardwood Tree Genomics: Unlocking Woody Plant Biology Frontiers in Plant Science 10.3389/fpls.2018.01799
Valdes-Lopez, O., Batek, J., Gomez-Hernandez, N., Nguyen, C. T., Isidra-Arellano, M. C., Zhang, N., Joshi, T., Xu, D., Hixson, K. K., Weitz, K. K., Aldrich, J. T., Pasa-Tolic, L. and Stacey, G. 2016 Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles Frontiers in Plant Science 10.3389/fpls.2016.00517
Wang, X., Liu, S., Tian, H., Wang, S. and Chen, J. G. 2015 The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis Frontiers in Plant Science 10.3389/fpls.2015.01064
Xie, M., Zhang, J., Tschaplinski, T.J., Tuskan, G.A., Chen, J-G., Muchero, W. 2018 Regulation of lignin biosynthesis and its role in growth-defense tradeoffs Frontiers in Plant Science 10.3389/fpls.2018.01427
Zhang, J., Xie, M., Tuskan, G.A., Muchero, W., and Chen, J-G. 2018 Recent advances in the transcriptional regulation of secondary cell wall biosynthesis in the woody plants Frontiers in Plant Science 10.3389/fpls.2018.01535
Zhao, K. M., Lin, F., Romero-Gamboa, S. P., Saha, P., Goh, H. J., An, G., Jung, K. H., Hazen, S. P. and Bartley, L. E. 2019 Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis Frontiers in Plant Science 10.3389/fpls.2019.01275
He, Z. L., Van Nostrand, J. D., Deng, Y. and Zhou, J. Z. 2011 Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities Frontiers of Environmental Science & Engineering in China 10.1007/s11783-011-0301-y
Groendyk, M. and Rothamer, D. A. 2019 Optical investigation of mixing-controlled combustion using a novel transgenic plant oil Fuel 10.1016/j.fuel.2019.03.094
He, Y., Barnes, S. E., Crunkleton, D. W. and Price, G. L. 2012 Comparison of ginger oil conversion over MFI, BEA, and FAU Fuel 10.1016/j.fuel.2012.01.033
Min, D. Y., Li, Q. Z., Chiang, V., Jameel, H., Chang, H. M. and Lucia, L. 2014 The influence of lignin-carbohydrate complexes on the cellulase-mediated saccharification I: Transgenic black cottonwood (western balsam poplar, California poplar) P-trichocarpa including the xylan down-regulated and the lignin down-regulated lines Fuel 10.1016/j.fuel.2013.11.047
Min, D. Y., Yang, C. M., Chiang, V., Jameel, H. and Chang, H. M. 2014 The influence of lignin-carbohydrate complexes on the cellulase-mediated saccharification II: Transgenic hybrid poplars (Populus nigra L. and Populus maximowiczii A.) Fuel 10.1016/j.fuel.2013.07.046
Sakai, S. and Rothamer, D. 2019 Impact of ethanol blending on particulate emissions from a spark-ignition direct-injection engine Fuel 10.1016/j.fuel.2018.09.037
Land, M., Hauser, L., Jun, S. R., Nookaew, I., Leuze, M. R., Ahn, T. H., Karpinets, T., Lund, O., Kora, G., Wassenaar, T., Poudel, S. and Ussery, D. W. 2015 Insights from 20 years of bacterial genome sequencing Functional & Integrative Genomics 10.1007/s10142-015-0433-4
Schneebeli, K., Mathesius, U., Zwart, A. B., Bragg, J. N., Vogel, J. P. and Watt, M. 2016 Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8 Functional Plant Biology 10.1071/fp15244
Yuan, Zhilin, Druzhinina, Irina S., Wang, Xinyu, Zhang, Xiaoguo, Peng, Long and Labbé, Jessy 2019 Insight into a highly polymorphic endophyte isolated from the roots of the halophytic seepweed Suaeda salsa: Laburnicola rhizohalophila sp. nov. (Didymosphaeriaceae, Pleosporales) Fungal Biology 10.1016/j.funbio.2019.10.001
Millet, L. J., Aufrecht, J., Labbe, J., Uehling, J., Vilgalys, R., Estes, M. L., Miquel Guennoc, C., Deveau, A., Olsson, S., Bonito, G., Doktycz, M. J. and Retterer, S. T. 2019 Increasing access to microfluidics for studying fungi and other branched biological structures Fungal Biology and Biotechnology 10.1186/s40694-019-0071-z
Bonito, Gregory, Hameed, Khalid, Ventura, Rafael, Krishnan, Jay, Schadt, Christopher W. and Vilgalys, Rytas 2016 Isolating a functionally relevant guild of fungi from the root microbiome of Populus Fungal Ecology 10.1016/j.funeco.2016.04.007
Brown, S. P., Veach, A. M., Rigdon-Huss, A. R., Grond, K., Lickteig, S. K., Lothamer, K., Oliver, A. K. and Jumpponen, A. 2015 Scraping the bottom of the barrel: are rare high throughput sequences artifacts? Fungal Ecology 10.1016/j.funeco.2014.08.006
Bruns, T. D. 2019 The developing relationship between the study of fungal communities and community ecology theory Fungal Ecology 10.1016/j.funeco.2018.12.009
Kuske, Cheryl R., Hesse, Cedar N., Challacombe, Jean F., Cullen, Daniel, Herr, Joshua R., Mueller, Rebecca C., Tsang, Adrian and Vilgalys, Rytas 2015 Prospects and challenges for fungal metatranscriptomics of complex communities Fungal Ecology 10.1016/j.funeco.2014.12.005
Oliver, A. K., Brown, S. P., Callaham, M. A. and Jumpponen, A. 2015 Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 % Fungal Ecology 10.1016/j.funeco.2015.03.003
Urbina, Hector, Schuster, Jack and Blackwell, Meredith 2013 The gut of Guatemalan passalid beetles: a habitat colonized by cellobiose- and xylose-fermenting yeasts Fungal Ecology 10.1016/j.funeco.2013.06.005
Vélez, Jessica M., Tschaplinski, Timothy J., Vilgalys, Rytas, Schadt, Christopher W., Bonito, Gregory, Hameed, Khalid, Engle, Nancy and Hamilton, Cyd E. 2017 Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees Fungal Ecology 10.1016/j.funeco.2017.03.001
Plett, J. M., Gibon, J., Kohler, A., Duffy, K., Hoegger, P. J., Velagapudi, R., Han, J., Kues, U., Grigoriev, I. V. and Martin, F. 2012 Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor Fungal Genetics and Biology 10.1016/j.fgb.2012.01.002
Presley, G. N., Zhang, J. W. and Schilling, J. S. 2018 A genomics-informed study of oxalate and cellulase regulation by brown rot wood-degrading fungi Fungal Genetics and Biology 10.1016/j.fgb.2016.08.004
Solomon, K. V., Henske, J. K., Gilmore, S. P., Lipzen, A., Grigoriev, I. V., Thompson, D. and O'Malley, M. A. 2018 Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts Fungal Genetics and Biology 10.1016/j.fgb.2018.09.004
Veneault-Fourrey, C., Commun, C., Kohler, A., Morin, E., Balestrini, R., Plett, J., Danchin, E., Coutinho, P., Wiebenga, A., de Vries, R. P., Henrissat, B. and Martin, F. 2014 Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment Fungal Genetics and Biology 10.1016/j.fgb.2014.08.007
Zhang, J. W., Mitchell, H. D., Markillie, L. M., Gaffrey, M. J., Orr, G. and Schilling, J. 2019 Reference genes for accurate normalization of gene expression in wood-decomposing fungi Fungal Genetics and Biology 10.1016/j.fgb.2018.11.005
Zhang, J. W. and Schilling, J. S. 2017 Role of carbon source in the shift from oxidative to hydrolytic wood decomposition by Postia placenta Fungal Genetics and Biology 10.1016/j.fgb.2017.06.003
Azodi, C. B., Bolger, E., McCarren, A., Roantree, M., de los Campos, G. and Shiu, S. H. 2019 Benchmarking Parametric and Machine Learning Models for Genomic Prediction of Complex Traits G3: Genes Genomes Genetics 10.1534/g3.119.400498
Bryan, A. C., Zhang, J., Guo, J., Ranjan, P., Singan, V., Barry, K., Schmutz, J., Weighill, D., Jacobson, D., Jawdy, S., Tuskan, G. A., Chen, J. G. and Muchero, W. 2018 A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein G3: Genes, Genomes and Genetics 10.1534/g3.118.200188
Cuevas, H. E., Prom, L. K. and Cruet-Burgos, C. M. 2019 Genome-Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm G3: Genes, Genomes and Genetics 10.1534/g3.119.400350
Kainer, D., Stone, E. A., Padovan, A., Foley, W. J. and Kulheim, C. 2018 Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybractea G3: Genes, Genomes and Genetics 10.1534/g3.118.200443
Ramstein, G. P. and Casler, M. D. 2019 Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample G3: Genes, Genomes and Genetics 10.1534/g3.118.200969
Felderhoff, T. J., McIntyre, L. M., Saballos, A. and Vermerris, W. 2016 Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor G3: Genes, Genomes, Genetics 10.1534/g3.116.030510
Mauro-Herrera, M., Wang, X. W., Barbier, H., Brutnell, T. P., Devos, K. M. and Doust, A. N. 2013 Genetic Control and Comparative Genomic Analysis of Flowering Time in Setaria (Poaceae) G3: Genes, Genomes, Genetics 10.1534/g3.112.005207
Milano, E. R., Lowry, D. B. and Juenger, T. E. 2016 The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum) G3: Genes, Genomes, Genetics 10.1534/g3.116.032763
Sardi, M., Krause, M., Heilberger, J. and Gasch, A. P. 2018 Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis G3: Genes, Genomes, Genetics 10.1534/g3.118.200677
Clifton-Brown, J., et al. 2018 Breeding progress and preparedness for mass-scale deployment of perenial lignocellulosic biomass crops switchgrass, miscanthus, willow, and poplar GCB Bioenergy 10.1111/gcbb.12566
Leuze, M. R., Karpinets, T. V., Syed, M. H., Beliaev, A. S. and Uberbacher, E. C. 2012 Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA Gene Regulation and Systems Biology 10.4137/GRSB.S9357
Higgins, D. A., Young, M. K. M., Tremaine, M., Sardi, M., Fletcher, J. M., Agnew, M., Liu, L., Dickinson, Q., Peris, D., Wrobel, R. L., Hittinger, C. T., Gasch, A. P., Singer, S. W., Simmons, B. A., Landick, R., Thelen, M. P. and Sato, T. K. 2018 Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast Genetics 10.1534/genetics.118.301161
Okada, M., Lanzatella, C., Saha, M. C., Bouton, J., Wu, R. L. and Tobias, C. M. 2010 Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions Genetics 10.1534/genetics.110.113910
Truong, S. K., McCormick, R. F., Rooney, W. L. and Mullet, J. E. 2015 Harnessing Genetic Variation in Leaf Angle to Increase Productivity of Sorghum bicolor Genetics 10.1534/genetics.115.178608
Everroad, R. Craig, Woebken, Dagmar, Singer, Steven W., Burow, Luke C., Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Detweiler, Angela, Prufert-Bebout, Leslie and Pett-Ridge, Jennifer 2013 Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1 Genome Announcements 10.1128/genomeA.00527-13
Klingeman, D. M., Utturkar, S., Lu, T. Y., Schadt, C. W., Pelletier, D. A. and Brown, S. D. 2015 Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere Genome Announcements 10.1128/genomeA.01344-15
Goodman, D. B., Kuznetsov, G., Lajoie, M. J., Ahern, B. W., Napolitano, M. G., Chen, K. Y., Chen, C. P. and Church, G. M. 2017 Millstone: software for multiplex microbial genome analysis and engineering Genome Biology 10.1186/s13059-017-1223-1
Jeong, D. H., Schmidt, S. A., Rymarquis, L. A., Park, S., Ganssmann, M., German, M. A., Accerbi, M., Zhai, J. X., Fahlgren, N., Fox, S. E., Garvin, D. F., Mockler, T. C., Carrington, J. C., Meyers, B. C. and Green, P. J. 2013 Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon Genome Biology 10.1186/gb-2013-14-12-r145
Kuznetsov, G., Goodman, D. B., Filsinger, G. T., Landon, M., Rohland, N., Aach, J., Lajoie, M. J. and Church, G. M. 2017 Optimizing complex phenotypes through model-guided multiplex genome engineering Genome Biology 10.1186/s13059-017-1217-z
Miller, C. S., Baker, B. J., Thomas, B. C., Singer, S. W. and Banfield, J. F. 2011 EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Genome Biology 10.1186/gb-2011-12-5-r44
Carlson, C. H., Choi, Y., Chan, A. P., Serapiglia, M. J., Town, C. D. and Smart, L. B. 2017 Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome Genome Biology and Evolution 10.1093/gbe/evx174
Reichenberger, E. R., Rosen, G., Hershberg, U. and Hershberg, R. 2015 Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment Genome Biology and Evolution 10.1093/gbe/evv063
Lovell, J. T., Schwartz, S., Lowry, D. B., Shakirov, E. V., Bonnette, J. E., Weng, X. Y., Wang, M., Johnson, J., Sreedasyam, A., Plott, C., Jenkins, J., Schmutz, J. and Juenger, T. E. 2016 Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C-4 grass Genome Research 10.1101/gr.198135.115
Rodgers-Melnick, E., Mane, S. P., Dharmawardhana, P., Slavov, G. T., Crasta, O. R., Strauss, S. H., Brunner, A. M. and DiFazio, S. P. 2012 Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus Genome Research 10.1101/gr.125146.111
Sharon, I., Kertesz, M., Hug, L. A., Pushkarev, D., Blauwkamp, T. A., Castelle, C. J., Amirebrahimi, M., Thomas, B. C., Burstein, D., Tringe, S. G., Williams, K. H. and Banfield, J. F. 2015 Accurate, multi-kb reads resolve complex populations and detect rare microorganisms Genome Research 10.1101/gr.183012.114
Suzuki, Y., Assad-Garcia, N., Kostylev, M., Noskov, V. N., Wise, K. S., Karas, B. J., Stam, J., Montague, M. G., Hanly, T. J., Enriquez, N. J., Ramon, A., Goldgof, G. M., Richter, R. A., Vashee, S., Chuang, R. Y., Winzeler, E. A., Hutchison, C. A., Gibson, D. G., Smith, H. O., Glass, J. I. and Venter, J. C. 2015 Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling Genome Research 10.1101/gr.182477.114
Yang, X., Tschaplinski, T. J., Hurst, G. B., Jawdy, S., Abraham, P. E., Lankford, P. K., Adams, R. M., Shah, M. B., Hettich, R. L., Lindquist, E., Kalluri, U. C., Gunter, L. E., Pennacchio, C. and Tuskan, G. A. 2011 Discovery and annotation of small proteins using genomics, proteomics, and computational approaches Genome Research 10.1101/gr.109280.110
Yoon, S. H., Reiss, D. J., Bare, J. C., Tenenbaum, D., Pan, M., Slagel, J., Moritz, R. L., Lim, S., Hackett, M., Menon, A. L., Adams, M. W. W., Barnebey, A., Yannone, S. M., Leigh, J. A. and Baliga, N. S. 2011 Parallel evolution of transcriptome architecture during genome reorganization Genome Research 10.1101/gr.122218.111
Yoon, S. H., Turkarslan, S., Reiss, D. J., Pan, M., Burn, J. A., Costa, K. C., Lie, T. J., Slagel, J., Moritz, R. L., Hackett, M., Leigh, J. A. and Baliga, N. S. 2013 A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen Genome Research 10.1101/gr.153916.112
Burow, L. C., Woebken, D., Marshall, I. P. G., Singer, S. W., Pett-Ridge, J., Prufert-Bebout, L., Spormann, A. M., Bebout, B. M., Weber, P. K. and Hoehler, T. M. 2014 Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community Geobiology 10.1111/gbi.12080
Stackhouse, B., Lau, M. C. Y., Vishnivetskaya, T., Burton, N., Wang, R., Southworth, A., Whyte, L. and Onstott, T. C. 2017 Atmospheric CH4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature Geobiology 10.1111/gbi.12193
Stanton, C. L., Reinhard, C. T., Kasting, J. F., Ostrom, N. E., Haslun, J. A., Lyons, T. W. and Glass, J. B. 2018 Nitrous oxide from chemodenitrification: A possible missing link in the Proterozoic greenhouse and the evolution of aerobic respiration Geobiology 10.1111/gbi.12311
Fahnestock, M. F., Bryce, J. G., McCalley, C. K., Montesdeoca, M., Bai, S., Li, Y., Driscoll, C. T., Crill, P. M., Rich, V. I. and Varner, R. K. 2019 Mercury reallocation in thawing subarctic peatlands Geochemical Perspectives Letters 10.7185/geochemlet.1922
Hodgkins, S. B., Tfaily, M. M., Podgorski, D. C., McCalley, C. K., Saleska, S. R., Crill, P. M., Rich, V. I., Chanton, J. P. and Cooper, W. T. 2016 Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland Geochimica Et Cosmochimica Acta 10.1016/j.gca.2016.05.015
Mayes M, Jagadamma S, Ambaye H, Petridis L, and Lauter V 2013 Neutron Reflectometry Reveals the Internal Structure of Natural Organic Matter Deposited onto an Aluminum Oxide Geoderma 10.1016/j.geoderma.2012.07.025
Xu, X., Shi, Z., Li, D. J., Rey, A., Ruan, H. H., Craine, J. M., Liang, J. Y., Zhou, J. Z. and Luo, Y. Q. 2016 Soil properties control decomposition of soil organic carbon: Results from data-assimilation analysis Geoderma 10.1016/j.geoderma.2015.08.038
Glass, J. B., Chen, S., Dawson, K. S., Horton, D. R., Vogt, S., Ingall, E. D., Twining, B. S. and Orphan, V. J. 2018 Trace Metal Imaging of Sulfate-Reducing Bacteria and Methanogenic Archaea at Single-Cell Resolution by Synchrotron X-Ray Fluorescence Imaging Geomicrobiology Journal 10.1080/01490451.2017.1321068
Jardine, A. B., Jardine, K. J., Fuentes, J. D., Martin, S. T., Martins, G., Durgante, F., Carneiro, V., Higuchi, N., Manzi, A. O. and Chambers, J. Q. 2015 Highly reactive light-dependent monoterpenes in the Amazon Geophysical Research Letters 10.1002/2014GL062573
Wieder, W. R., Sulman, B. N., Hartman, M. D., Koven, C. D. and Bradford, M. A. 2019 Arctic Soil Governs Whether Climate Change Drives Global Losses or Gains in Soil Carbon Geophysical Research Letters 10.1029/2019gl085543
Luo, Y. Q., Ahlstrom, A., Allison, S. D., Batjes, N. H., Brovkin, V., Carvalhais, N., Chappell, A., Ciais, P., Davidson, E. A., Finzi, A. C., Georgiou, K., Guenet, B., Hararuk, O., Harden, J. W., He, Y. J., Hopkins, F., Jiang, L. F., Koven, C., Jackson, R. B., Jones, C. D., Lara, M. J., Liang, J. Y., McGuire, A. D., Parton, W., Peng, C. H., Randerson, J. T., Salazar, A., Sierra, C. A., Smith, M. J., Tian, H. Q., Todd-Brown, K. E. O., Torn, M., van Groenigen, K. J., Wang, Y. P., West, T. O., Wei, Y. X., Wieder, W. R., Xia, J. Y., Xu, X., Xu, X. F. and Zhou, T. 2016 Toward more realistic projections of soil carbon dynamics by Earth system models Global Biogeochemical Cycles 10.1002/2015gb005239
Carrell, A. A., Kolton, M., Glass, J. B., Pelletier, D. A., Warren, M. J., Kostka, J. E., Iversen, C. M., Hanson, P. J. and Weston, D. J. 2019 Experimental warming alters the community composition, diversity, and N2 fixation activity of peat moss (Sphagnum fallax) microbiomes Global Change Biology 10.1111/gcb.14715
Deng, Y., He, Z. L., Xiong, J. B., Yu, H., Xu, M. Y., Hobbie, S. E., Reich, P. B., Schadt, C. W., Kent, A., Pendall, E., Wallenstein, M. and Zhou, J. Z. 2016 Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities Global Change Biology 10.1111/gcb.13098
Feng, W. T., Liang, J. Y., Hale, L. E., Jung, C. G., Chen, J., Zhou, J. Z., Xu, M. G., Yuan, M. T., Wu, L. Y., Bracho, R., Pegoraro, E., Schuur, E. A. G. and Luo, Y. Q. 2017 Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming Global Change Biology 10.1111/gcb.13755
Li, D. J., Zhou, X. H., Wu, L. Y., Zhou, J. Z. and Luo, Y. Q. 2013 Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual-dominated prairie Global Change Biology 10.1111/gcb.12273
Li, J. W., Wang, G. S., Mayes, M. A., Allison, S. D., Frey, S. D., Shi, Z., Hu, X. M., Luo, Y. Q. and Melillo, J. M. 2019 Reduced carbon use efficiency and increased microbial turnover with soil warming Global Change Biology 10.1111/gcb.14517
Li, Y., Guan, K. Y., Schnitkey, G. D., DeLucia, E. and Peng, B. 2019 Excessive rainfall leads to maize yield loss of a comparable magnitude to extreme drought in the United States Global Change Biology 10.1111/gcb.14628
Liang, J. Y., Xia, J. Y., Shi, Z., Jiang, L. F., Ma, S., Lu, X. J., Mauritz, M., Natali, S. M., Pegoraro, E., Penton, C. R., Plaza, C., Salmon, V. G., Celis, G., Cole, J. R., Konstantinidis, K. T., Tiedje, J. M., Zhou, J. Z., Schuur, E. A. G. and Luo, Y. Q. 2018 Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra Global Change Biology 10.1111/gcb.14325
Shi, Z., Lin, Y., Wilcox, K. R., Souza, L., Jiang, L. F., Jiang, J., Jung, C. G., Xu, X., Yuan, M. T., Guo, X., Wu, L. Y., Zhou, J. Z. and Luo, Y. Q. 2018 Successional change in species composition alters climate sensitivity of grassland productivity Global Change Biology 10.1111/gcb.14333
Ware, I. M., Van Nuland, M. E., Schweitzer, J. A., Yang, Z., Schadt, C. W., Sidak-Loftis, L. C., Stone, N. E., Busch, J. D., Wagner, D. M. and Bailey, J. K. 2019 Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools Global Change Biology 10.1111/gcb.14553
Wieder, W. R., Hartman, M. D., Sulman, B. N., Wang, Y. P., Koven, C. D. and Bonan, G. B. 2018 Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models Global Change Biology 10.1111/gcb.13979
Xu, X., Niu, S. L., Sherry, R. A., Zhou, X. H., Zhou, J. Z. and Luo, Y. Q. 2012 Interannual variability in responses of belowground net primary productivity (NPP) and NPP partitioning to long-term warming and clipping in a tallgrass prairie Global Change Biology 10.1111/j.1365-2486.2012.02651.x
Xu, X., Shi, Z., Chen, X. C., Lin, Y., Niu, S. L., Jiang, L. F., Luo, R. S. and Luo, Y. Q. 2016 Unchanged carbon balance driven by equivalent responses of production and respiration to climate change in a mixed-grass prairie Global Change Biology 10.1111/gcb.13192
Yang, Y. F., Wu, L. W., Lin, Q. Y., Yuan, M. T., Xu, D. P., Yu, H., Hu, Y. G., Duan, J. C., Li, X. Z., He, Z. L., Xue, K., van Nostrand, J., Wang, S. P. and Zhou, J. Z. 2013 Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland Global Change Biology 10.1111/gcb.12065
Yuan, M. M. M., Zhang, J., Xue, K., Wu, L. Y., Deng, Y., Deng, J., Hale, L. R., Zhou, X. S., He, Z. L., Yang, Y. F., Van Nostrand, J. D., Schuur, E. A. G., Konstantinidis, K. T., Penton, C. R., Cole, J. R., Tiedje, J. M., Luo, Y. Q. and Zhou, J. Z. 2018 Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil Global Change Biology 10.1111/gcb.13820
Clark, L. V., Dwiyanti, M. S., Anzoua, K. G., Brummer, J. E., Ghimire, B. K., Glowacka, K., Hall, M., Heo, K., Jin, X. L., Lipka, A. E., Peng, J. H., Yamada, T., Yoo, J. H., Yu, C. Y., Zhao, H., Long, S. P. and Sacks, E. J. 2019 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 10.1111/gcbb.12620
Clark, L. V., Dwiyanti, M. S., Anzoua, K. G., Brummer, J. E., Ghimire, B. K., Glowacka, K., Hall, M., Heo, K., Jin, X. L., Lipka, A. E., Peng, J. H., Yamada, T., Yoo, J. H., Yu, C. Y., Zhao, H., Long, S. P. and Sacks, E. J. 2019 Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential Global Change Biology Bioenergy 10.1111/gcbb.12606
Clifton-Brown, J., Harfouche, A., Casler, M. D., Jones, H. D., Macalpine, W. J., Murphy-Bokern, D., Smart, L. B., Adler, A., Ashman, C., Awty-Carroll, D., Bastien, C., Bopper, S., Botnari, V., Brancourt-Hulmel, M., Chen, Z. Y., Clark, L. V., Cosentino, S., Dalton, S., Davey, C., Dolstra, O., Donnison, I., Flavell, R., Greef, J., Hanley, S., Hastings, A., Hertzberg, M., Hsu, T. W., Huang, L. S., Iurato, A., Jensen, E., Jin, X. L., Jorgensen, U., Kiesel, A., Kim, D. S., Liu, J., McCalmont, J. P., McMahon, B. G., Mos, M., Robson, P., Sacks, E. J., Sandu, A., Scalici, G., Schwarz, K., Scordia, D., Shafiei, R., Shield, I., Slavov, G., Stanton, B. J., Swaminathan, K., Taylor, G., Torres, A. F., Trindade, L. M., Tschaplinski, T., Tuskan, G. A., Yamada, T., Yu, C. Y., Zalesny, R. S., Zong, J. Q. and Lewandowski, I. 2019 Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar Global Change Biology Bioenergy 10.1111/gcbb.12566
Dong, H. X., Clark, L. V., Lipka, A. E., Brummer, J. E., Glowacka, K., Hall, M. C., Heo, K., Jin, X. L., Peng, J. H., Yamada, T., Ghimire, B. K., Yoo, J. H., Yu, C. Y., Zhao, H., Long, S. P. and Sacks, E. J. 2019 Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis Global Change Biology Bioenergy 10.1111/gcbb.12615
Dong, H. X., Green, S. V., Nishiwaki, A., Yamada, T., Stewart, J. R., Deuter, M. and Sacks, E. J. 2019 Winter hardiness of Miscanthus (I): Overwintering ability and yield of new Miscanthus xgiganteus genotypes in Illinois and Arkansas Global Change Biology Bioenergy 10.1111/gcbb.12588
Dong, H. X., Liu, S. Y., Clark, L. V., Sharma, S., Gifford, J. M., Juvik, J. A., Lipka, A. E. and Sacks, E. J. 2018 Genetic mapping of biomass yield in three interconnected Miscanthus populations Global Change Biology Bioenergy 10.1111/gcbb.12472
Dong, H. X., Liu, S. Y., Clark, L. V., Sharma, S., Gifford, J. M., Juvik, J. A., Lipka, A. E. and Sacks, E. J. 2019 Winter hardiness of Miscanthus (II): Genetic mapping for overwintering ability and adaptation traits in three interconnected Miscanthus populations Global Change Biology Bioenergy 10.1111/gcbb.12587
Duncan, D. S., Oates, L. G., Gelfand, I., Millar, N., Robertson, G. P. and Jackson, R. D. 2019 Environmental factors function as constraints on soil nitrous oxide fluxes in bioenergy feedstock cropping systems Global Change Biology Bioenergy 10.1111/gcbb.12572
Kim, S., Dale, B. E., Jin, M., Thelen, K. D., Zhang, X., Meier, P., Reddy, A. D., Jones, C. D., Izaurralde, R. C., Balan, V., Runge, T. and Sharara, M. 2019 Integration in a depot-based decentralized biorefinery system: Corn stover-based cellulosic biofuel Global Change Biology Bioenergy 10.1111/gcbb.12613
Kravchenko, A. N., Guber, A. K., Quigley, M. Y., Koestel, J., Gandhi, H. and Ostrom, N. E. 2018 X-ray computed tomography to predict soil N2O production via bacterial denitrification and N2O emission in contrasting bioenergy cropping systems Global Change Biology Bioenergy 10.1111/gcbb.12552
Liu, S. Y., Clark, L. V., Swaminathan, K., Gifford, J. M., Juvik, J. A. and Sacks, E. J. 2016 High-density genetic map of Miscanthussinensis reveals inheritance of zebra stripe Global Change Biology Bioenergy 10.1111/gcbb.12275
Pignon, C. P., Spitz, I., Sacks, E. J., Jorgensen, U., Korup, K. and Long, S. P. 2019 Siberian Miscanthus sacchariflorus accessions surpass the exceptional chilling tolerance of the most widely cultivated clone of Miscanthus x giganteus Global Change Biology Bioenergy 10.1111/gcbb.12599
Zhang, L., Juenger, T. E., Lowry, D. B. and Behrman, K. D. 2019 Climatic impact, future biomass production, and local adaptation of four switchgrass cultivars Global Change Biology Bioenergy 10.1111/gcbb.12609
Zhang, Y. P., Oates, L. G., Serate, J., Xie, D., Pohlmann, E., Bukhman, Y. V., Karlen, S. D., Young, M. K., Higbee, A., Eilert, D., Sanford, G. R., Piotrowski, J. S., Cavalier, D., Ralph, J., Coon, J. J., Sato, T. K. and Ong, R. G. 2018 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 10.1111/gcbb.12533
Bouxin, F. P., Strub, H., Dutta, T., Aguilhon, J., Morgan, T. J., Mingardon, F., George, A. 2018 Elucidating transfer hydrogenation mechanisms in non-catalytic lignin depolymerization Green Chemistry 10.1039/C7GC03239K
Chang, H., Motagamwala, A. H., Huber, G. W. and Dumesic, J. A. 2019 Synthesis of biomass-derived feedstocks for the polymers and fuels industries from 5-(hydroxymethyl)furfural (HMF) and acetone Green Chemistry 10.1039/c9gc01859j
De Bruyn, M., Sener, C., Petrolini, D. D., McClelland, D. J., He, J. Y., Ball, M. R., Liu, Y. F., Martins, L., Dumesic, J. A., Huber, G. W. and Weckhuysen, B. M. 2019 Catalytic hydrogenation of dihydrolevoglucosenone to levoglucosanol with a hydrotalcite/mixed oxide copper catalyst Green Chemistry 10.1039/c9gc00564a
Ding, J. H., Yoo, C. G., Pu, Y. Q., Meng, X. Z., Bhagia, S., Yu, C. W. and Ragauskas, A. J. 2019 Cellulolytic enzyme-aided extraction of hemicellulose from switchgrass and its characteristics Green Chemistry 10.1039/c9gc00252a
Giummarella, N., Pu, Y. Q., Ragauskas, A. J. and Lawoko, M. 2019 A critical review on the analysis of lignin carbohydrate bonds Green Chemistry 10.1039/c8gc03606c
Kothari, N., Bhagia, S., Zaher, M., Pu, Y. Q., Mittal, A., Yoo, C. G., Himmel, M. E., Ragauskas, A. J., Kumar, R. and Wyman, C. E. 2019 Cellulose hydrolysis by Clostridium thermocellum is agnostic to substrate structural properties in contrast to fungal cellulases Green Chemistry 10.1039/c9gc00262f
Kumar, R., Bhagia, S., Smith, M. D., Petridis, L., Ong, R. G., Cai, C. M., Mittal, A., Himmel, M. H., Balan, V., Dale, B. E., Ragauskas, A. J., Smith, J. C. and Wyman, C. E. 2018 Cellulose-hemicellulose interactions at elevated temperatures increase cellulose recalcitrance to biological conversion Green Chemistry 10.1039/c7gc03518g
Langan P, Petridis L, O'Neill HM, Pingali SV, Foston M, Nishiyama Y, Schulz R, Lindner B, Hanson BL, Harton S, Heller WT, Urban V, Evans BR, Gnanakaran S, Ragauskas AJ, Smith JC, and Davison BH 2014 Common Processes Drive the Thermochemical Pretreatment of Lignocellulosic Biomass Green Chemistry 10.1039/C3GC41962B
Li, N., Li, Y. D., Yoo, C. G., Yang, X. H., Lin, X. L., Ralph, J. and Pan, X. J. 2018 An uncondensed lignin depolymerized in the solid state and isolated from lignocellulosic biomass: a mechanistic study Green Chemistry 10.1039/c8gc00953h
Li, Y. D., Demir, B., Ramos, L. M. V., Chen, M. J., Dumesice, J. A. and Ralph, O. 2019 Kinetic and mechanistic insights into hydrogenolysis of lignin to monomers in a continuous flow reactor Green Chemistry 10.1039/c9gc00986h
McClelland, D. J., Galebach, P. H., Motagamwala, A. H., Wittrig, A. M., Karlen, S. D., Buchanan, J. S., Dumesic, J. A. and Huber, G. W. 2019 Supercritical methanol depolymerization and hydrodeoxygenation of lignin and biomass over reduced copper porous metal oxides Green Chemistry 10.1039/c9gc00589g
Perez, J. M., Kontur, W. S., Alherech, M., Coplien, J., Karlen, S. D., Stahl, S. S., Donohue, T. J. and Noguera, D. R. 2019 Funneling aromatic products of chemically depolymerized lignin into 2-pyrone-4-6-dicarboxylic acid with Novosphingobium aromaticivorans Green Chemistry 10.1039/c8gc03504k
Shinde, S. D., Meng, X. Z., Kumar, R. and Ragauskas, A. J. 2018 Recent advances in understanding the pseudo-lignin formation in a lignocellulosic biorefinery Green Chemistry 10.1039/c8gc00353j
Smith M, Mostofian B, Cheng X, Petridis L, Cai C, Wyman C, and Smith J 2016 Cosolvent Pretreatment in Cellulosic Biofuel Production Effect of Tetrahydrofuran-Water on Lignin Structure and Dynamics Green Chemistry 10.1039/C5GC01952D
Smith MD, Cai CM, Cheng X, Petridis L, Smith JC 2018 Temperature-dependent phase behaviour of tetrahydrofuran–water alters solubilization of xylan to improve co-production of furfurals from lignocellulosic biomass Green Chemistry 10.1039/C7GC03608F
Song, Y., Motagamwala, A. H., Karlen, S. D., Dumesic, J. A., Ralph, J., Mobley, J. K. and Crocker, M. 2019 A comparative study of secondary depolymerization methods on oxidized lignins Green Chemistry 10.1039/c9gc01663e
Vermaas, J.V., Petridis, L., Ralph, J., Crowley, M.F., and Beckham, G.T. 2018 Systematic parameterization of lignin for the CHARMM force field Green Chemistry 10.1039/C8GC03209B
Vermaas, J. V., Petridis, L., Ralph, J., Crowley, M. F. and Beckham, G. T. 2019 Systematic parameterization of lignin for the CHARMM force field Green Chemistry 10.1039/c8gc03209b
Vural D, Gainaru C, O'Neill H, Pu Y, Smith MD, Parks JM, Pingali SV, Mamontov E, Davison BH, Sokolov AP, Ragauskas AJ, Smith JC, Petridis L 2018 Impact of hydration and temperature history on the structure and dynamics of lignin Green Chemistry 10.1039/C7GC03796A
Liang, L., Yan, J., He, Q., Luong, T., Pray, T. R., Simmons, B. A., and Sun, N. 2018 Scale-up of Biomass Conversion using 1-Ethyl-3-methylimidazolium Acetate as the Solvent Green Energy & Environment 10.1016/j.gee.2018.07.002
Frolking, S., Talbot, J. and Subin, Z. M. 2014 Exploring the relationship between peatland net carbon balance and apparent carbon accumulation rate at century to millennial time scales Holocene 10.1177/0959683614538078
Yelle, D. J., Ralph, J. and Frihart, C. R. 2011 Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 2. Non-catalyzed reactions with the wood cell wall Holzforschung 10.1515/hf.2011.029
Liu, D. G., Mewalal, R., Hu, R. B., Tuskan, G. A. and Yang, X. H. 2017 New technologies accelerate the exploration of non-coding RNAs in horticultural plants Horticulture Research 10.1038/hortres.2017.31
Zhang, Z. J., Wang, H., Zhou, J. Z., Li, H. Y., He, Z. L., Van Nostrand, J. D., Wang, Z. D. and Xu, X. H. 2015 Redox potential and microbial functional gene diversity in wetland sediments under simulated warming conditions: implications for phosphorus mobilization Hydrobiologia 10.1007/s10750-014-2039-6
Abraha, M., Chen, J. Q., Hamilton, S. K. and Robertson, G. P. 2019 Long-term evapotranspiration rates for rainfed corn versus perennial bioenergy crops in a mesic landscape Hydrological Processes 10.1002/hyp.13630
Hamilton, S. K., Hussain, M. Z., Lowrie, C., Basso, B. and Robertson, G. P. 2018 Evapotranspiration is resilient in the face of land cover and climate change in a humid temperate catchment Hydrological Processes 10.1002/hyp.11447
Yang, Q. C., Zhang, X. S., Almendinger, J. E., Huang, M. Y., Leng, G. Y., Zhou, Y. Y., Zhao, K. G., Asrar, G. R., Li, X. and Qiu, J. L. 2019 Improving the SWAT forest module for enhancing water resource projections: A case study in the St. Croix River basin Hydrological Processes 10.1002/hyp.13370
Chen, C. Q., Watve, A., Pramanik, S. and Zhu, Q. 2013 The BoND-Tree: An Efficient Indexing Method for Box Queries in Nonordered Discrete Data Spaces IEEE Transactions on Knowledge and Data Engineering 10.1109/tkde.2012.132
Zhou, J. A. and Qi, J. Y. 2011 Adaptive Imaging for Lesion Detection Using a Zoom-in PET System IEEE Transactions on Medical Imaging 10.1109/tmi.2010.2064173
Rosen, G. L. and Essinger, S. D. 2010 Comparison of Statistical Methods to Classify Environmental Genomic Fragments IEEE Transactions on Nanobioscience 10.1109/tnb.2010.2081375
Rozler, M. and Chang, W. 2011 Collimator Interchange System for Adaptive Cardiac Imaging in C-SPECT IEEE Transactions on Nuclear Science 10.1109/tns.2011.2163190
Rozler, M., Liang, H. N. and Chang, W. 2012 Development of a Cost-Effective Modular Pixelated NaI(Tl) Detector for Clinical SPECT Applications IEEE Transactions on Nuclear Science 10.1109/tns.2012.2210908
Chen, X., Hu, X. H., Lim, T. Y., Shen, X. J., Park, E. K. and Rosen, G. L. 2012 Exploiting the Functional and Taxonomic Structure of Genomic Data by Probabilistic Topic Modeling IEEE-ACM Transactions on Computational Biology and Bioinformatics 10.1109/tcbb.2011.113
Badr, K., Hilliard, M., Roberts, N., He, Q. P. and Wang, J. 2019 Photoautotroph-Methanotroph Coculture - A Flexible Platform for Efficient Biological CO2-CH4 Co-utilization IFAC-PapersOnLine 10.1016/j.ifacol.2019.06.179
Altpeter, F., Parajuli, S., Kannan, B., Luo, G. B., Karan, R., Liu, H., Garcia-Ruiz, E., Zhao, H. M. and Shanklin, J. 2019 Converting Sugarcane into Oilcane by Metabolic Engineering In Vitro Cellular & Developmental Biology-Animal 10.1007/s11626-019-00354-3
Altpeter, F., Oz, T. M., Altpeter, A., Karan, R. and Merotto, A. 2019 Precision Nucleotide Editing in Sugarcane Following Homology Directed Repair of Targeted DNA Breaks In Vitro Cellular & Developmental Biology-Plant 10.1007/s11627-019-09993-3
Cano, S., Parajuli, S., Kannan, B., Liu, H., Garcia-Ruiz, E., Zhao, H. M., Shanklin, J. and Altpeter, F. 2019 Environmental Impacts on Triacyl Glycerol Accumulation in Vegetative Tissues of Oilcane In Vitro Cellular & Developmental Biology-Plant 10.1007/s11627-019-09993-3
Kannan, B., Altpeter, A., Nguyen, T. H., South, P., Long, S. and Altpeter, F. 2019 Over-expression of Miscanthus Pyruvate Orthophosphate Dikinase (PPDK) in Energycane for Improving Cold Tolerance and Biomass Yield In Vitro Cellular & Developmental Biology-Plant 10.1007/s11627-019-09993-3
Mohan, C., Wang, D. D. and Altpeter, F. 2019 Establishing a Rapid Readout System for Genome Editing of Sugarcane In Vitro Cellular & Developmental Biology-Plant 10.1007/s11627-019-09993-3
Kong, L. X. and Maravelias, C. T. 2018 An Optimization-Based Approach for Simultaneous Chemical Process and Heat Exchanger Network Synthesis Industrial & Engineering Chemistry Research 10.1021/acs.iecr.8b00065
Ryu, J. and Maravelias, C. T. 2019 Simultaneous Process and Heat Exchanger Network Synthesis Using a Discrete Temperature Grid Industrial & Engineering Chemistry Research 10.1021/acs.iecr.8b04083
Singh, S. K., Savoy, A. W., Yuan, Z. Y., Luo, H., Stahl, S. S., Hegg, E. L. and Hodge, D. B. 2019 Integrated Two-Stage Alkaline-Oxidative Pretreatment of Hybrid Poplar. Part 1: Impact of Alkaline Pre-Extraction Conditions on Process Performance and Lignin Properties Industrial & Engineering Chemistry Research 10.1021/acs.iecr.9b01124
Smith, J. D., Neto, A. A., Cremaschi, S. and Crunkleton, D. W. 2013 CFD-Based Optimization of a Flooded Bed Algae Bioreactor Industrial & Engineering Chemistry Research 10.1021/ie302478d
Langan P, Evans BR, Foston M, Heller WT, O'Neill H, Petridis L, Pingali SV, Ragauskas AJ, Smith JC, Urban VS, and Davison BH 2012 Neutron Technologies for Bioenergy Research Industrial Biotechnology 10.1089/ind.2012.0012
Dou, J., Bian, H., Yelle, D. J., Ago, M., Vajanto, K., Vuorinen, T. and Zhu, J. 2019 Lignin containing cellulose nanofibril production from willow bark at 80 degrees C using a highly recyclable acid hydrotrope Industrial Crops and Products 10.1016/j.indcrop.2018.11.033
Yang, X. P., Todd, J., Arundale, R., Binder, J. B., Luo, Z. L., Islam, M. S., Sood, S. and Wang, J. P. 2019 Identifying loci controlling fiber composition in polyploid sugarcane (Saccharum spp.) through genome-wide association study Industrial Crops and Products 10.1016/j.indcrop.2019.01.023
Hasim, S., Allison, D. P., Retterer, S. T., Hopke, A., Wheeler, R. T., Doktycz, M. J. and Reynolds, T. B. 2017 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 10.1128/IAI.00601-16
Cheng X, Parks JM, Petridis L, Lindner B, Schulz R, Guo HB, Srinivas G, and Smith JC 2012 Molecular Simulation in the Energy Biosciences Innovations in Biomolecular Modeling and Simulations 10.1039/9781849735049-00087
Zhou J, Riccardi D, Beste A, Smith JC, and Parks JM 2014 Mercury methylation by HgcA Theory supports carbanion transfer to Hg II Inorganic Chemistry 10.1021/ic401992y
da Costa, R. R., Hu, H. F., Li, H. J. and Poulsen, M. 2019 Symbiotic Plant Biomass Decomposition in Fungus-Growing Termites Insects 10.3390/insects10040087
Rivera, J. G. L., Lee, Y. and Liao, J. C. 2015 An entropy-like index of bifurcational robustness for metabolic systems Integrative Biology 10.1039/c4ib00257a
Chen, Q., Cheng, X., Wei, D. and Xu, Q. 2015 Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase Interdisciplinary Sciences: Computational Life Sciences 10.1007/s12539-014-0235-8
Chu Y, and Guo H 2015 QM/MM MD and free energy simulation study of methyl transfer processes catalyzed by PKMTs and PRMTs Interdisciplinary Sciences: Computational Life Sciences 10.1007/s12539-014-0228-7
Guo HB, Gorin A, and Guo H 2009 A Peptide-Linkage Deletion Procedure for Estimate of Energetic Contributions of Individual Peptide Groups in a Complex Environment Application to Parallel β-Sheets Interdisciplinary Sciences: Computational Life Sciences 10.1007/s12539-008-0011-8
Mostofian, B., Smith, J. C. and Cheng, X. 2011 The solvation structures of cellulose microfibrils in ionic liquids Interdisciplinary Sciences: Computational Life Sciences 10.1007/s12539-011-0111-8
Xu Q, Ye X, Li LY, Cheng ZM, and Guo H 2009 Structural Basis for the Action of Xyloglucan Endotransglycosylases/hydrolases Insights from Homology Modeling Interdisciplinary Sciences: Computational Life Sciences 10.1007/s12539-010-0070-5
Yang, H., Watts, H. D., Gibilterra, V., Weiss, T. B., Petridis, L., Cosgrove, D. J. and Kubicki, J. D. 2019 Quantum Calculations on Plant Cell Wall Component Interactions Interdisciplinary Sciences: Computational Life Sciences 10.1007/s12539-018-0293-4
Zhang, J. W., Hu, D. H., Orr, G. and Schilling, J. 2019 Fluorescence in situ mRNA hybridization for gene expression detection in a wood decay fungus International Biodeterioration & Biodegradation 10.1016/j.ibiod.2019.104731
Guo, H. B., Ma, Y., Tuskan, G. A., Yang, X. H. and Guo, H. 2018 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 10.1155/2018/9784161
Yao, J., Guo, H. and Yang, X. 2015 PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction International Journal of Genomics 10.1155/2015/608042
Burrows, E. H., Chaplen, F. W. R. and Ely, R. L. 2008 Optimization of media nutrient composition for increased photofermentative hydrogen production by Synechocystis sp PCC 6803 International Journal of Hydrogen Energy 10.1016/j.ijhydene.2008.07.102
Jiao, Yongqin, Navid, Ali, Stewart, Benjamin J., McKinlay, James B., Thelen, Michael P. and Pett-Ridge, Jennifer 2012 Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum and Rhodopseudomonas palustris for hydrogen production International Journal of Hydrogen Energy 10.1016/j.ijhydene.2012.05.100
McCully, A. L. and McKinlay, J. B. 2016 Disrupting Calvin cycle phosphoribulokinase activity in Rhodopseudomonas palustris increases the H-2 yield and specific production rate proportionately International Journal of Hydrogen Energy 10.1016/j.ijhydene.2016.01.003
Friedman, B. A. and Levine, G. C. 2010 Topological Entanglement Entropy In The Second Landau Level International Journal of Modern Physics B 10.1142/s0217979210056864
Czarnecki, O., Yang, J., Weston, D. J., Tuskan, G. A. and Chen, J. G. 2013 A dual role of strigolactones in phosphate acquisition and utilization in plants International Journal of Molecular Sciences 10.3390/ijms14047681
Jardine, K. J., Fernandes de Souza, V., Oikawa, P., Higuchi, N., Bill, M., Porras, R., Niinemets, U. and Chambers, J. Q. 2017 Integration of C(1) and C(2) Metabolism in Trees International Journal of Molecular Sciences 10.3390/ijms18102045
Pereira, P. N. and Cushman, J. C. 2019 Exploring the Relationship between Crassulacean Acid Metabolism (CAM) and Mineral Nutrition with a Special Focus on Nitrogen International Journal of Molecular Sciences 10.3390/ijms20184363
Walewski L, Krachtus D, Fischer S, Smith JC, Bala P, and Lesyng B 2006 SCC-DFTB Energy Barriers for Single and Double Proton Transfer Processes in the Model Molecular Systems Malonaldehyde and Porphycene International Journal of Quantum Chemistry 10.1002/qua.20810
Bortniak, V. L., Pelletier, D. A. and Newman, J. D. 2019 Chryseobacterium populi sp. nov., isolated from Populus deltoides endosphere International Journal of Systematic and Evolutionary Microbiology 10.1099/ijsem.0.003140
Maune, M. W. and Tanner, R. S. 2012 Description of Anaerobaculum hydrogeniformans sp nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum International Journal of Systematic and Evolutionary Microbiology 10.1099/ijs.0.024349-0
Allen, L. Z., Allen, E. E., Badger, J. H., McCrow, J. P., Paulsen, I. T., Elbourne, L. D. H., Thiagarajan, M., Rusch, D. B., Nealson, K. H., Williamson, S. J., Venter, J. C. and Allen, A. E. 2012 Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic ISME Journal 10.1038/ismej.2011.201
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Belnap, C. P., Pan, C., Denef, V. J., Samatova, N. F., Hettich, R. L. and Banfield, J. F. 2011 Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions ISME Journal 10.1038/ismej.2010.200
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Lau, M. C. Y., Stackhouse, B. T., Layton, A. C., Chauhan, A., Vishnivetskaya, T. A., Chourey, K., Ronholm, J., Mykytczuk, N. C. S., Bennett, P. C., Lamarche-Gagnon, G., Burton, N., Pollard, W. H., Omelon, C. R., Medvigy, D. M., Hettich, R. L., Pfiffner, S. M., Whyte, L. G. and Onstott, T. C. 2015 An active atmospheric methane sink in high Arctic mineral cryosols ISME Journal 10.1038/ismej.2015.13
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Li, J. H., Mau, R. L., Dijkstra, P., Koch, B. J., Schwartz, E., Liu, X. J. A., Morrissey, E. M., Blazewicz, S. J., Pett-Ridge, J., Stone, B. W., Hayer, M. and Hungate, B. A. 2019 Predictive genomic traits for bacterial growth in culture versus actual growth in soil ISME Journal 10.1038/s41396-019-0422-z
Li, X. Y., Deng, Y., Li, Q., Lu, C. Y., Wang, J. J., Zhang, H. W., Zhu, J. G., Zhou, J. H. and He, Z. L. 2013 Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone ISME Journal 10.1038/ismej.2012.120
Liu, N., Li, H. J., Chevrette, M. G., Zhang, L., Cao, L., Zhou, H. K., Zhou, X. G., Zhou, Z. H., Pope, P. B., Currie, C. R., Huang, Y. P. and Wang, Q. 2019 Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite ISME Journal 10.1038/s41396-018-0255-1
Luo, C. W., Tsementzi, D., Kyrpides, N. C. and Konstantinidis, K. T. 2012 Individual genome assembly from complex community short-read metagenomic datasets ISME Journal 10.1038/ismej.2011.147
Mayali, Xavier, Weber, Peter K., Brodie, Eoin L., Mabery, Shalini, Hoeprich, Paul D. and Pett-Ridge, Jennifer 2012 High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use ISME Journal 10.1038/ismej.2011.175
Mosier, A. C., Li, Z., Thomas, B. C., Hettich, R. L., Pan, C. L. and Banfield, J. F. 2015 Elevated temperature alters proteomic responses of individual organisms within a biofilm community ISME Journal 10.1038/ismej.2014.113
Oshkin, I. Y., Beck, D. A. C., Lamb, A. E., Tchesnokova, V., Benuska, G., McTaggart, T. L., Kalyuzhnaya, M. G., Dedysh, S. N., Lidstrom, M. E. and Chistoserdova, L. 2015 Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response ISME Journal 10.1038/ismej.2014.203
Papp, K., Mau, R. L., Hayer, M., Koch, B. J., Hungate, B. A. and Schwartz, E. 2018 Quantitative stable isotope probing with (H2O)-O-18 reveals that most bacterial taxa in soil synthesize new ribosomal RNA ISME Journal 10.1038/s41396-018-0233-7
Pepe-Ranney, C., Koechli, C., Potrafka, R., Andam, C., Eggleston, E., Garcia-Pichel, F. and Buckley, D. H. 2016 Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation ISME Journal 10.1038/ismej.2015.106
Raveh-Sadka, T., Firek, B., Sharon, I., Baker, R., Brown, C. T., Thomas, B. C., Morowitz, M. J. and Banfield, J. F. 2016 Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants ISME Journal 10.1038/ismej.2016.83
Reith, F., Brugger, J., Zammit, C. M., Gregg, A. L., Goldfarb, K. C., Andersen, G. L., DeSantis, T. Z., Piceno, Y. M., Brodie, E. L., Lu, Z. M., He, Z. L., Zhou, J. Z. and Wakelin, S. A. 2012 Influence of geogenic factors on microbial communities in metallogenic Australian soils ISME Journal 10.1038/ismej.2012.48
Singleton, C. M., McCalley, C. K., Woodcroft, B. J., Boyd, J. A., Evans, P. N., Hodgkins, S. B., Chanton, J. P., Frolking, S., Crill, P. M., Saleska, S. R., Rich, V. I. and Tyson, G. W. 2018 Methanotrophy across a natural permafrost thaw environment ISME Journal 10.1038/s41396-018-0065-5
Skennerton, C. T., Haroon, M. F., Briegel, A., Shi, J., Jensen, G. J., Tyson, G. W. and Orphan, V. J. 2016 Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps ISME Journal 10.1038/ismej.2016.55
Smith, G. R., Steidinger, B. S., Bruns, T. D. and Peay, K. G. 2018 Competition-colonization tradeoffs structure fungal diversity ISME Journal 10.1038/s41396-018-0086-0
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Wang, B. Z., Qin, W., Ren, Y., Zhou, X., Jung, M. Y., Han, P., Eloe-Fadrosh, E. A., Li, M., Zheng, Y., Lu, L., Yan, X., Ji, J. B., Liu, Y., Liu, L. M., Heiner, C., Hall, R., Martens-Habbena, W., Herbold, C. W., Rhee, S. K., Bartlett, D. H., Huang, L., Ingalls, A. E., Wagner, M., Stahl, D. A. and Jia, Z. J. 2019 Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons ISME Journal 10.1038/s41396-019-0493-x
Woebken, Dagmar, Burow, Luke C., Behnam, Faris, Mayali, Xavier, Schintlmeister, Arno, Fleming, Erich D., Prufert-Bebout, Leslie, Singer, Steven W., Cortés, Alejandro López, Hoehler, Tori M., Pett-Ridge, Jennifer, Spormann, Alfred M., Wagner, Michael, Weber, Peter K. and Bebout, Brad M. 2015 Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach ISME Journal 10.1038/ismej.2014.144
Woebken, Dagmar, Burow, Luke C., Prufert-Bebout, Leslie, Bebout, Brad M., Hoehler, Tori M., Pett-Ridge, Jennifer, Spormann, Alfred M., Weber, Peter K. and Singer, Steven W. 2012 Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis ISME Journal 10.1038/ismej.2011.200
Wrighton, K. C., Castelle, C. J., Varaljay, V. A., Satagopan, S., Brown, C. T., Wilkins, M. J., Thomas, B. C., Sharon, I., Williams, K. H., Tabita, F. R. and Banfield, J. F. 2016 RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria ISME Journal 10.1038/ismej.2016.53
Wu, L. W., Yang, Y. F., Wang, S. P., Yue, H. W., Lin, Q. Y., Hu, Y. G., He, Z. L., Van Nostrand, J. D., Hale, L., Li, X. Z., Gilbert, J. A. and Zhou, J. Z. 2017 Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling ISME Journal 10.1038/ismej.2017.75
Xu, M. Y., Zhang, Q., Xia, C. Y., Zhong, Y. M., Sun, G. P., Guo, J., Yuan, T., Zhou, J. Z. and He, Z. L. 2014 Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments ISME Journal 10.1038/ismej.2014.42
Yang, Y. F., Gao, Y., Wang, S. P., Xu, D. P., Yu, H., Wu, L. W., Lin, Q. Y., Hu, Y. G., Li, X. Z., He, Z. L., Deng, Y. and Zhou, J. Z. 2014 The microbial gene diversity along an elevation gradient of the Tibetan grassland ISME Journal 10.1038/ismej.2013.146
Youngblut, N. D., Wirth, J. S., Henriksen, J. R., Smith, M., Simon, H., Metcalf, W. W. and Whitaker, R. J. 2015 Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment ISME Journal 10.1038/ismej.2015.31
Yu, X. Q., Polz, M. F. and Alm, E. J. 2019 Interactions in self-assembled microbial communities saturate with diversity ISME Journal 10.1038/s41396-019-0356-5
Yue, H. W., Wang, M. M., Wang, S. P., Gilbert, J. A., Sun, X., Wu, L. W., Lin, Q. Y., Hu, Y. G., Li, X. Z., He, Z. L., Zhou, J. Z. and Yang, Y. F. 2015 The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands ISME Journal 10.1038/ismej.2015.19
Zhang, X. M., Johnston, E. R., Li, L. H., Konstantinidis, K. T. and Han, X. G. 2017 Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe ISME Journal 10.1038/ismej.2016.180
Zhou, J. Z., Wu, L. Y., Deng, Y., Zhi, X. Y., Jiang, Y. H., Tu, Q. C., Xie, J. P., Van Nostrand, J. D., He, Z. L. and Yang, Y. F. 2011 Reproducibility and quantitation of amplicon sequencing-based detection ISME Journal 10.1038/ismej.2011.11
Bondar AN, and Smith JC 2009 Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping Israel Journal of Chemistry 10.1560/IJC.49.2.155
Hong L, Petridis L, and Smith JC 2014 Biomolecular Structure and Dynamics with Neutrons The View from Simulation Israel Journal of Chemistry 10.1002/ijch.201300137
Aggarwal M, Kovalevsky A, Velazquez H, Zoeuml S, Smith J, and McKenna R 2016 Neutron Structure of Human Carbonic Anhydrase II in Complex with Methazolamide Mapping the Solvent and H-Bonding Patterns of an Effective Clinical Drug IUCrJ 10.1107/S2052252516010514
Zee, C. T., Glynn, C., Gallagher-Jones, M., Miao, J., Santiago, C. G., Cascio, D., Gonen, T., Sawaya, M. R. and Rodriguez, J. A. 2019 Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ IUCrJ 10.1107/s2052252518017621
Kagan, M. Y., Efremov, D. V., Marienko, M. S. and Val'kov, V. V. 2011 Triplet p-Wave Superconductivity in the Low-Density Extended Hubbard Model with Coulomb Repulsion JETP Letters 10.1134/s0021364011120083
Johnson, C. W., Salvachua, D., Rorrer, N. A., Black, B. A., Vardon, D. R., St John, P. C., Cleveland, N. S., Dominick, G., Elmore, J. R., Grundl, N., Khanna, P., Martinez, C. R., Michener, W. E., Peterson, D. J., Ramirez, K. J., Singh, P., VanderWall, T. A., Wilson, A. N., Yi, X. N., Biddy, M. J., Bomble, Y. J., Guss, A. M. and Beckham, G. T. 2019 Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways Joule 10.1016/j.joule.2019.05.011
Deng, J., McCalley, C. K., Frolking, S., Chanton, J., Crill, P., Varner, R., Tyson, G., Rich, V., Hines, M., Saleska, S. R. and Li, C. S. 2017 Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling Journal of Advances in Modeling Earth Systems 10.1002/2016ms000817
Agarwal, U. P., Ralph, S. A., Padmakshan, D., Liu, S. and Foster, C. E. 2019 Estimation of Syringyl Units in Wood Lignins by FT-Raman Spectroscopy Journal of Agricultural and Food Chemistry 10.1021/acs.jafc.8b06707
del Rio, J. C., Rencoret, J., Gutierrez, A., Kim, H. and Ralph, J. 2018 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 10.1021/acs.jafc.8b00880
Dou, J. Z., Kim, H., Li, Y. D., Padmakshan, D., Yue, F. X., Ralph, J. and Vuorinen, T. 2018 Structural Characterization of Lignins from Willow Bark and Wood Journal of Agricultural and Food Chemistry 10.1021/acs.jafc.8b02014
Gao, R. L., Lu, F. C., Zhu, Y. M., Hahn, M. G. and Ralph, J. 2016 Flexible Method for Conjugation of Phenolic Lignin Model Compounds to Carrier Proteins Journal of Agricultural and Food Chemistry 10.1021/acs.jafc.6b04273
Lapierre, C., Voxeur, A., Boutet, S. and Ralph, J. 2019 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 10.1021/acs.jafc.9b05840
Lapierre, C., Voxeur, A., Karlen, S. D., Helm, R. F. and Ralph, J. 2018 Evaluation of Feruloylated and p-Coumaroylated Arabinosyl Units in Grass Arabinoxylans by Acidolysis in Dioxane/Methanol Journal of Agricultural and Food Chemistry 10.1021/acs.jafc.8b01618
Cantrell, S. A. and Cantrell, J. H. 2011 Renormalization, resonance bifurcation, and phase contrast in dynamic atomic force microscopy Journal of Applied Physics 10.1063/1.3660745
Brown, S. D., Klingeman, D. M., Lu, T. Y., Johnson, C. M., Utturkar, S. M., Land, M. L., Schadt, C. W., Doktycz, M. J. and Pelletier, D. A. 2012 Draft genome sequence of Rhizobium sp. strain PDO1-076, a bacterium isolated from Populus deltoides Journal of Bacteriology 10.1128/JB.00198-12
Brown, S. D., Utturkar, S. M., Klingeman, D. M., Johnson, C. M., Martin, S. L., Land, M. L., Lu, T. Y., Schadt, C. W., Doktycz, M. J. and Pelletier, D. A. 2012 Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides Journal of Bacteriology 10.1128/JB.01243-12
Christman, H. D., Campbell, E. L. and Meeks, J. C. 2011 Global Transcription Profiles of the Nitrogen Stress Response Resulting in Heterocyst or Hormogonium Development in Nostoc punctiforme Journal of Bacteriology 10.1128/jb.05999-11
Chubiz, L. M. and Marx, C. J. 2017 Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1 Journal of Bacteriology 10.1128/jb.00827-16
Gall, D. L., Ralph, J., Donohue, T. J. and Noguera, D. R. 2013 Benzoyl Coenzyme A Pathway-Mediated Metabolism of meta-Hydroxy-Aromatic Acids in Rhodopseudomonas palustris Journal of Bacteriology 10.1128/jb.00634-13
Good, N. M., Martinez-Gomez, N. C., Beck, D. A. C. and Lidstrom, M. E. 2015 Ethylmalonyl Coenzyme A Mutase Operates as a Metabolic Control Point in Methylobacterium extorquens AM1 Journal of Bacteriology 10.1128/jb.02478-14
Gordon, G. C. and McKinlay, J. B. 2014 Calvin Cycle Mutants of Photoheterotrophic Purple Nonsulfur Bacteria Fail To Grow Due to an Electron Imbalance Rather than Toxic Metabolite Accumulation Journal of Bacteriology 10.1128/jb.01299-13
Hirakawa, H., Oda, Y., Phattarasukol, S., Armour, C. D., Castle, J. C., Raymond, C. K., Lappala, C. R., Schaefer, A. L., Harwood, C. S. and Greenberg, E. P. 2011 Activity of the Rhodopseudomonas palustris p-Coumaroyl-Homoserine Lactone-Responsive Transcription Factor RpaR Journal of Bacteriology 10.1128/jb.01479-10
Hu, B. and Lidstrom, M. 2012 CcrR, a TetR Family Transcriptional Regulator, Activates the Transcription of a Gene of the Ethylmalonyl Coenzyme A Pathway in Methylobacterium extorquens AM1 Journal of Bacteriology 10.1128/jb.00061-12
Kontur, W. S., Schackwitz, W. S., Ivanova, N., Martin, J., LaButti, K., Deshpande, S., Tice, H. N., Pennacchio, C., Sodergren, E., Weinstock, G. M., Noguera, D. R. and Donohue, T. J. 2012 Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome Journal of Bacteriology 10.1128/jb.01214-12
Martinez-Gomez, N. C., Good, N. M. and Lidstrom, M. E. 2015 Methenyl-Dephosphotetrahydromethanopterin Is a Regulatory Signal for Acclimation to Changes in Substrate Availability in Methylobacterium extorquens AM1 Journal of Bacteriology 10.1128/jb.02595-14
Orr, J. S., Christensen, D. G., Wolfe, A. J. and Rao, C. V. 2019 Extracellular Acidic pH Inhibits Acetate Consumption by Decreasing Gene Transcription of the Tricarboxylic Acid Cycle and the Glyoxylate Shunt Journal of Bacteriology 10.1128/jb.00410-18
Reaves, M. L. and Rabinowitz, J. D. 2011 Characteristic Phenotypes Associated with ptsN-Null Mutants in Escherichia coli K-12 Are Absent in Strains with Functional ilvG Journal of Bacteriology 10.1128/jb.00325-11
Schilling, B., Basisty, N., Christensen, D. G., Sorensen, D., Orr, J. S., Wolfe, A. J. and Rao, C. V. 2019 Global Lysine Acetylation in Escherichia coli Results from Growth Conditions That Favor Acetate Fermentation Journal of Bacteriology 10.1128/jb.00768-18
Stein, L. Y., Bringel, F., DiSpirito, A. A., Han, S., Jetten, M. S. M., Kalyuzhnaya, M. G., Kits, K. D., Klotz, M. G., den Camp, Hjmo, Semrau, J. D., Vuilleumier, S., Bruce, D. C., Cheng, J. F., Davenport, K. W., Goodwin, L., Han, S. S., Hauser, L., Lajus, A., Land, M. L., Lapidus, A., Lucas, S., Medigue, C., Pitluck, S. and Woyke, T. 2011 Genome Sequence of the Methanotrophic Alphaproteobacterium Methylocystis sp Strain Rockwell (ATCC 49242) Journal of Bacteriology 10.1128/jb.00278-11
Svenning, M. M., Hestnes, A. G., Wartiainen, I., Stein, L. Y., Klotz, M. G., Kalyuzhnaya, M. G., Spang, A., Bringel, F., Vuilleumier, S., Lajus, A., Medigue, C., Bruce, D. C., Cheng, J. F., Goodwin, L., Ivanova, N., Han, J., Han, C. S., Hauser, L., Held, B., Land, M. L., Lapidus, A., Lucas, S., Nolan, M., Pitluck, S. and Woyke, T. 2011 Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96 Journal of Bacteriology 10.1128/jb.05380-11
Wise, K. S., Calcutt, M. J., Foecking, M. F., Madupu, R., Deboy, R. T., Roske, K., Hvinden, M. L., Martin, T. R., Durkin, A. S., Glass, J. I. and Methe, B. A. 2012 Complete Genome Sequences of Mycoplasma leachii Strain PG50(T) and the Pathogenic Mycoplasma mycoides subsp mycoides Small Colony Biotype Strain Gladysdale Journal of Bacteriology 10.1128/jb.00761-12
Lu, F. C. and Ralph, J. 2011 Solution-State NMR of Lignocellulosic Biomass Journal of Biobased Materials and Bioenergy 10.1166/jbmb.2011.1131
Amos, R.A., Pattathil, S., Yang, J-Y., Atmodjo, M.A., Urbanowicz, B.R., Moremen, K.W., and Mohnen, D. 2018 A two-phase model for the non-processive biosynthesis of homogalacturonan polysaccharides by the GAUT1:GAUT7 complex Journal of Biological Chemistry 10.1074/jbc.RA118.004463
Berim, A. and Gang, D. R. 2013 The Roles of a Flavone-6-Hydroxylase and 7-O-Demethylation in the Flavone Biosynthetic Network of Sweet Basil Journal of Biological Chemistry 10.1074/jbc.M112.420448
Crosby, H. A., Pelletier, D. A., Hurst, G. B. and Escalante-Semerena, J. C. 2012 System-wide studies of N-lysine acetylation in Rhodopseudomonas palustris reveal substrate specificity of protein acetyltransferases Journal of Biological Chemistry 10.1074/jbc.M112.352104
Dajnowicz S, Parks JM, Hu X, Gesler K, Kovalevsky AY, Mueser TC 2017 Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5′-phosphate in aspartate aminotransferase Journal of Biological Chemistry 10.1074/jbc.M116.774588
Goins CM, Dajnowicz S, Smith MD, Parks JM, Ronning DR 2018 Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into Antigen 85 catalysis Journal of Biological Chemistry 10.1074/jbc.RA117.001681
Horn, P. J., Ledbetter, N. R., James, C. N., Hoffman, W. D., Case, C. R., Verbeck, G. F. and Chapman, K. D. 2011 Visualization of Lipid Droplet Composition by Direct Organelle Mass Spectrometry Journal of Biological Chemistry 10.1074/jbc.M110.186353
Johnson, S. R., Bhat, W. W., Bibik, J., Turmo, A., Hamberger, B., Hamberger, B. and Evolutionary Mint, Genomics 2019 A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae) Journal of Biological Chemistry 10.1074/jbc.RA118.006025
Kontur, W. S., Olmsted, C. N., Yusko, L. M., Niles, A. V., Walters, K. A., Beebe, E. T., Vander Meulen, K. A., Karlen, S. D., Gall, D. L., Noguera, D. R. and Donohue, T. J. 2019 A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's (R)-aryl ether bond reveals the diversity of bacterial -etherases Journal of Biological Chemistry 10.1074/jbc.RA118.006548
McKinlay, J. B., Oda, Y., Ruhl, M., Posto, A. L., Sauer, U. and Harwood, C. S. 2014 Non-growing Rhodopseudomonas palustris Increases the Hydrogen Gas Yield from Acetate by Shifting from the Glyoxylate Shunt to the Tricarboxylic Acid Cycle Journal of Biological Chemistry 10.1074/jbc.M113.527515
Pingali SV, O'Neill HM, McGaughey J, Urban VS, Rempe CS, Petridis L, Smith JC, Evans BR, and Heller WT 2011 Small-Angle Neutron Scattering Reveals pH-Dependent Conformational Changes in Trichoderma reesei Cellobiohydrolase I Implications for Enzymatic Activity Journal of Biological Chemistry 10.1074/jbc.M111.263004
Scott, I. M., Rubinstein, G. M., Poole, F. L., Lipscomb, G. L., Schut, G. J., Williams-Rhaesa, A. M., Stevenson, D. M., Amador-Noguez, D., Kelly, R. M. and Adams, M. W. W. 2019 The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis Journal of Biological Chemistry 10.1074/jbc.RA118.007120
Tsednee, Munkhtsetseg, Castruita, Madeli, Salomé, Patrice A., Sharma, Ajay, Lewis, Brianne E., Schmollinger, Stefan R., Strenkert, Daniela, Holbrook, Kristen, Otegui, Marisa S., Khatua, Kaustav, Das, Sayani, Datta, Ankona, Chen, Si, Ramon, Christina, Ralle, Martina, Weber, Peter K., Stemmler, Timothy L., Pett-Ridge, Jennifer, Hoffman, Brian M. and Merchant, Sabeeha S. 2019 Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in Mn-deficient conditions Journal of Biological Chemistry 10.1074/jbc.RA119.009130
Wang HL, Cheng X, and Sine SM 2012 Intramembrane Proton Binding Site Linked to Activation of Bacterial Pentameric Ion Channel Journal of Biological Chemistry 10.1074/jbc.M111.305839
Yurkovich, J. T., Zielinski, D. C., Yang, L., Paglia, G., Rolfsson, O., Sigurjonsson, O. E., Broddrick, J. T., Bordbar, A., Wichuk, K., Brynjolfsson, S., Palsson, S., Gudmundsson, S. and Palsson, B. O. 2017 Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks Journal of Biological Chemistry 10.1074/jbc.M117.804914
Hays, S. G., Yan, L. L. W., Silver, P. A. and Ducat, D. C. 2017 Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction Journal of Biological Engineering 10.1186/s13036-017-0048-5
Karas, B. J., Molparia, B., Jablanovic, J., Hermann, W. J., Lin, Y. C., Dupont, C. L., Tagwerker, C., Yonemoto, I. T., Noskov, V. N., Chuang, R. Y., Allen, A. E., Glass, J. I., Hutchison, C. A., Smith, H. O., Venter, J. C. and Weyman, P. D. 2013 Assembly of eukaryotic algal chromosomes in yeast Journal of Biological Engineering 10.1186/1754-1611-7-30
Rosen, G. L., Polikar, R., Caseiro, D. A., Essinger, S. D. and Sokhansanj, B. A. 2011 Discovering the Unknown: Improving Detection of Novel Species and Genera from Short Reads Journal of Biomedicine and Biotechnology 10.1155/2011/495849
Brothers MC, Nesbitt AE, Hallock MJ, Rupasinghe SG, Tang M, Harris J, Baudry J, Schuler MA, and Rienstra CM 2012 VITAL NMR Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy Journal of Biomolecular NMR 10.1007/s10858-011-9576-3
Chen, S. J., Sinsuebphon, N., Rudkouskaya, A., Barroso, M., Intes, X. and Michalet, X. 2019 In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short-lifetime near-infrared dyes and time-gated imaging Journal of Biophotonics 10.1002/jbio.201800185
Oh, E. J., Wei, N., Kwak, S., Kim, H. and Jin, Y. S. 2019 Overexpression of RCK1 improves acetic acid tolerance in Saccharomyces cerevisiae Journal of Biotechnology 10.1016/j.jbiotec.2018.12.013
Zhang, S., Jagtap, S. S., Deewan, A. and Rao, C. V. 2019 pH selectively regulates citric acid and lipid production in Yarrowia lipolytica W29 during nitrogen-limited growth on glucose Journal of Biotechnology 10.1016/j.jbiotec.2018.10.012
Walker, T. W., Motagamwala, A. H., Dumesic, J. A. and Huber, G. W. 2019 Fundamental catalytic challenges to design improved biomass conversion technologies Journal of Catalysis 10.1016/j.jcat.2018.11.028
Adeyo, O., Horn, P. J., Lee, S. K., Binns, D. D., Chandrahas, A., Chapman, K. D. and Goodman, J. M. 2011 The yeast lipin orthologue Pah1p is important for biogenesis of lipid droplets Journal of Cell Biology 10.1083/jcb.201010111
Chen Q, Buolamwini JK, Smith JC, Li A, Xu Q, Cheng X, and Wei DQ 2013 Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase Journal of Chemical Information and Modeling 10.1021/ci400537n
Kapoor, K., McGill, N., Peterson, C. B., Meyers, H. V., Blackburn, M. N. and Baudry, J. 2016 Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex Journal of Chemical Information and Modeling 10.1021/acs.jcim.5b00596
Riccardi D, Parks JM, Johs A, and Smith JC 2015 HackaMol An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales Journal of Chemical Information and Modeling 10.1021/ci500359e
Sharma, H., Cheng, X. and Buolamwini, J. K. 2012 Homology model-guided 3D-QSAR studies of HIV-1 integrase inhibitors Journal of Chemical Information and Modeling 10.1021/ci200485a
Yao, J., Chu, Y., An, R. and Guo, H. 2012 Understanding product specificity of protein lysine methyltransferases from QM/MM molecular dynamics and free energy simulations: the effects of mutation on SET7/9 beyond the Tyr/Phe switch Journal of Chemical Information and Modeling 10.1021/ci200364m
Yue Y, and Guo H 2014 Quantum Mechanical/Molecular Mechanical Study of Catalytic Mechanism and Role of Key Residues in Methylation Reactions Catalyzed by Dimethylxanthine Methyltransferase in Caffeine Biosynthesis Journal of Chemical Information and Modeling 10.1021/ci400640v
Chaudret R., Parks J.M., and Yang W. 2013 Pseudobond Parameters for QM/MM Studies Involving Nucleosides, Nucleotides, and Their Analogs Journal of Chemical Physics 10.1063/1.4772182
Hu X, Elghobashi-Meinhardt N, Gembris D, and Smith JC 2011 Response of Water to Electric Fields at Temperatures Below the Glass Transition A Molecular Dynamics Analysis Journal of Chemical Physics 10.1063/1.3643077
Klein H, Cheng X, Smith JC, and Shen T 2011 Transfer Matrix Approach to the Hydrogen-Bonding in Cellulose Ia Fibrils Describes the Recalcitrance to Thermal Deconstruction Journal of Chemical Physics 10.1063/1.3626274
Lindner, B., Yi, Z., Prinz, J. H., Smith, J. C. and Noe, F. 2013 Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models Journal of Chemical Physics 10.1063/1.4824070
Lindsay RJ, Siess J, Lohry DP, McGee TS, Ritchie JS, Johnson QR, Shen T 2018 Characterizing protein conformations by correlation analysis of coarse-grained contact matricesPhysical Chemistry Chemical Journal of Chemical Physics 10.1063/1.5004141
Nellas, R. B., Glover, M. M., Hamelberg, D. and Shen, T. 2012 High-pressure effect on the dynamics of solvated peptides Journal of Chemical Physics 10.1063/1.3700183
Noé F, Horenko I, Schütte C, and Smith JC 2007 Hierarchical Analysis of Conformational Dynamics in Biomolecules Transition Networks of Metastable States Journal of Chemical Physics 10.1063/1.2714539
Prinz JH, Chodera J, Pande V, Swope W, Smith JC, and Noe F 2011 Optimal Use of Data in Parallel Tempering Simulations for the Construction of Discrete-State Markov Models of Biomolecular Dynamics Journal of Chemical Physics 10.1063/1.3592153
Wang S, Shen T, and Wolynes P 2011 The Interplay of Nonlinearity and Architecture in Equilibrium Cytoskeletal Mechanics Journal of Chemical Physics 10.1063/1.3518450
Xu, Z., Cheng, X. and Yang, H. 2011 Treecode-based generalized Born method Journal of Chemical Physics 10.1063/1.3552945
Chu Y, Xu Q, and Guo H 2010 Understanding Energetic Origins of Product Specificity of SET8 from QM/MM Free Energy Simulations What Causes the Stop of Methyl Addition during Histone Lysine Methylation Journal of Chemical Theory and Computation 10.1021/ct9006458
Glass D, Krishnan M, Nutt D, and Smith JC 2010 Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models Journal of Chemical Theory and Computation 10.1021/ct9006508
Imhof, P., Noe, F., Fischer, S. and Smith, J. C. 2006 AM1/d Parameters for Magnesium in Metalloenzymes Journal of Chemical Theory and Computation 10.1021/ct600092c
Johnson Q, Doshi U, Shen T, and Hamelberg D 2010 Water’s Contribution to the Energetic Roughness from Peptide Dynamics Journal of Chemical Theory and Computation 10.1021/ct100183s
Noé F, Krachtus D, Smith JC, and Fischer S 2006 Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins Journal of Chemical Theory and Computation 10.1021/ct050162r
Nutt DR, and Smith JC 2007 Molecular Dynamics Simulations of Proteins Can the Explicit Water Model Be Varied Journal of Chemical Theory and Computation 10.1021/ct700053u
Pavlova, A., Parks, J. M. and Gumbart, J. C. 2018 Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations Journal of Chemical Theory and Computation 10.1021/acs.jctc.7b01236
Riccardi D, Guo HB, Parks JM, Gu B, Liang L, and Smith JC 2013 Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations Journal of Chemical Theory and Computation 10.1021/ct300296k
Schulz, R., Lindner, B., Petridis, L. and Smith, J. C. 2009 Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer Journal of Chemical Theory and Computation 10.1021/ct900292r
Srinivas, G., Cheng, X. and Smith, J. C. 2011 A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils Journal of Chemical Theory and Computation 10.1021/ct200181t
Ulmschneider JP, Smith JC, Killian A, and Ulmschneider MB 2009 Peptide Partitioning and Folding into Lipid Bilayers Journal of Chemical Theory and Computation 10.1021/ct900256k
Cocuron, J. C., Casas, M. I., Yang, F., Grotewold, E. and Alonso, A. P. 2019 Beyond the wall: High-throughput quantification of plant soluble and cell-wall bound phenolics by liquid chromatography tandem mass spectrometry Journal of Chromatography A 10.1016/j.chroma.2018.12.059
Cocuron, J. C., Tsogtbaatar, E. and Alonso, A. P. 2017 High-throughput quantification of the levels and labeling abundance of free amino acids by liquid chromatography tandem mass spectrometry Journal of Chromatography A 10.1016/j.chroma.2017.02.028
Yang, S., Hoggard, J. C., Lidstrom, M. E. and Synovec, R. E. 2013 Comprehensive discovery of C-13 labeled metabolites in the bacterium Methylobacterium extorquens AM1 using gas chromatography-mass spectrometry Journal of Chromatography A 10.1016/j.chroma.2013.08.059
Yang, S., Nadeau, J. S., Humston-Fulmer, E. M., Hoggard, J. C., Lidstrom, M. E. and Synovec, R. E. 2012 Gas chromatography-mass spectrometry with chemometric analysis for determining C-12 and C-13 labeled contributions in metabolomics and C-13 flux analysis Journal of Chromatography A 10.1016/j.chroma.2012.03.072
Xiao Z, Baudry J, Cao L, Huang J, Chen H, Yates CR, Li W, Dong B, Waters CM, Smith JC, Quarles LD 2018 Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis Journal of Clinical Investigation 10.1172/JCI93725
Berezniak T, Jaeschke A, Smith JC, and Imhof P 2012 Stereoselection in the Diels-Alderase Ribozyme A Molecular Dynamics Study Journal of Computational Chemistry 10.1002/jcc.22993
Collignon B, Schulz R, Smith JC, and Baudry J 2011 Task-Parallel MPI Implementation of Autodock4 for Docking of Very Large Databases of Compounds Using High Performance Super-Computers Journal of Computational Chemistry 10.1002/jcc.21696
Ellingson, S. R., Smith, J. C. and Baudry, J. 2013 VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers Journal of Computational Chemistry 10.1002/jcc.23367
Jenkins, D. D., Harris, J. B., Howell, E. E., Hinde, R. J. and Baudry, J. 2013 STAAR: statistical analysis of aromatic rings Journal of Computational Chemistry 10.1002/jcc.23164
Johnson QR, Lindsay RJ, Shen T 2018 CAMERRA An Analysis Tool for the Computation of Allosteric Mechanism by Evaluating Residue-Residue Associations Journal of Computational Chemistry 10.1002/jcc.25192
Lv, C., Aitchison, E. W., Wu, D., Zheng, L., Cheng, X. and Yang, W. 2016 Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling Journal of Computational Chemistry 10.1002/jcc.23982
Petridis, L. and Smith, J. C. 2009 A molecular mechanics force field for lignin Journal of Computational Chemistry 10.1002/jcc.21075
Pool R, Heringa J, Hoefling M, Schulz R, and Smith JC 2012 Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of GROMACS through the GromPy Python Interface Module to the GROMACS Simulation C-library Journal of Computational Chemistry 10.1002/jcc.22947
Voltz, K., Trylska, J., Tozzini, V., Kurkal-Siebert, V., Langowski, J. and Smith, J. 2008 Coarse-grained force field for the nucleosome from self-consistent multiscaling Journal of Computational Chemistry 10.1002/jcc.20902
Jung, H. and Meile, C. 2019 Upscaling of microbially driven first-order reactions in heterogeneous porous media Journal of Contaminant Hydrology 10.1016/j.jconhyd.2019.04.006
Peay, K. G. 2018 Timing of mutualist arrival has a greater effect on Pinus muricata seedling growth than interspecific competition Journal of Ecology 10.1111/1365-2745.12915
Hussain, M. Z., Bhardwaj, A. K., Basso, B., Robertson, G. P. and Hamilton, S. K. 2019 Nitrate Leaching from Continuous Corn, Perennial Grasses, and Poplar in the US Midwest Journal of Environmental Quality 10.2134/jeq2019.04.0156
Yang, X., Liu, D., Tschaplinski, T.J., and Tuskan, G.A. 2019 Comparative genomics can provide new insights into the evolutionary mechanisms and genefunction in CAM plants Journal of Experimental Biology 10.1093/jxb/erz408
Braun, D. M., Wang, L. and Ruan, Y. L. 2014 Understanding and manipulating sucrose phloem loading, unloading, metabolism, and signalling to enhance crop yield and food security Journal of Experimental Botany 10.1093/jxb/ert416
Cushman, J. C., Davis, S. C., Yang, X. H. and Borland, A. M. 2015 Development and use of bioenergy feedstocks for semi-arid and arid lands Journal of Experimental Botany 10.1093/jxb/erv087
DePaoli, H. C., Borland, A. M., Tuskan, G. A., Cushman, J. C. and Yang, X. H. 2014 Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities Journal of Experimental Botany 10.1093/jxb/eru038
Jansson, C., Vogel, J., Hazen, S., Brutnell, T. and Mockler, T. 2018 Climate-smart crops with enhanced photosynthesis Journal of Experimental Botany 10.1093/jxb/ery213
Lara-Chavez, A., Lowman, S., Kim, S., Tang, Y. H., Zhang, J. Y., Udvardi, M., Nowak, J., Flinn, B. and Mei, C. S. 2015 Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN Journal of Experimental Botany 10.1093/jxb/erv096
Liu, D., Chen, M., Mendoza, B., Cheng, H., Hu, R., Li, L., Trinh, C. T., Tuskan, G. A. and Yang, X. 2019 CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants Journal of Experimental Botany 10.1093/jxb/erz415
Swamy, P. S., Hu, H., Pattathil, S., Maloney, V. J., Xiao, H., Xue, L. J., Chung, J. D., Johnson, V. E., Zhu, Y. Y., Peter, G. F., Hahn, M. G., Mansfield, S. D., Harding, S. A. and Tsai, C. J. 2015 Tubulin perturbation leads to unexpected cell wall modifications and affects stomatal behaviour in Populus Journal of Experimental Botany 10.1093/jxb/erv383
Yerramsetty, P., Agar, E. M., Yim, W. C., Cushman, J. C. and Berry, J. O. 2017 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 10.1093/jxb/erx264
Zambrano, V. A. B., Lawson, T., Olmos, E., Fernandez-Garcia, N. and Borland, A. M. 2014 Leaf anatomical traits which accommodate the facultative engagement of crassulacean acid metabolism in tropical trees of the genus Clusia Journal of Experimental Botany 10.1093/jxb/eru022
Burke, S. A., Wik, M., Lang, A., Contosta, A. R., Palace, M., Crill, M. and Varner, R. K. 2019 Long-Term Measurements of Methane Ebullition From Thaw Ponds Journal of Geophysical Research-Biogeosciences 10.1029/2018jg004786
Deng, J., Li, C. S. and Frolking, S. 2015 Modeling impacts of changes in temperature and water table on C gas fluxes in an Alaskan peatland Journal of Geophysical Research-Biogeosciences 10.1002/2014jg002880
Stackhouse, B. T., Vishnivetskaya, T. A., Layton, A., Chauhan, A., Pfiffner, S., Mykytczuk, N. C., Sanders, R., Whyte, L. G., Hedin, L., Saad, N., Myneni, S. and Onstott, T. C. 2015 Effects of simulated spring thaw of permafrost from mineral cryosol on CO2 emissions and atmospheric CH4 uptake Journal of Geophysical Research-Biogeosciences 10.1002/2015jg003004
Wik, M., Johnson, J. E., Crill, P. M., DeStasio, J. P., Erickson, L., Halloran, M. J., Fahnestock, M. F., Crawford, M. K., Phillips, S. C. and Varner, R. K. 2018 Sediment Characteristics and Methane Ebullition in Three Subarctic Lakes Journal of Geophysical Research-Biogeosciences 10.1029/2017jg004298
Wilson, R. M., Fitzhugh, L., Whiting, G. J., Frolking, S., Harrison, M. D., Dimova, N., Burnett, W. C. and Chanton, J. P. 2017 Greenhouse gas balance over thaw-freeze cycles in discontinuous zone permafrost Journal of Geophysical Research-Biogeosciences 10.1002/2016jg003600
Guan Y, Ranoa DRE, Jiang S, Mutha S, Li X, Baudry J, and Tapping RI 2010 Human TLRs 10 and 1 Share Common Mechanisms of Innate Immune Sensing but Not Signaling Journal of Immunology 10.4049/jimmunol.0901888
Groom, J., Chung, C., Kim, S-K., Guss, A., and Westpheling, J. 2018 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 & Biotechnology 10.1007/s10295-018-2049-x
Kim, S. K., Chung, D., Himmel, M. E., Bomble, Y. J. and Westpheling, J. 2019 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 10.1007/s10295-019-02150-0
Li, Z. J., Qiao, K. J., Liu, N. and Stephanopoulos, G. 2017 Engineering Yarrowia lipolytica for poly-3-hydroxybutyrate production Journal of Industrial Microbiology & Biotechnology 10.1007/s10295-016-1864-1
Papanek, B., O'Dell, K. B., Manga, P., Giannone, R. J., Klingeman, D. M., Hettich, R. L., Brown, S. D. and Guss, A. M. 2018 Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains Journal of Industrial Microbiology & Biotechnology 10.1007/s10295-018-2073-x
Riley, L. A., Ji, L., Schmitz, R. J., Westpheling, J. and Guss, A. M. 2019 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 10.1007/s10295-019-02218-x
Shi, S. B., Ang, E. L. and Zhao, H. M. 2018 In vivo biosensors: mechanisms, development, and applications Journal of Industrial Microbiology & Biotechnology 10.1007/s10295-018-2004-x
Guo, J., Yang, X., Weston, D. J. and Chen, J. G. 2011 Abscisic acid receptors: past, present and future Journal of Integrative Plant Biology 10.1111/j.1744-7909.2011.01044.x
Poire, R., Chochois, V., Sirault, X. R. R., Vogel, J. P., Watt, M. and Furbank, R. T. 2014 Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon Journal of Integrative Plant Biology 10.1111/jipb.12198
Chapman, K. D., Dyer, J. M. and Mullen, R. T. 2012 Biogenesis and functions of lipid droplets in plants Journal of Lipid Research 10.1194/jlr.R021436
Tsui, H. S., Pham, N. V. B., Amer, B. R., Bradley, M. C., Gosschalk, J. E., Gallagher-Jones, M., Ibarra, H., Clubb, R. T., Blaby-Haas, C. E. and Clarke, C. F. 2019 Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function Journal of Lipid Research 10.1194/jlr.M093534
Rasmussen, M., Hastings, A., Smith, M. J., Agusto, F. B., Chen-Charpentier, B. M., Hoffman, F. M., Jiang, J., Todd-Brown, K. E. O., Wang, Y., Wang, Y. P. and Luo, Y. Q. 2016 Transit times and mean ages for nonautonomous and autonomous compartmental systems Journal of Mathematical Biology 10.1007/s00285-016-0990-8
Haynes KM, Abdali N, Jhawar V, Zgurskaya HI, Parks JM, Green AT, Baudry J, Rybenkov VV, Smith JC, Walker JK 2017 Identification and Structure–Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli Journal of Medicinal Chemistry 10.1021/acs.jmedchem.7b00453
Bondar AN, Fischer S, and Smith JC 2011 Water Pathways in the Bacteriorhodopsin Proton Pump Journal of Membrane Biology 10.1007/s00232-010-9329-3
Cournia Z, Allen T, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman T, Delemotte L, Del Val C, Freidman R, Gkeka P, Hege HC, Henin J, Kasimova M, Kolocouris A, Klein ML, Khalid S, Lemieu J, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, and Bondar AN 2015 Membrane Proteins Environmental Effects on Structure, Function and Dynamics Journal of Membrane Biology 10.1007/s00232-015-9802-0
Elghobashi-Meinhardt N, Phatak P, Bondar A, Elstner M, Smith JC 2018 Catalysis of Ground State cis→trans Isomerization of Bacteriorhodopsin’s Retinal Chromophore by a Hydrogen-Bond Network Journal of Membrane Biology 10.1007/s00232-018-0027-x
Nelson, C. E., Beri, N. R. and Gardner, J. G. 2016 Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates Journal of Microbiological Methods 10.1016/j.mimet.2016.09.013
La Reau, A. J. and Suen, G. 2018 The Ruminococci: key symbionts of the gut ecosystem Journal of Microbiology 10.1007/s12275-018-8024-4
Glasgow, E. M., Vander Meulen, K. A., Takasuka, T. E., Bianchetti, C. M., Bergeman, L. F., Deutsch, S. and Fox, B. G. 2019 Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases Journal of Molecular Biology 10.1016/j.jmb.2019.01.024
Guo HB, Johs A, Parks JM, Oliff L, Miller SM, Summers AO, Liang L, and Smith JC 2010 Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg II Journal of Molecular Biology 10.1016/j.jmb.2010.03.020
Johs A, Harwood IM, Parks JM, Nauss RE, Smith JC, Liang L, and Miller SM 2011 Structural Characterization of Intramolecular Hg2+ Transfer between Flexibly Linked Domains of Mercuric Ion Reductase Journal of Molecular Biology 10.1016/j.jmb.2011.08.042
Koppole S, Smith JC, and Fischer S 2006 Simulations of the Myosin II Motor Reveal a Nucleotide-State Sensing Element that Controls the Recovery Stroke Journal of Molecular Biology 10.1016/j.jmb.2006.06.022
Lajoie, M. J., Soll, D. and Church, G. M. 2016 Overcoming Challenges in Engineering the Genetic Code Journal of Molecular Biology 10.1016/j.jmb.2015.09.003
Mesentean, S., Koppole, S., Smith, J. C. and Fischer, S. 2007 The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor Journal of Molecular Biology 10.1016/j.jmb.2006.12.058
Tuukkanen, A. T., Freire, D., Chan, S., Arbing, M. A., Reed, R. W., Evans, T. J., Zenkeviciute, G., Kim, J., Kahng, S., Sawaya, M. R., Chaton, C. T., Wilmanns, M., Eisenberg, D., Parret, A. H. A. and Korotkov, K. V. 2019 Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems Journal of Molecular Biology 10.1016/j.jmb.2018.11.003
Zahran M, Daidone I, Smith JC, and Imhof P 2010 Mechanism of DNA Recognition by the Restriction Enzyme EcoRV Journal of Molecular Biology 10.1016/j.jmb.2010.06.026
Montague, M., Barnes, C., Smith, H. O., Chuang, R. Y. and Vashee, S. 2009 The Evolution of RecD Outside of the RecBCD Complex Journal of Molecular Evolution 10.1007/s00239-009-9290-x
Chen, Q., Luan, Z. J., Yu, H. L., Cheng, X. and Xu, J. H. 2015 Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding Journal of Molecular Graphics and Modeling 10.1016/j.jmgm.2015.10.015
Cashman DJ, Zhu T, Simmerman RF, Scott C, Bruce BD, and Baudry J 2014 Molecular Interactions between Photosystem I and Ferredoxin: An Integrated Energy Frustration and Experimental Model Journal of Molecular Recognition 10.1002/jmr.2384
Noé F, Oswald M, Reinelt G, Fischer S, and Smith JC 2006 Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the αL β αR Transitions in Octaalanine Journal of Multiscale Modelling and Simulation 10.1137/050641922
Sarafian, T. A., Yacoub, A., Kunz, A., Aranki, B., Serobyan, G., Cohn, W., Whitelegge, J. P. and Watson, J. B. 2019 Enhanced mitochondrial inhibition by 3,4-dihydroxyphenyl-acetaldehyde (DOPAL)-oligomerized alpha-synuclein Journal of Neuroscience Research 10.1002/jnr.24513
Kurkal-Siebert V, Daniel R, Finney JL, Tehei M, Dunn RV, and Smith JC 2006 Enzyme Hydration, Activity and Flexibility A Neutron Scattering Approach Journal of Noncrystalline Solids 10.1016/j.jnoncrysol.2006.01.115
Young, M. Todd, Hinkle, Jacob, Kannan, Ramakrishnan and Ramanathan, Arvind 2020 Distributed Bayesian optimization of deep reinforcement learning algorithms Journal of Parallel and Distributed Computing 10.1016/j.jpdc.2019.07.008
Wilken, S., Choi, C. J. and Worden, A. Z. 2019 Contrasting Mixotrophic Lifestyles Reveal Different Ecological Niches in Two Closely Related Marine Protists Journal of Phycology 10.1111/jpy.12920
Guo, H. B., He, F., Gu, B., Liang, L. and Smith, J. C. 2012 Time-dependent density functional theory assessment of UV absorption of benzoic acid derivatives Journal of Physical Chemistry A 10.1021/jp3084293
Lian P, Johnston RC, Parks JM, Smith JC 2018 Quantum Chemical Calculation of pKas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines and Thiols in Aqueous Solution Journal of Physical Chemistry A 10.1021/acs.jpca.8b01751
Mintz, B. J. and Parks, J. M. 2012 Benchmark interaction energies for biologically relevant noncovalent complexes containing divalent sulfur Journal of Physical Chemistry A 10.1021/jp209536e
Arbelo-Lopez HD, Simakov NA, Smith JC, Lopez-Garriga J, and Wymore T 2016 Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme Journal of Physical Chemistry B 10.1021/acs.jpcb.6b02839
Balog E, Perahia D, Smith JC, and Merzel F 2011 Vibrational Softening of a Protein on Ligand Binding Journal of Physical Chemistry B 10.1021/jp108493g
Bondar AN, Baudry J, Suhai S, Fischer S, and Smith JC 2008 Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions Journal of Physical Chemistry B 10.1021/jp801916f
Clark, A. K., Wilder, J. H., Grayson, A. W., Johnson, Q. R., Lindsay, R. J., Nellas, R. B., Fernandez, E. J. and Shen, T. 2016 The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor Journal of Physical Chemistry B 10.1021/acs.jpcb.6b02057
Cournia, Z., Ullmann, G. M. and Smith, J. C. 2007 Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study Journal of Physical Chemistry B 10.1021/jp065172i
Daidone, I., Thukral, L., Smith, J. C. and Amadei, A. 2015 Monitoring the folding kinetics of a beta-hairpin by time-resolved IR spectroscopy in silico Journal of Physical Chemistry B 10.1021/acs.jpcb.5b01477
Devarajan, A., Markutsya, S., Lamm, M. H., Cheng, X., Smith, J. C., Baluyut, J. Y., Kholod, Y., Gordon, M. S. and Windus, T. L. 2013 Ab initio study of molecular interactions in cellulose Ialpha Journal of Physical Chemistry B 10.1021/jp406266u
Ellingson, S. R., Miao, Y., Baudry, J. and Smith, J. C. 2015 Multi-conformer ensemble docking to difficult protein targets Journal of Physical Chemistry B 10.1021/jp506511p
Glass DC, Krishnan M, Smith JC, and Baudry J 2013 Three Entropic Classes of Side Chains in a Globular Protein Journal of Physical Chemistry B 10.1021/jp400564q
Harris, B. J., Cheng, X. and Frymier, P. 2014 All-atom molecular dynamics simulation of a photosystem i/detergent complex Journal of Physical Chemistry B 10.1021/jp507157e
Harris BJ, Cheng X, and Frymier P 2016 Structure and Function of Photosystem I–[FeFe] Hydrogenase Protein Fusions An All-Atom Molecular Dynamics Study Journal of Physical Chemistry B 10.1021/acs.jpcb.5b07812
Hembree W, and Baudry J 2011 Three-dimensional Mapping of Micro-environmental Control of Methyl Rotational Barriers Journal of Physical Chemistry B 10.1021/jp201887v
Jing X, Falcon WE, Baudry J, Serpersu EH 2017 Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability Can We Draw a Line Journal of Physical Chemistry B 10.1021/acs.jpcb.7b04519
Johnson, Q. R., Lindsay, R. J., Raval, S. R., Dobbs, J. S., Nellas, R. B. and Shen, T. 2014 Effects of branched O-glycosylation on a semiflexible peptide linker Journal of Physical Chemistry B 10.1021/jp410788r
Johnston RC, Zhou J, Smith JC, and Parks JM 2016 Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin Journal of Physical Chemistry B 10.1021/acs.jpcb.6b02701
Krishnan, M. and Smith, J. C. 2012 Reconstruction of protein side-chain conformational free energy surfaces from NMR-derived methyl axis order parameters Journal of Physical Chemistry B 10.1021/jp2104853
Krishnan M, Kurkal-Siebert V, and Smith JC 2008 Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin Journal of Physical Chemistry B 10.1021/jp076641z
Moritsugu, K., Njunda, B. M. and Smith, J. C. 2010 Theory and normal-mode analysis of change in protein vibrational dynamics on ligand binding Journal of Physical Chemistry B 10.1021/jp909677p
Moritsugu, K. and Smith, J. C. 2006 Temperature-dependent protein dynamics: a simulation-based probabilistic diffusion-vibration Langevin description Journal of Physical Chemistry B 10.1021/jp055314t
Moritsugu K, Kidera A, and Smith JC 2014 Solvent Friction Effects Propagate over the Entire Protein Molecule through Low-Frequency Collective Modes Journal of Physical Chemistry B 10.1021/jp503956m
Mostofian B, Cheng X, and Smith JC 2014 Replica-Exchange Molecular Dynamics Simulations of Cellulose Solvated in Water and in the Ionic Liquid 1-Butyl-3-Methylimidazolium Chloride Journal of Physical Chemistry B 10.1021/jp502889c
Noé F, Daidone I, Smith JC, di Nola A, and Amadei A 2008 Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation Journal of Physical Chemistry B 10.1021/jp801391t
Pan J, Cheng X, Heberle FA, Mostofian B, Kucerka N, Drazba P, and Katsaras J 2012 Interactions between Ether Phospholipids and Cholesterol As Determined by Scattering and Molecular Dynamics Simulations Journal of Physical Chemistry B 10.1021/jp310345j
Polimeni M, Petridis L, Smith JC, Arcangeli C 2017 Dynamics at a Peptide–TiO2 Anatase 101 Interface Journal of Physical Chemistry B 10.1021/acs.jpcb.7b04707
Sangha, A. K., Petridis, L., Cheng, X. and Smith, J. C. 2016 Relative Binding Affinities of Monolignols to Horseradish Peroxidase Journal of Physical Chemistry B 10.1021/acs.jpcb.6b00789
Sangha AK, Davison BH, Standaert RF, Davis MF, Smith JC, and Parks JM 2014 Chemical Factors that Control Lignin Polymerization Journal of Physical Chemistry B 10.1021/jp411998t
Sangha AK, Parks JM, Standaert RF, Ziebell A, Davis M, and Smith JC 2012 Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study Journal of Physical Chemistry B 10.1021/jp2122449
Shen, T., Qi, X. and Nellas, R. B. 2013 Nucleation dynamics of active particles Journal of Physical Chemistry B 10.1021/jp402024s
Simakov, N., Leonard, D. A., Smith, J. C., Wymore, T. and Szarecka, A. 2017 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 10.1021/acs.jpcb.6b07884
Smith, M. D., Mostofian, B., Petridis, L., Cheng, X. and Smith, J. C. 2016 Molecular Driving Forces behind the Tetrahydrofuran-Water Miscibility Gap Journal of Physical Chemistry B 10.1021/acs.jpcb.5b09770
Srinivas, G., Cheng, X. and Smith, J. C. 2014 Coarse-grain model for natural cellulose fibrils in explicit water Journal of Physical Chemistry B 10.1021/jp407953p
Wolter T, Elstner M, Fischer S, Smith JC, and Bondar AN 2015 Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States Journal of Physical Chemistry B 10.1021/jp505818r
Wymore T, Field MJ, Langan P, Smith JC, and Parks JM 2014 Hydrolysis of DFP and the Nerve Agent S -Sarin by DFPase Proceeds along Two Different Reaction Pathways Implications for Engineering Bioscavengers Journal of Physical Chemistry B 10.1021/jp410422c
Xu, Q., Li, L. and Guo, H. 2010 Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations Journal of Physical Chemistry B 10.1021/jp102785s
Xu Q, Guo HB, Gorin A, and Guo H 2007 Stabilization of a Transition-State Analogue at the Active Site of Yeast Cytosine Deaminase Importance of Proton Transfers Journal of Physical Chemistry B 10.1021/jp0670743
Xu Q, Yao J, Wlodawer A, and Guo H 2011 Clarification of the Mechanism of Acylation Reaction and Origin of Substrate Specificity of the Serine-Carboxyl Peptidase Sedolisin through QM/MM Free Energy Simulations Journal of Physical Chemistry B 10.1021/jp1122294
Yao J, Xu Q, Chen F, and Guo H 2011 QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity Journal of Physical Chemistry B 10.1021/jp1086812
Yi Z, Miao Y, Baudry J, Jain N, and Smith JC 2012 Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering Journal of Physical Chemistry B 10.1021/jp2102868
Nickels, J. D., Chatterjee, S., Mostofian, B., Stanley, C. B., Ohl, M., Zolnierczuk, P., Schulz, R., Myles, D. A. A., Standaert, R. F., Elkins, J. G., Cheng, X. and Katsaras, J. 2017 Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane Journal of Physical Chemistry Letters 10.1021/acs.jpclett.7b01877
Riccardi D, Guo HB, Parks JM, Gu B, Summers AO, Miller SM, Liang L, and Smith JC 2013 Why Mercury Prefers Soft Ligands Journal of Physical Chemistry Letters 10.1021/jz401075b
Petridis L, and Smith JC 2008 Cellulosic Ethanol Progress towards a Simulation Model of Lignocellulosic Biomass Journal of Physics Conference Series 10.1088/1742-6596/125/1/012055
Cortini R, Cheng X, Smith JC, and Kornyshev AA 2017 The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations Journal of Physics: Condensed Matter 10.1088/1361-648X/aa4e68
Jeong, D. H. and Green, P. J. 2013 The role of rice microRNAs in abiotic stress responses Journal of Plant Biology 10.1007/s12374-013-0213-4
Denis, Elizabeth H., Ilhardt, Peter D., Tucker, Abigail E., Huggett, Nicholas L., Rosnow, Joshua J. and Moran, James J. 2019 Spatially tracking carbon through the root-rhizosphere-soil system using laser ablation-IRMS Journal of Plant Nutrition and Soil Science 10.1002/jpln.201800301
Sandhu, H. S., Comstock, J. C., Gilbert, R. A., Gordon, V. S., Korndorfer, P., El-Hout, N. and Arundale, R. A. 2015 Registration of 'UFCP 78-1013' Sugarcane Cultivar Journal of Plant Registrations 10.3198/jpr2014.08.0050crc
Estenson, K., Hurst, G. B., Standaert, R. F., Bible, A. N., Garcia, D., Chourey, K., Doktycz, M. J. and Morrell-Falvey, J. L. 2018 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 10.1021/acs.jproteome.7b00708
Li, Z., Adams, R. M., Chourey, K., Hurst, G. B., Hettich, R. L. and Pan, C. 2012 Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos Journal of Proteome Research 10.1021/pr200748h
Li, Z., Czarnecki, O., Chourey, K., Yang, J., Tuskan, G. A., Hurst, G. B., Pan, C. and Chen, J. G. 2014 Strigolactone-regulated proteins revealed by iTRAQ-based quantitative proteomics in Arabidopsis Journal of Proteome Research 10.1021/pr400925t
McClintock C, Parks J, Bern M, GhattyVenkataKrishna P, and Hettich R 2013 Comparative Informatics Analysis to Evaluate Site-Specific Protein Oxidation in Multidimensional LC–MS/MS Data Journal of Proteome Research 10.1021/pr400141p
Van, P. T., Schmid, A. K., King, N. L., Kaur, A., Pan, M., Whitehead, K., Koide, T., Facciotti, M. T., Goo, Y. A., Deutsch, E. W., Reiss, D. J., Mallick, P. and Baliga, N. S. 2008 Halobacterium salinarum NRC-1 PeptideAtlas: Toward strategies for targeted proteomics and improved proteome coverage Journal of Proteome Research 10.1021/pr800031f
Vincent, D., Kohler, A., Claverol, S., Solier, E., Joets, J., Gibon, J., Lebrun, M. H., Plomion, C. and Martin, F. 2012 Secretome of the free-living mycelium from the ectomycorrhizal basidiomycete Laccaria bicolor Journal of Proteome Research 10.1021/pr200895f
Nichols, J. E., Peteet, D. M., Frolking, S. and Karavias, J. 2017 A probabilistic method of assessing carbon accumulation rate at Imnavait Creek Peatland, Arctic Long Term Ecological Research Station, Alaska Journal of Quaternary Science 10.1002/jqs.2952
Nie, B., He, C. L. and Liu, L. J. 2013 Surface-enhanced Raman scattering within silver-nanoparticle-decorated nanometric apertures Journal of Raman Spectroscopy 10.1002/jrs.4380
Yang, S., Synovec, R. E., Kalyuzhnaya, M. G. and Lidstrom, M. E. 2011 Development of a solid phase extraction protocol coupled with liquid chromatography mass spectrometry to analyze central carbon metabolites in lake sediment microcosms Journal of Separation Science 10.1002/jssc.201100533
Bondar AN, Suhai S, Fischer S, Smith JC, and Elstner M 2007 Suppression of the Back Proton-Transfer from Asp85 to the Retinal Schiff Base in Bacteriorhodopsin: A Theoretical Analysis of Structural Elements Journal of Structural Biology 10.1016/j.jsb.2006.10.007
Rasyidah Mohamad Razar, Ali Missaoui 2018 Phenotyping Winter Dormancy in Switchgrass to Extend the Growing Season and Improve Biomass Yield Journal of Sustainable Bioenergy Systems 10.4236/jsbs.2018.81001
Baudry, Jerome 2006 van der Waals Interactions and Decrease of the Rotational Barrier of Methyl-Sized Rotators:  A Theoretical Study Journal of the American Chemical Society 10.1021/ja060731k
Berezniak T, Zahran M, Imhof P, Jaeschke A, and Smith JC 2010 Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme Journal of the American Chemical Society 10.1021/ja101370e
Fu, D., Yang, W. L. and Xie, X. L. S. 2017 Label-free Imaging of Neurotransmitter Acetylcholine at Neuromuscular Junctions with Stimulated Raman Scattering Journal of the American Chemical Society 10.1021/jacs.6b10727
Krishnan M, and Smith JC 2009 Response of Small-Scale, Methyl Rotors to Protein-Ligand Association A Simulation Analysis of Calmodulin-Peptide Binding Journal of the American Chemical Society 10.1021/ja901276n
Kurkal-Siebert V, and Smith JC 2006 Low-Temperature Protein Physics A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K Journal of the American Chemical Society 10.1021/ja055962q
Miao, Y., Yi, Z., Glass, D. C., Hong, L., Tyagi, M., Baudry, J., Jain, N. and Smith, J. C. 2012 Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein Journal of the American Chemical Society 10.1021/ja3097898
Mostofian, B., Cai, C. M., Smith, M. D., Petridis, L., Cheng, X., Wyman, C. E. and Smith, J. C. 2016 Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications Journal of the American Chemical Society 10.1021/jacs.6b03285
Nickels, J. D., Cheng, X., Mostofian, B., Stanley, C., Lindner, B., Heberle, F. A., Perticaroli, S., Feygenson, M., Egami, T., Standaert, R. F., Smith, J. C., Myles, D. A., Ohl, M. and Katsaras, J. 2015 Mechanical Properties of Nanoscopic Lipid Domains Journal of the American Chemical Society 10.1021/jacs.5b08894
Nutt, D. R. and Smith, J. C. 2008 Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations Journal of the American Chemical Society 10.1021/ja8034027
Parks, J. M., Guo, H., Momany, C., Liang, L., Miller, S. M., Summers, A. O. and Smith, J. C. 2009 Mechanism of Hg-C protonolysis in the organomercurial lyase MerB Journal of the American Chemical Society 10.1021/ja9016123
Patri, A. S., Mostofian, B., Pu, Y. Q., Ciaffone, N., Soliman, M., Smith, M. D., Kumar, R., Cheng, X. L., Wyrnan, C. E., Tetard, L., Ragauskas, A. J., Smith, J. C., Petridis, L. and Cai, C. M. 2019 A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction Journal of the American Chemical Society 10.1021/jacs.8b10242
Perticaroli S, Ehlers G, Stanley C, Mamontov E, O'Neill H, Zhang Q, Cheng X, Myles DA, Katsaras J, Nickels JD 2016 Description of Hydration Water in Protein GFP Solution Journal of the American Chemical Society 10.1021/jacs.6b08845
Petridis, L., Schulz, R. and Smith, J. C. 2011 Simulation analysis of the temperature dependence of lignin structure and dynamics Journal of the American Chemical Society 10.1021/ja206839u
Phatak, P., Frahmcke, J. S., Wanko, M., Hoffmann, M., Strodel, P., Smith, J. C., Suhai, S., Bondar, A. N. and Elstner, M. 2009 Long-distance proton transfer with a break in the bacteriorhodopsin active site Journal of the American Chemical Society 10.1021/ja809767v
Rafiee, M., Alherech, M., Karlen, S. D. and Stahl, S. S. 2019 Electrochemical Aminoxyl-Mediated Oxidation of Primary Alcohols in Lignin to Carboxylic Acids: Polymer Modification and Depolymerization Journal of the American Chemical Society 10.1021/jacs.9b07243
Rajeshwar T R, Smith JC, and Krishnan M 2014 Hidden Regularity and Universal Classification of Fast Side Chain Motions in Proteins Journal of the American Chemical Society 10.1021/ja5024783
Shen, T., Langan, P., French, A. D., Johnson, G. P. and Gnanakaran, S. 2009 Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence Journal of the American Chemical Society 10.1021/ja9034158
Spies A, Reese JG, Dodd D, Pankow KL, Blanke SR, and Baudry J 2009 Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase Journal of the American Chemical Society 10.1021/ja809660g
Thukral, L., Smith, J. C. and Daidone, I. 2009 Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations Journal of the American Chemical Society 10.1021/ja9064365
Ulmschneider, J. P., Smith, J. C., White, S. H. and Ulmschneider, M. B. 2011 In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions Journal of the American Chemical Society 10.1021/ja204042f
Ulmschneider MB, Doux JPF, Killian JA, Smith JC, and Ulmschneider JP 2010 Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides Journal of the American Chemical Society 10.1021/ja5024783
Welsher, K., McManus, S. A., Hsia, C. H., Yin, S. H. and Yang, H. 2015 Discovery of Protein- and DNA-Imperceptible Nanoparticle Hard Coating Using Gel-Based Reaction Tuning Journal of the American Chemical Society 10.1021/ja511297d
Xu, Q., Guo, H., Wlodawer, A. and Guo, H. 2006 The importance of dynamics in substrate-assisted catalysis and specificity Journal of the American Chemical Society 10.1021/ja058831y
Zhang, Z. Y., Chen, L., Liu, L., Su, X. Y. and Rabinowitz, J. D. 2017 Chemical Basis for Deuterium Labeling of Fat and NADPH Journal of the American Chemical Society 10.1021/jacs.7b08012
Hutchins, P. D., Russell, J. D. and Coon, J. J. 2019 Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries Journal of the American Society for Mass Spectrometry 10.1007/s13361-018-02125-y
Meyer, J. G., D'Souza, A. K., Sorensen, D. J., Rardin, M. J., Wolfe, A. J., Gibson, B. W. and Schilling, B. 2016 Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH) Journal of the American Society for Mass Spectrometry 10.1007/s13361-016-1476-z
Nshanian, M., Lantz, C., Wongkongkathep, P., Schrader, T., Klarner, F. G., Blumke, A., Despres, C., Ehrmann, M., Smet-Nocca, C., Bitan, G. and Loo, J. A. 2019 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 10.1007/s13361-018-2027-6
Khandaker, M. S. K., Dudek, D. M., Beers, E. P. and Dillard, D. A. 2017 Expression, crosslinking, and developing modulus master curves of recombinant resilin Journal of the Mechanical Behavior of Biomedical Materials 10.1016/j.jmbbm.2017.01.009
Khandaker, M. S. K., Dudek, D. M., Beers, E. P., Dillard, D. A. and Bevan, D. R. 2016 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 10.1016/j.jmbbm.2016.01.017
Allison, D. P., Sullivan, C. J., Mortensen, N. P., Retterer, S. T. and Doktycz, M. 2011 Bacterial immobilization for imaging by atomic force microscopy Journal of Visualized Experiments 10.3791/2880
Aufrecht, J. A., Ryan, J. M., Hasim, S., Allison, D. P., Nebenfuhr, A., Doktycz, M. J. and Retterer, S. T. 2017 Imaging the Root Hair Morphology of Arabidopsis Seedlings in a Two-layer Microfluidic Platform Journal of Visualized Experiments 10.3791/55971
Miquel Guennoc, C., Rose, C., Guinnet, F., Miquel, I., Labbe, J. and Deveau, A. 2017 A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy Journal of Visualized Experiments 10.3791/54771
Fadrosh, D. W., Andrews-Pfannkoch, C. and Williamson, S. J. 2011 Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography JoVE-Journal of Visualized Experiments 10.3791/3146
Gao, J., Sasse, J., Lewald, K. M., Zhalnina, K., Cornmesser, L. T., Duncombe, T. A., Yoshikuni, Y., Vogel, J. P., Firestone, M. K. and Northen, T. R. 2018 Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions JoVE-Journal of Visualized Experiments 10.3791/57170
Levine, M. Z., Gregorio, N. E., Jewett, M. C., Watts, K. R. and Oza, J. P. 2019 Escherichia coil-Based Cell-Free Protein Synthesis: Protocols for a robust, flexible, and accessible platform technology Jove-Journal of Visualized Experiments 10.3791/58882
Murphy, K. M., Chung, S., Fogla, S., Minsky, H. B., Zhu, K. Y. and Zerbe, P. 2019 A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products JoVE-Journal of Visualized Experiments 10.3791/59992
Tfaily, M. M., Wilson, R. M., Brewer, H. M., Chu, R. K., Heyman, H. M., Hoyt, D. W., Kyle, J. E. and Purvine, S. O. 2019 Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures JoVE-Journal of Visualized Experiments 10.3791/59035
Chen, J. Q., Sciusco, P., Ouyang, Z. T., Zhang, R., Henebry, G. M., John, R. and Roy, D. P. 2019 Linear downscaling from MODIS to landsat: connecting landscape composition with ecosystem functions Landscape Ecology 10.1007/s10980-019-00928-2
Bier, Raven L., Wernegreen, Jennifer J., Vilgalys, Rytas J., Ellis, Joseph Christopher and Bernhardt, Emily S. 2019 Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage Limnology and Oceanography 10.1002/lno.11301
Noé F, and Smith JC 2007 Transition Networks A Unifying Theme for Molecular Simulation and Computer Science Mathematical Modeling of Biological Systems 10.1007/978-0-8176-4558-8_11
Todd, J., Sandhu, H., Hale, A., Glaz, B. and Wang, J. P. 2017 Phenotypic evaluation of a diversity panel selected from the world collection of sugarcane (Saccharum spp) and related grasses Maydica none
Feng, J. J., Penton, C. R., He, Z. L., Van Nostrand, J. D., Yuan, M. T. M., Wu, L. Y., Wang, C., Qin, Y. J., Shi, Z. J., Guo, X., Schuur, E. A. G., Luo, Y. Q., Bracho, R., Konstantinidis, K. T., Cole, J. R., Tiedje, J. M., Yang, Y. F. and Zhou, J. Z. 2019 Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils mBio 10.1128/mBio.02521-18
Filippova, E. V., Zemaitaitis, B., Aung, T., Wolfe, A. J. and Anderson, W. F. 2018 Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB mBio 10.1128/mBio.01993-17
Herivaux, A., Duge de Bernonville, T., Roux, C., Clastre, M., Courdavault, V., Gastebois, A., Bouchara, J. P., James, T. Y., Latge, J. P., Martin, F. and Papon, N. 2017 The Identification of Phytohormone Receptor Homologs in Early Diverging Fungi Suggests a Role for Plant Sensing in Land Colonization by Fungi mBio 10.1128/mBio.01739-16
Hu, P., Tom, L., Singh, A., Thomas, B. C., Baker, B. J., Piceno, Y. M., Andersen, G. L. and Banfield, J. F. 2016 Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs mBio 10.1128/mBio.01669-15
James, K. L., Rios-Hernandez, L. A., Wofford, N. Q., Mouttaki, H., Sieber, J. R., Sheik, C. S., Nguyen, H. H., Yang, Y. N., Xie, Y. M., Erde, J., Rohlin, L., Karr, E. A., Loo, J. A., Loo, R. R. O., Hurst, G. B., Gunsalus, R. P., Szweda, L. I. and McInerney, M. J. 2016 Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation mBio 10.1128/mBio.01208-16
Johnson, T. A., Stedtfeld, R. D., Wang, Q., Cole, J. R., Hashsham, S. A., Looft, T., Zhu, Y. G. and Tiedje, J. M. 2016 Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture mBio 10.1128/mBio.02214-15
Karaoz, U., Couradeau, E., da Rocha, U. N., Lim, H. C., Northen, T., Garcia-Pichel, F. and Brodie, E. L. 2018 Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity mBio 10.1128/mBio.01366-16
Kerkhoven, E. J., Kim, Y. M., Wei, S. W., Nicora, C. D., Fillmore, T. L., Purvine, S. O., Webb-Robertson, B. J., Smith, R. D., Baker, S. E., Metz, T. O. and Nielsen, J. 2017 Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica mBio 10.1128/mBio.00857-17
Khalfaoui-Hassani, B., Wu, H., Blaby-Haas, C. E., Zhang, Y., Sandri, F., Verissimo, A. F., Koch, H. G. and Daldal, F. 2018 Widespread Distribution and Functional Specificity of the Copper Importer CcoA: Distinct Cu Uptake Routes for Bacterial Cytochrome c Oxidases mBio 10.1128/mBio.00065-18
Kothari, A., Wu, Y. W., Chandonia, J. M., Charrier, M., Rajeev, L., Rocha, A. M., Joyner, D. C., Hazen, T. C., Singer, S. W. and Mukhopadhyay, A. 2019 Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes mBio 10.1128/mBio.02899-18
Levar, C. E., Chan, C. H., Mehta-Kolte, M. G. and Bond, D. R. 2014 An Inner Membrane Cytochrome Required Only for Reduction of High Redox Potential Extracellular Electron Acceptors mBio 10.1128/mBio.02034-14
McCully, A. L., LaSarre, B. and McKinlay, J. B. 2017 Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists mBio 10.1128/mBio.01620-17
Nakayasu, E. S., Burnet, M. C., Walukiewicz, H. E., Wilkins, C. S., Shukla, A. K., Brooks, S., Plutz, M. J., Lee, B. D., Schilling, B., Wolfe, A. J., Muller, S., Kirby, J. R., Rao, C. V., Cort, J. R. and Payne, S. H. 2017 Ancient Regulatory Role of Lysine Acetylation in Central Metabolism mBio 10.1128/mBio.01894-17
Schaefer, A. L., Oda, Y., Coutinho, B. G., Pelletier, D. A., Weiburg, J., Venturi, V., Greenberg, E. P. and Harwood, C. S. 2016 A LuxR Homolog in a Cottonwood Tree Endophyte That Activates Gene Expression in Response to a Plant Signal or Specific Peptides mBio 10.1128/mBio.01101-16
Shi, S. J., Nuccio, E., Herman, D. J., Rijkers, R., Estera, K., Li, J. B., da Rocha, U. N., He, Z. L., Pett-Ridge, J., Brodie, E. L., Zhou, J. Z. and Firestone, M. 2015 Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons mBio 10.1128/mBio.00746-15
Siegel, S. D., Amer, B. R., Wu, C. G., Sawaya, M. R., Gosschalk, J. E., Clubb, R. T. and Ton-That, H. 2019 Structure and Mechanism of LcpA, a Phosphotransferase That Mediates Glycosylation of a Gram-Positive Bacterial Cell Wall-Anchored Protein mBio 10.1128/mBio.01580-18
Skennerton, C. T., Chourey, K., Iyer, R., Hettich, R. L., Tyson, G. W. and Orphan, V. J. 2017 Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea mBio 10.1128/mBio.00530-17
Smith, G. J., Angle, J. C., Solden, L. M., Borton, M. A., Morin, T. H., Daly, R. A., Johnston, M. D., Stefanik, K. C., Wolfe, R., Gil, B. and Wrighton, K. C. 2018 Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland mBio 10.1128/mBio.00815-18
Stuart, Rhona K., Mayali, Xavier, Boaro, Amy A., Zemla, Adam, Everroad, R. Craig, Nilson, Daniel, Weber, Peter K., Lipton, Mary, Bebout, Brad M., Pett-Ridge, Jennifer and Thelen, Michael P. 2016 Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm mBio 10.1128/mBio.00650-16
Van Goethem, M. W., Swenson, T. L., Trubl, G., Roux, S. and Northen, T. R. 2019 Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust mBio 10.1128/mBio.02287-19
Wang, Q., Quensen, J. F., Fish, J. A., Lee, T. K., Sun, Y. N., Tiedje, J. M. and Cole, J. R. 2013 Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool mBio 10.1128/mBio.00592-13
Wilmes, P., Bowen, B. P., Thomas, B. C., Mueller, R. S., Denef, V. J., VerBerkmoes, N. C., Hettich, R. L., Northen, T. R. and Banfield, J. F. 2010 Metabolome-Proteome Differentiation Coupled to Microbial Divergence mBio 10.1128/mBio.00246-10
Xue, K., Yuan, M. T. M., Xie, J. P., Li, D. J., Qin, Y. J., Hale, L. E., Wu, L. Y., Deng, Y., He, Z. L., Van Nostrand, J. D., Luo, Y. Q., Tiedje, J. M. and Zhou, J. Z. 2016 Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming mBio 10.1128/mBio.00976-16
Zhalnina, K., Zengler, K., Newman, D. and Northen, T. R. 2018 Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry mBio 10.1128/mBio.01175-18
Zhang, J. W., Silverstein, K. A. T., Castano, J. D., Figueroa, M. and Schilling, J. S. 2019 Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers mBio 10.1128/mBio.02176-19
Zhou, J. Z., Deng, Y., Luo, F., He, Z. L., Tu, Q. C. and Zhi, X. Y. 2010 Functional Molecular Ecological Networks mBio 10.1128/mBio.00169-10
Zhou, J. Z., Deng, Y., Luo, F., He, Z. L. and Yang, Y. F. 2011 Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2 mBio 10.1128/mBio.00122-11
Zhou, J. Z., He, Z. L., Yang, Y. F., Deng, Y., Tringe, S. G. and Alvarez-Cohen, L. 2015 High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats mBio 10.1128/mBio.02288-14
Zhou, J. Z., Jiang, Y. H., Deng, Y., Shi, Z., Zhou, B. Y., Xue, K., Wu, L. Y., He, Z. L. and Yang, Y. F. 2013 Random Sampling Process Leads to Overestimation of beta-Diversity of Microbial Communities mBio 10.1128/mBio.00324-13
Abdel-Mawgoud, A. M., Markham, K. A., Palmer, C. M., Liu, N., Stephanopoulos, G. and Alper, H. S. 2018 Metabolic engineering in the host Yarrowia lipolytica Metabolic Engineering 10.1016/j.ymben.2018.07.016
Au, J., Choi, J., Jones, S. W., Venkataramanan, K. P. and Antoniewicz, M. R. 2014 Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for C-13 metabolic flux analysis Metabolic Engineering 10.1016/j.ymben.2014.08.002
Broddrick, J. T., Welkie, D. G., Jallet, D., Golden, S. S., Peers, G. and Palsson, B. O. 2019 Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes Metabolic Engineering 10.1016/j.ymben.2018.11.001
Clark, R. L., McGinley, L. L., Purdy, H. M., Korosh, T. C., Reed, J. L., Root, T. W. and Pfleger, B. F. 2018 Light-optimized growth of cyanobacterial cultures: Growth phases and productivity of biomass and secreted molecules in light-limited batch growth Metabolic Engineering 10.1016/j.ymben.2018.03.017
Contador, C. A., Rizk, M. L., Asenjo, J. A. and Liao, J. C. 2009 Ensemble modeling for strain development of L-lysine-producing Escherichia coli Metabolic Engineering 10.1016/j.ymben.2009.04.002
Cui, J., Olson, D.G., Lynd, L.R. 2018 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 10.1016/j.ymben.2018.09.006
Dash, S., Olson, D.G., Chan, S.H.J., Amador-Noguez, D., Lynd, L.R., and Maranas, C.D. 2019 Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum Metabolic Engineering 10.1016/j.ymben.2019.06.006
Garcia, S. and Trinh, C. T. 2019 Multiobjective strain design: A framework for modular cell engineering Metabolic Engineering 10.1016/j.ymben.2018.09.003
Ghosh, I. N., Martien, J., Hebert, A. S., Zhang, Y. P., Coon, J. J., Amador-Noguez, D. and Landick, R. 2019 OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate Metabolic Engineering 10.1016/j.ymben.2018.12.008
Guo, L. Y., Wang, P., Jaini, R., Dudareva, N., Chapple, C. and Morgan, J. A. 2018 Dynamic modeling of subcellular phenylpropanoid metabolism in Arabidopsis lignifying cells Metabolic Engineering 10.1016/j.ymben.2018.07.003
Henson, W. R., Campbell, T., DeLorenzo, D. M., Gao, Y., Berla, B., Kim, S. J., Foston, M., Moon, T. S. and Dantas, G. 2018 Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus Metabolic Engineering 10.1016/j.ymben.2018.06.009
Hing, N. Y. K., Liang, F. Y., Lindblad, P. and Morgan, J. A. 2019 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 10.1016/j.ymben.2019.08.014
Jacobson, T. B., Adamczyk, P. A., Stevenson, D. M., Regner, M., Ralph, J., Reed, J. L. and Amador-Noguez, D. 2019 H-2 and C-13 metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis Metabolic Engineering 10.1016/j.ymben.2019.05.006
Jazmin, L. J., Xu, Y., Cheah, Y. E., Adebiyi, A. O., Johnson, C. H. and Young, J. D. 2017 Isotopically nonstationary C-13 flux analysis of cyanobacterial isobutyraldehyde production Metabolic Engineering 10.1016/j.ymben.2017.05.001
Karim, A. S., Heggestad, J. T., Crowe, S. A. and Jewett, M. C. 2018 Controlling cell-free metabolism through physiochemical perturbations Metabolic Engineering 10.1016/j.ymben.2017.11.005
Kim, S. K. and Westpheling, J. 2018 Engineering a spermidine biosynthetic pathway in Clostridium thermocellum results in increased resistance to furans and increased ethanol production Metabolic Engineering 10.1016/j.ymben.2018.09.002
Lee, Y., Rivera, J. G. L. and Liao, J. C. 2014 Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways Metabolic Engineering 10.1016/j.ymben.2014.06.006
Lian, J. Z., Mishra, S. and Zhao, H. M. 2018 Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications Metabolic Engineering 10.1016/j.ymben.2018.04.011
Liu, N., Qiao, K. J. and Stephanopoulos, G. 2016 C-13 Metabolic Flux Analysis of acetate conversion to lipids by Yarrowia lipolytica Metabolic Engineering 10.1016/j.ymben.2016.06.006
Liu, R. M., Liang, L. Y., Choudhury, A., Bassalo, M. C., Garst, A. D., Tarasava, K. and Gill, R. T. 2018 Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production Metabolic Engineering 10.1016/j.ymben.2018.04.007
Liu, R. M., Liang, L. Y., Choudhury, A., Garst, A. D., Eckert, C. A., Oh, E. J., Winkler, J. and Gill, R. T. 2019 Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production Metabolic Engineering 10.1016/j.ymben.2018.07.007
Mehrer, C. R., Rand, J. M., Incha, M. R., Cook, T. B., Demir, B., Motagamwala, A. H., Kim, D., Dumesic, J. A. and Pfleger, B. F. 2019 Growth-coupled bioconversion of levulinic acid to butanone Metabolic Engineering 10.1016/j.ymben.2019.06.003
Rivera, J. G. L., Theisen, M. K., Chen, P. W. and Liao, J. C. 2017 Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites Metabolic Engineering 10.1016/j.ymben.2017.03.011
Roell, G. W., Carr, R. R., Campbell, T., Shang, Z. Y., Henson, W. R., Czajka, J. J., Martin, H. G., Zhang, F. Z., Foston, M., Dantas, G., Moon, T. S. and Tang, Y. J. J. 2019 A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630 Metabolic Engineering 10.1016/j.ymben.2019.06.013
Seppala, S., Wilken, S. E., Knop, D., Solomon, K. V. and O'Malley, M. A. 2017 The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown Metabolic Engineering 10.1016/j.ymben.2017.09.008
Vasdekis, A. E. and Stephanopoulos, G. 2015 Review of methods to probe single cell metabolism and bioenergetics Metabolic Engineering 10.1016/j.ymben.2014.09.007
Walker, C., Ryu, S. and Trinh, C. T. 2019 Exceptional solvent tolerance in Yarrowia lipolytica is enhanced by sterols Metabolic Engineering 10.1016/j.ymben.2019.03.003
Wang, X., He, Q. N., Yang, Y. F., Wang, J. W., Haning, K., Hu, Y., Wu, B., He, M. X., Zhang, Y. P., Bao, J., Contreras, L. M. and Yang, S. H. 2018 Advances and prospects in metabolic engineering of Zymomonas mobilis Metabolic Engineering 10.1016/j.ymben.2018.04.001
Wasylenko, T. M., Ahn, W. S. and Stephanopoulos, G. 2015 The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica Metabolic Engineering 10.1016/j.ymben.2015.02.007
Wong, W. W. and Liao, J. C. 2009 Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters Metabolic Engineering 10.1016/j.ymben.2009.08.004
Zhang, X. L., Tervo, C. J. and Reed, J. L. 2016 Metabolic assessment of E. coli as a Biofactory for commercial products Metabolic Engineering 10.1016/j.ymben.2016.01.007
Lee, J-W., Niraula, N.P., Trinh, C.T. 2018 Harnessing a P450 fatty acid decorboxylase from Macrococcus caseolyticus for microbial biosynthesis of odd chain terminal alkenes Metabolic Engineering Communications 10.1016/j.mec.2018.e00076
Standaert, R. F., Giannone, R. J. and Michener, J. K. 2018 Identification of parallel and divergent optimization solutions for homologous metabolic enzymes Metabolic Engineering Communications 10.1016/j.meteno.2018.04.002
Fischer, C. R., Wilmes, P., Bowen, B. P., Northen, T. R. and Banfield, J. F. 2012 Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities Metabolomics 10.1007/s11306-011-0344-x
Hamerly, T., Tripet, B. P., Tigges, M., Giannone, R. J., Wurch, L., Hettich, R. L., Podar, M., Copie, V. and Bothner, B. 2015 Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis Metabolomics 10.1007/s11306-014-0747-6
Ackerman, C. M., Weber, P. K., Xiao, T., Thai, B., Kuo, T. J., Zhang, E., Pett-Ridge, J. and Chang, C. J. 2018 Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease Metallomics 10.1039/c7mt00349h
Blaby-Haas, Crysten E., Castruita, Madeli, Fitz-Gibbon, Sorel T., Kropat, Janette and Merchant, Sabeeha S. 2016 Ni induces the CRR1-dependent regulon revealing overlap and distinction between hypoxia and Cu deficiency responses in Chlamydomonas reinhardtii Metallomics 10.1039/c6mt00063k
Myrold, D. D., Pett-Ridge, J. and Bottomley, P. J. 2011 Nitrogen mineralization and assimilation at millimeter scales Methods in Enzymology 10.1016/B978-0-12-386489-5.00004-X
Dekas, A. E. and Orphan, V. J. 2011 Identification Of Diazotrophic Microorganisms In Marine Sediment Via Fluorescence In Situ Hybridization Coupled To Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS) Methods in Enzymology: Research on Nitrification and Related Processes, Vol 486, Part A 10.1016/b978-0-12-381294-0.00012-2
Basso, V. and Veneault-Fourrey, C. 2020 Role of Jasmonates in Beneficial Microbe-Root Interactions Methods in Molecular Biology 10.1007/978-1-0716-0142-6_4
Blaby, I. K. and Blaby-Haas, C. E. 2018 Gene Expression Analysis by Arylsulfatase Assays in the Green Alga Chlamydomonas reinhardtii Methods in Molecular Biology 10.1007/978-1-4939-7724-6_11
Blaby-Haas, C. E., Page, M. D. and Merchant, S. S. 2018 Using YFP as a Reporter of Gene Expression in the Green Alga Chlamydomonas reinhardtii Methods in Molecular Biology 10.1007/978-1-4939-7724-6_10
Cheng X, and Ivanov I 2012 Molecular Dynamics Methods in Molecular Biology 10.1007/978-1-62703-050-2_11
Heinemann, J. 2019 Cluster Analysis of Untargeted Metabolomic Experiments Methods in Molecular Biology 10.1007/978-1-4939-8757-3_16
Mayali, X., Weber, P. K., Nuccio, E., Lietard, J., Somoza, M., Blazewicz, S. J. and Pett-Ridge, J. 2019 Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS Methods in Molecular Biology 10.1007/978-1-4939-9721-3_6
Plett, J. M., Montanini, B., Kohler, A., Ottonello, S. and Martin, F. 2011 Tapping genomics to unravel ectomycorrhizal symbiosis Methods in Molecular Biology 10.1007/978-1-61779-040-9_19
Schaefer, A. L., Harwood, C. S. and Greenberg, E. P. 2018 "Hot Stuff": The Many Uses of a Radiolabel Assay in Detecting Acyl-Homoserine Lactone Quorum-Sensing Signals Methods in Molecular Biology 10.1007/978-1-4939-7309-5_3
Shen, T. and Wong, C. F. 2015 Brownian dynamics simulation of peptides with the University of Houston Brownian Dynamics (UHBD) program Methods in Molecular Biology 10.1007/978-1-4939-2285-7_5
Zuniga, C., Zaramela, L. and Zengler, K. 2017 Elucidation of complexity and prediction of interactions in microbial communities Microbial Biotechnology 10.1111/1751-7915.12855
Eng, T., Demling, P., Herbert, R. A., Chen, Y., Benites, V., Martin, J., Mukhopadhyay, A. 2018 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 10.1186/s12934-018-1006-8
Roell, G. W., Zha, J., Carr, R. R., Koffas, M. A., Fong, S. S. and Tang, Y. J. J. 2019 Engineering microbial consortia by division of labor Microbial Cell Factories 10.1186/s12934-019-1083-3
Seppala, S., Solomon, K. V., Gilmore, S. P., Henske, J. K. and O'Malley, M. A. 2016 Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters Microbial Cell Factories 10.1186/s12934-016-0611-7
Wehrs, M., Prahl, J. P., Moon, J., Li, Y., Tanjore, D., Keasling, J. D., … Mukhopadhyay, A. 2018 Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae Microbial Cell Factories 10.1186/s12934-018-1045-1
Wei, Y. J., Bergenholm, D., Gossing, M., Siewers, V. and Nielsen, J. 2018 Expression of cocoa genes in Saccharomyces cerevisiae improves cocoa butter production Microbial Cell Factories 10.1186/s12934-018-0866-2
Zhang, H. R., Li, Z. J., Pereira, B. and Stephanopoulos, G. 2015 Engineering E-coli-E-coli cocultures for production of muconic acid from glycerol Microbial Cell Factories 10.1186/s12934-015-0319-0
Geng, Haifeng, Sale, Kenneth L., Tran-Gyamfi, Mary Bao, Lane, Todd W. and Yu, Eizadora T. 2016 Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures Microbial Ecology 10.1007/s00248-016-0746-4
Mason, O. U., Case, D. H., Naehr, T. H., Lee, R. W., Thomas, R. B., Bailey, J. V. and Orphan, V. J. 2015 Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA Microbial Ecology 10.1007/s00248-015-0615-6
Tu, Q. C., Zhou, X. S., He, Z. L., Xue, K., Wu, L. Y., Reich, P., Hobbie, S. and Zhou, J. Z. 2016 The Diversity and Co-occurrence Patterns of N-2-Fixing Communities in a CO2-Enriched Grassland Ecosystem Microbial Ecology 10.1007/s00248-015-0659-7
La Reau, A. J., Meier-Kolthoff, J. P. and Suen, G. 2016 Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association Microbial Genomics 10.1099/mgen.0.000099
Ando, D., and García Martín, H. 2019 Genome-Scale 13C Fluxomics Modeling for Metabolic Engineering of Saccharomyces cerevisiae Microbial Metabolomics: Methods and Protocols 10.1007/978-1-4939-8757-3_19
Baidoo, E. E. K., and Teixeira Benites, V. 2019 Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications Microbial Metabolomics: Methods and Protocols 10.1007/978-1-4939-8757-3_2
Baidoo, E. E. K. 2019 Microbial Metabolomics: A General Overview Microbial Metabolomics: Methods and Protocols 10.1007/978-1-4939-8757-3_1
Heinemann, J. 2019 Machine Learning in Untargeted Metabolomics Experiments Microbial Metabolomics: Methods and Protocols 10.1007/978-1-4939-8757-3_17
Joshua, C. J. 2019 Metabolomics: A Microbial Physiology and Metabolism Perspective Microbial Metabolomics: Methods and Protocols 10.1007/978-1-4939-8757-3_3
Navid, Ali 2012 Development of Constraint-Based System-Level Models of Microbial Metabolism Microbial Systems Biology: Methods and Protocols 10.1007/978-1-61779-827-6_18
Pett-Ridge, Jennifer and Weber, Peter K. 2012 NanoSIP: NanoSIMS Applications for Microbial Biology Microbial Systems Biology: Methods and Protocols 10.1007/978-1-61779-827-6_13
Al-Hinai, M. A., Jones, S. W. and Papoutsakis, E. T. 2015 The Clostridium Sporulation Programs: Diversity and Preservation of Endospore Differentiation Microbiology and Molecular Biology Reviews 10.1128/mmbr.00025-14
Zhou, J. Z. and Ning, D. L. 2017 Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiology and Molecular Biology Reviews 10.1128/mmbr.00002-17
Day, L. A., De Leon, K. B., Kempher, M. L., Zhou, J. and Wall, J. D. 2019 Complete Genome Sequence of Desulfovibrio desulfuricans IC1, a Sulfonate-Respiring Anaerobe Microbiology Resource Announcements 10.1128/MRA.00456-19
Hatmaker, E. A., Klingeman, D. M., Martin, R. K., Guss, A. M. and Elkins, J. G. 2019 Complete Genome Sequence of Caloramator sp. Strain E03, a Novel Ethanologenic, Thermophilic, Obligately Anaerobic Bacterium Microbiology Resource Announcements 10.1128/MRA.00708-19
Hatmaker, E. A., Klingeman, D. M., O'Dell, K. B., Riley, L. A., Papanek, B. and Guss, A. M. 2019 Complete Genome Sequences of Two Megasphaera elsdenii Strains, NCIMB 702410 and ATCC 25940 Microbiology Resource Announcements 10.1128/MRA.01430-18
O'Dell, K.B., Hatmaker, E.A., Guss, A.M., Mormile, M.R. 2018 Complete genome sequence of salinispaera sp. Strain LB1, a moderately halo-acidophilic bacterium isolated from Lake Brown, western Australia Microbiology Resource Announcements 10.1128/MRA.01047-18
Podar, M., Turner, J., Burdick, L. H. and Pelletier, D. A. 2019 Complete Genome Sequence of Terriglobus albidus Strain ORNL, an Acidobacterium Isolated from the Populus deltoides Rhizosphere Microbiology Resource Announcements 10.1128/MRA.01065-19
Walker, C., Ryu, S., Na, Hyunsoo, Zane, M., LaButti, K., Lipzen, A., Haridas, S., Barry, K., Grigoriev, IV., Quarterman, J., Slininger, P., Dien, B., Trinh, C.T. 2018 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 10.1128/MRA.01040-18
Xue, Y., Jonassen, I., Ovreas, L. and Tas, N. 2019 Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost Microbiology Resource Announcements 10.1128/MRA.00516-19
Blackwell, Meredith 2017 Made for Each Other: Ascomycete Yeasts and Insects Microbiology Spectrum 10.1128/microbiolspec.FUNK-0081-2016
Spatafora, Joseph W., Aime, M. Catherine, Grigoriev, Igor V., Martin, Francis, Stajich, Jason E. and Blackwell, Meredith 2017 The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies Microbiology Spectrum 10.1128/microbiolspec.FUNK-0053-2016
Taylor, J. W., Branco, S., Gao, C., Hann-Soden, C., Montoya, L., Sylvain, I. and Gladieux, P. 2017 Sources of Fungal Genetic Variation and Associating It with Phenotypic Diversity Microbiology Spectrum 10.1128/microbiolspec.FUNK-0057-2016
Chu, H. J., Wang, S. P., Yue, H. W., Lin, Q. Y., Hu, Y. G., Li, X. Z., Zhou, J. Z. and Yang, Y. F. 2014 Contrasting soil microbial community functional structures in two major landscapes of the Tibetan alpine meadow MicrobiologyOpen 10.1002/mbo3.190
Wang, M. M., Liu, S. S., Wang, F., Sun, B., Zhou, J. Z. and Yang, Y. F. 2015 Microbial responses to southward and northward Cambisol soil transplant MicrobiologyOpen 10.1002/mbo3.302
Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A. and Schadt, C. W. 2018 The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome Microbiome 10.1186/s40168-018-0413-8
Lan, Y. M., Kriete, A. and Rosen, G. L. 2013 Selecting age-related functional characteristics in the human gut microbiome Microbiome 10.1186/2049-2618-1-2
Lan, Y. M., Rosen, G. and Hershberg, R. 2016 Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains Microbiome 10.1186/s40168-016-0162-5
Liu, Y. F., Galzerani, D. D., Mbadinga, S. M., Zaramela, L. S., Gu, J. D., Mu, B. Z. and Zengler, K. 2018 Metabolic capability and in situ activity of microorganisms in an oil reservoir Microbiome 10.1186/s40168-017-0392-1
Starr, E. P., Shi, S. J., Blazewicz, S. J., Probst, A. J., Herman, D. J., Firestone, M. K. and Banfield, J. F. 2018 Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon Microbiome 10.1186/s40168-018-0499-z
Veach, A. M., Morris, R., Yip, D. Z., Yang, Z. K., Engle, N. L., Cregger, M. A., Tschaplinski, T. J. and Schadt, C. W. 2019 Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin Microbiome 10.1186/s40168-019-0668-8
Wang, Q., Fish, J. A., Gilman, M., Sun, Y. N., Brown, C. T., Tiedje, J. M. and Cole, J. R. 2015 Xander: employing a novel method for efficient gene-targeted metagenomic assembly Microbiome 10.1186/s40168-015-0093-6
Carpenter, Kevin J., Weber, Peter K., Davisson, M. Lee, Pett-Ridge, Jennifer, Haverty, Michael I. and Keeling, Patrick J. 2013 Correlated SEM, FIB-SEM, TEM, and NanoSIMS Imaging of Microbes from the Hindgut of a Lower Termite: Methods for In Situ Functional and Ecological Studies of Uncultivable Microbes Microscopy and Microanalysis 10.1017/S1431927613013482
Guo HB, Parks JM, Johs A, and Smith JC 2011 Mercury Detoxification by Bacteria Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage Modeling of Molecular Properties 10.1002/9783527636402.ch20
Pan, C. L., Fischer, C. R., Hyatt, D., Bowen, B. P., Hettich, R. L. and Banfield, J. F. 2011 Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities Molecular & Cellular Proteomics 10.1074/mcp.M110.006049
Peshkin, L., Gupta, M., Ryazanova, L. and Wuhr, M. 2019 Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance Molecular & Cellular Proteomics 10.1074/mcp.TIR119.001317
Brademan, D. R., Riley, N. M., Kwiecien, N. W. and Coon, J. J. 2019 Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications Molecular and Cellular Proteomics 10.1074/mcp.TIR118.001209
Kuang, M. C., Kominek, J., Alexander, W. G., Cheng, J. F., Wrobel, R. L. and Hittinger, C. T. 2018 Repeated Cis-Regulatory Tuning of a Metabolic Bottleneck Gene during Evolution Molecular Biology and Evolution 10.1093/molbev/msy102
Langdon, Q. K., Peris, D., Kyle, B. and Hittinger, C. T. 2018 spplDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing Molecular Biology and Evolution 10.1093/molbev/msy166
Nagy, L. G., Riley, R., Bergmann, P. J., Krizsan, K., Martin, F. M., Grigoriev, I. V., Cullen, D. and Hibbett, D. S. 2017 Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution Molecular Biology and Evolution 10.1093/molbev/msw238
Nguyen, T. A., Brescic, J., Vinyard, D. J., Chandrasekar, T. and Dismukes, G. C. 2012 Identification of an Oxygenic Reaction Center psbADC Operon in the Cyanobacterium Gloeobacter violaceus PCC 7421 Molecular Biology and Evolution 10.1093/molbev/msr224
Priyann, A., Woodcroft, B. J., Rai, V., Moghul, I., Munagala, A., Ter, F., Chowdhary, H., Pieniak, I., Maynard, L. J., Gibbins, M. A., Moon, H., Davis-Richardson, A., Uludag, M., Watson-Haigh, N. S., Challis, R., Nakamura, H., Favreau, E., Gomez, E. A., Pluskal, T., Leonard, G., Rumpf, W. and Wurm, Y. 2019 Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases Molecular Biology and Evolution 10.1093/molbev/msz185
Gibney, P. A., Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y. F., Bennett, B. D., Rabinowitz, J. D. and Botstein, D. 2018 Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast Molecular Biology of the Cell 10.1091/mbc.E17-11-0666
Chaiboonchoe, A., Ghamsari, L., Dohai, B., Ng, P., Khraiwesh, B., Jaiswal, A., Jijakli, K., Koussa, J., Nelson, D. R., Cai, H., Yang, X. P., Chang, R. L., Papin, J., Yu, H. Y., Balaji, S. and Salehi-Ashtiani, K. 2016 Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation Molecular Biosystems 10.1039/c6mb00237d
Cheung, R., Insigne, K. D., Yao, D., Burghard, C. P., Wang, J., Hsiao, Y. H. E., Jones, E. M., Goodman, D. B., Xiao, X. S. and Kosuri, S. 2019 A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions Molecular Cell 10.1016/j.molcel.2018.10.037
Xu, Y. F., Zhao, X., Glass, D. S., Absalan, F., Perlman, D. H., Broach, J. R. and Rabinowitz, J. D. 2012 Regulation of Yeast Pyruvate Kinase by Ultrasensitive Allostery Independent of Phosphorylation Molecular Cell 10.1016/j.molcel.2012.07.013
Bonito, G., Reynolds, H., Robeson, M. S., 2nd, Nelson, J., Hodkinson, B. P., Tuskan, G., Schadt, C. W. and Vilgalys, R. 2014 Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants Molecular Ecology 10.1111/mec.12821
Paula, F. S., Rodrigues, J. L. M., Zhou, J. Z., Wu, L. Y., Mueller, R. C., Mirza, B. S., Bohannan, B. J. M., Nusslein, K., Deng, Y., Tiedje, J. M. and Pellizari, V. H. 2014 Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities Molecular Ecology 10.1111/mec.12786
Clark, L. V. and Schreier, A. D. 2017 Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables Molecular Ecology Resources 10.1111/1755-0998.12639
Tu, Q. C., Yu, H., He, Z. L., Deng, Y., Wu, L. Y., Van Nostrand, J. D., Zhou, A. F., Voordeckers, J., Lee, Y. J., Qin, Y. J., Hemme, C. L., Shi, Z., Xue, K., Yuan, T., Wang, A. J. and Zhou, J. Z. 2014 GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis Molecular Ecology Resources 10.1111/1755-0998.12239
Pi M, Kapoor K, Wu Y, Ye R, Senogles SE, Nishimoto SK, Hwang DJ, Miller DD, Narayanan R, Smith JC, Baudry J, and Quarles LD 2015 Structural and Functional Evidence for Testosterone Activation of GPRC6A in Peripheral Tissues Molecular Endocrinology 10.1210/me.2015-1161
Veneault-Fourrey, Claire, Plett, Jonathan M. and Martin, Francis 2013 Who is Controlling whom within the Ectomycorrhizal Symbiosis: Insights from Genomic and Functional Analyses Molecular Microbial Ecology of the Rhizosphere 1&2 10.1002/9781118297674.ch47
Blake, A. D., Beri, N. R., Guttman, H. S., Cheng, R. and Gardner, J. G. 2018 The complex physiology of Cellvibrio japonicus xylan degradation relies on a single cytoplasmic -xylosidase for xylo-oligosaccharide utilization Molecular Microbiology 10.1111/mmi.13903
Burgos, R., Wood, G. E., Young, L., Glass, J. I. and Totten, P. A. 2012 RecA mediates MgpB and MgpC phase and antigenic variation in Mycoplasma genitalium, but plays a minor role in DNA repair Molecular Microbiology 10.1111/j.1365-2958.2012.08130.x
Close D, Cooper S, Wang X, Giannone RJ, Engle NL, Tschaplinski TJ, Hedstrom L, Parks JM, Michener JK 2018 Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis Molecular Microbiology 10.1111/mmi.14393
Donohue, T. J. 2019 Shedding light on a Group IV (ECF11) alternative sigma factor Molecular Microbiology 10.1111/mmi.14280
Nelson, C. E., Rogowski, A., Morland, C., Wilhide, J. A., Gilbert, H. J. and Gardner, J. G. 2017 Systems analysis in Cellvibrio japonicus resolves predicted redundancy of beta-glucosidases and determines essential physiological functions Molecular Microbiology 10.1111/mmi.13625
Schilling, B., Christensen, D., Davis, R., Sahu, A. K., Hu, L. I., Walker-Peddakotla, A., Sorensen, D. J., Zemaitaitis, B., Gibson, B. W. and Wolfe, A. J. 2015 Protein acetylation dynamics in response to carbon overflow in Escherichia coli Molecular Microbiology 10.1111/mmi.13161
Wurtmann, E. J., Ratushny, A. V., Pan, M., Beer, K. D., Aitchison, J. D. and Baliga, N. S. 2014 An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation Molecular Microbiology 10.1111/mmi.12564
Pi M, Kapoor K, Ye R, Smith JC, Baudry J, Quarles LD 2018 GPCR6A is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea Molecular Nutrition & Food Research 10.1002/mnfr.201700770
Toutounchian, J. J., Pagadala, J., Miller, D. D., Baudry, J., Park, F., Chaum, E., Morales-Tirado, V. and Yates, C. R. 2017 Novel Small Molecule JP-153 Targets the Src-FAK-Paxillin Signaling Complex to Inhibit VEGF-Induced Retinal Angiogenesis Molecular Pharmacology 10.1124/mol.116.105031
Harding, S. A. and Tsai, C. J. 2019 Cell wall pectins in tree growth and woody biomass utilization Molecular Physiology and Biotechnology of Trees 10.1016/bs.abr.2018.11.008
Fahlgren, N., Feldman, M., Gehan, M. A., Wilson, M. S., Shyu, C., Bryant, D. W., Hill, S. T., McEntee, C. J., Warnasooriya, S. N., Kumar, I., Ficor, T., Turnipseed, S., Gilbert, K. B., Brutnell, T. P., Carrington, J. C., Mockler, T. C. and Baxter, I. 2015 A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria Molecular Plant 10.1016/j.molp.2015.06.005
Filichkin, S. A., Cumbie, J. S., Dharmawardhana, P., Jaiswal, P., Chang, J. H., Palusa, S. G., Reddy, A. S. N., Megraw, M. and Mockler, T. C. 2015 Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis Molecular Plant 10.1016/j.molp.2014.10.011
Hedenstrom, M., Wiklund-Lindstrom, S., Oman, T., Lu, F. C., Gerber, L., Schatz, P., Sundberg, B. and Ralph, J. 2009 Identification of Lignin and Polysaccharide Modifications in Populus Wood by Chemometric Analysis of 2D NMR Spectra from Dissolved Cell Walls Molecular Plant 10.1093/mp/ssp047
Jia, Q. D. and Chen, F. 2016 Catalytic Functions of the Isoprenyl Diphosphate Synthase Superfamily in Plants: A Growing Repertoire Molecular Plant 10.1016/j.molp.2015.12.020
Widhalm, J. R. and Dudareva, N. 2015 A Familiar Ring to It: Biosynthesis of Plant Benzoic Acids Molecular Plant 10.1016/j.molp.2014.12.001
Cecchini, N. M., Jung, H. W., Engle, N. L., Tschaplinski, T. J. and Greenberg, J. T. 2015 ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis Molecular Plant-Microbe Interactions 10.1094/MPMI-06-14-0187-R
Cecchini, N. M., Roychoudhry, S., Speed, D. J., Steffes, K., Tambe, A., Zodrow, K., Konstantinoff, K., Jung, H. W., Engle, N. L., Tschaplinski, T. J. and Greenberg, J. T. 2019 Underground Azelaic Acid-Conferred Resistance to Pseudomonas syringae in Arabidopsis Molecular Plant-Microbe Interactions 10.1094/MPMI-07-18-0185-R
Chowda-Reddy, R. V., Palmer, N., Edme, S., Sarath, G., Kovacs, F., Yuen, G., Mitchell, R. and Tatineni, S. 2019 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 10.1094/mpmi-09-18-0247-r
Karpinets, T. V., Park, B. H., Syed, M. H., Klotz, M. G. and Uberbacher, E. C. 2014 Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants Molecular Plant-Microbe Interactions 10.1094/MPMI-12-13-0368-R
Liao, H. L., Bonito, G., Rojas, J. A., Hameed, K., Wu, S., Schadt, C. W., Labbe, J., Tuskan, G. A., Martin, F., Grigoriev, I. V. and Vilgalys, R. 2019 Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition Molecular Plant-Microbe Interactions 10.1094/MPMI-05-18-0133-R
Weston, D. J., Pelletier, D. A., Morrell-Falvey, J. L., Tschaplinski, T. J., Jawdy, S. S., Lu, T. Y., Allen, S. M., Melton, S. J., Martin, M. Z., Schadt, C. W., Karve, A. A., Chen, J. G., Yang, X., Doktycz, M. J. and Tuskan, G. A. 2012 Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis, and fitness Molecular Plant-Microbe Interactions 10.1094/MPMI-09-11-0253
Ellingson S, Smith JC, and Baudry J 2014 Polypharmacology and Supercomputer-Based Docking Opportunities and Challenges Molecular Simulation 10.1080/08927022.2014.899699
Yao J, Xu Q, and Guo H 2013 QM/MM and Free Energy Simulations of Deacylation Reaction Catalyzed by Sedolisin, a Serine Carboxyl Peptidase Molecular Simulation 10.1080/08927022.2012.714467
Bassalo, M. C., Garst, A. D., Choudhury, A., Grau, W. C., Oh, E. J., Spindler, E., Lipscomb, T. and Gill, R. T. 2018 Deep scanning lysine metabolism in Escherichia coli Molecular Systems Biology 10.15252/msb.20188371
Brooks, A. N., Reiss, D. J., Allard, A., Wu, W. J., Salvanha, D. M., Plaisier, C. L., Chandrasekaran, S., Pan, M., Kaur, A. and Baliga, N. S. 2014 A system-level model for the microbial regulatory genome Molecular Systems Biology 10.15252/msb.20145160
Brynildsen, M. P. and Liao, J. C. 2009 An integrated network approach identifies the isobutanol response network of Escherichia coli Molecular Systems Biology 10.1038/msb.2009.34
Chang, R. L., Ghamsari, L., Manichaikul, A., Hom, E. F. Y., Balaji, S., Fu, W. Q., Shen, Y., Hao, T., Palsson, B. O., Salehi-Ashtiani, K. and Papin, J. A. 2011 Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism Molecular Systems Biology 10.1038/msb.2011.52
Ebrahim, Ali, Almaas, Eivind, Bauer, Eugen, Bordbar, Aarash, Burgard, Anthony P., Chang, Roger L., Dräger, Andreas, Famili, Iman, Feist, Adam M., Fleming, Ronan M. T., Fong, Stephen S., Hatzimanikatis, Vassily, Herrgård, Markus J., Holder, Allen, Hucka, Michael, Hyduke, Daniel, Jamshidi, Neema, Lee, Sang Yup, Le Novère, Nicolas, Lerman, Joshua A., Lewis, Nathan E., Ma, Ding, Mahadevan, Radhakrishnan, Maranas, Costas, Nagarajan, Harish, Navid, Ali, Nielsen, Jens, Nielsen, Lars K., Nogales, Juan, Noronha, Alberto, Pal, Csaba, Palsson, Bernhard O., Papin, Jason A., Patil, Kiran R., Price, Nathan D., Reed, Jennifer L., Saunders, Michael, Senger, Ryan S., Sonnenschein, Nikolaus, Sun, Yuekai and Thiele, Ines 2015 Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology 10.15252/msb.20156157
Kaur, A., Van, P. T., Busch, C. R., Robinson, C. K., Pan, M., Pang, W. L., Reiss, D. J., DiRuggiero, J. and Baliga, N. S. 2010 Coordination of frontline defense mechanisms under severe oxidative stress Molecular Systems Biology 10.1038/msb.2010.50
Koide, T., Reiss, D. J., Bare, J. C., Pang, W. L., Facciotti, M. T., Schmid, A. K., Pan, M., Marzolf, B., Van, P. T., Lo, F. Y., Pratap, A., Deutsch, E. W., Peterson, A., Martin, D. and Baliga, N. S. 2009 Prevalence of transcription promoters within archaeal operons and coding sequences Molecular Systems Biology 10.1038/msb.2009.42
Moser, F., Borujeni, A. E., Ghodasara, A. N., Cameron, E., Park, Y. and Voigt, C. A. 2018 Dynamic control of endogenous metabolism with combinatorial logic circuits Molecular Systems Biology 10.15252/msb.20188605
Sanchez, B. J., Zhang, C., Nilsson, A., Lahtvee, P. J., Kerkhoven, E. J. and Nielsen, J. 2017 Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints Molecular Systems Biology 10.15252/msb.20167411
Schmid, A. K., Reiss, D. J., Pan, M., Koide, T. and Baliga, N. S. 2009 A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability Molecular Systems Biology 10.1038/msb.2009.40
Xu, Y. F., Letisse, F., Absalan, F., Lu, W. Y., Kuznetsova, E., Brown, G., Caudy, A. A., Yakunin, A. F., Broach, J. R. and Rabinowitz, J. D. 2013 Nucleotide degradation and ribose salvage in yeast Molecular Systems Biology 10.1038/msb.2013.21
Yaung, S. J., Deng, L. X., Li, N., Braff, J. L., Church, G. M., Bry, L., Wang, H. H. and Gerber, G. K. 2015 Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics Molecular Systems Biology 10.15252/msb.20145866
Johnson, Q. R., Lindsay, R. J., Petridis, L. and Shen, T. 2015 Investigation of Carbohydrate Recognition via Computer Simulation Molecules 10.3390/molecules20057700
Wall JS, Martin EB, Richey T, Stuckey AC, Macy S, Wooliver C, Williams A, Foster JS, McWilliams-Koeppen P, Ubebacher E, Cheng X, and Kennel SJ 2015 Preclinical Validation of the Heparin-Reactive Peptide p5+14 as a Molecular Imaging Agent for Visceral Amyloidosis Molecules 10.3390/molecules20057657
Yue Y, Chu Y, and Guo H 2015 Computational Study of Symmetric Methylation on Histone Arginine Catalyzed by Protein Arginine Methyltransferase PRMT5 through QM/MM MD and Free Energy Simulations Molecules 10.3390/molecules200610032
Neumann, A. P. and Suen, G. 2018 The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential mSphere 10.1128/mSphere.00593-18
Pomraning, K. R., Bredeweg, E. L., Kerkhoven, E. J., Barry, K., Haridas, S., Hundley, H., Baker, S. E. 2018 Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica mSphere 10.1128/mSphere.00541-18
Pomraning, K. R., Bredeweg, E. L. and Baker, S. E. 2017 Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica mSphere 10.1128/mSphere.00038-17
Pomraning, K. R., Bredeweg, E. L., Kerkhoven, E. J., Barry, K., Haridas, S., Hundley, H., LaButti, K., Lipzen, A., Yan, M., Magnuson, J. K., Simmons, B. A., Grigoriev, I. V., Nielsen, J. and Baker, S. E. 2018 Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica mSphere 10.1128/mSphere.00541-18
Tran, V. G., Cao, M. F., Fatma, Z., Song, X. F. and Zhao, H. M. 2019 Development of a CRISPR/Cas9-Based Too for Gene Deletion in Issatchenkia orientalis mSphere 10.1128/mSphere.00345-19
Blair, P. M., Land, M. L., Piatek, M. J., Jacobson, D. A., Lu, T. Y. S., Doktycz, M. J. and Pelletier, D. A. 2018 Exploration of the Biosynthetic Potential of the Populus Microbiome mSystems 10.1128/mSystems.00045-18
Bowsher, A. W., Kearns, P. J. and Shade, A. 2019 16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil mSystems 10.1128/mSystems.00003-19
Bradley, P. H., Gibney, P. A., Botstein, D., Troyanskaya, O. G. and Rabinowitz, J. D. 2019 Minor Isozymes Tailor Yeast Metabolism to Carbon Availability mSystems 10.1128/mSystems.00170-18
Dunivin, T. K., Choi, J., Howe, A. and Shade, A. 2019 RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids mSystems 10.1128/mSystems.00349-18
Levering, J., Dupont, C. L., Allen, A. E., Palsson, B. O. and Zengler, K. 2017 Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels mSystems 10.1128/mSystems.00142-16
Martien, J. I., Hebert, A. S., Stevenson, D. M., Regner, M. R., Khana, D. B., Coon, J. J. and Amador-Noguez, D. 2019 Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production mSystems 10.1128/mSystems.00284-18
Martino, C., Morton, J. T., Marotz, C. A., Thompson, L. R., Tripathi, A., Knight, R. and Zengler, K. 2019 A Novel Sparse Compositional Technique Reveals Microbial Perturbations mSystems 10.1128/mSystems.00016-19
Narrowe, A. B., Borton, M. A., Hoyt, D. W., Smith, G. J., Daly, R. A., Angle, J. C., Eder, E. K., Wong, A. R., Wolfe, R. A., Pappas, A., Bohrer, G., Miller, C. S. and Wrighton, K. C. 2019 Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils mSystems 10.1128/mSystems.00320-19
Price, M. N. and Arkin, A. P. 2019 Curated BLAST for Genomes mSystems 10.1128/mSystems.00072-19
Price, M. N., Ray, J., Iavarone, A. T., Carlson, H. K., Ryan, E. M., Malmstrom, R. R., Arkin, A. P. and Deutschbauer, A. M. 2019 Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism mSystems 10.1128/mSystems.00297-18
Scarborough, M. J., Lawson, C. E., Hamilton, J. J., Donohue, T. J. and Noguera, D. R. 2018 Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome mSystems 10.1128/mSystems.00221-18
Shi, Z., Yin, H. Q., Van Nostrand, J. D., Voordeckers, J. W., Tu, Q., Deng, Y., Yuan, M. T., Zhou, A. F., Zhang, P., Xiao, N. J., Ning, D. L., He, Z. L., Wu, L. Y. and Zhou, J. Z. 2019 Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities mSystems 10.1128/mSystems.00296-19
Succurro, A., Segre, D. and Ebenhoh, O. 2019 Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth mSystems 10.1128/mSystems.00230-18
Thommes, M., Wang, T. Y., Zhao, Q., Paschalidis, I. C. and Segre, D. 2019 Designing Metabolic Division of Labor in Microbial Communities mSystems 10.1128/mSystems.00263-18
Timm, C. M., Carter, K. R., Carrell, A. A., Jun, S. R., Jawdy, S. S., Velez, J. M., Gunter, L. E., Yang, Z., Nookaew, I., Engle, N. L., Lu, T. S., Schadt, C. W., Tschaplinski, T. J., Doktycz, M. J., Tuskan, G. A., Pelletier, D. A. and Weston, D. J. 2018 Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome mSystems 10.1128/mSystems.00070-17
Trubl, G., Jang, H. B., Roux, S., Emerson, J. B., Solonenko, N., Vik, D. R., Solden, L., Ellenbogen, J., Runyon, A. T., Bolduc, B., Woodcroft, B. J., Saleska, S. R., Tyson, G. W., Wrighton, K. C., Sullivan, M. B. and Rich, V. I. 2018 Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing mSystems 10.1128/mSystems.00076-18
Prinz JH, Held M, Smith JC, and Noe F 2011 Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes Multiscale Modeling and Simulation 10.1137/100789191
Aime, M. C., Urbina, H., Liber, J. A., Bonito, G. and Oono, R. 2018 Two new endophytic Atractiellomycetes, Atractidochium hillariae and Proceropycnis hameedii Mycologia 10.1080/00275514.2018.1446650
Bonito, G., Hameed, K., Toome-Heller, M., Healy, R., Reid, C., Liao, H. L., Aime, M. C., Schadt, C. and Vilgalys, R. 2017 Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from the Populus root microbiome Mycologia 10.1080/00275514.2016.1271689
Bruns, T. D., Hale, M. L. and Nguyen, N. H. 2019 Rhizopogon olivaceotinctus increases its inoculum potential in heated soil independent of competitive release from other ectomycorrhizal fungi Mycologia 10.1080/00275514.2019.1657354
Deshpande, V., Wang, Q., Greenfield, P., Charleston, M., Porras-Alfaro, A., Kuske, C. R., Cole, J. R., Midgley, D. J. and Nai, T. D. 2016 Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences Mycologia 10.3852/14-293
Guevara, G., Bonito, G., Trappe, J. M., Cazares, E., Williams, G., Healy, R. A., Schadt, C. and Vilgalys, R. 2013 New North American truffles (Tuber spp.) and their ectomycorrhizal associations Mycologia 10.3852/12-087
Urbina, Hector, Frank, Robert and Blackwell, Meredith 2013 Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the Sugiyamaella yeast clade Mycologia 10.3852/12-094
Rineau, F., Lmalem, H., Ahren, D., Shah, F., Johansson, T., Coninx, L., Ruytinx, J., Nguyen, H., Grigoriev, I., Kuo, A., Kohler, A., Morin, E., Vangronsveld, J., Martin, F. and Colpaert, J. V. 2017 Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes Mycorrhiza 10.1007/s00572-016-0758-4
Tarkka, M. T., Drigo, B. and Deveau, A. 2018 Mycorrhizal microbiomes Mycorrhiza 10.1007/s00572-018-0865-5
Plett, J. M., Kohler, A. and Martin, F. 2012 6 De-Constructing a Mutualist: How the Molecular Blueprints of Model Symbiotic Fungi Are Changing Our Understanding of Mutualism The Mycota (A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research) 10.1007/978-3-642-30826-0_6
Urbina, Hector and Blackwell, Meredith 2013 New combinations, Scheffersomyces amazonensis and S. ergatensis Mycotaxon 10.5248/123.233
Chaves-Lopez, C., Nguyen, H. N., Oliveira, R. C., Nadres, E. T., Paparella, A. and Rodrigues, D. F. 2018 A morphological, enzymatic and metabolic approach to elucidate apoptotic-like cell death in fungi exposed to h- and alpha-molybdenum trioxide nanoparticles Nanoscale 10.1039/c8nr06470a
Anthony, K. M. W., Zimov, S. A., Grosse, G., Jones, M. C., Anthony, P. M., Chapin, F. S., Finlay, J. C., Mack, M. C., Davydov, S., Frenzel, P. and Frolking, S. 2014 A shift of thermokarst lakes from carbon sources to sinks during the Holocene epoch Nature 10.1038/nature13560
Blees, A., Januliene, D., Hofmann, T., Koller, N., Schmidt, C., Trowitzsch, S., Moeller, A. and Tampe, R. 2017 Structure of the human MHC-I peptide-loading complex Nature 10.1038/nature24627
Bonawitz, N. D., Kim, J. I., Tobimatsu, Y., Ciesielski, P. N., Anderson, N. A., Ximenes, E., Maeda, J., Ralph, J., Donohoe, B. S., Ladisch, M. and Chapple, C. 2014 Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant Nature 10.1038/nature13084
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H. and Banfield, J. F. 2015 Unusual biology across a group comprising more than 15% of domain Bacteria Nature 10.1038/nature14486
Gu, L. C., Li, C., Aach, J., Hill, D. E., Vidal, M. and Church, G. M. 2014 Multiplex single-molecule interaction profiling of DNA-barcoded proteins Nature 10.1038/nature13761
Mandell, D. J., Lajoie, M. J., Mee, M. T., Takeuchi, R., Kuznetsov, G., Norville, J. E., Gregg, C. J., Stoddard, B. L. and Church, G. M. 2015 Biocontainment of genetically modified organisms by synthetic protein design Nature 10.1038/nature14121
McCalley, C. K., Woodcroft, B. J., Hodgkins, S. B., Wehr, R. A., Kim, E. H., Mondav, R., Crill, P. M., Chanton, J. P., Rich, V. I., Tyson, G. W. and Saleska, S. R. 2014 Methane dynamics regulated by microbial community response to permafrost thaw Nature 10.1038/nature13798
McGlynn, S. E., Chadwick, G. L., Kempes, C. P. and Orphan, V. J. 2015 Single cell activity reveals direct electron transfer in methanotrophic consortia Nature 10.1038/nature15512
McQuaid, J. B., Kustka, A. B., Obornik, M., Horak, A., McCrow, J. R., Karas, B. J., Zheng, H., Kindeberg, T., Andersson, A. J., Barbeau, K. A. and Allen, A. E. 2018 Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms Nature 10.1038/nature25982
Reaves, M. L., Young, B. D., Hosios, A. M., Xu, Y. F. and Rabinowitz, J. D. 2013 Pyrimidine homeostasis is accomplished by directed overflow metabolism Nature 10.1038/nature12445
VanBuren, R., Bryant, D., Edger, P. P., Tang, H. B., Burgess, D., Challabathula, D., Spittle, K., Hall, R., Gu, J., Lyons, E., Freeling, M., Bartels, D., Ten Hallers, B., Hastie, A., Michael, T. P. and Mockler, T. C. 2015 Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum Nature 10.1038/nature15714
Woodcroft, B. J., Singleton, C. M., Boyd, J. A., Evans, P. N., Emerson, J. B., Zayed, A. A. F., Hoelzle, R. D., Lamberton, T. O., McCalley, C. K., Hodgkins, S. B., Wilson, R. M., Purvine, S. O., Nicora, C. D., Li, C. S., Frolking, S., Chanton, J. P., Cril, P. M., Saleska, S. R., Rich, V. I. and Tyson, G. W. 2018 Genome-centric view of carbon processing in thawing permafrost Nature 10.1038/s41586-018-0338-1
Yooseph, S., Nealson, K. H., Rusch, D. B., McCrow, J. P., Dupont, C. L., Kim, M., Johnson, J., Montgomery, R., Ferriera, S., Beeson, K., Williamson, S. J., Tovchigrechko, A., Allen, A. E., Zeigler, L. A., Sutton, G., Eisenstadt, E., Rogers, Y. H., Friedman, R., Frazier, M. and Venter, J. C. 2010 Genomic and functional adaptation in surface ocean planktonic prokaryotes Nature 10.1038/nature09530
Amiram, M., Haimovich, A. D., Fan, C. G., Wang, Y. S., Aerni, H. R., Ntai, I., Moonan, D. W., Ma, N. J., Rovner, A. J., Hong, S. H., Kelleher, N. L., Goodman, A. L., Jewett, M. C., Soll, D., Rinehart, J. and Isaacs, F. J. 2015 Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids Nature Biotechnology 10.1038/nbt.3372
Arkin, A. P., Cottingham, R. W., Henry, C. S., Harris, N. L., Stevens, R. L., Maslov, S., Dehal, P., Ware, D., Perez, F., Canon, S., Sneddon, M. W., Henderson, M. L., Riehl, W. J., Murphy-Olson, D., Chan, S. Y., Kamimura, R. T., Kumari, S., Drake, M. M., Brettin, T. S., Glass, E. M., Chivian, D., Gunter, D., Weston, D. J., Allen, B. H., Baumohl, J., Best, A. A., Bowen, B., Brenner, S. E., Bun, C. C., Chandonia, J. M., Chia, J. M., Colasanti, R., Conrad, N., Davis, J. J., Davison, B. H., DeJongh, M., Devoid, S., Dietrich, E., Dubchak, I., Edirisinghe, J. N., Fang, G., Faria, J. P., Frybarger, P. M., Gerlach, W., Gerstein, M., Greiner, A., Gurtowski, J., Haun, H. L., He, F., Jain, R., Joachimiak, M. P., Keegan, K. P., Kondo, S., Kumar, V., Land, M. L., Meyer, F., Mills, M., Novichkov, P. S., Oh, T., Olsen, G. J., Olson, R., Parrello, B., Pasternak, S., Pearson, E., Poon, S. S., Price, G. A., Ramakrishnan, S., Ranjan, P., Ronald, P. C., Schatz, M. C., Seaver, S. M. D., Shukla, M., Sutormin, R. A., Syed, M. H., Thomason, J., Tintle, N. L., Wang, D., Xia, F., Yoo, H., Yoo, S. and Yu, D. 2018 KBase: The United States Department of Energy Systems Biology Knowledgebase Nature Biotechnology 10.1038/nbt.4163
Atsumi, S., Higashide, W. and Liao, J. C. 2009 Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde Nature Biotechnology 10.1038/nbt.1586
Bao, Z. H., HamediRad, M., Xue, P., Xiao, H., Tasan, I., Chao, R., Liang, J. and Zhao, H. M. 2018 Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision Nature Biotechnology 10.1038/nbt.4132
Bennetzen, J. L., Schmutz, J., Wang, H., Percifield, R., Hawkins, J., Pontaroli, A. C., Estep, M., Feng, L., Vaughn, J. N., Grimwood, J., Jenkins, J., Barry, K., Lindquist, E., Hellsten, U., Deshpande, S., Wang, X. W., Wu, X. M., Mitros, T., Triplett, J., Yang, X. H., Ye, C. Y., Mauro-Herrera, M., Wang, L., Li, P. H., Sharma, M., Sharma, R., Ronald, P. C., Panaud, O., Kellogg, E. A., Brutnell, T. P., Doust, A. N., Tuskan, G. A., Rokhsar, D. and Devos, K. M. 2012 Reference genome sequence of the model plant Setaria Nature Biotechnology 10.1038/nbt.2196
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., 2018 Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis Nature Biotechnology 10.1038/nbt.4067
Brown, C. T., Olm, M. R., Thomas, B. C. and Banfield, J. F. 2016 Measurement of bacterial replication rates in microbial communities Nature Biotechnology 10.1038/nbt.3704
DiCarlo, J. E., Chavez, A., Dietz, S. L., Esvelt, K. M. and Church, G. M. 2015 Safeguarding CRISPR-Cas9 gene drives in yeast Nature Biotechnology 10.1038/nbt.3412
Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L. H. and Church, G. M. 2013 CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering Nature Biotechnology 10.1038/nbt.2675
Qiao, K. J., Wasylenko, T. M., Zhou, K., Xu, P. and Stephanopoulos, G. 2017 Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism Nature Biotechnology 10.1038/nbt.3763
Zhang, F., Cong, L., Lodato, S., Kosuri, S., Church, G. M. and Arlotta, P. 2011 Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription Nature Biotechnology 10.1038/nbt.1775
DeLoache, W. C., Russ, Z. N., Narcross, L., Gonzales, A. M., Martin, V. J. J. and Dueber, J. E. 2015 An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose Nature Chemical Biology 10.1038/nchembio.1816
Doucette, C. D., Schwab, D. J., Wingreen, N. S. and Rabinowitz, J. D. 2011 alpha-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition Nature Chemical Biology 10.1038/nchembio.685
Hong-Hermesdorf, Anne, Miethke, Marcus, Gallaher, Sean D., Kropat, Janette, Dodani, Sheel C., Chan, Jefferson, Barupala, Dulmini, Domaille, Dylan W., Shirasaki, Dyna I., Loo, Joseph A., Weber, Peter K., Pett-Ridge, Jennifer, Stemmler, Timothy L., Chang, Christopher J. and Merchant, Sabeeha S. 2014 Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas Nature Chemical Biology 10.1038/nchembio.1662
Oslund, R. C., Su, X. Y., Haugbro, M., Kee, J. M., Esposito, M., David, Y., Wang, B. Y., Ge, E., Perlman, D. H., Kang, Y. B., Muir, T. W. and Rabinowitz, J. D. 2017 Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate Nature Chemical Biology 10.1038/nchembio.2453
Park, J. O., Rubin, S. A., Xu, Y. F., Amador-Noguez, D., Fan, J., Shlomi, T. and Rabinowitz, J. D. 2016 Metabolite concentrations, fluxes and free energies imply efficient enzyme usage Nature Chemical Biology 10.1038/nchembio.2077
Park, J. O., Tanner, L. B., Wei, M. H., Khana, D. B., Jacobson, T. B., Zhang, Z. Y., Rubin, S. A., Li, S. H. J., Higgins, M. B., Stevenson, D. M., Amador-Noguez, D. and Rabinowitz, J. D. 2019 Near-equilibrium glycolysis supports metabolic homeostasis and energy yield Nature Chemical Biology 10.1038/s41589-019-0364-9
Xu, Y. F., Amador-Noguez, D., Reaves, M. L., Feng, X. J. and Rabinowitz, J. D. 2012 Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase Nature Chemical Biology 10.1038/nchembio.941
Guo, X., Feng, J. J., Shi, Z., Zhou, X. S., Yuan, M. T., Tao, X. Y., Hale, L., Yuan, T., Wang, J. J., Qin, Y. J., Zhou, A. F., Fu, Y., Wu, L. Y., He, Z. L., Van Nostrand, J. D., Ning, D. L., Liu, X. D., Luo, Y. Q., Tiedje, J. M., Yang, Y. F. and Zhou, J. Z. 2018 Climate warming leads to divergent succession of grassland microbial communities Nature Climate Change 10.1038/s41558-018-0254-2
Xue, K., Yuan, M. M., Shi, Z. J., Qin, Y. J., Deng, Y., Cheng, L., Wu, L. Y., He, Z. L., Van Nostrand, J. D., Bracho, R., Natali, S., Schuur, E. A. G., Luo, C. W., Konstantinidis, K. T., Wang, Q., Cole, J. R., Tiedje, J. M., Luo, Y. Q. and Zhou, J. Z. 2016 Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming Nature Climate Change 10.1038/nclimate2940
Zhou, J. Z., Xue, K., Xie, J. P., Deng, Y., Wu, L. Y., Cheng, X. H., Fei, S. F., Deng, S. P., He, Z. L., Van Nostrand, J. D. and Luo, Y. Q. 2012 Microbial mediation of carbon-cycle feedbacks to climate warming Nature Climate Change 10.1038/nclimate1331
Abdel-Ghany, S. E., Hamilton, M., Jacobi, J. L., Ngam, P., Devitt, N., Schilkey, F., Ben-Hur, A. and Reddy, A. S. N. 2016 A survey of the sorghum transcriptome using single-molecule long reads Nature Communications 10.1038/ncomms11706
Akhil Kumar , Lin Wang, Chiam Yu Ng, Costas D. Maranas 2018 Pathway design using de novo steps through uncharted biochemical spaces Nature Communications 10.1038/s41467-017-02362-x
Al-Bassam, M. M., Kim, J. N., Zaramela, L. S., Kellman, B. P., Zuniga, C., Wozniak, J. M., Gonzalez, D. J. and Zengler, K. 2018 Optimization of carbon and energy utilization through differential translational efficiency Nature Communications 10.1038/s41467-018-06993-6
Anderson, E.M., Stone, M.L., Katahira, R., Reed, M., Muchero, W., Ramirez, K.J., Beckham, G.T., and Roman-Leshkov, Y. 2019 Differences in S/G ratio in natural poplar variants do not predict catalytic depolymerization monomer yields Nature Communications 10.1038/s41467-019-09986-1
Angle, J. C., Morin, T. H., Solden, L. M., Narrowe, A. B., Smith, G. J., Borton, M. A., Rey-Sanchez, C., Daly, R. A., Mirfenderesgi, G., Hoyt, D. W., Riley, W. J., Miller, C. S., Bohrer, G. and Wrighton, K. C. 2017 Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions Nature Communications 10.1038/s41467-017-01753-4
Anthony, K. W., von Deimling, T. S., Nitze, I., Frolking, S., Emond, A., Daanen, R., Anthony, P., Lindgren, P., Jones, B. and Grosse, G. 2018 21st-century modeled permafrost carbon emissions accelerated by abrupt thaw beneath lakes Nature Communications 10.1038/s41467-018-05738-9
Baran, R., Brodie, E. L., Mayberry-Lewis, J., Hummel, E., Da Rocha, U. N., Chakraborty, R., Bowen, B. P., Karaoz, U., Cadillo-Quiroz, H., Garcia-Pichel, F. and Northen, T. R. 2015 Exometabolite niche partitioning among sympatric soil bacteria Nature Communications 10.1038/ncomms9289
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. 2019 4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase Nature Communications 10.1038/s41467-019-10082-7
Boock, J. T., Freedman, A. J. E., Tompsett, G. A., Muse, S. K., Allen, A. J., Jackson, L. A., Castro-Dominguez, B., Timko, M. T., Prather, K. L. J. and Thompson, J. R. 2019 Engineered microbial biofuel production and recovery under supercritical carbon dioxide Nature Communications 10.1038/s41467-019-08486-6
Burstein, D., Sun, C. L., Brown, C. T., Sharon, I., Anantharaman, K., Probst, A. J., Thomas, B. C. and Banfield, J. F. 2016 Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems Nature Communications 10.1038/ncomms10613
Couradeau, E., Karaoz, U., Lim, H. C., Nunes da Rocha, U., Northen, T., Brodie, E. and Garcia-Pichel, F. 2016 Bacteria increase arid-land soil surface temperature through the production of sunscreens Nature Communications 10.1038/ncomms10373
Couradeau, E., Sasse, J., Goudeau, D., Nath, N., Hazen, T. C., Bowen, B. P., Chakraborty, R., Malmstrom, R. R. and Northen, T. R. 2019 Probing the active fraction of soil microbiomes using BONCAT-FACS Nature Communications 10.1038/s41467-019-10542-0
DeLoache, W. C., Russ, Z. N. and Dueber, J. E. 2016 Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways Nature Communications 10.1038/ncomms11152
Garsmeur, O., Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K., D’Hont, A. 2018 A mosaic monoploid reference sequence for the highly complex genome of sugarcane Nature Communications 10.1038/s41467-018-05051-5
Grady, K. L., Sorensen, J. W., Stopnisek, N., Guittar, J. and Shade, A. 2019 Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops Nature Communications 10.1038/s41467-019-11974-4
Heckmann, D., Zielinski, D. C. and Palsson, B. O. 2018 Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates Nature Communications 10.1038/s41467-018-07649-1
Hodgkins, S. B., Richardson, C. J., Dommain, R., Wang, H. J., Glaser, P. H., Verbeke, B., Winkler, B. R., Cobb, A. R., Rich, V. I., Missilmani, M., Flanagan, N., Ho, M., Hoyt, A. M., Harvey, C. F., Vining, S. R., Hough, M. A., Moore, T. R., Richard, P. J. H., De la Cruz, F. B., Toufaily, J., Hamdan, R., Cooper, W. T. and Chanton, J. P. 2018 Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance Nature Communications 10.1038/s41467-018-06050-2
Juarez, J. F., Lecube-Azpeitia, B., Brown, S. L., Johnston, C. D. and Church, G. M. 2018 Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators Nature Communications 10.1038/s41467-018-05525-6
Kalyuzhnaya, M. G., Yang, S., Rozova, O. N., Smalley, N. E., Clubb, J., Lamb, A., Gowda, G. A. N., Raftery, D., Fu, Y., Bringel, F., Vuilleumier, S., Beck, D. A. C., Trotsenko, Y. A., Khmelenina, V. N. and Lidstrom, M. E. 2013 Highly efficient methane biocatalysis revealed in a methanotrophic bacterium Nature Communications 10.1038/ncomms3785
Karas, B. J., Diner, R. E., Lefebvre, S. C., McQuaid, J., Phillips, A. P. R., Noddings, C. M., Brunson, J. K., Valas, R. E., Deerinck, T. J., Jablanovic, J., Gillard, J. T. F., Beeri, K., Ellisman, M. H., Glass, J. I., Hutchison, C. A., Smith, H. O., Venter, J. C., Allen, A. E., Dupont, C. L. and Weyman, P. D. 2015 Designer diatom episomes delivered by bacterial conjugation Nature Communications 10.1038/ncomms7925
Khodayari, A. and Maranas, C. D. 2016 A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains Nature Communications 10.1038/ncomms13806
Kraychenko, A. N., Guber, A. K., Razavi, B. S., Koestel, J., Quigley, M. Y., Robertson, G. P. and Kuzyakov, Y. 2019 Microbial spatial footprint as a driver of soil carbon stabilization Nature Communications 10.1038/s41467-019-11057-4
Lee, H. H., Kalhor, R., Goela, N., Bolot, J. and Church, G. M. 2019 Terminator-free template-independent enzymatic DNA synthesis for digital information storage Nature Communications 10.1038/s41467-019-10258-1
Lian, J. Z., HamediRad, M., Hu, S. M. and Zhao, H. M. 2017 Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system Nature Communications 10.1038/s41467-017-01695-x
Liang, J. Y., Zhou, Z. G., Huo, C. F., Shi, Z., Cole, J. R., Huang, L., Konstantinidis, K. T., Li, X. M., Liu, B., Luo, Z. K., Penton, C. R., Schuur, E. A. G., Tiedje, J. M., Wang, Y. P., Wu, L. Y., Xia, J. Y., Zhou, J. Z. and Luo, Y. Q. 2018 More replenishment than priming loss of soil organic carbon with additional carbon input Nature Communications 10.1038/s41467-018-05667-7
Liu, J. J., Zhang, G. C., Kwak, S., Oh, E. J., Yun, E. J., Chomvong, K., Cate, J. H. D. and Jin, Y. S. 2019 Overcoming the thermodynamic equilibrium of an isomerization reaction through oxidoreductive reactions for biotransformation Nature Communications 10.1038/s41467-019-09288-6
Liu, Y. X., Huynh, D. T. and Yeates, T. O. 2019 A 3.8 angstrom resolution cryo-EM structure of a small protein bound to an imaging scaffold Nature Communications 10.1038/s41467-019-09836-0
Love, J. T., Jenkins, J., Lowry, D. B., Mamidi, S., Sreedasyam, A., Weng, X. Y., Barry, K., Bonnette, J., Campitelli, B., Daum, C., Gordon, S. P., Gould, B. A., Khasanova, A., Lipzen, A., MacQueen, A., Palacio-Mejia, J. D., Plott, C., Shakirov, E. V., Shu, S. Q., Yoshinaga, Y., Zane, M., Kudrna, D., Talag, J. D., Rokhsar, D., Grimwood, J., Schmutz, J. and Juenger, T. E. 2018 The genomic landscape of molecular responses to natural drought stress in Panicum hallii Nature Communications 10.1038/s41467-018-07669-x
Martinez-Hernandez, F., Fornas, O., Gomez, M. L., Bolduc, B., de la Cruz Pena, M. J., Martinez, J. M., Anton, J., Gasol, J. M., Rosselli, R., Rodriguez-Valera, F., Sullivan, M. B., Acinas, S. G. and Martinez-Garcia, M. 2017 Single-virus genomics reveals hidden cosmopolitan and abundant viruses Nature Communications 10.1038/ncomms15892
Matheus Carnevali, P. B., Schulz, F., Castelle, C. J., Kantor, R. S., Shih, P. M., Sharon, I., Banfield, J. F. 2019 Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria Nature Communications 10.1038/s41467-018-08246-y
Mellmer, M. A., Sanpitakseree, C., Demir, B., Ma, K. W., Elliott, W. A., Bai, P., Johnson, R. L., Walker, T. W., Shanks, B. H., Rioux, R. M., Neurock, M. and Dumesic, J. A. 2019 Effects of chloride ions in acid-catalyzed biomass dehydration reactions in polar aprotic solvents Nature Communications 10.1038/s41467-019-09090-4
Mondav, R., Woodcroft, B. J., Kim, E. H., McCalley, C. K., Hodgkins, S. B., Crill, P. M., Chanton, J., Hurst, G. B., VerBerkmoes, N. C., Saleska, S. R., Hugenholtz, P., Rich, V. I. and Tyson, G. W. 2014 Discovery of a novel methanogen prevalent in thawing permafrost Nature Communications 10.1038/ncomms4212
Mutalik, V. K., Novichkov, P. S., Price, M. N., Owens, T. K., Callaghan, M., Carim, S., Deutschbauer, A. M. and Arkin, A. P. 2019 Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria Nature Communications 10.1038/s41467-018-08177-8
Nagarajan, H., Embree, M., Rotaru, A. E., Shrestha, P. M., Feist, A. M., Palsson, B. O., Lovley, D. R. and Zengler, K. 2013 Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association Nature Communications 10.1038/ncomms3809
Nagy, L. G., Ohm, R. A., Kovacs, G. M., Floudas, D., Riley, R., Gacser, A., Sipiczki, M., Davis, J. M., Doty, S. L., de Hoog, G. S., Lang, B. F., Spatafora, J. W., Martin, F. M., Grigoriev, I. V. and Hibbett, D. S. 2014 Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts Nature Communications 10.1038/ncomms5471
Ortega, D. R., Yang, C., Ames, P., Baudry, J., Parkinson, J. S. and Zhulin, I. B. 2013 A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors Nature Communications 10.1038/ncomms3881
Pacheco, A. R., Moel, M. and Segre, D. 2019 Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems Nature Communications 10.1038/s41467-018-07946-9
Peter, M., Kohler, A., Ohm, R. A., Kuo, A., Krutzmann, J., Morin, E., Arend, M., Barry, K. W., Binder, M., Choi, C., Clum, A., Copeland, A., Grisel, N., Haridas, S., Kipfer, T., LaButti, K., Lindquist, E., Lipzen, A., Maire, R., Meier, B., Mihaltcheva, S., Molinier, V., Murat, C., Poggeler, S., Quandt, C. A., Sperisen, C., Tritt, A., Tisserant, E., Crous, P. W., Henrissat, B., Nehls, U., Egli, S., Spatafora, J. W., Grigoriev, I. V. and Martin, F. M. 2016 Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum Nature Communications 10.1038/ncomms12662
Qiu, Y., Nagarajan, H., Embree, M., Shieu, W., Abate, E., Juarez, K., Cho, B. K., Elkins, J. G., Nevin, K. P., Barrett, C. L., Lovley, D. R., Palsson, B. O. and Zengler, K. 2013 Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks Nature Communications 10.1038/ncomms2743
Ruegg, T. L., Pereira, J. h., Chen, J. C., DeGiovanni, A., Novichkov, P., Mutalik, V. K., Thelen, M. P. 2018 Jungle Express is a versatile repressor system for tight transcriptional control Nature Communications 10.1038/s41467-018-05857-3
Sadre, R., Kuo, P. Y., Chen, J. X., Yang, Y., Banerjee, A., Benning, C. and Hamberger, B. 2019 Cytosolic lipid droplets as engineered organelles for production and accumulation of terpenoid biomaterials in leaves Nature Communications 10.1038/s41467-019-08515-4
Saifuddin, M., Bhatnagar, J. M., Segre, D. and Finzi, A. C. 2019 Microbial carbon use efficiency predicted from genome-scale metabolic models Nature Communications 10.1038/s41467-019-11488-z
Smith, S. R., Dupont, C. L., McCarthy, J. K., Broddrick, J. T., Obornik, M., Horak, A., Fussy, Z., Cihlar, J., Kleessen, S., Zheng, H., McCrow, J. P., Hixson, K. K., Araujo, W. L., Nunes-Nesi, A., Fernie, A., Nikoloski, Z., Palsson, B. O. and Allen, A. E. 2019 Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom Nature Communications 10.1038/s41467-019-12407-y
Straub, C. T., Khatibi, P. A., Wang, J. P., Conway, J. M., Williams-Rhaesa, A. M., Peszlen, I. M., Chiang, V. L., Adams, M. W. W. and Kelly, R. M. 2019 Quantitative fermentation of unpretreated transgenic poplar by Caldicellulosiruptor bescii Nature Communications 10.1038/s41467-019-11376-6
Swenson, T. L., Karaoz, U., Swenson, J. M., Bowen, B. P. and Northen, T. R. 2018 Linking soil biology and chemistry in biological soil crust using isolate exometabolomics Nature Communications 10.1038/s41467-017-02356-9
Valdovinos, F. S., Berlow, E. L., de Espanes, P. M., Ramos-Jiliberto, R., Vazquez, D. P. and Martinez, N. D. 2018 Species traits and network structure predict the success and impacts of pollinator invasions Nature Communications 10.1038/s41467-018-04593-y
Valliere, M. A., Korman, T. P., Woodall, N. B., Khitrov, G. A., Taylor, R. E., Baker, D. and Bowie, J. U. 2019 A cell-free platform for the prenylation of natural products and application to cannabinoid production Nature Communications 10.1038/s41467-019-08448-y
Vasdekis, A. E., Alanazi, H., Silverman, A. M., Williams, C. J., Canul, A. J., Cliff, J. B., Dohnalkova, A. C. and Stephanopoulos, G. 2019 Eliciting the impacts of cellular noise on metabolic trade-offs by quantitative mass imaging Nature Communications 10.1038/s41467-019-08717-w
Widhalm, J. R., Gutensohn, M., Yoo, H., Adebesin, F., Qian, Y. C., Guo, L. Y., Jaini, R., Lynch, J. H., McCoy, R. M., Shreve, J. T., Thimmapuram, J., Rhodes, D., Morgan, J. A. and Dudareva, N. 2015 Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network Nature Communications 10.1038/ncomms9142
Wurch, L., Giannone, R. J., Belisle, B. S., Swift, C., Utturkar, S., Hettich, R. L., Reysenbach, A. L. and Podar, M. 2016 Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment Nature Communications 10.1038/ncomms12115
Yang, X. H., Hu, R. B., Yin, H. F., Jenkins, J., Shu, S. Q., Tang, H. B., Liu, D. G., Weighill, D. A., Yim, W. C., Ha, J. M., Heyduk, K., Goodstein, D. M., Guo, H. B., Moseley, R. C., Fitzek, E., Jawdy, S., Zhang, Z. H., Xie, M., Hartwell, J., Grimwood, J., Abraham, P. E., Mewalal, R., Beltran, J. D., Boxall, S. F., Dever, L. V., Palla, K. J., Albion, R., Garcia, T., Mayer, J. A., Lim, S. D., Wai, C. M., Peluso, P., Van Buren, R., De Paoli, H. C., Borland, A. M., Guo, H., Chen, J. G., Muchero, W., Yin, Y. B., Jacobson, D. A., Tschaplinski, T. J., Hettich, R. L., Ming, R., Winter, K., Leebens-Mack, J. H., Smith, J. A. C., Cushman, J. C., Schmutz, J. and Tuskan, G. A. 2017 The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism Nature Communications 10.1038/s41467-017-01491-7
Yoo, H., Widhalm, J. R., Qian, Y. C., Maeda, H., Cooper, B. R., Jannasch, A. S., Gonda, I., Lewinsohn, E., Rhodes, D. and Dudareva, N. 2013 An alternative pathway contributes to phenylalanine biosynthesis in plants via a cytosolic tyrosine:phenylpyruvate aminotransferase Nature Communications 10.1038/ncomms3833
Guo, X., Zhou, X. S., Hale, L., Yuan, M. T., Ning, D. L., Feng, J. J., Shi, Z., Li, Z. X., Feng, B., Gao, Q., Wu, L. W., Shi, W. L., Zhou, A. F., Fu, Y., Wu, L. Y., He, Z. L., Van Nostrand, J. D., Qiu, G. Z., Liu, X. D., Luo, Y. Q., Tiedje, J. M., Yang, Y. F. and Zhou, J. Z. 2019 Climate warming accelerates temporal scaling of grassland soil microbial biodiversity Nature Ecology and Evolution 10.1038/s41559-019-0848-8
Langdon, Q. K., Peris, D., Baker, E. P., Opulente, D. A., Nguyen, H. V., Bond, U., Goncalves, P., Sampaio, J. P., Libkind, D. and Hittinger, C. T. 2019 Fermentation innovation through complex hybridization of wild and domesticated yeasts Nature Ecology and Evolution 10.1038/s41559-019-0998-8
Morrissey, E. M., Mau, R. L., Hayer, M., Liu, X. J. A., Schwartz, E., Dijkstra, P., Koch, B. J., Allen, K., Blazewicz, S. J., Hofmockel, K., Pett-Ridge, J. and Hungate, B. A. 2019 Evolutionary history constrains microbial traits across environmental variation Nature Ecology and Evolution 10.1038/s41559-019-0918-y
Zhou, Y. J., Kerkhoven, E. J. and Nielsen, J. 2018 Barriers and opportunities in bio-based production of hydrocarbons Nature Energy 10.1038/s41560-018-0197-x
Kohler, A., Kuo, A., Nagy, L. G., Morin, E., Barry, K. W., Buscot, F., Canback, B., Choi, C., Cichocki, N., Clum, A., Colpaert, J., Copeland, A., Costa, M. D., Dore, J., Floudas, D., Gay, G., Girlanda, M., Henrissat, B., Herrmann, S., Hess, J., Hogberg, N., Johansson, T., Khouja, H. R., LaButti, K., Lahrmann, U., Levasseur, A., Lindquist, E. A., Lipzen, A., Marmeisse, R., Martino, E., Murat, C., Ngan, C. Y., Nehls, U., Plett, J. M., Pringle, A., Ohm, R. A., Perotto, S., Peter, M., Riley, R., Rineau, F., Ruytinx, J., Salamov, A., Shah, F., Sun, H., Tarkka, M., Tritt, A., Veneault-Fourrey, C., Zuccaro, A., Mycorrhizal Genomics Initiative, Consortium, Tunlid, A., Grigoriev, I. V., Hibbett, D. S. and Martin, F. 2015 Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists Nature Genetics 10.1038/ng.3223
Levy, A., Gonzalez, I. S., Mittelviefhaus, M., Clingenpeel, S., Paredes, S. H., Miao, J. M., Wang, K. R., Devescovi, G., Stillman, K., Monteiro, F., Alvarez, B. R., Lundberg, A. D. S., Lu, T. Y., Lebeis, S., Jin, Z., McDonald, M., Klein, A. P., Feltcher, M. E., Rio, T. G., Grant, S. R., Doty, S. L., Ley, R. E., Zhao, B. Y., Venturi, V., Pelletier, D. A., Vorholt, J. A., Tringe, S. G., Woyke, T. and Dangl, J. L. 2018 Genomic features of bacterial adaptation to plants Nature Genetics 10.1038/s41588-017-0012-9
Levy, A., Salas Gonzalez, I., Mittelviefhaus, M., Clingenpeel, S., Herrera Paredes, S., Miao, J., Wang, K., Devescovi, G., Stillman, K., Monteiro, F., Rangel Alvarez, B., Lundberg, D. S., Lu, T. Y., Lebeis, S., Jin, Z., McDonald, M., Klein, A. P., Feltcher, M. E., Rio, T. G., Grant, S. R., Doty, S. L., Ley, R. E., Zhao, B., Venturi, V., Pelletier, D. A., Vorholt, J. A., Tringe, S. G., Woyke, T. and Dangl, J. L. 2017 Genomic features of bacterial adaptation to plants Nature Genetics 10.1038/s41588-017-0012-9
Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M. L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., Yim, W. C., Priest, H. D., Zheng, C., Woodhouse, M., Edger, P. P., Guyot, R., Guo, H. B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F. J., Harkess, A., McKain, M. R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L. Y., Shirley, N., Lin, Y. R., Liu, L. Y., Hernandez, A. G., Wright, C. L., Bulone, V., Tuskan, G. A., Heath, K., Zee, F., Moore, P. H., Sunkar, R., Leebens-Mack, J. H., Mockler, T., Bennetzen, J. L., Freeling, M., Sankoff, D., Paterson, A. H., Zhu, X., Yang, X., Smith, J. A., Cushman, J. C., Paull, R. E. and Yu, Q. 2015 The pineapple genome and the evolution of CAM photosynthesis Nature Genetics 10.1038/ng.3435
Ming, R., VanBuren, R., Wai, C. M., Tang, H. B., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M. L., Chen, J., Biggers, E., Zhang, J. S., Huang, L. X., Zhang, L. M., Miao, W. J., Zhang, J., Ye, Z. Y., Miao, C. Y., Lin, Z. C., Wang, H., Zhou, H. Y., Yim, W. C., Priest, H. D., Zheng, C. F., Woodhouse, M., Edger, P. P., Guyot, R., Guo, H. B., Guo, H., Zheng, G. Y., Singh, R., Sharma, A., Min, X. J., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F. J., Harkess, A., McKain, M. R., Liao, Z. Y., Fang, J. P., Liu, J., Zhang, X. D., Zhang, Q., Hu, W. C., Qin, Y., Wang, K., Chen, L. Y., Shirley, N., Lin, Y. R., Liu, L. Y., Hernandez, A. G., Wright, C. L., Bulone, V., Tuskan, G. A., Heath, K., Zee, F., Moore, P. H., Sunkar, R., Leebens-Mack, J. H., Mockler, T., Bennetzen, J. L., Freeling, M., Sankoff, D., Paterson, A. H., Zhu, X. G., Yang, X. H., Smith, J. A. C., Cushman, J. C., Paull, R. E. and Yu, Q. Y. 2015 The pineapple genome and the evolution of CAM photosynthesis Nature Genetics 10.1038/ng.3435
Mondo, S. J., Dannebaum, R. O., Kuo, R. C., Louie, K. B., Bewick, A. J., LaButti, K., Haridas, S., Kuo, A., Salamov, A., Ahrendt, S. R., Lau, R., Bowen, B. P., Lipzen, A., Sullivan, W., Andreopoulos, B. B., Clum, A., Lindquist, E., Daum, C., Northen, T. R., Kunde-Ramamoorthy, G., Schmitz, R. J., Gryganskyi, A., Culley, D., Magnuson, J., James, T. Y., O'Malley, M. A., Stajich, J. E., Spatafora, J. W., Visel, A. and Grigoriev, I. V. 2017 Widespread adenine N6-methylation of active genes in fungi Nature Genetics 10.1038/ng.3859
Zhang, J. S., Zhang, X. T., Tang, H. B., Zhang, Q., Hua, X. T., Ma, X. K., Zhu, F., Jones, T., Zhu, X. G., Bowers, J., Wai, C. M., Zheng, C. F., Shil, Y., Chen, S., Xu, X. M., Yue, J. J., Nelsons, D. R., Huang, L. X., Li, Z., Xu, H. M., Zhou, D., Wang, Y. J., Hu, W. C., Lin, J. S., Deng, Y. J., Pandey, N., Mancini, M., Zerpa, D., Nguyen, J. K., Wang, L. M., Yu, L., Xin, Y. H., Ge, L. F., Arro, J., Han, J. O., Chakrabarty, S., Pushko, M., Zhang, W. P., Ma, Y. H., Ma, P. P., Lv, M. J., Chen, F. M., Zheng, G. Y., Xu, J. S., Yang, Z. H., Deng, F., Chen, X. Q., Liao, Z. Y., Zhang, X. X., Lin, Z. C., Lin, H., Yan, H. S., Kuang, Z., Zhong, W. M., Liang, P. P., Wang, G. F., Yuan, Y., Shi, J. X., Hou, J. X., Lin, J. X., Jin, J. J., Cao, P. J., Shen, Q. C., Jiang, Q., Zhou, P., Ma, Y. Y., Zhang, X. D., Xu, R. R., Liu, J., Zhou, Y. M., Jia, H. F., Ma, Q., Qi, R., Zhang, Z. L., Fang, J. P., Fang, H. K., Song, J. J., Wang, M. J., Dong, G. R., Wang, G., Chen, Z., Ma, T., Liu, H., Dhungana, S. R., Huss, S. E., Yang, X. P., Sharma, A., Trujillo, J. H., Martinez, M. C., Hudson, M., Riascos, J. J., Schuler, M., Chen, L. Q., Braun, D. M., Li, L., Yu, Q. Y., Wang, J. P., Wang, K., Schatz, M. C., Heckerman, D., Van Sluys, M. A., Souza, G. M., Moore, P. H., Sankoff, D., VanBuren, R., Paterson, A. H., Nagai, C. and Ming, R. 2018 Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L Nature Genetics 10.1038/s41588-018-0237-2
Chavez, A., Scheiman, J., Vora, S., Pruitt, B. W., Tuttle, M., Iyer, E. P. R., Lin, S. L., Kiani, S., Guzman, C. D., Wiegand, D. J., Ter-Ovanesyan, D., Braff, J. L., Davidsohn, N., Housden, B. E., Perrimon, N., Weiss, R., Aach, J., Collins, J. J. and Church, G. M. 2015 Highly efficient Cas9-mediated transcriptional programming Nature Methods 10.1038/nmeth.3312
Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J. and Church, G. M. 2013 Orthogonal Cas9 proteins for RNA-guided gene regulation and editing Nature Methods 10.1038/nmeth.2681
Kiani, S., Chavez, A., Tuttle, M., Hal, R. N., Chari, R., Ter-Ovanesyan, D., Qian, J., Pruitt, B. W., Beal, J., Vora, S., Buchthal, J., Kowal, E. J. K., Ebrahimkhani, M. R., Collins, J. J., Weiss, R. and Church, G. 2015 Cas9 gRNA engineering for genome editing, activation and repression Nature Methods 10.1038/nmeth.3580
Mali, P., Esvelt, K. M. and Church, G. M. 2013 Cas9 as a versatile tool for engineering biology Nature Methods 10.1038/nmeth.2649
Manichaikul, A., Ghamsari, L., Hom, E. F. Y., Lin, C. W., Murray, R. R., Chang, R. L., Balaji, S., Hao, T., Shen, Y., Chavali, A. K., Thiele, I., Yang, X. P., Fan, C. Y., Mello, E., Hill, D. E., Vidal, M., Salehi-Ashtiani, K. and Papin, J. A. 2009 Metabolic network analysis integrated with transcript verification for sequenced genomes Nature Methods 10.1038/nmeth.1348
Martin, Michael C., Dabat-Blondeau, Charlotte, Unger, Miriam, Sedlmair, Julia, Parkinson, Dilworth Y., Bechtel, Hans A., Illman, Barbara, Castro, Jonathan M., Keiluweit, Marco, Buschke, David, Ogle, Brenda, Nasse, Michael J. and Hirschmugl, Carol J. 2013 3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography Nature Methods 10.1038/nmeth.2596
Morton, J. T., Aksenov, A. A., Nothias, L. F., Foulds, J. R., Quinn, R. A., Badri, M. H., Swenson, T. L., Van Goethem, M. W., Northen, T. R., Vazquez-Baeza, Y., Wang, M., Bokulich, N. A., Watters, A., Song, S. J., Bonneau, R., Dorrestein, P. C. and Knight, R. 2019 Learning representations of microbe-metabolite interactions Nature Methods 10.1038/s41592-019-0616-3
Taylor, N. D., Garruss, A. S., Moretti, R., Chan, S., Arbing, M. A., Cascio, D., Rogers, J. K., Isaacs, F. J., Kosuri, S., Baker, D., Fields, S., Church, G. M. and Raman, S. 2016 Engineering an allosteric transcription factor to respond to new ligands Nature Methods 10.1038/nmeth.3696
Trigg, S. A., Garza, R. M., MacWilliams, A., Nery, J. R., Bartlett, A., Castanon, R., Goubil, A., Feeney, J., O'Malley, R., Huang, S. S. C., Zhang, Z. Z., Galli, M. and Ecker, J. R. 2017 CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping Nature Methods 10.1038/nmeth.4343
Zengler, Karsten, Hofmockel, Kirsten, Baliga, Nitin S., Behie, Scott W., Bernstein, Hans C., Brown, James B., Dinneny, José R., Floge, Sheri A., Forry, Samuel P., Hess, Matthias, Jackson, Scott A., Jansson, Christer, Lindemann, Stephen R., Pett-Ridge, Jennifer, Maranas, Costas, Venturelli, Ophelia S., Wallenstein, Matthew D., Shank, Elizabeth A. and Northen, Trent R. 2019 EcoFABs: advancing microbiome science through standardized fabricated ecosystems Nature Methods 10.1038/s41592-019-0465-0
Ceja-Navarro, J. A., Karaoz, U., Bill, M., Hao, Z., White, R. A., 3rd, Arellano, A., Ramanculova, L., Filley, T. R., Berry, T. D., Conrad, M. E., Blackwell, M., Nicora, C. D., Kim, Y. M., Reardon, P. N., Lipton, M. S., Adkins, J. N., Pett-Ridge, J. and Brodie, E. L. 2019 Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle Nature Microbiology 10.1038/s41564-019-0384-y
Emerson, J. B., Roux, S., Brum, J. R., Bolduc, B., Woodcroft, B. J., Jang, H. B., Singleton, C. M., Soden, L. M., Naas, A. E., Boyd, J. A., Hodgkins, S. B., Wilson, R. M., Trubl, G., Li, C. S., Frokings, S., Pope, P. B., Wrighton, K. C., Crill, P. M., Chanton, J. P., Saleska, S. R., Tyson, G. W., Rich, V. I. and Sullivan, M. B. 2018 Host-linked soil viral ecology along a permafrost thaw gradient Nature Microbiology 10.1038/s41564-018-0190-y
Haitjema, C. H., Gilmore, S. P., Henske, J. K., Solomon, K. V., de Groot, R., Kuo, A., Mondo, S. J., Salamov, A. A., LaButti, K., Zhao, Z. Y., Chiniquy, J., Barry, K., Brewer, H. M., Purvine, S. O., Wright, A. T., Hainaut, M., Boxma, B., van Alen, T., Hackstein, J. H. P., Henrissat, B., Baker, S. E., Grigoriev, I. V. and O'Malley, M. A. 2017 A parts list for fungal cellulosomes revealed by comparative genomics Nature Microbiology 10.1038/nmicrobiol.2017.87
Lee, H. H., Ostrov, N., Wong, B. G., Gold, M. A., Khalil, A. S. and Church, G. M. 2019 Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi Nature Microbiology 10.1038/s41564-019-0423-8
Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P. A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P. and Tyson, G. W. 2017 Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Nature Microbiology 10.1038/s41564-017-0012-7
Paul, B. G., Burstein, D., Castelle, C. J., Handa, S., Arambula, D., Czornyj, E., Thomas, B. C., Ghosh, P., Miller, J. F., Banfield, J. F. and Valentine, D. L. 2017 Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea Nature Microbiology 10.1038/nmicrobiol.2017.45
Zhalnina, K., Louie, K. B., Hao, Z., Mansoori, N., da Rocha, U. N., Shi, S. J., Cho, H. J., Karaoz, U., Loque, D., Bowen, B. P., Firestone, M. K., Northen, T. R. and Brodie, E. L. 2018 Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly Nature Microbiology 10.1038/s41564-018-0129-3
Zuniga, C., Li, C. T., Yu, G., Al-Bassam, M. M., Li, T. T., Jiang, L. Q., Zaramela, L. S., Guarnieri, M., Betenbaugh, M. J. and Zengler, K. 2019 Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities Nature Microbiology 10.1038/s41564-019-0567-6
Zuniga, C., Li, C. T., Yu, G., Al-Bassam, M. M., Li, T. T., Jiang, L. Q., Zaramela, L. S., Guarnieri, M., Betenbaugh, M. J. and Zengler, K. 2019 Author Correction: Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities Nature Microbiology 10.1038/s41564-019-0621-4
Welsher, K. and Yang, H. 2014 Multi-resolution 3D visualization of the early stages of cellular uptake of peptide-coated nanoparticles Nature Nanotechnology 10.1038/nnano.2014.12
Hu X, Hong L, Smith MD, Neusius T, Cheng X, and Smith JC 2016 The Dynamics of Single Protein Molecules is Non-Equilibrium and Self-Similar over Thirteen Decades in Time Nature Physics 10.1038/nphys3553
Abraham, P. E., Yin, H. F., Borland, A. M., Weighill, D., Lim, S. D., De Paoli, H. C., Engle, N., Jones, P. C., Agh, R., Weston, D. J., Wullschleger, S. D., Tschaplinski, T., Jacobson, D., Cushman, J. C., Hettich, R. L., Tuskan, G. A. and Yang, X. H. 2016 Transcript, protein and metabolite temporal dynamics in the CAM plant Agave Nature Plants 10.1038/nplants.2016.178
Allen, J. M., Folk, R. A., Soltis, P. S., Soltis, D. E. and Guralnick, R. P. 2019 Biodiversity synthesis across the green branches of the tree of life Nature Plants 10.1038/s41477-018-0322-7
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. 2018 A Golgi UDP-GlcNAc transporter delivers substrates for N-linked glycans and sphingolipids Nature Plants 10.1038/s41477-018-0235-5
Labbe, J., Muchero, W., Czarnecki, O., Wang, J., Wang, X., Bryan, A. C., Zheng, K., Yang, Y., Xie, M., Zhang, J., Wang, D., Meidl, P., Wang, H., Morrell-Falvey, J. L., Cope, K. R., Maia, L. G. S., Ane, J. M., Mewalal, R., Jawdy, S. S., Gunter, L. E., Schackwitz, W., Martin, J., Le Tacon, F., Li, T., Zhang, Z., Ranjan, P., Lindquist, E., Yang, X., Jacobson, D. A., Tschaplinski, T. J., Barry, K., Schmutz, J., Chen, J. G. and Tuskan, G. A. 2019 Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase Nature Plants 10.1038/s41477-019-0469-x
Muller, L. M., Flokova, K., Schnabel, E., Sun, X. P., Fei, Z. J., Frugoli, J., Bouwmeester, H. J. and Harrison, M. J. 2019 A CLE-SUNN module regulates strigolactone content and fungal colonization in arbuscular mycorrhiza Nature Plants 10.1038/s41477-019-0501-1
Oyarce, P., De Meester, B., Fonseca, F., de Vries, L., Goeminne, G., Pallidis, A., De Rycke, R., Tsuji, Y., Li, Y. D., Van den Bosch, S., Sels, B., Ralph, J., Vanholme, R. and Boerjan, W. 2019 Introducing curcumin biosynthesis in Arabidopsis enhances lignocellulosic biomass processing Nature Plants 10.1038/s41477-018-0350-3
Toju, H., Peay, K. G., Yamamichi, M., Narisawa, K., Hiruma, K., Naito, K., Fukuda, S., Ushio, M., Nakaoka, S., Onoda, Y., Yoshida, K., Schlaeppi, K., Bai, Y., Sugiura, R., Ichihashi, Y., Minamisawa, K. and Kiers, E. T. 2018 Core microbiomes for sustainable agroecosystems Nature Plants 10.1038/s41477-018-0139-4
Tuskan, G. A. 2019 The unexpected malleability of lignin Nature Plants 10.1038/s41477-019-0360-9
Ulvskov, P., and Scheller, H. V. 2018 Cell walls have a new family Nature Plants 10.1038/s41477-018-0222-x
Vanholme, R., Sundin, L., Seetso, K. C., Kim, H., Liu, X. Y., Li, J., De Meester, B., Hoengenaert, L., Goeminne, G., Morreel, K., Haustraete, J., Tsai, H. H., Schmidt, W., Vanholme, B., Ralph, J. and Boerjan, W. 2019 COSY catalyses trans-cis isomerization and lactonization in the biosynthesis of coumarins Nature Plants 10.1038/s41477-019-0510-0
Xiong, W., Morgan, J. A., Ungerer, J., Wang, B., Maness, P. C. and Yu, J. P. 2015 The plasticity of cyanobacterial metabolism supports direct CO2 conversion to ethylene Nature Plants 10.1038/nplants.2015.53
Gallagher, R. R., Li, Z., Lewis, A. O. and Isaacs, F. J. 2014 Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA Nature Protocols 10.1038/nprot.2014.082
Ma, N. J., Moonan, D. W. and Isaacs, F. J. 2014 Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering Nature Protocols 10.1038/nprot.2014.081
Meng, X., Crestini, C., Ben, H., Hao, N., Pu, Y., Ragauskas, A. J. and Argyropoulos, D. S. 2019 Determination of hydroxyl groups in biorefinery resources via quantitative (31)P NMR spectroscopy Nature Protocols 10.1038/s41596-019-0191-1
Cavicchioli, R., Ripple, W. J., Timmis, K. N., Azam, F., Bakken, L. R., Baylis, M., Behrenfeld, M. J., Boetius, A., Boyd, P. W., Classen, A. T., Crowther, T. W., Danovaro, R., Foreman, C. M., Huisman, J., Hutchins, D. A., Jansson, J. K., Karl, D. M., Koskella, B., Welch, D. B. M., Martiny, J. B. H., Moran, M. A., Orphan, V. J., Reay, D. S., Remais, J. V., Rich, V. I., Singh, B. K., Stein, L. Y., Stewart, F. J., Sullivan, M. B., van Oppen, M. J. H., Weaver, S. C., Webb, E. A. and Webster, N. S. 2019 Scientists' warning to humanity: microorganisms and climate change Nature Reviews Microbiology 10.1038/s41579-019-0222-5
Evans, P. N., Boyd, J. A., Leu, A. O., Woodcroft, B., Parks, D. H., Hugenholtz, P. and Tyson, G. W. 2019 An evolving view of methane metabolism in the Archaea Nature Reviews Microbiology 10.1038/s41579-018-0136-7
Lawson, C. E., Harcombe, W. R., Hatzenpichler, R., Lindemann, S. R., Loffler, F. E., O'Malley, M. A., Martin, H. G., Pfleger, B. F., Raskin, L., Venturelli, O. S., Weissbrodt, D. G., Noguera, D. R. and McMahon, K. D. 2019 Common principles and best practices for engineering microbiomes Nature Reviews Microbiology 10.1038/s41579-019-0255-9
Lewis, N. E., Nagarajan, H. and Palsson, B. O. 2012 Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods Nature Reviews Microbiology 10.1038/nrmicro2737
Martin, F., Kohler, A., Murat, C., Veneault-Fourrey, C. and Hibbett, D. S. 2016 Unearthing the roots of ectomycorrhizal symbioses Nature Reviews Microbiology 10.1038/nrmicro.2016.149
Zengler, K. and Zaramela, L. S. 2018 The social network of microorganisms - how auxotrophies shape complex communities Nature Reviews Microbiology 10.1038/s41579-018-0004-5
Boyer, D. R., Li, B. S., Sun, C. Q., Fan, W. J., Sawaya, M. R., Jiang, L. and Eisenberg, D. S. 2019 Structures of fibrils formed by alpha-synuclein hereditary disease mutant H50Q reveal new polymorphs Nature Structural and Molecular Biology 10.1038/s41594-019-0322-y
Cao, Q., Boyer, D. R., Sawaya, M. R., Ge, P. and Eisenberg, D. S. 2019 Cryo-EM structures of four polymorphic TDP-43 amyloid cores Nature Structural and Molecular Biology 10.1038/s41594-019-0248-4
Merzel F, Johnson MR, and Smith JC 2012 Normal Modes and Neutrons Defining Collective, Functional Biomolecular Motions Neutron News 10.1080/10448632.2012.695714
Friedman, B. A., Levine, G. C. and Luna, D. 2011 Entanglement entropy of random fractional quantum Hall systems New Journal of Physics 10.1088/1367-2630/13/5/055006
Broddrick, J. T., Du, N., Smith, S. R., Tsuji, Y., Jallet, D., Ware, M. A., Peers, G., Matsuda, Y., Dupont, C. L., Mitchell, B. G., Palsson, B. O. and Allen, A. E. 2019 Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum New Phytologist 10.1111/nph.15685
Bruns, T. D., Corradi, N., Redecker, D., Taylor, J. W. and Opik, M. 2018 Glomeromycotina: what is a species and why should we care? New Phytologist 10.1111/nph.14913
Chen, Eric C. H., Morin, Emmanuelle, Beaudet, Denis, Noel, Jessica, Yildirir, Gokalp, Ndikumana, Steve, Charron, Philippe, St-Onge, Camille, Giorgi, John, Krüger, Manuela, Marton, Timea, Ropars, Jeanne, Grigoriev, Igor V., Hainaut, Matthieu, Henrissat, Bernard, Roux, Christophe, Martin, Francis and Corradi, Nicolas 2018 High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis New Phytologist 10.1111/nph.14989
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 2019 Multi-trait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits New Phytologist 10.1111/nph.15777
da Costa, R. M. F., Pattathil, S., Avci, U., Lee, S. J., Hazen, S. P., Winters, A., Hahn, M. G. and Bosch, M. 2017 A cell wall reference profile for Miscanthus bioenergy crops highlights compositional and structural variations associated with development and organ origin New Phytologist 10.1111/nph.14306
Dickie, I. A., Alexander, I., Lennon, S., Opik, M., Selosse, M. A., van der Heijden, M. G. and Martin, F. M. 2015 Evolving insights to understanding mycorrhizas New Phytologist 10.1111/nph.13290
Dore, J., Perraud, M., Dieryckx, C., Kohler, A., Morin, E., Henrissat, B., Lindquist, E., Zimmermann, S. D., Girard, V., Kuo, A., Grigoriev, I. V., Martin, F., Marmeisse, R. and Gay, G. 2015 Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis New Phytologist 10.1111/nph.13546
Fochi, V., Chitarra, W., Kohler, A., Voyron, S., Singan, V. R., Lindquist, E. A., Barry, K. W., Girlanda, M., Grigoriev, I. V., Martin, F., Balestrini, R. and Perotto, S. 2017 Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas New Phytologist 10.1111/nph.14279
Gallego-Giraldo, L., Pose, S., Pattathil, S., Peralta, A. G., Hahn, M. G., Ayre, B. G., Sunuwar, J., Hernandez, J., Patel, M., Shah, J., Rao, X., Knox, J. P. and Dixon, R. A. 2018 Elicitors and defense gene induction in plants with altered lignin compositions New Phytologist 10.1111/nph.15258
Grabowski, P. P., Evans, J., Daum, C., Deshpande, S., Barry, K. W., Kennedy, M., Ramstein, G., Kaeppler, S. M., Buell, C. R., Jiang, Y. W. and Casler, M. D. 2017 Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data New Phytologist 10.1111/nph.14101
Hacquard, S. and Schadt, C. W. 2015 Towards a holistic understanding of the beneficial interactions across the Populus microbiome New Phytologist 10.1111/nph.13133
Hossain, M. S., Kawakatsu, T., Do Kim, K., Zhang, N., Nguyen, C. T., Khan, S. M., Batek, J. M., Joshi, T., Schmutz, J., Grimwood, J., Schmitz, R. J., Xu, D., Jackson, S. A., Ecker, J. R. and Stacey, G. 2017 Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs New Phytologist 10.1111/nph.14421
Jensen, J. K., Busse-Wicher, M., Poulsen, C. P., Fangel, J. U., Smith, P. J., Yang, J. Y., Pena, M. J., Dinesen, M. H., Martens, H. J., Melkonian, M., Wong, G. K. S., Moremen, K. W., Wilkerson, C. G., Scheller, H. V., Dupree, P., Ulvskov, P., Urbanowicz, B. R. and Harholt, J. 2018 Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis New Phytologist 10.1111/nph.15050
Johnsen, H. R., Striberny, B., Olsen, S., Vidal-Melgosa, S., Fangel, J. U., Willats, W. G. T., Rose, J. K. C. and Krause, K. 2015 Cell wall composition profiling of parasitic giant dodder (Cuscuta reflexa) and its hosts: a priori differences and induced changes New Phytologist 10.1111/nph.13378
Johnson, D., Martin, F., Cairney, J. W. and Anderson, I. C. 2012 The importance of individuals: intraspecific diversity of mycorrhizal plants and fungi in ecosystems New Phytologist 10.1111/j.1469-8137.2012.04087.x
Johnson, S. R., Bhat, W. W., Sadre, R., Miller, G. P., Garcia, A. S. and Hamberger, B. 2019 Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution New Phytologist 10.1111/nph.15778
Kainer, D., Padovan, A., Degenhardt, J., Krause, S., Mondal, P., Foley, W. J. and Kulheim, C. 2019 High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus New Phytologist 10.1111/nph.15887
Karve, A. A., Jawdy, S. S., Gunter, L. E., Allen, S. M., Yang, X., Tuskan, G. A., Wullschleger, S. D. and Weston, D. J. 2012 Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes New Phytologist 10.1111/j.1469-8137.2012.04288.x
Konotchick, T., Dupont, C. L., Valas, R. E., Badger, J. H. and Allen, A. E. 2013 Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season New Phytologist 10.1111/nph.12160
Kostka, J. E., Weston, D. J., Glass, J. B., Lilleskov, E. A., Shaw, A. J. and Turetsky, M. R. 2016 The Sphagnum microbiome: new insights from an ancient plant lineage New Phytologist 10.1111/nph.13993
Labbe, J., Uehling, J., Payen, T. and Plett, J. 2014 Fungal biology: compiling genomes and exploiting them New Phytologist 10.1111/nph.12891
Liu, L. J., Zinkgraf, M., Petzold, H. E., Beers, E. P., Filkov, V. and Groover, A. 2015 The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function New Phytologist 10.1111/nph.13151
Looney, B. P., Meidl, P., Piatek, M. J., Miettinen, O., Martin, F. M., Matheny, P. B. and Labbe, J. L. 2018 Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates New Phytologist 10.1111/nph.15001
Martin, F., Cullen, D., Hibbett, D., Pisabarro, A., Spatafora, J. W., Baker, S. E. and Grigoriev, I. V. 2011 Sequencing the fungal tree of life New Phytologist 10.1111/j.1469-8137.2011.03688.x
Murik, O., Tirichine, L., Prihoda, J., Thomas, Y., Araujo, W. L., Allen, A. E., Fernie, A. R. and Bowler, C. 2019 Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom New Phytologist 10.1111/nph.15479
Plett, J. M., Khachane, A., Ouassou, M., Sundberg, B., Kohler, A. and Martin, F. 2014 Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots New Phytologist 10.1111/nph.12655
Riley, R., Charron, P., Idnurm, A., Farinelli, L., Dalpe, Y., Martin, F. and Corradi, N. 2014 Extreme diversification of the mating type-high-mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus New Phytologist 10.1111/nph.12462
Sasse, J., Kant, J., Cole, B. J., Klein, A. P., Arsova, B., Schlaepfer, P., Gao, J., Lewald, K., Zhalnina, K., Kosina, S., Bowen, B. P., Treen, D., Vogel, J., Visel, A., Watt, M., Dangl, J. L. and Northen, T. R. 2019 Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass New Phytologist 10.1111/nph.15662
Selosse, M. A. and Martin, F. 2013 Mycorrhizas and New Phytologist: une vraie histoire d'amour New Phytologist 10.1111/nph.12545
Sheehan, H., Feng, T., Walker-Hale, N., Lopez-Nieves, S., Pucker, B., Guo, R., Yim, W. C., Badgami, R., Timoneda, A., Zhao, L. J., Tiley, H., Copetti, D., Sanderson, M. J., Cushman, J. C., Moore, M. J., Smith, S. A. and Brockington, S. F. 2019 Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales New Phytologist 10.1111/nph.16089
Smith, S. R., Gle, C., Abbriano, R. M., Traller, J. C., Davis, A., Trentacoste, E., Vernet, M., Allen, A. E. and Hildebrand, M. 2016 Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana New Phytologist 10.1111/nph.13843
Sonawane, B. V. and Cousins, A. B. 2019 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 10.1111/nph.15585
Strullu-Derrien, C., Selosse, M. A., Kenrick, P. and Martin, F. M. 2018 The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics New Phytologist 10.1111/nph.15076
Sun, X. P., Chen, W. B., Ivanov, S., MacLean, A. M., Wight, H., Ramaraj, T., Mudge, J., Harrison, M. J. and Fei, Z. J. 2019 Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts New Phytologist 10.1111/nph.15472
Valverde-Barrantes, O. J., Freschet, G. T., Roumet, C. and Blackwood, C. B. 2017 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 10.1111/nph.14571
van der Heijden, M. G., Martin, F. M., Selosse, M. A. and Sanders, I. R. 2015 Mycorrhizal ecology and evolution: the past, the present, and the future New Phytologist 10.1111/nph.13288
Weston, David J., Turetsky, Merritt R., Johnson, Matthew G., Granath, Gustaf, Lindo, Zoë, Belyea, Lisa R., Rice, Steven K., Hanson, David T., Engelhardt, Katharina A. M., Schmutz, Jeremy, Dorrepaal, Ellen, Euskirchen, Eugénie S., Stenøien, Hans K., Szövényi, Péter, Jackson, Michelle, Piatkowski, Bryan T., Muchero, Wellington, Norby, Richard J., Kostka, Joel E., Glass, Jennifer B., Rydin, Håkan, Limpens, Juul, Tuittila, Eeva-Stiina, Ullrich, Kristian K., Carrell, Alyssa, Benscoter, Brian W., Chen, Jin-Gui, Oke, Tobi A., Nilsson, Mats B., Ranjan, Priya, Jacobson, Daniel, Lilleskov, Erik A., Clymo, R. S. and Shaw, A. Jonathan 2018 The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project New Phytologist 10.1111/nph.14860
Yan, X. J., Liu, J., Kim, H., Liu, B. G., Huang, X., Yang, Z. C., Lin, Y. C. J., Chen, H., Yang, C. M., Wang, J. P., Muddiman, D. C., Ralph, J., Sederoff, R. R., Li, Q. Z. and Chiang, V. L. 2019 CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa New Phytologist 10.1111/nph.15505
Yip, D. Z., Veach, A. M., Yang, Z. K., Cregger, M. A. and Schadt, C. W. 2019 Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides) New Phytologist 10.1111/nph.15346
Zhang, F., Anasontzis, G. E., Labourel, A., Champion, C., Haon, M., Kemppainen, M., Commun, C., Deveau, A., Pardo, A., Veneault-Fourrey, C., Kohler, A., Rosso, M. N., Henrissat, B., Berrin, J. G. and Martin, F. 2018 The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted beta-1,4 endoglucanase that plays a key role in symbiosis development New Phytologist 10.1111/nph.15113
Zhang, J., Yang, Y., Zheng, K., Xie, M., Feng, K., Jawdy, S. S., Gunter, L. E., Ranjan, P., Singan, V. R., Engle, N., Lindquist, E., Barry, K., Schmutz, J., Zhao, N., Tschaplinski, T. J., LeBoldus, J., Tuskan, G. A., Chen, J. G. and Muchero, W. 2018 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 10.1111/nph.15297
Zhao, C. S., Lasses, T., Bako, L., Kong, D. Y., Zhao, B. Y., Chanda, B., Bombarely, A., Cruz-Ramirez, A., Scheres, B., Brunner, A. M. and Beers, E. P. 2017 XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED New Phytologist 10.1111/nph.14704
Zivanovic, S., Thapa, A., Koorie, M., Animilli, S., Gunasekaran, A., Melancon, J. and Genov, D. 2012 Surface Plasmon Enhanced P3HT: PCBM Photovoltaic Devices Next Generation 10.1117/12.970325
Lopez-Garriga J, Wymore T, Pietri R, Roman-Morales EM, Rios-Gonzalez B, and Arbelo H 2014 P90 Hydrogen Sulfide Activation by Hemeproteins Implications of the Sulfheme Scenario Nitric Oxide 10.1016/j.niox.2014.03.140
Kerkhoven, E. J., Pomraning, K. R., Baker, S. E. and Nielsen, J. 2016 Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica npj Systems Biology and Applications 10.1038/npjsba.2016.5
Li, C. T., Yelsky, J., Chen, Y. Q., Zuniga, C., Eng, R., Jiang, L. Q., Shapiro, A., Huang, K. W., Zengler, K. and Betenbaugh, M. J. 2019 Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity npj Systems Biology and Applications 10.1038/s41540-019-0110-7
Afrasiabi, C., Samad, B., Dineen, D., Meacham, C. and Sjolander, K. 2013 The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification Nucleic Acids Research 10.1093/nar/gkt399
Boyd, J. A., Woodcroft, B. J. and Tyson, G. W. 2018 GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes Nucleic Acids Research 10.1093/nar/gky174
Caldwell, B. J., Zakharova, E., Filsinger, G. T., Wormier, T. M., Hempfling, J. P., Chun-Der, L., Pei, D., Church, G. M. and Bell, C. E. 2019 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 10.1093/nar/gky1309
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M. and Tiedje, J. M. 2009 The Ribosomal Database Project: improved alignments and new tools for rRNA analysis Nucleic Acids Research 10.1093/nar/gkn879
Cole, J. R., Wang, Q., Fish, J. A., Chai, B. L., McGarrell, D. M., Sun, Y. N., Brown, C. T., Porras-Alfaro, A., Kuske, C. R. and Tiedje, J. M. 2014 Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucleic Acids Research 10.1093/nar/gkt1244
DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X., Aach, J. and Church, G. M. 2013 Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems Nucleic Acids Research 10.1093/nar/gkt135
Egbert, R. G., Rishi, H. S., Adler, B. A., McCormick, D. M., Toro, E., Gill, R. T. and Arkin, A. P. 2019 A versatile platform strain for high-fidelity multiplex genome editing Nucleic Acids Research 10.1093/nar/gkz085
Fujishima, K., Sugahara, J., Miller, C. S., Baker, B. J., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, J. F. and Kanai, A. 2011 A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity Nucleic Acids Research 10.1093/nar/gkr692
Gregg, C. J., Lajoie, M. J., Napolitano, M. G., Mosberg, J. A., Goodman, D. B., Aach, J., Isaacs, F. J. and Church, G. M. 2014 Rational optimization of tolC as a powerful dual selectable marker for genome engineering Nucleic Acids Research 10.1093/nar/gkt1374
Jabre, I., Reddy, A. S. N., Kalyna, M., Chaudhary, S., Khokhar, W., Byrne, L. J., Wilson, C. M. and Syed, N. H. 2019 Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Research 10.1093/nar/gkz121
Joshi, T., Fitzpatrick, M. R., Chen, S. Y., Liu, Y., Zhang, H. X., Endacott, R. Z., Gaudiello, E. C., Stacey, G., Nguyen, H. T. and Xu, D. 2014 Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding Nucleic Acids Research 10.1093/nar/gkt905
Karpinets, T. V., Park, B. H. and Uberbacher, E. C. 2012 Analyzing large biological datasets with association networks Nucleic Acids Research 10.1093/nar/gks403
Kelly, L., Huang, K. H., Ding, H. M. and Chisholm, S. W. 2012 ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage Nucleic Acids Research 10.1093/nar/gkr1022
King, Z. A., Lu, J., Drager, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O. and Lewis, N. E. 2016 BiGG Models: A platform for integrating, standardizing and sharing genome-scale models Nucleic Acids Research 10.1093/nar/gkv1049
Lajoie, M. J., Gregg, C. J., Mosberg, J. A., Washington, G. C. and Church, G. M. 2012 Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering Nucleic Acids Research 10.1093/nar/gks751
Lan, Y. M., Morrison, J. C., Hershberg, R. and Rosen, G. L. 2014 POGO-DB-a database of pairwise-comparisons of genomes and conserved orthologous genes Nucleic Acids Research 10.1093/nar/gkt1094
Lee, D. F., Lu, J., Chang, S., Loparo, J. J. and Xie, X. L. S. 2016 Mapping DNA polymerase errors by single-molecule sequencing Nucleic Acids Research 10.1093/nar/gkw436
Lindsay, R. J., Pham, B., Shen, T. and McCord, R. P. 2018 Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework Nucleic Acids Research 10.1093/nar/gky604
Ling, J. Q., Daoud, R., Lajoie, M. J., Church, G. M., Soll, D. and Lang, B. F. 2014 Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria Nucleic Acids Research 10.1093/nar/gkt842
Liu, X. Y., Gupta, S. T. P., Bhimsaria, D., Reed, J. L., Rodriguez-Martinez, J. A., Ansari, A. Z. and Raman, S. 2019 De novo design of programmable inducible promoters Nucleic Acids Research 10.1093/nar/gkz772
Luo, C. W., Rodriguez, L. M. and Konstantinidis, K. T. 2014 MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences Nucleic Acids Research 10.1093/nar/gku169
Pieper, U., Webb, B. M., Barkan, D. T., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E. C., Pettersen, E. F., Huang, C. C., Datta, R. S., Sampathkumar, P., Madhusudhan, M. S., Sjolander, K., Ferrin, T. E., Burley, S. K. and Sali, A. 2011 ModBase, a database of annotated comparative protein structure models, and associated resources Nucleic Acids Research 10.1093/nar/gkq1091
Prestat, E., David, M. M., Hultman, J., Tas, N., Lamendella, R., Dvornik, J., Mackelprang, R., Myrold, D. D., Jumpponen, A., Tringe, S. G., Holman, E., Mavromatis, K. and Jansson, J. K. 2014 FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus Nucleic Acids Research 10.1093/nar/gku702
Rogers, J. K., Guzman, C. D., Taylor, N. D., Raman, S., Anderson, K. and Church, G. M. 2015 Synthetic biosensors for precise gene control and real-time monitoring of metabolites Nucleic Acids Research 10.1093/nar/gkv616
Schmid, A. K., Pan, M., Sharma, K. and Baliga, N. S. 2011 Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon Nucleic Acids Research 10.1093/nar/gkq1211
Tu, Q. C., He, Z. L. and Zhou, J. Z. 2014 Strain/species identification in metagenomes using genome-specific markers Nucleic Acids Research 10.1093/nar/gku138
Yoneda, A., Henson, W. R., Goldner, N. K., Park, K. J., Forsberg, K. J., Kim, S. J., Pesesky, M. W., Foston, M., Dantas, G. and Moon, T. S. 2016 Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630 Nucleic Acids Research 10.1093/nar/gkw055
Schadel, C., Luo, Y. Q., Evans, R. D., Fei, S. F. and Schaeffer, S. M. 2013 Separating soil CO2 efflux into C-pool-specific decay rates via inverse analysis of soil incubation data Oecologia 10.1007/s00442-012-2577-4
Liu, S., Streich, J., Borevita, J.O., Rice, K.J., Li, T., Li, B. 2018 Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations Oikos 10.1111/oik.05548
Urano, D., Chen, J. G., Botella, J. R. and Jones, A. M. 2013 Heterotrimeric G protein signalling in the plant kingdom Open Biology 10.1098/rsob.120186
Vasdekis, A. E., Alanazi, H., Silverman, A. M., Canul, A. J., Dohnalkova, A. C., Cliff, J. B. and Stephanopoulos, G. 2019 Imaging the competition between growth and production of self-assembled lipid droplets at the single-cell level Optical Methods for Inspection, Characterization, and Imaging of Biomaterials Iv 10.1117/12.2531007
Saar, B. G., Holtom, G. R., Freudiger, C. W., Ackermann, C., Hill, W. and Xie, X. S. 2009 Intracavity wavelength modulation of an optical parametric oscillator for coherent Raman microscopy Optics Express 10.1364/oe.17.012532
Kieu, K., Saar, B. G., Holtom, G. R., Xie, X. S. and Wise, F. W. 2009 High-power picosecond fiber source for coherent Raman microscopy Optics Letters 10.1364/ol.34.002051
Yang, W. L., Li, A., Suo, Y. Z., Lu, F. K. and Xie, X. S. 2017 Simultaneous two-color stimulated Raman scattering microscopy by adding a fiber amplifier to a 2 ps OPO-based SRS microscope Optics Letters 10.1364/ol.42.000523
Kim, H. and Ralph, J. 2010 Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d(6)/pyridine-d(5) Organic & Biomolecular Chemistry 10.1039/b916070a
Wilson, R. M., Tfaily, M. M., Rich, V. I., Keller, J. K., Bridgham, S. D., Zalman, C. M., Meredith, L., Hanson, P. J., Hines, M., Pfeifer-Meister, L., Saleska, S. R., Crill, P., Cooper, W. T., Chanton, J. P. and Kostka, J. E. 2017 Hydrogenation of organic matter as a terminal electron sink sustains high CO2:CH4 production ratios during anaerobic decomposition Organic Geochemistry 10.1016/j.orggeochem.2017.06.011
Joubert, Wayne, Nance, James, Climer, Sharlee, Weighill, Deborah and Jacobson, Daniel 2019 Parallel accelerated Custom Correlation Coefficient calculations for genomics applications Parallel Computing 10.1016/j.parco.2019.02.003
Joubert, Wayne, Nance, James, Weighill, Deborah and Jacobson, Daniel 2018 Parallel accelerated vector similarity calculations for genomics applications Parallel Computing 10.1016/j.parco.2018.03.009
Beck, D. A. C., Kalyuzhnaya, M. G., Malfatti, S., Tringe, S. G., del Rio, T. G., Ivanova, N., Lidstrom, M. E. and Chistoserdova, L. 2013 A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae PeerJ 10.7717/peerj.23
Berry, J. C., Fahlgren, N., Pokorny, A. A., Bart, R. S. and Veley, K. M. 2018 An automated, high-throughput method for standardizing image color profiles to improve image-based plant phenotyping PeerJ 10.7717/peerj.5727
Bolduc, B., Jang, H. B., Doulcier, G., You, Z. Q., Roux, S. and Sullivan, M. B. 2017 vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria PeerJ 10.7717/peerj.3243
Gehan, M. A., Fahlgren, N., Abbasi, A., Berry, J. C., Callen, S. T., Chavez, L., Doust, A. N., Feldman, M. J., Gilbert, K. B., Hodge, J. G., Hoyer, J. S., Lin, A., Liu, S. X., Lizarraga, C., Lorence, A., Miller, M., Platon, E., Tessman, M. and Sax, T. 2017 PlantCV v2: Image analysis software for high-throughput plant phenotyping PeerJ 10.7717/peerj.4088
Henning, J. A., Weston, D. J., Pelletier, D. A., Timm, C. M., Jawdy, S. S. and Classen, A. T. 2016 Root bacterial endophytes alter plant phenotype, but not physiology PeerJ 10.7717/peerj.2606
Rinke, C., Low, S., Woodcroft, B., Raina, J. B., Skarshewski, A., Le, X. Y. H., Butler, M. K., Stocker, R., Seymour, J., Tyson, G. W. and Hugenholtz, P. 2016 Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics PeerJ 10.7717/peerj.2486
Roux, S., Emerson, J. B., Eloe-Fadrosh, E. A. and Sullivan, M. B. 2017 Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity PeerJ 10.7717/peerj.3817
Roux, S., Trubl, G., Goudeau, D., Nath, N., Couradeau, E., Ahlgren, N. A., Zhan, Y., Marsan, D., Chen, F., Fuhrman, J. A., Northen, T. R., Sullivan, M. B., Rich, V. I., Malmstrom, R. R. and Eloe-Fadrosh, E. A. 2019 Optimizing de novo genome assembly from PCR-amplified metagenomes PeerJ 10.7717/peerj.6902
Roux, S., Trubl, G., Goudeau, D., Nath, N., Couradeau, E., Ahlgren, N. A., Zhan, Y. C., Marsan, D., Chen, F., Fuhrman, J. A., Northen, T. R., Sullivan, M. B., Rich, V. I., Malmstrom, R. R. and Eloe-Fadrosh, E. A. 2019 Optimizing de novo genome assembly from PCR-amplified metagenomes PeerJ 10.7717/peerj.6902
Speth, D. R. and Orphan, V. J. 2018 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 10.7717/peerj.5614
Trembath-Reichert, E., Case, D. H. and Orphan, V. J. 2016 Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments PeerJ 10.7717/peerj.1913
Trubl, G., Roux, S., Solonenko, N., Li, Y. F., Bolduc, B., Rodriguez-Ramos, J., Eloe-Fadrosh, E. A., Rich, V. I. and Sullivan, M. B. 2019 Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils PeerJ 10.7717/peerj.7265
Yim, W. C. and Cushman, J. C. 2017 Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments PeerJ 10.7717/peerj.3486
Carper, Dana L., Lawrence, Travis J., Carrell, Alyssa A., Pelletier, Dale A. and Weston, David J. 2019 DISCo-microbe: Design of an identifiable synthetic community of microbes PeerJ Preprints 10.7287/peerj.preprints.27898v1
Glass, J. I. 2012 Synthetic Genomics And The Construction Of A Synthetic Bacterial Cell Perspectives in Biology and Medicine 10.1353/pbm.2012.0040
Bondar AN, Smith JC, and Fischer S 2006 Structural and Energetic Determinants of Proton Transfer in Bacteriorhodopsin Photochemical and Photobiological Sciences 10.1039/b516451f
Bondar, AN, Smith JC 2017 Protonation–state Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins Photochemistry and Photobiology 10.1111/php.12790
Tfaily, M. M., Corbett, J. E., Wilson, R., Chanton, J. P., Glaser, P. H., Cawley, K. M., Jaffe, R. and Cooper, W. T. 2015 Utilization of PARAFAC-Modeled Excitation-Emission Matrix (EEM) Fluorescence Spectroscopy to Identify Biogeochemical Processing of Dissolved Organic Matter in a Northern Peatland Photochemistry and Photobiology 10.1111/php.12448
Yoneda, A., Wittmann, B. J., King, J. D., Blankenship, R. E. and Dantas, G. 2016 Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp CCMEE 5410 Photosynthesis Research 10.1007/s11120-016-0279-1
Field MJ, and Wymore TW 2014 Multiscale Modeling of Nerve Agent Hydrolysis Mechanisms a Tale of Two Nobel Prizes Physica Scripta 10.1088/0031-8949/89/10/108004
Qi X, Nellas R, Byrn M, Russell M, Bible A, Alexandre G, and Shen T 2013 Swimming Motility Plays a Key Role in the Stochastic Dynamics of Cell Clumping Physical Biology 10.1088/1478-3975/10/2/026005
Balog E, Smith JC, and Perahia D 2006 Conformational Heterogeneity and Low-Frequency Vibrational Modes of Proteins Physical Chemistry Chemical Physics 10.1039/b610075a
Carmona C, Langan P, Smith JC, and Petridis L 2015 Why Genetic Modification of Lignin Leads to Low-Recalcitrance Biomass Physical Chemistry Chemical Physics 10.1039/c4cp05004e
Johnson, Q. R., Mostofian, B., Fuente Gomez, G., Smith, J. C. and Cheng, X. 2018 Effects of carotenoids on lipid bilayers Physical Chemistry Chemical Physics 10.1039/c7cp07126d
Moyer P, Smith MD, Abdoulmoumine N, Chmely SC, Smith JC, Petridis L, Labbé N 2018 Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions Physical Chemistry Chemical Physics 10.1039/C7CP07195G
Paslack, C., Smith, J. C., Heyden, M. and Schafer, L. V. 2019 Hydration-mediated stiffening of collective membrane dynamics by cholesterol Physical Chemistry Chemical Physics 10.1039/c9cp01431d
Perticaroli, S., Mostofian, B., Ehlers, G., Neuefeind, J. C., Diallo, S. O., Stanley, C. B., Daemen, L., Egami, T., Katsaras, J., Cheng, X. and Nickels, J. D. 2017 Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid Physical Chemistry Chemical Physics 10.1039/c7cp04013j
Smith, M. D., Petridis, L., Cheng, X., Mostofian, B. and Smith, J. C. 2016 Enhanced sampling simulation analysis of the structure of lignin in the THF-water miscibility gap Physical Chemistry Chemical Physics 10.1039/c5cp07088k
Vural D, Smith JC, Petridis L 2018 Dynamics of the lignin glass transition Physical Chemistry Chemical Physics 10.1039/c8cp03144d
Caravan, B., Friedman, B. A. and Levine, G. C. 2014 Scaling of entanglement entropy in point-contact, free-fermion systems Physical Review A 10.1103/PhysRevA.89.052305
Levine, G. C., Friedman, B. A. and Bantegui, M. J. 2011 Detecting many-body entanglement in noninteracting ultracold atomic Fermi gases Physical Review A 10.1103/PhysRevA.83.013623
Levine, G. C., Bantegui, M. J. and Burg, J. A. 2012 Full counting statistics in a disordered free fermion system Physical Review B 10.1103/PhysRevB.86.174202
Levine, G. C. and Friedman, B. A. 2011 Projective approach to the entanglement entropy of one-dimensional fermions Physical Review B 10.1103/PhysRevB.83.125118
Neusius, T., Daidone, I., Sokolov, I. M. and Smith, J. C. 2011 Configurational subdiffusion of peptides: a network study Physical Review E 10.1103/PhysRevE.83.021902
Neusius, T., Sokolov, I. M. and Smith, J. C. 2009 Subdiffusion in time-averaged, confined random walks Physical Review E 10.1103/PhysRevE.80.011109
Petridis, L., Pingali, S. V., Urban, V., Heller, W. T., O'Neill, H. M., Foston, M., Ragauskas, A. and Smith, J. C. 2011 Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation Physical Review E 10.1103/PhysRevE.83.061911
Vural, D., Hong, L., Smith, J. C. and Glyde, H. R. 2013 Long-time mean-square displacements in proteins Physical Review E 10.1103/PhysRevE.88.052706
Vural, D., Hong, L., Smith, J. C. and Glyde, H. R. 2015 Motional displacements in proteins: The origin of wave-vector-dependent values Physical Review E 10.1103/PhysRevE.91.052705
Godec, A., Smith, J. C. and Merzel, F. 2013 Soft collective fluctuations governing hydrophobic association Physical Review Letters 10.1103/PhysRevLett.111.127801
Godec A, Smith JC, and Merzel F 2011 Increase of both Order and Disorder in the First Hydration Shell with Increasing Solute Polarity Physical Review Letters 10.1103/PhysRevLett.107.267801
Hong, L., Glass, D. C., Nickels, J. D., Perticaroli, S., Yi, Z., Tyagi, M., O'Neill, H., Zhang, Q., Sokolov, A. P. and Smith, J. C. 2013 Elastic and conformational softness of a globular protein Physical Review Letters 10.1103/PhysRevLett.110.028104
Hong, L., Smolin, N., Lindner, B., Sokolov, A. P. and Smith, J. C. 2011 Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein Physical Review Letters 10.1103/PhysRevLett.107.148102
Hong, L., Smolin, N. and Smith, J. C. 2014 de Gennes narrowing describes the relative motion of protein domains Physical Review Letters 10.1103/PhysRevLett.112.158102
Hong L, Glass DC, and Smith JC 2012 Surface Hydration Amplifies Single-Well Protein Atom Diffusion Propagating into the Macromolecular Core Physical Review Letters 10.1103/PhysRevLett.108.238102
Kurkal-Siebert V, Agarwal R, and Smith JC 2008 Hydration-Dependent Dynamical Transition in Protein Protein Interactions at Approximately 240 K Physical Review Letters 10.1103/PhysRevLett.100.138102
Liu, Z., Huang, J., Tyagi, M., O'Neill, H., Zhang, Q., Mamontov, E., Jain, N., Wang, Y., Zhang, J., Smith, J. C. and Hong, L. 2017 Dynamical Transition of Collective Motions in Dry Proteins Physical Review Letters 10.1103/PhysRevLett.119.048101
Meinhold, L., Merzel, F. and Smith, J. C. 2007 Lattice dynamics of a protein crystal Physical Review Letters 10.1103/PhysRevLett.99.138101
Neusius, T., Daidone, I., Sokolov, I. M. and Smith, J. C. 2008 Subdiffusion in peptides originates from the fractal-like structure of configuration space Physical Review Letters 10.1103/PhysRevLett.100.188103
Nutt DR, and Smith JC 2007 Choosing an Appropriate Water Model for Use in Biomolecular Simulations Physics and Chemistry of Ice 10.1039/9781847557773-00099
Komarov, S., Yin, Y. Z., Wu, H. Y., Wen, J., Krawczynski, H., Meng, L. J. and Tai, Y. C. 2012 Investigation of the limitations of the highly pixilated CdZnTe detector for PET applications Physics in Medicine and Biology 10.1088/0031-9155/57/22/7355
Qi, J. Y., Yang, Y. F., Zhou, J., Wu, Y. B. and Cherry, S. R. 2011 Experimental assessment of resolution improvement of a zoom-in PET Physics in Medicine and Biology 10.1088/0031-9155/56/17/n01
St James, S., Yang, Y. F., Bowen, S. L., Qi, J. Y. and Cherry, S. R. 2010 Simulation study of spatial resolution and sensitivity for the tapered depth of interaction PET detectors for small animal imaging Physics in Medicine and Biology 10.1088/0031-9155/55/2/n04
St James, S., Yang, Y. F., Wu, Y. B., Farrell, R., Dokhale, P., Shah, K. S. and Cherry, S. R. 2009 Experimental characterization and system simulations of depth of interaction PET detectors using 0.5 mm and 0.7 mm LSO arrays Physics in Medicine and Biology 10.1088/0031-9155/54/14/015
Zhou, J. and Qi, J. Y. 2009 Theoretical analysis and simulation study of a high-resolution zoom-in PET system Physics in Medicine and Biology 10.1088/0031-9155/54/17/008
Zhou, J. and Qi, J. Y. 2011 Fast and efficient fully 3D PET image reconstruction using sparse system matrix factorization with GPU acceleration Physics in Medicine and Biology 10.1088/0031-9155/56/20/015
Petzold, H. E., Zhao, M. Z. and Beers, E. P. 2012 Expression and functions of proteases in vascular tissues Physiologia Plantarum 10.1111/j.1399-3054.2011.01538.x
Craven, K., and Ray, P. 2019 More than serendipity: the potential to manage soil carbon and emissions while promoting low-input agriculture with serendipitoid mycorrhizae Phytobiomes Journal 10.1094/PBIOMES-12-18-0058-P
Garcia, B.J., Labbe, J., Jones, P., Abraham, P., Hodge, I., Climer, S., Jawdy, S., Gunter, L., Tuskan, G., Yang, X., Tschaplinski, T., and Jacobson, D.J. 2018 Phytobiome and transcriptional adaptation of Populus deltoides to acute progressive drought and cyclic drought Phytobiomes Journal 10.1094/PBIOMES-04-18-0021-R
Garcia, Benjamin J., Labbé, Jessy L., Jones, Piet, Abraham, Paul E., Hodge, Ian, Climer, Sharlee, Jawdy, Sara, Gunter, Lee, Tuskan, Gerald A., Yang, Xiaohan, Tschaplinski, Timothy J. and Jacobson, Daniel A. 2018 Phytobiome and Transcriptional Adaptation of Populus deltoides to Acute Progressive Drought and Cyclic Drought Phytobiomes Journal 10.1094/pbiomes-04-18-0021-r
Jaini, R., Wang, P., Dudareva, N., Chapple, C. and Morgan, J. A. 2017 Targeted Metabolomics of the Phenylpropanoid Pathway in Arabidopsis thaliana using Reversed Phase Liquid Chromatography Coupled with Tandem Mass Spectrometry Phytochemical Analysis 10.1002/pca.2672
Berim, A. and Gang, D. R. 2013 Characterization of two candidate flavone 8-O-methyltransferases suggests the existence of two potential routes to nevadensin in sweet basil Phytochemistry 10.1016/j.phytochem.2013.05.001
Elder, T., del Rio, J. C., Ralph, J., Rencoret, J., Kim, H. and Beckham, G. T. 2019 Radical coupling reactions of piceatannol and monolignols: A density functional theory study Phytochemistry 10.1016/j.phytochem.2019.04.003
Jervis, J., Hildreth, S. B., Sheng, X. Y., Beers, E. P., Brunner, A. M. and Helm, R. F. 2015 A metabolomic assessment of NAC154 transcription factor overexpression in field grown poplar stem wood Phytochemistry 10.1016/j.phytochem.2015.02.013
Piva, L. R. O., Jardine, K. J., Gimenez, B. O., de Oliveira Perdiz, R., Menezes, V. S., Durgante, F. M., Cobello, L. O., Higuchi, N. and Chambers, J. Q. 2019 Volatile monoterpene 'fingerprints' of resinous Protium tree species in the Amazon rainforest Phytochemistry 10.1016/j.phytochem.2019.01.014
Zhao N, Yao J, Chaipransongsuk M, Li G, Guan J, Tschaplinski TJ, Guo H, and Chen F 2013 Molecular and Biochemical Characterization of the Jasmonic Acid Methyltransferase Gene from Black Cottonwood Populus trichocarpa Phytochemistry 10.1016/j.phytochem.2013.06.014
Berim, A. and Gang, D. R. 2016 Methoxylated flavones: occurrence, importance, biosynthesis Phytochemistry Reviews 10.1007/s11101-015-9426-0
Abraham, N., Chitrampalam, P., Nelson, B., Poudel, R. S., Chittem, K., Borowicz, P., Brueggeman, R., Jain, S. and LeBoldus, J. M. 2019 Microscopic, Biochemical, and Molecular Comparisons of Moderately Resistant and Susceptible Populus Genotypes Inoculated with Sphaerulina musiva Phytopathology 10.1094/phyto-03-19-0105-r
Yang, X. P., Sood, S., Luo, Z. L., Todd, J. and Wang, J. P. 2019 Genome-Wide Association Studies Identified Resistance Loci to Orange Rust and Yellow Leaf Virus Diseases in Sugarcane (Saccharum spp.) Phytopathology 10.1094/phyto-08-18-0282-r
Berim, A., Kim, M. J. and Gang, D. R. 2015 Identification of a Unique 2-Oxoglutarate-Dependent Flavone 7-O-Demethylase Completes the Elucidation of the Lipophilic Flavone Network in Basil Plant and Cell Physiology 10.1093/pcp/pcu152
Wu, P. P., Peng, M. S., Li, Z. G., Yuan, N., Hu, Q., Foster, C. E., Saski, C., Wu, G. H., Sun, D. F. and Luo, H. 2019 DRMY1, a Myb-Like Protein, Regulates Cell Expansion and Seed Production in Arabidopsis thaliana Plant and Cell Physiology 10.1093/pcp/pcy207
Bowsher, A. W., Evans, S., Tiemann, L. K. and Friesen, M. L. 2018 Effects of soil nitrogen availability on rhizodeposition in plants: a review Plant and Soil 10.1007/s11104-017-3497-1
Lowman, S., Kim-Dura, S., Mei, C. S. and Nowak, J. 2016 Strategies for enhancement of switchgrass (Panicum virgatum L.) performance under limited nitrogen supply based on utilization of N-fixing bacterial endophytes Plant and Soil 10.1007/s11104-015-2640-0
Smercina, D. N., Evans, S. E., Friesen, M. L. and Tiemann, L. K. 2019 Optimization of the N-15(2) incorporation and acetylene reduction methods for free-living nitrogen fixation Plant and Soil 10.1007/s11104-019-04307-3
Veach, Allison M., Yip, Daniel, Engle, Nancy L., Yang, Zamin K., Bible, Amber, Morrell-Falvey, Jennifer, Tschaplinski, Timothy J., Kalluri, Udaya C. and Schadt, Christopher W. 2018 Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants Plant and Soil 10.1007/s11104-018-3692-8
Wang, M. M., Wang, S. P., Wu, L. W., Xu, D. P., Lin, Q. Y., Hu, Y. G., Li, X. Z., Zhou, J. Z. and Yang, Y. F. 2016 Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils Plant and Soil 10.1007/s11104-016-2897-y
Xu, X., Sherry, R. A., Niu, S. L., Zhou, J. Z. and Luo, Y. Q. 2012 Long-term experimental warming decreased labile soil organic carbon in a tallgrass prairie Plant and Soil 10.1007/s11104-012-1265-9
Daly, P., McClellan, C., Maluk, M., Oakey, H., Lapierre, C., Waugh, R., Stephens, J., Marshall, D., Barakate, A., Tsuji, Y., Goeminne, G., Vanholme, R., Boerjan, W., Ralph, J. and Halpin, C. 2019 RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family Plant Biotechnology Journal 10.1111/pbi.13001
Lim, S. D., Yim, W. C., Liu, D. G., Hu, R. B., Yang, X. H. and Cushman, J. C. 2018 A Vitis vinifera basic helix-loop-helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield Plant Biotechnology Journal 10.1111/pbi.12898
Lin, J., Mazarei, M., Zhao, N., Hatcher, C. N., Wuddineh, W. A., Rudis, M., Tschaplinski, T. J., Pantalone, V. R., Arelli, P. R., Hewezi, T., Chen, F. and Stewart, C. N., Jr. 2016 Transgenic soybean overexpressing GmSAMT1 exhibits resistance to multiple-HG types of soybean cyst nematode Heterodera glycines Plant Biotechnology Journal 10.1111/pbi.12566
Liu, F. S., Zhao, Q. R., Mano, N., Ahmed, Z., Nitschke, F., Cai, Y. Q., Chapman, K. D., Steup, M., Tetlow, I. J. and Emes, M. J. 2016 Modification of starch metabolism in transgenic Arabidopsis thaliana increases plant biomass and triples oilseed production Plant Biotechnology Journal 10.1111/pbi.12453
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. 2018 Gene regulatory networks of lignin biosynthesis in switchgrass (Panicum virgatum) Plant Biotechnology Journal 10.1111/pbi.13000
Weyman, P. D., Beeri, K., Lefebvre, S. C., Rivera, J., McCarthy, J. K., Heuberger, A. L., Peers, G., Allen, A. E. and Dupont, C. L. 2015 Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis Plant Biotechnology Journal 10.1111/pbi.12254
Yang, X. P., Song, J., Todd, J., Peng, Z., Paudel, D., Luo, Z. L., Ma, X. K., You, Q., Hanson, E., Zhao, Z. F., Zhao, Y., Zhang, J., Ming, R. and Wang, J. P. 2019 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 10.1111/pbi.12992
Zhang, J., Xie, M., Li, M., Ding, J., Pu, Y., Bryan, A. C., 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., Tuskan, G. A., Muchero, W. and Chen, J. G. 2020 Overexpression of a Prefoldin beta subunit gene reduces biomass recalcitrance in the bioenergy crop Populus Plant Biotechnology Journal 10.1111/pbi.13254
Zhang, J. S., Zhang, Q., Li, L. T., Tang, H. B., Zhang, Q., Chen, Y., Arrow, J., Zhang, X. T., Wang, A. Q., Miao, C. Y. and Ming, R. 2019 Recent polyploidization events in three Saccharum founding species Plant Biotechnology Journal 10.1111/pbi.12962
Anderson, N. A., Tobimatsu, Y., Ciesielski, P. N., Ximenes, E., Ralph, J., Donohoe, B. S., Ladisch, M. and Chapple, C. 2015 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 10.1105/tpc.15.00373
Boxall, S. F., Dever, L. V., Knerova, J., Gould, P. D. and Hartwell, J. 2017 Phosphorylation of Phosphoenolpyruvate Carboxylase Is Essential for Maximal and Sustained Dark CO2 Fixation and Core Circadian Clock Operation in the Obligate Crassulacean Acid Metabolism Species Kalanchoe fedtschenkoi Plant Cell 10.1105/tpc.17.00301
Cai, Y. Q., Goodman, J. M., Pyc, M., Mullen, R. T., Dyer, J. M. and Chapman, K. D. 2015 Arabidopsis SEIPIN Proteins Modulate Triacylglycerol Accumulation and Influence Lipid Droplet Proliferation Plant Cell 10.1105/tpc.15.00588
Cope, K. R., Bascaules, A., Irving, T. B., Venkateshwaran, M., Maeda, J., Garcia, K., Rush, T. A., Ma, C., Labbe, J., Jawdy, S., Steigerwald, E., Setzke, J., Fung, E., Schnell, K. M. G., Wang, Y. Q., Schlief, N., Bucking, H., Strauss, S. H., Maillet, F., Jargeat, P., Becard, G., Puech-Pages, V. and Ane, J. M. 2019 The Ectomycorrhizal Fungus Laccaria bicolor Produces Lipochitooligosaccharides and Uses the Common Symbiosis Pathway to Colonize Populus Roots Plant Cell 10.1105/tpc.18.00676
Hu, J. P., Baker, A., Bartel, B., Linka, N., Mullen, R. T., Reumann, S. and Zolman, B. K. 2012 Plant Peroxisomes: Biogenesis and Function Plant Cell 10.1105/tpc.112.096586
Li, X., Bonawitz, N. D., Weng, J. K. and Chapple, C. 2010 The Growth Reduction Associated with Repressed Lignin Biosynthesis in Arabidopsis thaliana Is Independent of Flavonoids Plant Cell 10.1105/tpc.110.074161
Liu, M. J., Sugimoto, K., Uygun, S., Panchy, N., Campbell, M. S., Yandell, M., Howe, G. A. and Shiu, S. H. 2018 Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato Plant Cell 10.1105/tpc.18.00194
McCarthy, J. K., Smith, S. R., McCrow, J. P., Tan, M., Zheng, H., Beeri, K., Roth, R., Lichtle, C., Goodenough, U., Bowler, C. P., Dupont, C. L. and Allen, A. E. 2017 Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom Plant Cell 10.1105/tpc.16.00910
Park, S., Gidda, S. K., James, C. N., Horn, P. J., Khuu, N., Seay, D. C., Keereetaweep, J., Chapman, K. D., Mullen, R. T. and Dyer, J. M. 2013 The alpha/beta Hydrolase CGI-58 and Peroxisomal Transport Protein PXA1 Coregulate Lipid Homeostasis and Signaling in Arabidopsis Plant Cell 10.1105/tpc.113.111898
Roth, M. S., Gallaher, S. D., Westcott, D. J., Iwai, M., Louie, K. B., Mueller, M., Walter, A., Foflonker, F., Bowen, B. P., Ataii, N. N., Song, J. H., Chen, J. H., Blaby-Haas, C. E., Larabell, C., Auer, M., Northen, T. R., Merchant, S. S. and Niyogi, K. K. 2019 Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis Plant Cell 10.1105/tpc.18.00742
Salome, P. A. and Merchant, S. S. 2019 A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism Plant Cell 10.1105/tpc.18.00952
Sekhon, R. S., Saski, C., Kumar, R., Flinn, B. S., Luo, F., Beissinger, T. M., Ackerman, A. J., Breitzman, M. W., Bridges, W. C., de Leon, N. and Kaepplere, S. M. 2019 Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize Plant Cell 10.1105/tpc.18.00930
Weng, J. K., Akiyama, T., Bonawitz, N. D., Li, X., Ralph, J. and Chapple, C. 2010 Convergent Evolution of Syringyl Lignin Biosynthesis via Distinct Pathways in the Lycophyte Selaginella and Flowering Plants Plant Cell 10.1105/tpc.109.073528
Weng, J. K., Akiyama, T., Ralph, J. and Chapple, C. 2011 Independent Recruitment of an O-Methyltransferase for Syringyl Lignin Biosynthesis in Selaginella moellendorffii Plant Cell 10.1105/tpc.110.081547
Xie, M., Muchero, W., Bryan, A.C., Yee, K., Guo, H-B., Zhang, J., Tschaplinski, T.J., Singan, V.R., Lindquist, E., Payyavula, R.S., Barros-Rios, J., Dixon, R., Engle, N., Sykes, R.W., Davis, M., Jawdy, S.S., Gunter, L.E., Thompson, O., DiFazio, S.P., Evans, M., Winkeler, K., Collins, C., Schmutz, J., Guo, H., Kalluri, U., Rodriguez, M., Feng, K., Chen, J-G., Tuskan, G.A. 2018 A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus Plant Cell 10.1105/tpc.18.00168
Xing, D. H., Wang, Y. J., Hamilton, M., Ben-Hur, A. and Reddy, A. S. N. 2015 Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing Plant Cell 10.1105/tpc.15.00641
Basso, V., Kohler, A., Miyauchi, S., Singan, V., Guinet, F., Simura, J., Novak, O., Barry, K. W., Amirebrahimi, M., Block, J., Daguerre, Y., Na, H., Grigoriev, I. V., Martin, F. and Veneault-Fourrey, C. 2019 An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots Plant Cell & Environment 10.1111/pce.13702
Borland, A. M., Wullschleger, S. D., Weston, D. J., Hartwell, J., Tuskan, G. A., Yang, X. H. and Cushman, J. C. 2015 Climate-resilient agroforestry: physiological responses to climate change and engineering of crassulacean acid metabolism (CAM) as a mitigation strategy Plant Cell & Environment 10.1111/pce.12479
Jardine, K., Wegener, F., Abrell, L., van Haren, J. and Werner, C. 2014 Phytogenic biosynthesis and emission of methyl acetate Plant Cell & Environment 10.1111/pce.12164
Jardine, K. J., Jardine, A. B., Holm, J. A., Lombardozzi, D. L., Negron-Juarez, R. I., Martin, S. T., Beller, H. R., Gimenez, B. O., Higuchi, N. and Chambers, J. Q. 2017 Monoterpene 'thermometer' of tropical forest-atmosphere response to climate warming Plant Cell & Environment 10.1111/pce.12879
Kebrom, T. H. and Mullet, J. E. 2015 Photosynthetic leaf area modulates tiller bud outgrowth in sorghum Plant Cell & Environment 10.1111/pce.12500
Lantz, A. T., Allman, J., Weraduwage, S. M. and Sharkey, T. D. 2019 Isoprene: New insights into the control of emission and mediation of stress tolerance by gene expression Plant Cell & Environment 10.1111/pce.13629
Niinemets, U., Fares, S., Harley, P. and Jardine, K. J. 2014 Bidirectional exchange of biogenic volatiles with vegetation: emission sources, reactions, breakdown and deposition Plant Cell & Environment 10.1111/pce.12322
Sukumar, P., Legue, V., Vayssieres, A., Martin, F., Tuskan, G. A. and Kalluri, U. C. 2013 Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions Plant Cell & Environment 10.1111/pce.12036
Watts-Williams, S. J., Emmett, B. D., Levesque-Tremblay, V., MacLean, A. M., Sun, X. P., Satterlee, J. W., Fei, Z. J. and Harrison, M. J. 2019 Diverse Sorghum bicolor accessions show marked variation in growth and transcriptional responses to arbuscular mycorrhizal fungi Plant Cell & Environment 10.1111/pce.13509
Weng, X. Y., Lovell, J. T., Schwartz, S. L., Cheng, C. D., Haque, T., Zhang, L., Razzaque, S. and Juenger, T. E. 2019 Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C-4 grass Plant Cell & Environment 10.1111/pce.13546
Ebert, B., Birdseye, D., Liwanag, A. J. M., Laursen, T., Rennie, E. A., Guo, X., Scheller, H. V. 2018 The Three Members of the Arabidopsis thaliana Glycosyltransferase Family 92 are Functional beta-1,4-Galactan Synthases Plant Cell Physiolology 10.1093/pcp/pcy180
Yoo, J. H., Seong, E. S., Ghimire, B. K., Heo, K., Jin, X., Yamada, T., Clark, L. V., Sacks, E. J. and Yu, C. Y. 2018 Establishment of Miscanthus sinensis with decreased lignin biosynthesis by Agrobacterium-mediated transformation using antisense COMT gene Plant Cell Tissue and Organ Culture 10.1007/s11240-018-1389-6
Yang, Xiaohan, Ye, Chu-Yu, Cheng, Zong-Ming, Tschaplinski, Timothy J., Wullschleger, Stan D., Yin, Weilun, Xia, Xinli and Tuskan, Gerald A. 2010 Genomic aspects of research involving polyploid plants Plant Cell, Tissue and Organ Culture 10.1007/s11240-010-9826-1
Mei, Y., Beernink, B. M., Ellison, E. E., Konecna, E., Neelakandan, A. K., Voytas, D. F. and Whitham, S. A. 2019 Protein expression and gene editing in monocots using foxtail mosaic virus vectors Plant Direct 10.1002/pld3.181
Cuevas, H. E., Prom, L. K., Cooper, E. A., Knoll, J. E. and Ni, X. Z. 2018 Genome-Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in the US Sorghum Association Panel Plant Genome 10.3835/plantgenome2017.11.0099
Gage, J. L., Vaillancourt, B., Hamilton, J. P., Manrique-Carpintero, N. C., Gustafson, T. J., Barry, K., Lipzen, A., Tracy, W. F., Mikel, M. A., Kaeppler, S. M., Buell, C. R. and de Leon, N. 2019 Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel Plant Genome 10.3835/plantgenome2018.09.0069
Murphy, R. L., Morishige, D. T., Brady, J. A., Rooney, W. L., Yang, S. S., Klein, P. E. and Mullet, J. E. 2014 Ghd7 (Ma(6)) Represses Sorghum Flowering in Long Days: Ghd7 Alleles Enhance Biomass Accumulation and Grain Production Plant Genome 10.3835/plantgenome2013.11.0040
Ruzicka, Daniel, Chamala, Srikar, Barrios-Masias, Felipe H., Martin, Francis, Smith, Sally, Jackson, Louise E., Barbazuk, W. Brad and Schachtman, Daniel P. 2013 Inside Arbuscular Mycorrhizal Roots - Molecular Probes to Understand the Symbiosis Plant Genome 10.3835/plantgenome2012.06.0007
Tornqvist, C. E., Taylor, M., Jiang, Y. W., Evans, J., Buell, C. R., Kaeppler, S. M. and Casler, M. D. 2018 Quantitative Trait Locus Mapping for Flowering Time in a Lowland x Upland Switchgrass Pseudo-F-2 Population Plant Genome 10.3835/plantgenome2017.10.0093
Tyler, L., Lee, S. J., Young, N. D., DeIulio, G. A., Benavente, E., Reagon, M., Sysopha, J., Baldini, R. M., Troia, A., Hazen, S. P. and Caicedo, A. L. 2016 Population Structure in the Model Grass Brachypodium distachyon Is Highly Correlated with Flowering Differences across Broad Geographic Areas Plant Genome 10.3835/plantgenome2015.08.0074
Berim, A., Park, J. J. and Gang, D. R. 2014 Unexpected roles for ancient proteins: flavone 8-hydroxylase in sweet basil trichomes is a Rieske-type, PAO-family oxygenase Plant Journal 10.1111/tpj.12642
Carbonell, A., Fahlgren, N., Mitchell, S., Cox, K. L., Reilly, K. C., Mockler, T. C. and Carrington, J. C. 2015 Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors Plant Journal 10.1111/tpj.12835
Chen, F., Tholl, D., Bohlmann, J. and Pichersky, E. 2011 The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom Plant Journal 10.1111/j.1365-313X.2011.04520.x
Dash, M., Yordanov, Y. S., Georgieva, T., Kumari, S., Wei, H. R. and Busov, V. 2015 A systems biology approach identifies new regulators of poplar root development under low nitrogen Plant Journal 10.1111/tpj.13002
Dash, M., Yordanov, Y. S., Georgieva, T., Tschaplinski, T. J., Yordanova, E. and Busov, V. 2017 Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress Plant Journal 10.1111/tpj.13413
Handakumbura, P. P., Brow, K., Whitney, I. P., Zhao, K. M., Sanguinet, K. A., Lee, S. J., Olins, J., Romero-Gamboa, S. P., Harrington, M. J., Bascom, C. J., MacKinnon, K. J. M., Veling, M. T., Liu, L. F., Lee, J. E., Vogel, J. P., O'Malley, R. C., Bezanilla, M., Bartley, L. E. and Hazen, S. P. 2018 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 10.1111/tpj.14047
Hoopes, G. M., Hamilton, J. P., Wood, J. C., Esteban, E., Pasha, A., Vaillancourt, B., Provart, N. J. and Buell, C. R. 2019 An updated gene atlas for maize reveals organ-specific and stress-induced genes Plant Journal 10.1111/tpj.14184
Horn, P. J. and Chapman, K. D. 2012 Lipidomics in tissues, cells and subcellular compartments Plant Journal 10.1111/j.1365-313X.2011.04868.x
Hsia, M. M., O'Malley, R., Cartwright, A., Nieu, R., Gordon, S. P., Kelly, S., Williams, T. G., Wood, D. F., Zhao, Y. J., Bragg, J., Jordan, M., Pauly, M., Ecker, J. R., Gu, Y. and Vogel, J. P. 2017 Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection Plant Journal 10.1111/tpj.13582
Iwai, M., Roth, M. S. and Niyogi, K. K. 2018 Subdiffraction-resolution live-cell imaging for visualizing thylakoid membranes Plant Journal 10.1111/tpj.14021
Kim, S. J., Zemelis-Durfee, S., Jensen, J. K., Wilkerson, C. G., Keegstra, K. and Brandizzi, F. 2018 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 10.1111/tpj.13830
Lan, W., Rencoret, J., Lu, F. C., Karlen, S. D., Smith, B. G., Harris, P. J., del Rio, J. C. and Ralph, J. 2016 Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny Plant Journal 10.1111/tpj.13315
McCormick, R. F., Truong, S. K., Sreedasyam, A., Jenkins, J., Shu, S. Q., Sims, D., Kennedy, M., Amirebrahimi, M., Weers, B. D., McKinley, B., Mattison, A., Morishige, D. T., Grimwood, J., Schmutz, J. and Mullet, J. E. 2018 The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization Plant Journal 10.1111/tpj.13781
Na, G., Mu, X. P., Grabowski, P., Schmutz, J. and Lu, C. F. 2019 Enhancing microRNA167A expression in seed decreases the alpha-linolenic acid content and increases seed size in Camelina sativa Plant Journal 10.1111/tpj.14223
Patel, D., Basu, M., Hayes, S., Majlath, I., Hetherington, F. M., Tschaplinski, T. J. and Franklin, K. A. 2013 Temperature-dependent shade avoidance involves the receptor-like kinase ERECTA Plant Journal 10.1111/tpj.12088
Petzold, H. E., Chanda, B., Zhao, C. S., Rigoulot, S. B., Beers, E. P. and Brunner, A. M. 2018 Divaricata and Radialis Interacting Factor (DRIF) also interacts with WOX and KNOX proteins associated with wood formation in Populus trichocarpa Plant Journal 10.1111/tpj.13831
Sechet, J., Htwe, S., Urbanowicz, B., Agyeman, A., Feng, W., Ishikawa, T., Mortimer, J. C. 2018 Suppressing Arabidopsis GGLT1 affects growth by reducing the L-galactose content and borate cross-linking of rhamnogalacturonan II Plant Journal 10.1111/tpj.14088
Sorensen, I., Pettolino, F. A., Bacic, A., Ralph, J., Lu, F. C., O'Neill, M. A., Fei, Z. Z., Rose, J. K. C., Domozych, D. S. and Willats, W. G. T. 2011 The charophycean green algae provide insights into the early origins of plant cell walls Plant Journal 10.1111/j.1365-313X.2011.04686.x
Stranne, M., Ren, Y., Fimognari, L., Birdseye, D., Yan, J., Bardor, M., Sakuragi, Y. 2018 TBL10 is required for O-acetylation of pectic rhamnogalacturonan-I in Arabidopsis thaliana Plant Journal 10.1111/tpj.14067
Takeda, Y., Tobimatsu, Y., Karlen, S. D., Koshiba, T., Suzuki, S., Yamamura, M., Murakami, S., Mukai, M., Hattori, T., Osakabe, K., Ralph, J., Sakamoto, M. and Umezawa, T. 2018 Downregulation of p-COUMAROYL ESTER 3-HYDROXYLASE in rice leads to altered cell wall structures and improves biomass saccharification Plant Journal 10.1111/tpj.13988
Tobimatsu, Y., Wagner, A., Donaldson, L., Mitra, P., Niculaes, C., Dima, O., Kim, J. I., Anderson, N., Loque, D., Boerjan, W., Chapple, C. and Ralph, J. 2013 Visualization of plant cell wall lignification using fluorescence-tagged monolignols Plant Journal 10.1111/tpj.12299
Wai, C. M., VanBuren, R., Zhang, J. S., Huang, L. X., Miao, W. J., Edger, P. P., Yim, W. C., Priest, H. D., Meyers, B. C., Mockler, T., Smith, J. A. C., Cushman, J. C. and Ming, R. 2017 Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple Plant Journal 10.1111/tpj.13630
Weng, J. K., Mo, H. P. and Chapple, C. 2010 Over-expression of F5H in COMT-deficient Arabidopsis leads to enrichment of an unusual lignin and disruption of pollen wall formation Plant Journal 10.1111/j.1365-313X.2010.04391.x
Ye, C. Y., Li, T., Yin, H., Weston, D. J., Tuskan, G. A., Tschaplinski, T. J. and Yang, X. 2013 Evolutionary analyses of non-family genes in plants Plant Journal 10.1111/tpj.12073
Zhao, C. S., Hanada, A., Yamaguchi, S., Kamiya, Y. and Beers, E. P. 2011 The Arabidopsis Myb genes MYR1 and MYR2 are redundant negative regulators of flowering time under decreased light intensity Plant Journal 10.1111/j.1365-313X.2011.04508.x
Zhuang, X. F., Kollner, T. G., Zhao, N., Li, G. L., Jiang, Y. F., Zhu, L. C., Ma, J. X., Degenhardt, J. and Chen, F. 2012 Dynamic evolution of herbivore-induced sesquiterpene biosynthesis in sorghum and related grass crops Plant Journal 10.1111/j.1365-313X.2011.04771.x
Zhuo, C., Rao, X., Azad, R., Pandey, R., Xiao, X., Harkelroad, A., Wang, X., Chen, F. and Dixon, R. A. 2019 Enzymatic basis for C-lignin monomer biosynthesis in the seed coat of Cleome hassleriana Plant Journal 10.1111/tpj.14340
Czarnecki, O., Bryan, A. C., Jawdy, S. S., Yang, X. H., Cheng, Z. M., Chen, J. G. and Tuskan, G. A. 2016 Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana Plant Methods 10.1186/s13007-016-0116-8
Wang, P., Guo, L. Y., Jaini, R., Klempien, A., McCoy, R. M., Morgan, J. A., Dudareva, N. and Chapple, C. 2018 A C-13 isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems Plant Methods 10.1186/s13007-018-0318-3
Rigoulot, S. B., Petzold, H. E., Williams, S. P., Brunner, A. M. and Beers, E. P. 2019 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 10.1007/s11103-019-00861-7
Sade, N., Wilhelmi, M. D. R., Ke, X. J., Brotman, Y., Wright, M., Khan, I., De Souza, W., Bassil, E., Tobias, C. M., Thilmony, R., Vogel, J. P. and Blumwald, E. 2018 Salt tolerance of two perennial grass Brachypodium sylvaticum accessions Plant Molecular Biology 10.1007/s11103-017-0696-3
Zhao, Y., Kim, J. Y., Karan, R., Jung, J. H., Pathak, B., Williamson, B., Kannan, B., Wang, D. D., Fan, C. Y., Yu, W. J., Dong, S. J., Srivastava, V. and Altpeter, F. 2019 Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane Plant Molecular Biology 10.1007/s11103-019-00856-4
Abraham, N. D., Chitrampal, P., Kerio, S. and LeBoldus, J. M. 2018 Multiplex qPCR for detection and quantification of Sphaerulina musiva in Populus stems Plant Pathology 10.1111/ppa.12913
Kabbage, M., Piotrowski, J. S., Thill, E., Westrick, N. M., Ralph, J., Hockemeyer, K. and Koch, P. L. 2020 Poacic acid suppresses dollar spot and snow mould in amenity turfgrass Plant Pathology 10.1111/ppa.13099
Andersson, B., Shen, C., Cantrell, M., Dandy, D. S. and Peers, G. 2019 The Fluctuating Cell-Specific Light Environment and Its Effects on Cyanobacterial Physiology Plant Physiology 10.1104/pp.19.00480
Berim, A., Hyatt, D. C. and Gang, D. R. 2012 A Set of Regioselective O-Methyltransferases Gives Rise to the Complex Pattern of Methoxylated Flavones in Sweet Basil Plant Physiology 10.1104/pp.112.204164
Chen, F. 2018 Lignin biosynthesis and control of lignin composition Plant Physiology 10.1104/pp.110.155119
Dever, L. V., Boxall, S. F., Knerova, J. and Hartwell, J. 2015 Transgenic Perturbation of the Decarboxylation Phase of Crassulacean Acid Metabolism Alters Physiology and Metabolism But Has Only a Small Effect on Growth Plant Physiology 10.1104/pp.114.251827
Fan, M. Z., Herburger, K., Jensen, J. K., Zemelis-Durfee, S., Brandizzi, F., Fry, S. C. and Wilkerson, C. G. 2018 A Trihelix Family Transcription Factor Is Associated with Key Genes in Mixed-Linkage Glucan Accumulation Plant Physiology 10.1104/pp.18.00978
Feldman, M. J., Ellsworth, P. Z., Fahlgren, N., Gehan, M. A., Cousins, A. B. and Baxter, I. 2018 Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C-4 Grass Setaria Plant Physiology 10.1104/pp.18.00146
Gidda, S. K., Park, S., Pyc, M., Yurchenko, O., Cai, Y. Q., Wu, P., Andrews, D. W., Chapman, K. D., Dyer, J. M. and Mullen, R. T. 2016 Lipid Droplet-Associated Proteins (LDAPs) Are Required for the Dynamic Regulation of Neutral Lipid Compartmentation in Plant Cells Plant Physiology 10.1104/pp.15.01977
Ha, C.M., Fine, D., Bhatia, A., Rao, X., Martin, M.Z., Engle, N.L., Wherritt, D.J., Tschaplinski, T.J. and Sumner, L.W., and Dixon, R.A. 2019 Ectopic defense gene expression is associated with growth defects in medicago thrncatula lignin pathway mutants Plant Physiology 10.1104/pp.19.00533
Hendry, J. I., Gopalakrishnan, S., Ungerer, J., Pakrasi, H. B., Tang, Y. J. J. and Maranasa, C. D. 2019 Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient C-13-Labeling Data Plant Physiology 10.1104/pp.18.01357
Ishikawa, T., Fang, L., Rennie, E. A., Sechet, J., Yan, J. W., Jing, B. B., Mortimer, J. C. 2018 GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) Is a GlcNAc-Containing Glycosylinositol Phosphorylceramide Glycosyltransferase Plant Physiology 10.1104/pp.18.00396
Jardine, K., Chambers, J., Alves, E. G., Teixeira, A., Garcia, S., Holm, J., Higuchi, N., Manzi, A., Abrell, L., Fuentes, J. D., Nielsen, L. K., Torn, M. S. and Vickers, C. E. 2014 Dynamic balancing of isoprene carbon sources reflects photosynthetic and photorespiratory responses to temperature stress Plant Physiology 10.1104/pp.114.247494
Kebrom, T. H. and Mullet, J. E. 2016 Transcriptome Profiling of Tiller Buds Provides New Insights into PhyB Regulation of Tillering and Indeterminate Growth in Sorghum Plant Physiology 10.1104/pp.16.00014
Lacayo, Catherine I., Malkin, Alexander J., Holman, Hoi-Ying N., Chen, Liang, Ding, Shi-You, Hwang, Mona S. and Thelen, Michael P. 2010 Imaging Cell Wall Architecture in Single Zinnia elegans Tracheary Elements Plant Physiology 10.1104/pp.110.155242
Lovell, J. T., Shakirov, E. V., Schwartz, S., Lowry, D. B., Aspinwall, M. J., Taylor, S. H., Bonnette, J., Palacio-Mejia, J. D., Hawkes, C. V., Fay, P. A. and Juenger, T. E. 2016 Promises and Challenges of Eco-Physiological Genomics in the Field: Tests of Drought Responses in Switchgrass Plant Physiology 10.1104/pp.16.00545
Park, H. J., Floss, D. S., Levesque-Tremblay, V., Bravo, A. and Harrison, M. J. 2015 Hyphal Branching during Arbuscule Development Requires Reduced Arbuscular Mycorrhizal Plant Physiology 10.1104/pp.15.01155
Penning, B. W., Hunter, C. T., Tayengwa, R., Eveland, A. L., Dugard, C. K., Olek, A. T., Vermerris, W., Koch, K. E., McCarty, D. R., Davis, M. F., Thomas, S. R., McCann, M. C. and Carpita, N. C. 2009 Genetic Resources for Maize Cell Wall Biology Plant Physiology 10.1104/pp.109.136804
Rencoret, J., Neiva, D., Marques, G., Gutierrez, A., Kim, H., Gominho, J., Pereira, H., Ralph, J. and del Rio, J. C. 2019 Hydroxystilbene Glucosides Are Incorporated into Norway Spruce Bark Lignin Plant Physiology 10.1104/pp.19.00344
Rigal, A., Yordanov, Y. S., Perrone, I., Karlberg, A., Tisserant, E., Bellini, C., Busov, V. B., Martin, F., Kohler, A., Bhalerao, R. and Legue, V. 2012 The AINTEGUMENTA LIKE1 homeotic transcription factor PtAIL1 controls the formation of adventitious root primordia in poplar Plant Physiology 10.1104/pp.112.204453
Schuetz, M., Benske, A., Smith, R. A., Watanabe, Y., Tobimatsu, Y., Ralph, J., Demura, T., Ellis, B. and Samuels, A. L. 2014 Laccases Direct Lignification in the Discrete Secondary Cell Wall Domains of Protoxylem Plant Physiology 10.1104/pp.114.245597
Uygun, S., Azodi, C. B. and Shiu, S. H. 2019 Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity Plant Physiology 10.1104/pp.19.00653
Vandavasi, V. G., Putnam, D. K., Zhang, Q., Petridis, L., Heller, W. T., Nixon, B. T., Haigler, C. H., Kalluri, U., Coates, L., Langan, P., Smith, J. C., Meiler, J. and O'Neill, H. 2016 A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers Plant Physiology 10.1104/pp.15.01356
Vayssieres, A., Pencik, A., Felten, J., Kohler, A., Ljung, K., Martin, F. and Legue, V. 2015 Development of the Poplar-Laccaria bicolor Ectomycorrhiza Modifies Root Auxin Metabolism, Signaling, and Response Plant Physiology 10.1104/pp.114.255620
Voiniciuc, C., Engle, K. A., Gunl, M., Dieluweit, S., Schmidt, M. H., Yang, J. Y., Moremen, K. W., Mohnen, D. and Usadel, B. 2018 Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage Plant Physiology 10.1104/pp.18.00584
Yu, X. H., Cai, Y. H., Chai, J., Schwender, J. and Shanklin, J. 2019 Expression of a Lychee PHOSPHATIDYLCHOLINE:DIACYLGLYCEROL CHOLINEPHOSPHOTRANSFERASE with an Escherichia coli CYCLOPROPANE SYNTHASE Enhances Cyclopropane Fatty Acid Accumulation in Camelina Seeds Plant Physiology 10.1104/pp.19.00396
Zuniga, C., Levering, J., Antoniewicz, M. R., Guarnieri, M. T., Betenbaugh, M. J. and Zengler, K. 2018 Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris Plant Physiology 10.1104/pp.17.00605
Zuniga, C., Li, C. T., Huelsman, T., Levering, J., Zielinski, D. C., McConnell, B. O., Long, C. P., Knoshaug, E. P., Guarnieri, M. T., Antoniewicz, M. R., Betenbaugh, M. J. and Zengler, K. 2016 Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions Plant Physiology 10.1104/pp.16.00593
Jiang, Y., Chen, H., Chen, X., Kollner, T. G., Jia, Q., Wymore, T. W., Wang, F. and Chen, F. 2015 Volatile squalene from a nonseed plant Selaginella moellendorffii: Emission and biosynthesis Plant Physiology and Biochemistry 10.1016/j.plaphy.2015.07.010
Kim, J., Liu, Y. M., Zhang, X. Z., Zhao, B. Y. and Childs, K. L. 2016 Analysis of salt-induced physiological and proline changes in 46 switchgrass (Panicum virgatum) lines indicates multiple response modes Plant Physiology and Biochemistry 10.1016/j.plaphy.2016.04.020
Ozseyhan, M. E., Kang, J. L., Mu, X. P. and Lu, C. F. 2018 Mutagenesis of the FAE1 genes significantly changes fatty acid composition in seeds of Camelina sativa Plant Physiology and Biochemistry 10.1016/j.plaphy.2017.11.021
Wang, B. X., Mei, C. S. and Seiler, J. R. 2015 Early growth promotion and leaf level physiology changes in Burkholderia phytofirmans strain PsJN inoculated switchgrass Plant Physiology and Biochemistry 10.1016/j.plaphy.2014.11.008
Zhao, N., Guan, J., Ferrer, J. L., Engle, N., Chern, M., Ronald, P., Tschaplinski, T. J. and Chen, F. 2010 Biosynthesis and emission of insect-induced methyl salicylate and methyl benzoate from rice Plant Physiology and Biochemistry 10.1016/j.plaphy.2010.01.023
Jia, X. Y., Chanda, B., Zhao, M. Z., Brunner, A. M. and Beers, E. P. 2015 Instability of the Arabidopsis mutant csn5a-2 caused by epigenetic modification of intronic T-DNA Plant Science 10.1016/j.plantsci.2015.05.015
Kausch, A. P., Nelson-Vasilchik, K., Hague, J., Mookkan, M., Quemada, H., Dellaporta, S., Fragoso, C. and Zhang, Z. Y. J. 2019 Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing Plant Science 10.1016/j.plantsci.2019.01.006
Liu, D. G., Palla, K. J., Hu, R. B., Moseley, R. C., Mendoza, C., Chen, M., Abraham, P. E., Labbe, J. L., Kalluri, U. C., Tschaplinski, T. J., Cushman, J. C., Borland, A. M., Tuskan, G. A. and Yang, X. H. 2018 Perspectives on the basic and applied aspects of crassulacean acid metabolism (CAM) research Plant Science 10.1016/j.plantsci.2018.06.012
Newhouse, A. E., Polin-McGuigan, L. D., Baier, K. A., Valletta, K. E., Rottmann, W. H., Tschaplinski, T. J., Maynard, C. A. and Powell, W. A. 2014 Transgenic American chestnuts show enhanced blight resistance and transmit the trait to T1 progeny Plant Science 10.1016/j.plantsci.2014.04.004
Zogli, P. and Libault, M. 2017 Plant response to biotic stress: Is there a common epigenetic response during plant-pathogenic and symbiotic interactions? Plant Science 10.1016/j.plantsci.2017.07.008
Bihmidine, S., Julius, B. T., Dweikat, I. and Braun, D. M. 2016 Tonoplast Sugar Transporters (SbTSTs) putatively control sucrose accumulation in sweet sorghum stems Plant Signaling & Behavior 10.1080/15592324.2015.1117721
Chen, J. G. 2015 Phosphorylation of RACK1 in plants Plant Signaling & Behavior 10.1080/15592324.2015.1022013
Schnabel, E., Karve, A., Kassaw, T., Mukherjee, A., Zhou, X., Hall, T. and Frugoli, J. 2012 The M. truncatula SUNN gene is expressed in vascular tissue, similarly to RDN1, consistent with the role of these nodulation regulation genes in long distance signaling Plant Signaling & Behavior 10.4161/psb.7.1.18491
Banerjee, A., Arnesen, J. A., Moser, D., Motsa, B. B., Johnson, S. R. and Hamberger, B. 2019 Engineering modular diterpene biosynthetic pathways in Physcomitrella patens Planta 10.1007/s00425-018-3053-0
Buanafina, M. M. D., Buanafina, M. F., Laremore, T., Shearer, E. A. and Fescemyer, H. W. 2019 Characterization of feruloyl esterases in maize pollen Planta 10.1007/s00425-019-03288-y
Evans, B. R., Foston, M., O'Neill, H. M., Reeves, D., Rempe, C., McGrath, K., Ragauskas, A. J. and Davison, B. H. 2019 Production of deuterated biomass by cultivation of Lemna minor (duckweed) in D2O Planta 10.1007/s00425-019-03097-3
Grant, E. H., Fujino, T., Beers, E. P. and Brunner, A. M. 2010 Characterization of NAC domain transcription factors implicated in control of vascular cell differentiation in Arabidopsis and Populus Planta 10.1007/s00425-010-1181-2
Hong, J. J., Park, Y. S., Bravo, A., Bhattarai, K. K., Daniels, D. A. and Harrison, M. J. 2012 Diversity of morphology and function in arbuscular mycorrhizal symbioses in Brachypodium distachyon Planta 10.1007/s00425-012-1677-z
Sillo, F., Fangel, J. U., Henrissat, B., Faccio, A., Bonfante, P., Martin, F., Willats, W. G. and Balestrini, R. 2016 Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray Planta 10.1007/s00425-016-2507-5
Zhu, R. Q., Shevchenko, O., Ma, C., Maury, S., Freitag, M. and Strauss, S. H. 2013 Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology Planta 10.1007/s00425-013-1858-4
Fan, J. L., Zhou, C., Yu, L. H., Li, P., Shanklin, J. and Xu, C. C. 2019 Diversion of Carbon Flux from Sugars to Lipids Improves the Growth of an Arabidopsis Starchless Mutant Plants-Basel 10.3390/plants8070229
Li, S., Courbet, G., Ourry, A. and Ainsworth, E. A. 2019 Elevated Ozone Concentration Reduces Photosynthetic Carbon Gain but Does Not Alter Leaf Structural Traits, Nutrient Composition or Biomass in Switchgrass Plants-Basel 10.3390/plants8040085
Cole, B. J., Feltcher, M. E., Waters, R. J., Wetmore, K. M., Mucyn, T. S., Ryan, E. M., Wang, G. Y., Ul-Hasan, S., McDonald, M., Yoshikuni, Y., Malmstrom, R. R., Deutschbauer, A. M., Dang, J. L. and Visel, A. 2017 Genome-wide identification of bacterial plant colonization genes PLoS Biology 10.1371/journal.pbio.2002860
Nickels, J. D., Chatterjee, S., Stanley, C. B., Qian, S., Cheng, X., Myles, D. A. A., Standaert, R. F., Elkins, J. G. and Katsaras, J. 2017 The in vivo structure of biological membranes and evidence for lipid domains PLoS Biology 10.1371/journal.pbio.2002214
Paredes, S. H., Gao, T. X., Law, T. F., Finkel, O. M., Mucyn, T., Teixeira, Pjpl, Gonzalez, I. S., Feltcher, M. E., Powers, M. J., Shank, E. A., Jones, C. D., Jojic, V., Dangl, J. L. and Castrillo, G. 2018 Design of synthetic bacterial communities for predictable plant phenotypes PLoS Biology 10.1371/journal.pbio.2003962
Steenwyk, J. L., Opulente, D. A., Kominek, J., Shen, X. X., Zhou, X. F., Labella, A. L., Bradley, N. P., Eichman, B. F., Cadez, N., Libkind, D., DeVirgilio, J., Hulfachor, A. B., Kurtzman, C. P., Hittinger, C. T. and Rokas, A. 2019 Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts PloS Biology 10.1371/journal.pbio.3000255
Biswas M, Voltz K, Smith JC, and Langowski J 2011 Role of Histone Tails in Structural Stability of the Nucleosome PLOS Computational Biology 10.1371/journal.pcbi.1002279
Collins, S. B., Reznik, E. and Segre, D. 2012 Temporal Expression-based Analysis of Metabolism PLoS Computational Biology 10.1371/journal.pcbi.1002781
Daidone, I., Neuweiler, H., Doose, S., Sauer, M. and Smith, J. C. 2010 Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains PLOS Computational Biology 10.1371/journal.pcbi.1000645
Feist, A. M., Nagarajan, H., Rotaru, A. E., Tremblay, P. L., Zhang, T., Nevin, K. P., Lovley, D. R. and Zengler, K. 2014 Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens PLoS Computational Biology 10.1371/journal.pcbi.1003575
Foster, C. J., Gopalakrishnan, S., Antoniewicz, M. A., Maranas, C.D. 2019 From escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline PLOS Computational Biology 10.1371/journal.pcbi.1007319
King, Z. A., Drager, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E. and Palsson, B. O. 2015 Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways PLoS Computational Biology 10.1371/journal.pcbi.1004321
Liu, J. K., Lloyd, C., Al-Bassam, M. M., Ebrahim, A., Kim, J. N., Olson, C., Aksenov, A., Dorrestein, P. and Zengler, K. 2019 Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen PLoS Computational Biology 10.1371/journal.pcbi.1006848
O'Connor, D. L., Runions, A., Sluis, A., Bragg, J., Vogel, J. P., Prusinkiewicz, P. and Hake, S. 2014 A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses PLoS Computational Biology 10.1371/journal.pcbi.1003447
Ortega D, Mo G, Lee K, Zhou H, Baudry J, Dahlquist F, and Zhulin I 2013 Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein PLOS Computational Biology 10.1371/journal.pcbi.1003337
Pang, W. L., Kaur, A., Ratushny, A. V., Cvetkovic, A., Kumar, S., Pan, M., Arkin, A. P., Aitchison, J. D., Adams, M. W. W. and Baliga, N. S. 2013 Metallochaperones Regulate Intracellular Copper Levels PLoS Computational Biology 10.1371/journal.pcbi.1002880
Rockwell, G., Guido, N. J. and Church, G. M. 2013 Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective PLoS Computational Biology 10.1371/journal.pcbi.1002882
Sarkar, D., Mueller, T. J., Liu, D., Pakrasi, H. B. and Maranas, C. D. 2019 A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism PLOS Computational Biology 10.1371/journal.pcbi.1006692
Theisen, M. K., Rivera, J. G. L. and Liao, J. C. 2016 Stability of Ensemble Models Predicts Productivity of Enzymatic Systems PLoS Computational Biology 10.1371/journal.pcbi.1004800
Thukral, L., Daidone, I. and Smith, J. C. 2011 Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations PLOS Computational Biology 10.1371/journal.pcbi.1002137
Weighill, D. A. and Jacobson, D. A. 2015 3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics PLOS Computational Biology 10.1371/journal.pcbi.1004079
Yelton, A. P., Thomas, B. C., Simmons, S. L., Wilmes, P., Zemla, A., Thelen, M. P., Justice, N. and Banfield, J. F. 2011 A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes PLoS Computational Biology 10.1371/journal.pcbi.1002230
Yurkovich, J. T., Yang, L. and Palsson, B. O. 2017 Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells PLoS Computational Biology 10.1371/journal.pcbi.1005424
Baker, E. P. and Hittinger, C. T. 2019 Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function PLOS Genetics 10.1371/journal.pgen.1007786
Labella, A. L., Opulente, D. A., Steenwyk, J. L., Hittinger, C. T. and Rokas, A. 2019 Variation and selection on codon usage bias across an entire subphylum PLOS Genetics 10.1371/journal.pgen.1008304
Myers, K. S., Riley, N. M., MacGilvray, M. E., Sato, T. K., McGee, M., Heilberger, J., Coon, J. J. and Gasch, A. P. 2019 Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast PLOS Genetics 10.1371/journal.pgen.1008037
Smith, S. R., Gillard, J. T. F., Kustka, A. B., McCrow, J. P., Badger, J. H., Zheng, H., New, A. M., Dupont, C. L., Obata, T., Fernie, A. R. and Allen, A. E. 2016 Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation PLoS Genetics 10.1371/journal.pgen.1006490
Wisniewski-Dye, F., Borziak, K., Khalsa-Moyers, G., Alexandre, G., Sukharnikov, L. O., Wuichet, K., Hurst, G. B., McDonald, W. H., Robertson, J. S., Barbe, V., Calteau, A., Rouy, Z., Mangenot, S., Prigent-Combaret, C., Normand, P., Boyer, M., Siguier, P., Dessaux, Y., Elmerich, C., Condemine, G., Krishnen, G., Kennedy, I., Paterson, A. H., Gonzalez, V., Mavingui, P. and Zhulin, I. B. 2011 Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments PLOS Genetics 10.1371/journal.pgen.1002430
Abraham, P. E., Garcia, B. J., Gunter, L. E., Jawdy, S. S., Engle, N., Yang, X., Jacobson, D. A., Hettich, R. L., Tuskan, G. A. and Tschaplinski, T. J. 2018 Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves PLoS ONE 10.1371/journal.pone.0190019
Allen, L. Z., Ishoey, T., Novotny, M. A., McLean, J. S., Lasken, R. S. and Williamson, S. J. 2011 Single Virus Genomics: A New Tool for Virus Discovery PLoS ONE 10.1371/journal.pone.0017722
Aufrecht, J. A., Fowlkes, J. D., Bible, A. N., Morrell-Falvey, J., Doktycz, M. J. and Retterer, S. T. 2019 Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network PLoS ONE 10.1371/journal.pone.0218316
Berthelier V, Harris JB, Estenson KN, and Baudry J 2015 Discovery of an Inhibitor of Z-Alpha1 Antitrypsin Polymerization PLoS ONE 10.1371/journal.pone.0126256
Blanchette, C., Lacayo, C. I., Fischer, N. O., Hwang, M. and Thelen, M. P. 2012 Enhanced cellulose degradation using cellulase-nanosphere complexes PLoS One 10.1371/journal.pone.0042116
Bradley, D. T., Bourke, T. W., Fairley, D. J., Borrow, R., Shields, M. D., Zipfel, P. F. and Hughes, A. E. 2015 Susceptibility to invasive meningococcal disease: polymorphism of complement system genes and Neisseria meningitidis factor H binding protein PLoS ONE 10.1371/journal.pone.0120757
Bragg, J. N., Wu, J. J., Gordon, S. P., Guttman, M. E., Thilmony, R., Lazo, G. R., Gu, Y. Q. and Vogel, J. P. 2012 Generation and Characterization of the Western Regional Research Center Brachypodium T-DNA Insertional Mutant Collection PLoS ONE 10.1371/journal.pone.0041916
Burnet, M. C., Dohnalkova, A. C., Neumann, A. P., Lipton, M. S., Smith, R. D., Suen, G. and Callister, S. J. 2015 Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85 PLoS ONE 10.1371/journal.pone.0143809
Cadez, N., Bellora, N., Ulloa, R., Hittinger, C. T. and Libkind, D. 2019 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 10.1371/journal.pone.0210792
Cashman D, Ortega D, Zhulin I, and Baudry J 2013 Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex PLoS ONE 10.1371/journal.pone.0070705
Chen, Y., Vu, J., Thompson, M. G., Sharpless, W. A., Chan, L. J. G., Gin, J. W., Petzold, C. J. 2019 A rapid methods development workflow for high-throughput quantitative proteomic applications PLoS ONE 10.1371/journal.pone.0211582
Choi, J., Rajagopal, A., Xu, Y. F., Rabinowitz, J. D. and O'Shea, E. K. 2017 A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae PLoS ONE 10.1371/journal.pone.0176085
Chowdhary, J., Loffler, F. E. and Smith, J. C. 2017 Community detection in sequence similarity networks based on attribute clustering PLoS ONE 10.1371/journal.pone.0178650
Christopherson, M. R., Suen, G., Bramhacharya, S., Jewell, K. A., Aylward, F. O., Mead, D. and Brumm, P. J. 2013 The Genome Sequences of Cellulomonas fimi and "Cellvibrio gilvus" Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of "Cellvibrio gilvus" to the Genus Cellulomonas, and Proposal of Cellulomonas gilvus sp nov PLoS ONE 10.1371/journal.pone.0053954
Chu Y, Yao J, and Guo H 2012 QM/MM MD and Free Energy Simulations of G9a-Like Protein GLP and Its Mutants Understanding the Factors that Determine the Product Specificity PLoS ONE 10.1371/journal.pone.0037674
Cui, J. Y., Good, N. M., Hu, B., Yang, J., Wang, Q. W., Sadilek, M. and Yang, S. 2016 Metabolomics Revealed an Association of Metabolite Changes and Defective Growth in Methylobacterium extorquens AM1 Overexpressing ecm during Growth on Methanol PLoS ONE 10.1371/journal.pone.0154043
Cui, Y., Lee, M. Y., Huo, N. X., Bragg, J., Yan, L. J., Yuan, C., Li, C., Holditch, S. J., Xie, J. Z., Luo, M. C., Li, D. W., Yu, J. L., Martin, J., Schackwitz, W., Gu, Y. Q., Vogel, J. P., Jackson, A. O., Liu, Z. Y. and Garvin, D. F. 2012 Fine Mapping of the Bsr1 Barley Stripe Mosaic Virus Resistance Gene in the Model Grass Brachypodium distachyon PLoS ONE 10.1371/journal.pone.0038333
Dash, M., Yordanov, Y. S., Georgieva, T., Wei, H. R. and Busov, V. 2018 Gene network analysis of poplar root transcriptome in response to drought stress identifies a PtaJAZ3PtaRAP2.6-centered hierarchical network PLoS ONE 10.1371/journal.pone.0208560
Douglas, S. M., Chubiz, L. M., Harcombe, W. R. and Marx, C. J. 2017 Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation PLoS ONE 10.1371/journal.pone.0174345
Douglas, S. M., Chubiz, L. M., Harcombe, W. R., Ytreberg, F. M. and Marx, C. J. 2016 Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium PLoS ONE 10.1371/journal.pone.0161837
Du, N., Gholami, P., Kline, D. I., DuPont, C. L., Dickson, A. G., Mendola, D., Martz, T., Allen, A. E. and Mitchell, B. G. 2018 Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures PLoS ONE 10.1371/journal.pone.0199125
Essinger, S. D., Reichenberger, E., Morrison, C., Blackwood, C. B. and Rosen, G. L. 2015 A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies PLoS ONE 10.1371/journal.pone.0109277
Frausto, R. F., Chung, D. D., Boere, P. M., Swamy, V. S., Duong, H. N. V., Kao, L., Azimov, R., Zhang, W. L., Carrigan, L., Wong, D., Morselli, M., Zakharevich, M., Hanser, E. M., Kassels, A. C., Kurtz, I., Pellegrini, M. and Aldave, A. J. 2019 ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing PloS ONE 10.1371/journal.pone.0218279
Frost, C. J., Nyamdari, B., Tsai, C. J. and Harding, S. A. 2012 The Tonoplast-Localized Sucrose Transporter in Populus (PtaSUT4) Regulates Whole-Plant Water Relations, Responses to Water Stress, and Photosynthesis PLoS ONE 10.1371/journal.pone.0044467
He H, Weir RL, Toutounchian JJ, Pagadala J, Steinle JJ, Baudry J, Miller DD, Yates CR 2017 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 10.1371/journal.pone.0180808
Hu, G. F., Liu, Y. M., Duo, T. Q., Zhao, B. Y., Cui, G. W., Ji, J., Kuang, X., Ervin, E. H. and Zhang, X. Z. 2018 Antioxidant metabolism variation associated with alkali-salt tolerance in thirty switchgrass (Panicum virgatum) lines PLoS ONE 10.1371/journal.pone.0199681
Jin, X. L., Chen, X. L., Xiao, L., Shi, C. H., Chen, L., Yu, B., Yi, Z. L., Yoo, J. H., Heo, K., Yu, C. Y., Yamada, T., Sacks, E. J. and Peng, J. H. 2017 Application of visible and near-infrared spectroscopy to classification of Miscanthus species PLoS ONE 10.1371/journal.pone.0171360
Labbe, J., Murat, C., Morin, E., Tuskan, G. A., Le Tacon, F. and Martin, F. 2012 Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor PLoS ONE 10.1371/journal.pone.0040197
Lacayo, C. I., Hwang, M. S., Ding, S. Y. and Thelen, M. P. 2013 Lignin depletion enhances the digestibility of cellulose in cultured xylem cells PLoS One 10.1371/journal.pone.0068266
Lan, Y. M., Wang, Q., Cole, J. R. and Rosen, G. L. 2012 Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms PLoS ONE 10.1371/journal.pone.0032491
Lee, C. K., Herbold, C. W., Polson, S. W., Wommack, K. E., Williamson, S. J., McDonald, I. R. and Cary, S. C. 2012 Groundtruthing Next-Gen Sequencing for Microbial Ecology-Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing PLoS ONE 10.1371/journal.pone.0044224
Lee, J. Z., Everroad, R. C., Karaoz, U., Detweiler, A. M., Pett-Ridge, J., Weber, P. K., Prufert-Bebout, L. and Bebout, B. M. 2018 Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat PLoS One 10.1371/journal.pone.0202792
Levering, J., Broddrick, J., Dupont, C. L., Peers, G., Beeri, K., Mayers, J., Gallina, A. A., Allen, A. E., Palsson, B. O. and Zengler, K. 2016 Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom PLoS ONE 10.1371/journal.pone.0155038
Leynaud-Kieffer, L. M. C., Curran, S. C., Kim, I., Magnuson, J. K., Gladden, J. M., Baker, S. E., and Simmons, B. A. 2019 A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable PLoS ONE 10.1371/journal.pone.0210243
Li, J., Gu, L. C., Aach, J. and Church, G. M. 2014 Improved Cell-Free RNA and Protein Synthesis System PLoS ONE 10.1371/journal.pone.0106232
Luo, C. W., Tsementzi, D., Kyrpides, N., Read, T. and Konstantinidis, K. T. 2012 Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample PLoS ONE 10.1371/journal.pone.0030087
Malone, B. M., Tan, F., Bridges, S. M. and Peng, Z. H. 2011 Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data PLoS ONE 10.1371/journal.pone.0025260
Matos, D. A., Cole, B. J., Whitney, I. P., MacKinnon, K. J. M., Kay, S. A. and Hazen, S. P. 2014 Daily Changes in Temperature, Not the Circadian Clock, Regulate Growth Rate in Brachypodium distachyon PLoS ONE 10.1371/journal.pone.0100072
Matos, D. A., Whitney, I. P., Harrington, M. J. and Hazen, S. P. 2013 Cell Walls and the Developmental Anatomy of the Brachypodium distachyon Stem Internode PLoS ONE 10.1371/journal.pone.0080640
Mayali, X., Weber, P. K., Mabery, S. and Pett-Ridge, J. 2014 Phylogenetic patterns in the microbial response to resource availability: amino acid incorporation in San Francisco Bay PLoS One 10.1371/journal.pone.0095842
McKinley, B. A., Olson, S. N., Ritter, K. B., Herb, D. W., Karien, S. D., Lu, F. H., Ralph, J., Rooney, W. L. and Mullet, J. E. 2018 Variation in energy sorghum hybrid TX08001 biomass composition and lignin chemistry during development under irrigated and non-irrigated field conditions PLoS ONE 10.1371/journal.pone.0195863
Muchero, W., Sewell, M. M., Ranjan, P., Gunter, L. E., Tschaplinski, T. J., Yin, T. and Tuskan, G. A. 2013 Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments PLoS ONE 10.1371/journal.pone.0054468
Orellana, M. V., Pang, W. L., Durand, P. M., Whitehead, K. and Baliga, N. S. 2013 A Role for Programmed Cell Death in the Microbial Loop PLoS ONE 10.1371/journal.pone.0062595
Oyetunde, T., Liu, D., Martin, H. G. and Tang, Y. J. J. 2019 Machine learning framework for assessment of microbial factory performance PloS ONE 10.1371/journal.pone.0210558
Pan, C. 2011 Measuring dissociation rate constants of protein complexes through subunit exchange: experimental design and theoretical modeling PloS ONE 10.1371/journal.pone.0028827
Payne, A. C., Andregg, M., Kemmish, K., Hamalainen, M., Bowell, C., Bleloch, A., Klejwa, N., Lehrach, W., Schatz, K., Stark, H., Marblestone, A., Church, G., Own, C. S. and Andregg, W. 2013 Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface PLoS ONE 10.1371/journal.pone.0069058
Pi M, Kapoor K, Ye R, Hwang D, Miller DD, Smith JC, Baudry J, Quarles LD 2018 Computationally identified novel agonists for GPRC6A PLoS ONE 10.1371/journal.pone.0195980
Rajeev, L., Luning, E. G., Zane, G. M., Juba, T. R., Kazakov, A. E., Novichkov, P. S., Wall, J. D. and Mukhopadhyay, A. 2019 LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species PLoS ONE 10.1371/journal.pone.0214960
Rempe, C. S., Burris, K. P., Woo, H. L., Goodrich, B., Gosnell, D. K., Tschaplinski, T. J. and Stewart, C. N., Jr. 2015 Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus PLoS ONE 10.1371/journal.pone.0123925
Rotsch, D., Brossard, T., Bihmidine, S., Ying, W. J., Gaddam, V., Harmata, M., Robertson, J. D., Swyers, M., Jurisson, S. S. and Braun, D. M. 2015 Radiosynthesis of 6 '-Deoxy-6 ' F-18 Fluorosucrose via Automated Synthesis and Its Utility to Study In Vivo Sucrose Transport in Maize (Zea mays) Leaves PLoS ONE 10.1371/journal.pone.0128989
Saha, R., Verseput, A. T., Berla, B. M., Mueller, T. J., Pakrasi, H. B. and Maranas, C. D. 2012 Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp ATCC 51142 and Synechocystis sp PCC 6803 PLoS ONE 10.1371/journal.pone.0048285
Saharay M, Guo H, and Smith JC 2010 Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS PLoS ONE 10.1371/journal.pone.0012947
Shakya, M., Gottel, N., Castro, H., Yang, Z. K., Gunter, L., Labbe, J., Muchero, W., Bonito, G., Vilgalys, R., Tuskan, G., Podar, M. and Schadt, C. W. 2013 A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees PLoS ONE 10.1371/journal.pone.0076382
Tuskan, G. A., Mewalal, R., Gunter, L. E., Palla, K. J., Carter, K., Jacobson, D. A., Jones, P. C., Garcia, B. J., Weighill, D. A., Hyatt, P. D., Yang, Y., Zhang, J., Reis, N., Chen, J. G. and Muchero, W. 2018 Defining the genetic components of callus formation: A GWAS approach PLoS ONE 10.1371/journal.pone.0202519
Urbina, H. and Blackwell, M. 2012 Multilocus phylogenetic study of the Scheffersomyces yeast clade and characterization of the N-terminal region of xylose reductase gene PLoS One 10.1371/journal.pone.0039128
Wagner, E. R., Myers, K. S., Riley, N. M., Coon, J. J. and Gasch, A. P. 2019 PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production PLoS ONE 10.1371/journal.pone.0212389
Wang, J. X., Chen, L., Wang, Y., Zhang, J. F., Liang, Y. C. and Xu, D. 2013 A Computational Systems Biology Study for Understanding Salt Tolerance Mechanism in Rice PLoS ONE 10.1371/journal.pone.0064929
Wang, Z., Zhang, X. C., Le, M. H., Xu, D., Stacey, G. and Cheng, J. L. 2011 A Protein Domain Co-Occurrence Network Approach for Predicting Protein Function and Inferring Species Phylogeny PLoS ONE 10.1371/journal.pone.0017906
Wen, C. Q., Wu, L. Y., Qin, Y. J., Van Nostrand, J. D., Ning, D. L., Sun, B., Xue, K., Liu, F. F., Deng, Y., Liang, Y. T. and Zhou, J. Z. 2017 Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform PLoS ONE 10.1371/journal.pone.0176716
Williamson, S. J., Allen, L. Z., Lorenzi, H. A., Fadrosh, D. W., Brami, D., Thiagarajan, M., McCrow, J. P., Tovchigrechko, A., Yooseph, S. and Venter, J. C. 2012 Metagenomic Exploration of Viruses throughout the Indian Ocean PLoS ONE 10.1371/journal.pone.0042047
Yaung, S. J., Esvelt, K. M. and Church, G. M. 2014 CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4 PLoS ONE 10.1371/journal.pone.0098811
Youngblut, N. D., Barnett, S. E. and Buckley, D. H. 2018 HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments PLoS ONE 10.1371/journal.pone.0189616
Zheng, T., Lanahan, A.A., Lynd, L.R., Olson, D.G. 2018 The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum PLoS ONE 10.1371/journal.pone.0195143
Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Andrew Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, and Korber B 2011 Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections PLoS Pathogens 10.1371/journal.ppat.1002209
Uehling, J., Deveau, A. and Paoletti, M. 2017 Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems PLoS Pathogens 10.1371/journal.ppat.1006578
Wei, S. T. S., Fernandez-Martinez, M. A., Chan, Y. K., Van Nostrand, J. D., de los Rios-Murillo, A., Chiu, J. M. Y., Ganeshram, A. M., Cary, S. C., Zhou, J. Z. and Pointing, S. B. 2015 Diverse metabolic and stress-tolerance pathways in chasmoendolithic and soil communities of Miers Valley, McMurdo Dry Valleys, Antarctica Polar Biology 10.1007/s00300-014-1598-3
Lan, W., Yue, F. X., Rencoret, J., del Rio, J. C., Boerjan, W., Lu, F. C. and Ralph, J. 2018 Elucidating Tricin-Lignin Structures: Assigning Correlations in HSQC Spectra of Monocot Lignins Polymers 10.3390/polym10080916
Nguyen, Nam, Blaby, Ian and Wang, Daifeng 2018 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 10.1145/3233547.3233622
Joubert, W., Weighill, D., Kainer, D., Climer, S., Justice, A., Fagnan, K. and Jacobson, D. 2018 Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for Chronic Pain and Opioid Addiction Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'18) 10.5555/3291656
Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H., Lopes, Mariana R., Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A., Wisecaver, Jennifer H., Long, Tanya M., Calvey, Christopher H., Aerts, Andrea L., Barry, Kerrie W., Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y., Deshpande, Shweta, Douglass, Alexander P., Hanson, Sara J., Klenk, Hans-Peter, LaButti, Kurt M., Lapidus, Alla, Lindquist, Erika A., Lipzen, Anna M., Meier-Kolthoff, Jan P., Ohm, Robin A., Otillar, Robert P., Pangilinan, Jasmyn L., Peng, Yi, Rokas, Antonis, Rosa, Carlos A., Scheuner, Carmen, Sibirny, Andriy A., Slot, Jason C., Stielow, J. Benjamin, Sun, Hui, Kurtzman, Cletus P., Blackwell, Meredith, Grigoriev, Igor V. and Jeffries, Thomas W. 2016 Comparative genomics of biotechnologically important yeasts Proceedings of the National Academy of Sciences 10.1073/pnas.1603941113
Arbing, M. A., Chan, S., Shin, A., Phan, T., Ahn, C. J., Rohlin, L. and Gunsalus, R. P. 2012 Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1120595109
Bastiaanse, H., Zinkgraf, M., Canning, C., Tsai, H., Lieberman, M., Comai, L., Henry, I. and Groover, A. 2019 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 10.1073/pnas.1903229116
Batista, C. E., Ye, J., Ribeiro, I. O., Guimaraes, P. C., Medeiros, A. S. S., Barbosa, R. G., Oliveira, R. L., Duvoisin, S., Jr., Jardine, K. J., Gu, D., Guenther, A. B., McKinney, K. A., Martins, L. D., Souza, R. A. F. and Martin, S. T. 2019 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 10.1073/pnas.1904154116
Bertrand, E. M., Allen, A. E., Dupont, C. L., Norden-Krichmar, T. M., Bai, J., Valas, R. E. and Saito, M. A. 2012 Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1201731109
Brawley, S. H., Blouin, N. A., Ficko-Blean, E., Wheeler, G. L., Lohr, M., Goodson, H. V., Jenkins, J. W., Blaby-Haas, C. E., Helliwell, K. E., Chan, C. X., Marriage, T. N., Bhattacharya, D., Klein, A. S., Badis, Y., Brodie, J., Cao, Y., Collen, J., Dittami, S. M., Gachon, C. M. M., Green, B. R., Karpowicz, S. J., Kim, J. W., Kudahl, U. J., Lin, S., Michel, G., Mittag, M., Olson, Bjsc, Pangilinan, J. L., Peng, Y., Qiu, H., Shu, S., Singer, J. T., Smith, A. G., Sprecher, B. N., Wagner, V., Wang, W., Wang, Z. Y., Yan, J., Yarish, C., Zauner-Riek, S., Zhuang, Y., Zou, Y., Lindquist, E. A., Grimwood, J., Barry, K. W., Rokhsar, D. S., Schmutz, J., Stiller, J. W., Grossman, A. R. and Prochnik, S. E. 2017 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 10.1073/pnas.1703088114
Broddrick, J. T., Rubin, B. E., Welkie, D. G., Du, N., Mih, N., Diamond, S., Lee, J. J., Golden, S. S. and Palsson, B. O. 2016 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 10.1073/pnas.1613446113
Brunk, E., Chang, R. L., Xia, J., Hefzi, H., Yurkovich, J. T., Kim, D., Buckmiller, E., Wang, H. H., Cho, B. K., Yang, C., Palsson, B. O., Church, G. M. and Lewis, N. E. 2018 Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1811971115
Chadwick, G. L., Otero, F. J., Gralnick, J. A., Bond, D. R. and Orphan, V. J. 2019 NanoSIMS imaging reveals metabolic stratification within current-producing biofilms Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1912498116
Chan, Y. K., Van Nostrand, J. D., Zhou, J. Z., Pointing, S. B. and Farrell, R. L. 2013 Functional ecology of an Antarctic Dry Valley Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1300643110
Chuck, G. S., Tobias, C., Sun, L., Kraemer, F., Li, C. L., Dibble, D., Arora, R., Bragg, J. N., Vogel, J. P., Singh, S., Simmons, B. A., Pauly, M. and Hake, S. 2011 Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1113971108
Coutinho, B. G., Mevers, E., Schaefer, A. L., Pelletier, D. A., Harwood, C. S., Clardy, J. and Greenberg, E. P. 2018 A plant-responsive bacterial-signaling system senses an ethanolamine derivative Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1809611115
Cuvelier, M. L., Allen, A. E., Monier, A., McCrow, J. P., Messie, M., Tringe, S. G., Woyke, T., Welsh, R. M., Ishoey, T., Lee, J. H., Binder, B. J., DuPont, C. L., Latasa, M., Guigand, C., Buck, K. R., Hilton, J., Thiagarajan, M., Caler, E., Read, B., Lasken, R. S., Chavez, F. P. and Worden, A. Z. 2010 Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1001665107
Czajka, J. J., Abernathy, M. h., Benites, V. T., Baidoo, E. E. K., Deming, J. W., and Tang, Y. J. 2018 Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1807804115
Diner, R. E., Nodding, C. M., Lian, N. C., Kang, A. K., McQuaid, J. B., Jablanovic, J., Espinoza, J. L., Nguyen, N. A., Anzelmatti, M. A., Jansson, J., Bielinski, V. A., Karas, B. J., Dupont, C. L., Allen, A. E. and Weyman, P. D. 2017 Diatom centromeres suggest a mechanism for nuclear DNA acquisition Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1700764114
Doust, A. N., Lukens, L., Olsen, K. M., Mauro-Herrera, M., Meyer, A. and Rogers, K. 2014 Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1308940110
Embree, M., Liu, J. K., Al-Bassam, M. M. and Zengler, K. 2015 Networks of energetic and metabolic interactions define dynamics in microbial communities Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1506034112
Fang, X., Sastry, A., Mih, N., Kim, D., Tan, J., Yurkovich, J. T., Lloyd, C. J., Gao, Y., Yang, L. and Palsson, B. O. 2017 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 10.1073/pnas.1702581114
Feng, S. H., Cokus, S. J., Zhang, X. Y., Chen, P. Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., Ukomadu, C., Sadler, K. C., Pradhan, S., Pellegrini, M. and Jacobsen, S. E. 2010 Conservation and divergence of methylation patterning in plants and animals Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1002720107
Gibney, P. A., Schieler, A., Chen, J. C., Rabinowitz, J. D. and Botstein, D. 2015 Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1506289112
Guo, H. B. and Guo, H. 2007 Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.0702981104
Harcombe, W. R., Chacon, J. M., Adamowicz, E. M., Chubiz, L. M. and Marx, C. J. 2018 Evolution of bidirectional costly mutualism from byproduct consumption Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1810949115
Hodgkins, S. B., Tfaily, M. M., McCalley, C. K., Logan, T. A., Crill, P. M., Saleska, S. R., Rich, V. I. and Chanton, J. P. 2014 Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1314641111
Hogle, S. L., Dupont, C. L., Hopkinson, B. M., King, A. L., Buck, K. N., Roe, K. L., Stuart, R. K., Allen, A. E., Mann, E. L., Johnson, Z. I. and Barbeau, K. A. 2018 Pervasive iron limitation at subsurface chlorophyll maxima of the California Current Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1813192115
Hu, P., Chakraborty, S., Kumar, A., Woolston, B., Liu, H. J., Emerson, D. and Stephanopoulos, G. 2016 Integrated bioprocess for conversion of gaseous substrates to liquids Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1516867113
James, C. N., Horn, P. J., Case, C. R., Gidda, S. K., Zhang, D. Y., Mullen, R. T., Dyer, J. M., Anderson, R. G. W. and Chapman, K. D. 2010 Disruption of the Arabidopsis CGI-58 homologue produces Chanarin-Dorfman-like lipid droplet accumulation in plants Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.0911359107
Johnston, E. R., Hatt, J. K., He, Z. L., Wu, L. Y., Guo, X., Luo, Y. Q., Schuur, E. A. G., Tiedje, J. M., Zhou, J. Z. and Konstantinidis, K. T. 2019 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 10.1073/pnas.1901307116
Kim, K. H., Eudes, A., Jeong, K., Yoo, C. G., Kim, C. S. and Ragauskas, A. 2019 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 10.1073/pnas.1904636116
Kosuri, S., Goodman, D. B., Cambray, G., Mutalik, V. K., Gao, Y., Arkin, A. P., Endy, D. and Church, G. M. 2013 Composability of regulatory sequences controlling transcription and translation in Escherichia coli Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1301301110
Krause, D. J., Kominek, J., Opulente, D. A., Shen, X. X., Zhou, X. F., Langdon, Q. K., DeVirgilio, J., Hulfachor, A. B., Kurtzman, C. P., Rokas, A. and Hittinge, C. T. 2018 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 10.1073/pnas.1806268115
Kremer, T. A., LaSarre, B., Posto, A. L. and McKinlay, J. B. 2015 N-2 gas is an effective fertilizer for bioethanol production by Zymomonas mobilis Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1420663112
Kunjapur, A. M., Stork, D. A., Kuru, E., Vargas-Rodriguez, O., Landon, M., Soll, D. and Church, G. M. 2018 Engineering posttranslational proofreading to discriminate nonstandard amino acids Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1715137115
Liao, L., Schaefer, A. L., Coutinho, B. G., Brown, P. J. B. and Greenberg, E. P. 2018 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 10.1073/pnas.1808351115
Lin, P. P., Jaeger, A. J., Wu, T. Y., Xu, S. C., Lee, A. S., Gao, F. K., Chen, P. W. and Liao, J. C. 2018 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 10.1073/pnas.1802191115
Lowry, D. B., Lovell, J. T., Zhang, L., Bonnette, J., Fay, P. A., Mitchell, R. B., Lloyd-Reilley, J., Boe, A. R., Wu, Y. Q., Rouquette, F. M., Wynia, R. L., Weng, X. Y., Behrman, K. D., Healey, A., Barrym, K., Lipzen, A., Bauer, D., Sharma, A., Jenkins, J., Schmutz, J., Fritschi, F. B. and Juenger, T. E. 2019 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 10.1073/pnas.1821543116
Machovina, M. M., Mallinson, S. J. B., Knott, B. C., Meyers, A. W., Garcia-Borras, M., Bu, L. T., Gado, J. E., Oliver, A., Schmidt, G. P., Hinchen, D. J., Crowley, M. F., Johnson, C. W., Neidle, E. L., Payne, C. M., Houk, K. N., Beckham, G. T., McGeehan, J. E. and DuBois, J. L. 2019 Enabling microbial syringol conversion through structure-guided protein engineering Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1820001116
Mack, D. G., Falta, M. T., McKee, A. S., Martin, A. K., Simonian, P. L., Crawford, F., Gordon, T., Mercer, R. R., Hoover, M. D., Marrack, P., Kappler, J. W., Tuder, R. M. and Fontenot, A. P. 2014 Regulatory T cells modulate granulomatous inflammation in an HLA-DP2 transgenic murine model of beryllium-induced disease Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1408048111
Marckmann, D., Trasnea, P. I., Schimpf, J., Winterstein, C., Andrei, A., Schmollinger, S., Blaby-Haas, C. E., Friedrich, T., Daldal, F. and Koch, H. G. 2019 The cbb 3-type cytochrome oxidase assembly factor CcoG is a widely distributed cupric reductase Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1913803116
McAndrew, R. P., Sathitsuksanoh, N., Mbughuni, M. M., Heins, R. A., Pereira, J. H., George, A., Sale, K. L., Fox, B. G., Simmons, B. A. and Adams, P. D. 2016 Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1608917113
Mee, M. T., Collins, J. J., Church, G. M. and Wang, H. H. 2014 Syntrophic exchange in synthetic microbial communities Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1405641111
Meinhold, L., Smith, J. C., Kitao, A. and Zewail, A. H. 2007 Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.0708199104
Moore, B. M., Wang, P. P., Fan, P. X., Leong, B., Schenck, C. A., Lloyd, J. P., Lehti-Shiu, M. D., Last, R. L., Pichersky, E. and Shiu, S. H. 2019 Robust predictions of specialized metabolism genes through machine learning Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1817074116
Muchero, W., Sondreli, K. L., Chen, J. G., Urbanowicz, B. R., Zhang, J., Singan, V., Yang, Y., Brueggeman, R. S., Franco-Coronado, J., Abraham, N., Yang, J. Y., Moremen, K. W., Weisberg, A. J., Chang, J. H., Lindquist, E., Barry, K., Ranjan, P., Jawdy, S., Schmutz, J., Tuskan, G. A. and LeBoldus, J. M. 2018 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 10.1073/pnas.1804428115
Murphy, R. L., Klein, R. R., Morishige, D. T., Brady, J. A., Rooney, W. L., Miller, F. R., Dugas, D. V., Klein, P. E. and Mullet, J. E. 2011 Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1106212108
Napolitano, M. G., Landon, M., Gregg, C. J., Lajoie, M. J., Govindarajan, L., Mosberg, J. A., Kuznetsov, G., Goodman, D. B., Vargas-Rodriguez, O., Isaacs, F. J., Soll, D. and Church, G. M. 2016 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 10.1073/pnas.1605856113
Ning, D. L., Deng, Y., Tiedje, J. M. and Zhou, J. Z. 2019 A general framework for quantitatively assessing ecological stochasticity Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1904623116
Noe, F., Doose, S., Daidone, I., Lollmann, M., Sauer, M., Chodera, J. D. and Smith, J. C. 2011 Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1004646108
Plett, J. M., Daguerre, Y., Wittulsky, S., Vayssieres, A., Deveau, A., Melton, S. J., Kohler, A., Morrell-Falvey, J. L., Brun, A., Veneault-Fourrey, C. and Martin, F. 2014 Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1322671111
Riley, R., Salamov, A. A., Brown, D. W., Nagy, L. G., Floudas, D., Held, B. W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E. A., Sun, H., LaButti, K. M., Schmutz, J., Jabbour, D., Luo, H., Baker, S. E., Pisabarro, A. G., Walton, J. D., Blanchette, R. A., Henrissat, B., Martin, F., Cullen, D., Hibbett, D. S. and Grigoriev, I. V. 2014 Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1400592111
Risser, D. D., Wong, F. C. Y. and Meeks, J. C. 2012 Biased inheritance of the protein PatN frees vegetative cells to initiate patterned heterocyst differentiation Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1207530109
Sivan, O., Antler, G., Turchyn, A. V., Marlow, J. J. and Orphan, V. J. 2014 Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1412269111
Strenkert, D., Schmollinger, S., Gallaher, S. D., Salome, P. A., Purvine, S. O., Nicora, C. D., Mettler-Altmann, T., Soubeyrand, E., Weber, A. P. M., Lipton, M. S., Basset, G. J. and Merchant, S. S. 2019 Multiomics resolution of molecular events during a day in the life of Chlamydomonas Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1815238116
Tisserant, E., Malbreil, M., Kuo, A., Kohler, A., Symeonidi, A., Balestrini, R., Charron, P., Duensing, N., Frei dit Frey, N., Gianinazzi-Pearson, V., Gilbert, L. B., Handa, Y., Herr, J. R., Hijri, M., Koul, R., Kawaguchi, M., Krajinski, F., Lammers, P. J., Masclaux, F. G., Murat, C., Morin, E., Ndikumana, S., Pagni, M., Petitpierre, D., Requena, N., Rosikiewicz, P., Riley, R., Saito, K., San Clemente, H., Shapiro, H., van Tuinen, D., Becard, G., Bonfante, P., Paszkowski, U., Shachar-Hill, Y. Y., Tuskan, G. A., Young, J. P., Sanders, I. R., Henrissat, B., Rensing, S. A., Grigoriev, I. V., Corradi, N., Roux, C. and Martin, F. 2013 Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1313452110
Vermaas, J. V., Dixon, R. A., Chen, F., Mansfield, S. D., Boerjan, W., Ralph, J., Crowley, M. F. and Beckham, G. T. 2019 Passive membrane transport of lignin-related compounds Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1904643116
Wan Q, Parks J, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L, 2015 Direct Determination of Protonation States and Visualization of Hydrogen Bonding in a Glycoside Hydrolase with Neutron Crystallography Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1504986112
Wannier, T. M., Kunjapur, A. M., Rice, D. P., McDonald, M. J., Desai, M. M. and Church, G. M. 2018 Adaptive evolution of genomically recoded Escherichia coli Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1715530115
Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C. and Siuzdak, G. 2009 Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.0812874106
Xu, J. Y., Liu, N., Qiao, K. J., Vogg, S. and Stephanopoulos, G. 2017 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 10.1073/pnas.1703321114
Xu, L., Naylor, D., Dong, Z. B., Simmons, T., Pierroz, G., Hixson, K. K., Kim, Y. M., Zink, E. M., Engbrecht, K. M., Wang, Y., Gao, C., DeGraaf, S., Madera, M. A., Sievert, J. A., Hollingsworth, J., Birdseye, D., Scheller, H. V., Hutmacher, R., Dahlberg, J., Jansson, C., Taylor, J. W., Lemaux, P. G. and Coleman-Derr, D. 2018 Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1807275115
Xu, P., Qiao, K. J., Ahn, W. S. and Stephanopoulos, G. 2016 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 10.1073/pnas.1607295113
Yang, S., Land, M. L., Klingeman, D. M., Pelletier, D. A., Lu, T. Y., Martin, S. L., Guo, H. B., Smith, J. C. and Brown, S. D. 2010 Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.0914506107
Yordanov, Y. S., Ma, C., Strauss, S. H. and Busov, V. B. 2014 EARLY BUD-BREAK 1 (EBB1) is a regulator of release from seasonal dormancy in poplar trees Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1405621111
Zhang, H. R., Pereira, B., Li, Z. J. and Stephanopoulos, G. 2015 Engineering Escherichia coli coculture systems for the production of biochemical products Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1506781112
Zhang, J. W., Presley, G. N., Hammel, K. E., Ryu, J. S., Menke, J. R., Figueroa, M., Hu, D. H., Orr, G. and Schilling, J. S. 2016 Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1608454113
Zhou, J. Z., Deng, Y., Zhang, P., Xue, K., Liang, Y. T., Van Nostrand, J. D., Yang, Y. F., He, Z. L., Wu, L. Y., Stahl, D. A., Hazen, T. C., Tiedje, J. M. and Arkin, A. P. 2014 Stochasticity, succession, and environmental perturbations in a fluidic ecosystem Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.1324044111
Brown SD, Guss AM, Karpinets TV, Parks JM, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwand A, Rodriguez M, Raman B, Shao X, Mielenz JR, Smith JC, Keller M, and Lynd LR 2011 Mutant Alcohol Dehydrogenase Leads to Improved Ethanol Tolerance in Clostridium thermocellum Proceedings of the National Academy of Sciences U S A 10.1073/pnas.1102444108
Daidone I, Ulmschneider MB, Di Nola A, Amadei A, and Smith JC 2007 Dehydration-Driven Solvent Exposure of Hydrophobic Surfaces as a Driving Force in Peptide Folding Proceedings of the National Academy of Sciences USA 10.1073/pnas.0701401104
Ellingson SR, and Baudry J 2011 High-Throughput Virtual Molecular Docking Hadoop Implementation of AutoDock4 on a Private Cloud Proceedings of the second international workshop on Emerging computational methods for the life sciences 10.1145/1996023
Chan, S.H.J., Friedman, E.S., Wu, G.D., and Maranas, C.D. 2019 Predicting the longitudinally and radially varying gut microbiota composition using multi-scale microbial metabolic modeling Processes 10.3390/pr7070394
Chan, S. H. J., Friedman, E. S., Wu, G. D. and Maranas, C. D. 2019 Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling Processes 10.3390/pr7070394
Chaves, J.E., Presley, G.N., and Michener, J.K., 2019 Modular engineering of biomass degradation pathways Processes 10.3390/pr7040230
Cheng, M. H., Wang, Z. Q., Dien, B. S., Slininger, P. J. W. and Singh, V. 2019 Economic Analysis of Cellulosic Ethanol Production from Sugarcane Bagasse Using a Sequential Deacetylation, Hot Water and Disk-Refining Pretreatment Processes 10.3390/pr7100642
Garcia, S. and Trinh, C. T. 2019 Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis Processes 10.3390/pr7060361
Kurambhatti, C., Kumar, D. and Singh, V. 2019 Impact of Fractionation Process on the Technical and Economic Viability of Corn Dry Grind Ethanol Process Processes 10.3390/pr7090578
Wilken, S., Saxena, M., Petzold, L. R. and O'Malley, M. A. 2018 In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi Processes 10.3390/pr6010007
Morton, S. A., Gupta, S., Petzold, C. J., and Ralston, C. 2018 Recent Advances in X-Ray Hydroxl Radical Footprinting at the Advanced Light Source Synchrotron Protein & Peptide Letters 10.2174/0929866526666181128125725
Xu J, and Smith JC 2010 Probing the Mechanism of Cellulosome Attachment to the Clostridium thermocellum Cell Surface Computer Simulation of the Type II Cohesin-Dockerin Complex and Its Variants Protein Engineering, Design and Selection 10.1093/protein/gzq049
Filippova, E. V., Wawrzak, Z., Ruan, J., Pshenychnyi, S., Schultz, R. M., Wolfe, A. J. and Anderson, W. F. 2016 Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli Protein Science 10.1002/pro.3050
Goodsell, D. S., Zardecki, C., Di Costanzo, L., Duarte, J. M., Hudson, B. P., Persikova, I., Segura, J., Shao, C. H., Voigt, M., Westbrook, J. D., Young, J. Y. and Burley, S. K. 2019 RCSB Protein Data Bank: Enabling biomedical research and drug discovery Protein Science 10.1002/pro.3730
Xu J, Crowley MF, and Smith JC 2009 Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol Insight into Cohesin-Dockerin Complexation from Computer Simulation Protein Science 10.1002/pro.105
Johnson, Q. R., Lindsay, R. J., Nellas, R. B. and Shen, T. 2016 Pressure-induced conformational switch of an interfacial protein Proteins 10.1002/prot.25031
Meinhold, L. and Smith, J. C. 2007 Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns Proteins 10.1002/prot.21246
Mesentean, S., Fischer, S. and Smith, J. C. 2006 Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping Proteins 10.1002/prot.20981
Miao, Y., Baudry, J., Smith, J. C. and McCammon, J. A. 2016 General trends of dihedral conformational transitions in a globular protein Proteins 10.1002/prot.24996
Splettstoesser, T., Holmes, K. C., Noe, F. and Smith, J. C. 2011 Structural modeling and molecular dynamics simulation of the actin filament Proteins 10.1002/prot.23017
Splettstoesser, T., Noe, F., Oda, T. and Smith, J. C. 2009 Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state Proteins 10.1002/prot.22350
Luxmi, R., Blaby-Haas, C., Kumar, D., Rauniyar, N., King, S. M., Mains, R. E. and Eipper, B. A. 2018 Proteases Shape the Chlamydomonas Secretome: Comparison to Classical Neuropeptide Processing Machinery Proteomes 10.3390/proteomes6040036
Basisty, N., Meyer, J. G., Wei, L., Gibson, B. W. and Schilling, B. 2018 Simultaneous Quantification of the Acetylome and Succinylome by "One-Pot' Affinity Enrichment Proteomics 10.1002/pmic.201800123
Qian C, Chen H, Johs A, Lu X, An J, Pierce EM, Parks JM, Elias DA, Hettich RL, Gu B 2018 Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes Proteomics 10.1002/pmic.201700479
Horn, P. J., Joshi, U., Behrendt, A. K., Chapman, K. D. and Verbeck, G. F. 2012 On-stage liquid-phase lipid microextraction coupled to nanospray mass spectrometry for detailed, nano-scale lipid analysis Rapid Communications in Mass Spectrometry 10.1002/rcm.6194
Ostrom, N. E., Gandhi, H., Coplen, T. B., Toyoda, S., Bohlke, J. K., Brand, W. A., Casciotti, K. L., Dyckmans, J., Giesemann, A., Mohn, J., Well, R., Yu, L. F. and Yoshida, N. 2018 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 10.1002/rcm.8157
Pett-Ridge, Jennifer and Firestone, Mary K. 2017 Using stable isotopes to explore root-microbe-mineral interactions in soil Rhizosphere 10.1016/j.rhisph.2017.04.016
Razavi, B. S., Zhang, X. C., Bilyera, N., Guber, A. and Zarebanadkouki, M. 2019 Soil zymography: Simple and reliable? Review of current knowledge and optimization of the method Rhizosphere 10.1016/j.rhisph.2019.100161
Cole, J. R. and Tiedje, J. M. 2014 History and impact of RDP A legacy from Carl Woese to microbiology RNA Biology 10.4161/rna.28306
Bondar AN, Suhai S, Smith JC, and Frangopol P 2007 Computer Simulations of Local Anesthetic Mechanisms Quantum Chemical Investigation of Procaine Romanian Reports in Physics none
Zhu, Y. M., Regner, M., Lu, F. C., Kim, H., Mohammadi, A., Pearson, T. J. and Ralph, J. 2013 Preparation of monolignol gamma-acetate, gamma-p-hydroxycinnamate, and gamma-p-hydroxybenzoate conjugates: selective deacylation of phenolic acetates with hydrazine acetate RSC Advances 10.1039/c3ra42818d
Smith, J. C. 2009 Supercomputers Tackle Biofuel Production Problems SciDAC Review none
Amann, R. I., Baichoo, S., Blencowe, B. J., Bork, P., Borodovsky, M., Brooksbank, C., Chain, P. S. G., Colwell, R. R., Daffonchio, D. G., Danchin, A., de Lorenzo, V., Dorrestein, P. C., Finn, R. D., Fraser, C. M., Gilbert, J. A., Hallam, S. J., Hugenholtz, P., Ioannidis, J. P. A., Jansson, J. K., Kim, J. F., Klenk, H. P., Klotz, M. G., Knight, R., Konstantinidis, K. T., Kyrpides, N. C., Mason, C. E., McHardy, A. C., Meyer, F., Ouzounis, C. A., Patrinos, A. A. N., Podar, M., Pollard, K. S., Ravel, J., Munoz, A. R., Roberts, R. J., Rossello-Mora, R., Sansone, S. A., Schloss, P. D., Schriml, L. M., Setubal, J. C., Sorek, R., Stevens, R. L., Tiedje, J. M., Turjanski, A., Tyson, G. W., Ussery, D. W., Weinstock, G. M., White, O., Whitman, W. B. and Xenarios, I. 2019 Toward unrestricted use of public genomic data Science 10.1126/science.aaw1280
Brunson, J. K., McKinnie, S. M. K., Chekan, J. R., McCrow, J. P., Miles, Z. D., Bertrand, E. M., Bielinski, V. A., Luhavaya, H., Obornik, M., Smith, G. J., Hutchins, D. A., Allen, A. E. and Moore, B. S. 2018 Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom Science 10.1126/science.aau0382
Budin, I., de Rond, T., Chen, Y., Chan, L. J. G., Petzold, C. J., AND Keasling, J. D. 2018 Viscous control of cellular respiration by membrane lipid composition Science 10.1126/science.aat7925
Goodman, D. B., Church, G. M. and Kosuri, S. 2013 Causes and Effects of N-Terminal Codon Bias in Bacterial Genes Science 10.1126/science.1241934
Hackett, S. R., Zanotelli, V. R. T., Xu, W. X., Goya, J., Park, J. O., Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D. and Rabinowitz, J. D. 2016 Systems-level analysis of mechanisms regulating yeast metabolic flux Science 10.1126/science.aaf2786
Lajoie, M. J., Kosuri, S., Mosberg, J. A., Gregg, C. J., Zhang, D. and Church, G. M. 2013 Probing the Limits of Genetic Recoding in Essential Genes Science 10.1126/science.1241460
Lajoie, M. J., Rovner, A. J., Goodman, D. B., Aerni, H. R., Haimovich, A. D., Kuznetsov, G., Mercer, J. A., Wang, H. H., Carr, P. A., Mosberg, J. A., Rohland, N., Schultz, P. G., Jacobson, J. M., Rinehart, J., Church, G. M. and Isaacs, F. J. 2013 Genomically Recoded Organisms Expand Biological Functions Science 10.1126/science.1241459
Lam, F. H., Ghaderi, A., Fink, G. R. and Stephanopoulos, G. 2014 Engineering alcohol tolerance in yeast Science 10.1126/science.1257859
Martin, F. M., Uroz, S. and Barker, D. G. 2017 Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria Science 10.1126/science.aad4501
Melillo, J. M., Frey, S. D., DeAngelis, K. M., Werner, W. J., Bernard, M. J., Bowles, F. P., Pold, G., Knorr, M. A. and Grandy, A. S. 2017 Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world Science 10.1126/science.aan2874
Ostrov, N., Landon, M., Guell, M., Kuznetsov, G., Teramoto, J., Cervantes, N., Zhou, M., Singh, K., Napolitano, M. G., Moosburner, M., Shrock, E., Pruitt, B. W., Conway, N., Goodman, D. B., Gardner, C. L., Tyree, G., Gonzales, A., Wanner, B. L., Norville, J. E., Lajoie, M. J. and Church, G. M. 2016 Design, synthesis, and testing toward a 57-codon genome Science 10.1126/science.aaf3639
Parks, J. M., Johs, A., Podar, M., Bridou, R., Hurt, R. A., Jr., Smith, S. D., Tomanicek, S. J., Qian, Y., Brown, S. D., Brandt, C. C., Palumbo, A. V., Smith, J. C., Wall, J. D., Elias, D. A. and Liang, L. 2013 The genetic basis for bacterial mercury methylation Science 10.1126/science.1230667
Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F. S., Pasternak, S., Liang, C. Z., Zhang, J. W., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M., Belter, E., Du, F. Y., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W. Z., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R. F., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J. K., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L. Y., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W., Ying, K., Yeh, C. T., Emrich, S. J., Jia, Y., Kalyanaraman, A., Hsia, A. P., Barbazuk, W. B., Baucom, R. S., Brutnell, T. P., Carpita, N. C., Chaparro, C., Chia, J. M., Deragon, J. M., Estill, J. C., Fu, Y., Jeddeloh, J. A., Han, Y. J., Lee, H., Li, P. H., Lisch, D. R., Liu, S. Z., Liu, Z. J., Nagel, D. H., McCann, M. C., SanMiguel, P., Myers, A. M., Nettleton, D., Nguyen, J., Penning, B. W., Ponnala, L., Schneider, K. L., Schwartz, D. C., Sharma, A., Soderlund, C., Springer, N. M., Sun, Q., Wang, H., Waterman, M., Westerman, R., Wolfgruber, T. K., Yang, L. X., Yu, Y., Zhang, L. F., Zhou, S. G., Zhu, Q., Bennetzen, J. L., Dawe, R. K., Jiang, J. M., Jiang, N., Presting, G. G., Wessler, S. R., Aluru, S., Martienssen, R. A., Clifton, S. W., McCombie, W. R., Wing, R. A. and Wilson, R. K. 2009 The B73 Maize Genome: Complexity, Diversity, and Dynamics Science 10.1126/science.1178534
Shaw, A. J., Lam, F. H., Hamilton, M., Consiglio, A., MacEwen, K., Brevnova, E. E., Greenhagen, E., LaTouf, W. G., South, C. R., van Dijken, H. and Stephanopoulos, G. 2016 Metabolic engineering of microbial competitive advantage for industrial fermentation processes Science 10.1126/science.aaf6159
Solomon, K. V., Haitjema, C. H., Henske, J. K., Gilmore, S. P., Borges-Rivera, D., Lipzen, A., Brewer, H. M., Purvine, S. O., Wright, A. T., Theodorou, M. K., Grigoriev, I. V., Regev, A., Thompson, D. A. and O'Malley, M. A. 2016 Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes Science 10.1126/science.aad1431
Wolfe-Simon, Felisa, Blum, Jodi Switzer, Kulp, Thomas R., Gordon, Gwyneth W., Hoeft, Shelley E., Pett-Ridge, Jennifer, Stolz, John F., Webb, Samuel M., Weber, Peter K., Davies, Paul C. W., Anbar, Ariel D. and Oremland, Ronald S. 2011 Response to Comments on “A Bacterium That Can Grow Using Arsenic Instead of Phosphorus” Science 10.1126/science.1202098
Wolfe-Simon, Felisa, Blum, Jodi Switzer, Kulp, Thomas R., Gordon, Gwyneth W., Hoeft, Shelley E., Pett-Ridge, Jennifer, Stolz, John F., Webb, Samuel M., Weber, Peter K., Davies, Paul C. W., Anbar, Ariel D. and Oremland, Ronald S. 2011 A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science 10.1126/science.1197258
Baker, E. P., Peris, D., Moriarty, R. V., Li, X. Y. C., Fay, J. C. and Hittinger, C. T. 2019 Mitochondrial DNA and temperature tolerance in lager yeasts Science Advances 10.1126/sciadv.aav1869
Hong L, Jain N, Cheng X, Bernal A, Tyagi M, and Smith JC 2016 Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering Science Advances 10.1126/sciadv.1600886
Huang, A., Nguyen, P. Q., Stark, J. C., Takahashi, M. K., Donghia, N., Ferrante, T., Dy, A. J., Hsu, K. J., Dubner, R. S., Pardee, K., Jewett, M. C. and Collins, J. J. 2018 BioBits (TM) Explorer: A modular synthetic biology education kit Science Advances 10.1126/sciadv.aat5105
Karlen, S. D., Zhang, C. C., Peck, M. L., Smith, R. A., Padmakshan, D., Helmich, K. E., Free, H. C. A., Lee, S., Smith, B. G., Lu, F. C., Sedbrook, J. C., Sibout, R., Grabber, J. H., Runge, T. M., Mysore, K. S., Harris, P. J., Bartley, L. E. and Ralph, J. 2016 Monolignol ferulate conjugates are naturally incorporated into plant lignins Science Advances 10.1126/sciadv.1600393
Li, X. Y. C., Peris, D., Hittinger, C. T., Sia, E. A. and Fay, J. C. 2019 Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast Science Advances 10.1126/sciadv.aav1848
Li, Y. D., Li, S., Kim, H., Motagamwala, A. H., Mobley, J. K., Yue, F., Tobimatsu, Y., Havkin-Frenkel, D., Chen, F., Dixon, R. A., Luterbacher, J. S., Dumesic, J. A. and Ralph, J. 2018 An "ideal lignin" facilitates full biomass utilization Science Advances 10.1126/sciadv.aau2968
O'Kane, P. T., Dudley, Q. M., McMillan, A. K., Jewett, M. C. and Mrksich, M. 2019 High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA Science Advances 10.1126/sciadv.aaw9180
Bladon, K. D., Bywater-Reyes, S., LeBoldus, J. M., Kerio, S., Segura, C., Ritokova, G. and Shaw, D. C. 2019 Increased streamflow in catchments affected by a forest disease epidemic Science of the Total Environment 10.1016/j.scitotenv.2019.07.127
Xiao Z, Riccardi D, Velazquez HA, Chin AL, Yates CR, Carrick JD, Baudry J, Smith JC, and Quarles LD 2017 A Computationally Identified Compound Antagonizes Excess FGF-23 Signaling in Renal Tubules and a Mouse Model of Hypophosphatemia Science Signaling 10.1126/scisignal.aaf5034
Utturkar, S. M., Klingeman, D. M., Bruno-Barcena, J. M., Chinn, M. S., Grunden, A. M., Kopke, M. and Brown, S. D. 2015 Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies Scientific Data 10.1038/sdata.2015.14
Basso, B., Shuai, G. Y., Zhang, J. S. and Robertson, G. P. 2019 Yield stability analysis reveals sources of large-scale nitrogen loss from the US Midwest Scientific Reports 10.1038/s41598-019-42271-1
Bordbar, A., Yurkovich, J. T., Paglia, G., Rolfsson, O., Sigurjonsson, O. E. and Palsson, B. O. 2017 Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics Scientific Reports 10.1038/srep46249
Corts, A. D., Thomason, L. C., Gill, R. T. and Gralnick, J. A. 2019 A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides Scientific Reports 10.1038/s41598-018-37025-4
DeLorenzo, D. M. and Moon, T. S. 2018 Selection of stable reference genes for RT-qPCR in Rhodococcus opacus PD630 Scientific Reports 10.1038/s41598-018-24486-w
Gardner, J. J., Hodge, B. M. S. and Boyle, N. R. 2019 Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems Scientific Reports 10.1038/s41598-019-53188-0
Hermann, S. L., Blackledge, C., Haan, N. L., Myers, A. T. and Landis, D. A. 2019 Predators of monarch butterfly eggs and neonate larvae are more diverse than previously recognised Scientific Reports 10.1038/s41598-019-50737-5
Ievlev, A. V., Belianinov, A., Jesse, S., Allison, D. P., Doktycz, M. J., Retterer, S. T., Kalinin, S. V. and Ovchinnikova, O. S. 2017 Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data Scientific Reports 10.1038/s41598-017-17049-y
Jia, Q., Chen, X., Kollner, T. G., Rinkel, J., Fu, J., Labbe, J., Xiong, W., Dickschat, J. S., Gershenzon, J. and Chen, F. 2019 Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi Scientific Reports 10.1038/s41598-019-45532-1
Kao-Kniffin, J., Woodcroft, B. J., Carver, S. M., Bockheim, J. G., Handelsman, J., Tyson, G. W., Hinkel, K. M. and Mueller, C. W. 2015 Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska Scientific Reports 10.1038/srep18165
Kimball, J., Cui, Y. Y., Chen, D. Q., Brown, P., Rooney, W. L., Stacey, G. and Balint-Kurti, P. J. 2019 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 10.1038/s41598-019-54802-x
Knoot, C. J. and Pakrasi, H. B. 2019 Diverse hydrocarbon biosynthetic enzymes can substitute for olefin synthase in the cyanobacterium Synechococcus sp. PCC 7002 Scientific Reports 10.1038/s41598-018-38124-y
Lam, P. Y., Tobimatsu, Y., Matsumoto, N., Suzuki, S., Lan, W., Takeda, Y., Yamamura, M., Sakamoto, M., Ralph, J., Lo, C. and Umezawa, T. 2019 OsCAldOMT1 is a bifunctional O-methyltransferase involved in the biosynthesis of tricin-lignins in rice cell walls Scientific Reports 10.1038/s41598-019-47957-0
Lloyd, J. P., Bowman, M. J., Azodi, C. B., Sowers, R. P., Moghe, G. D., Childs, K. L. and Shiu, S. H. 2019 Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae Scientific Reports 10.1038/s41598-019-47797-y
Mueller, T. J., Ungerer, J. L., Pakrasi, H. B. and Maranas, C. D. 2017 Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973 Scientific Reports 10.1038/srep41569
Ng, C. Y., Wang, L., Chowdhury, A. and Maranas, C. D. 2019 Pareto Optimality Explanation of the Glycolytic Alternatives in Nature Scientific Reports 10.1038/s41598-019-38836-9
Noirot-Gros, M. F., Forrester, S., Malato, G., Larsen, P. E. and Noirot, P. 2019 CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens Scientific Reports 10.1038/s41598-019-52400-5
O’neill H., Pingali S.V., Petridis L, He J., Mamontov E., Hong L, Urban V., Evans B., Langan .P, Smith J.C, Davison B.H. 2017 Dynamics of water bound to crystalline cellulose Scientific Reports 10.1038/s41598-017-12035-w
Patabadige, D. E. W., Millet, L. J., Aufrecht, J. A., Shankles, P. G., Standaert, R. F., Retterer, S. T. and Doktycz, M. J. 2019 Label-free time- and space-resolved exometabolite sampling of growing plant roots through nanoporous interfaces Scientific Reports 10.1038/s41598-019-46538-5
Plett, J. M., Yin, H., Mewalal, R., Hu, R., Li, T., Ranjan, P., Jawdy, S., De Paoli, H. C., Butler, G., Burch-Smith, T. M., Guo, H. B., Ju Chen, C., Kohler, A., Anderson, I. C., Labbe, J. L., Martin, F., Tuskan, G. A. and Yang, X. 2017 Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis Scientific Reports 10.1038/s41598-017-00400-8
Rastogi, A., Maheswari, U., Dorrell, R. G., Vieira, F. R. J., Maumus, F., Kustka, A., McCarthy, J., Allen, A. E., Kersey, P., Bowler, C. and Tirichine, L. 2018 Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms Scientific Reports 10.1038/s41598-018-23106-x
Reese, Kristen L., Fisher, Carolyn L., Lane, Pamela D., Jaryenneh, James D., Moorman, Matthew W., Jones, A. Daniel, Frank, Matthias and Lane, Todd W. 2019 Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes Scientific Reports 10.1038/s41598-019-50125-z
Smith MD, Cheng X, Petridis L, Mostofian B, Smith JC 2017 Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose A Molecular Dynamics Analysis Scientific Reports 10.1038/s41598-017-15048-7
Stone, K. A., He, Q. P. and Wang, J. 2019 Two Experimental Protocols for Accurate Measurement of Gas Component Uptake and Production Rates in Bioconversion Processes Scientific Reports 10.1038/s41598-019-42469-3
Tian, L., Cervenka, N. D., Low, A. M., Olson, D. G. and Lynd, L. R. 2019 A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol Scientific Reports 10.1038/s41598-018-37979-5
Torres-Cortes, G., Garcia, B. J., Compant, S., Rezki, S., Jones, P., Preveaux, A., Briand, M., Roulet, A., Bouchez, O., Jacobson, D. and Barret, M. 2019 Differences in resource use lead to coexistence of seed-transmitted microbial populations Scientific Reports 10.1038/s41598-019-42865-9
Xue, L. J., Frost, C. J., Tsai, C. J. and Harding, S. A. 2016 Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression Scientific Reports 10.1038/srep33655
Yang, L., Yurkovich, J. T., Lloyd, C. J., Ebrahim, A., Saunders, M. A. and Palsson, B. O. 2016 Principles of proteome allocation are revealed using proteomic data and genome-scale models Scientific Reports 10.1038/srep36734
Yoo, C. Y., Mano, N., Finkler, A., Weng, H., Day, I. S., Reddy, A. S. N., Poovaiah, B. W., Fromm, H., Hasegawa, P. M. and Mickelbart, M. V. 2019 A Ca2+/CaM-regulated transcriptional switch modulates stomatal development in response to water deficit Scientific Reports 10.1038/s41598-019-47529-2
Yuan, Z., Druzhinina, I. S., Labbe, J., Redman, R., Qin, Y., Rodriguez, R., Zhang, C., Tuskan, G. A. and Lin, F. 2016 Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity Scientific Reports 10.1038/srep32467
Zhang, Q., Jun, S. R., Leuze, M., Ussery, D. and Nookaew, I. 2017 Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer Scientific Reports 10.1038/srep40712
Zhang, Y., Blaby-Haas, C. E., Steimle, S., Verissimo, A. F., Garcia-Angulo, V. A., Koch, H. G., Daldal, F. and Khalfaoui-Hassani, B. 2019 Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria Scientific Reports 10.1038/s41598-018-37988-4
Zheng, K., Wang, X., Weighill, D. A., Guo, H. B., Xie, M., Yang, Y., Yang, J., Wang, S., Jacobson, D. A., Guo, H., Muchero, W., Tuskan, G. A. and Chen, J. G. 2016 Characterization of DWARF14 Genes in Populus Scientific Reports 10.1038/srep21593
Smith JC, Becker T, Fischer S, Noé F, Tournier AL, Ullmann GM, and Kurkal V 2006 Physical and Functional Aspects of Protein Dynamics Soft Condensed Matter Physics in Molecular and Cell Biology none
Pan J, Cheng X, Sharp M, Ho CS, Khadka N, and Katsaras J 2015 Structural and Mechanical Properties of Cardiolipin Lipid Bilayers Determined Using Neutron Spin Echo, Small Angle Neutron and X-ray Scattering, and Molecular Dynamics Simulations Soft Matter 10.1039/C4SM02227K
Pan J., Cheng X., Monticelli L., Heberle F.A., Kucerka N., Tieleman D.P., and Katsaras J. 2014 The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations Soft Matter 10.1039/C4SM00066H
Abraham MJ, Murtola T, Schulz R, Pall S, Smith JC, Hess B, and Lindahl E 2015 GROMACS High Performance Molecular Simulations through Multi-Level parallelism from Laptops to Supercomputers SoftwareX 10.1016/j.softx.2015.06.001
Bracho, R., Natali, S., Pegoraro, E., Crummer, K. G., Schadel, C., Celis, G., Hale, L., Wu, L. Y., Yin, H. Q., Tiedje, J. M., Konstantinidis, K. T., Luo, Y. Q., Zhou, J. Z. and Schuur, E. A. G. 2016 Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations Soil Biology & Biochemistry 10.1016/j.soilbio.2016.02.008
Feng, W. T., Shi, Z., Jiang, J., Xia, J. Y., Liang, J. Y., Zhou, J. Z. and Luo, Y. Q. 2016 Methodological uncertainty in estimating carbon turnover times of soil fractions Soil Biology & Biochemistry 10.1016/j.soilbio.2016.06.003
Geyer, K. M., Dijkstra, P., Sinsabaugh, R. and Frey, S. D. 2019 Clarifying the interpretation of carbon use efficiency in soil through methods comparison Soil Biology & Biochemistry 10.1016/j.soilbio.2018.09.036
Ilhardt, Peter D., Nuñez, Jamie R., Denis, Elizabeth H., Rosnow, Joshua J., Krogstad, Eirik J., Renslow, Ryan S. and Moran, James J. 2019 High-resolution elemental mapping of the root-rhizosphere-soil continuum using laser-induced breakdown spectroscopy (LIBS) Soil Biology & Biochemistry 10.1016/j.soilbio.2018.12.029
Koechli, C., Campbell, A. N., Pepe-Ranney, C. and Buckley, D. H. 2019 Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing Soil Biology & Biochemistry 10.1016/j.soilbio.2018.12.013
Kravchenko, A. N., Guber, A. K., Razavi, B. S., Koestel, J., Blagodatskaya, E. V. and Kuzyakov, Y. 2019 Spatial patterns of extracellular enzymes: Combining X-ray computed micro-tomography and 2D zymography Soil Biology & Biochemistry 10.1016/j.soilbio.2019.06.002
Li, D. J., Schaedel, C., Haddix, M. L., Paul, E. A., Conant, R., Li, J. W., Zhou, J. Z. and Luo, Y. Q. 2013 Differential responses of soil organic carbon fractions to warming: Results from an analysis with data assimilation Soil Biology & Biochemistry 10.1016/j.soilbio.2013.07.008
Liang, J. Y., Li, D. J., Shi, Z., Tiedje, J. M., Zhou, J. Z., Schuur, E. A. G., Konstantinidis, K. T. and Luo, Y. Q. 2015 Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation Soil Biology & Biochemistry 10.1016/j.soilbio.2014.10.005
Minerovic, A. J., Valverde-Barrantes, O. J. and Blackwood, C. B. 2018 Physical and microbial mechanisms of decomposition vary in importance among root orders and tree species with differing chemical and morphological traits Soil Biology & Biochemistry 10.1016/j.soilbio.2018.06.006
Ouyang, Y., Evans, S. E., Friesen, M. L. and Tiemann, L. K. 2018 Effect of nitrogen fertilization on the abundance of nitrogen cycling genes in agricultural soils: A meta-analysis of field studies Soil Biology & Biochemistry 10.1016/j.soilbio.2018.08.024
Papp, K., Hungate, B. A. and Schwartz, E. 2019 mRNA, rRNA and DNA quantitative stable isotope probing with (H2O)-O-18 indicates use of old rRNA among soil Thaumarchaeota Soil Biology & Biochemistry 10.1016/j.soilbio.2018.12.016
Pegoraro, E., Mauritz, M., Bracho, R., Ebert, C., Dijkstra, P., Hungate, B. A., Konstantinidis, K. T., Luo, Y. Q., Schadel, C., Tiedje, J. M., Zhou, J. Z. and Schuur, E. A. G. 2019 Glucose addition increases the magnitude and decreases the age of soil respired carbon in a long-term permafrost incubation study Soil Biology & Biochemistry 10.1016/j.soilbio.2018.10.009
Roley, S. S., Xue, C., Hamilton, S. K., Tiedje, J. M. and Robertson, G. P. 2019 Isotopic evidence for episodic nitrogen fixation in switchgrass (Panicum virgatum L.) Soil Biology & Biochemistry 10.1016/j.soilbio.2018.11.006
Shi, S. J., Herman, D. J., He, Z. L., Pett-Ridge, J., Wu, L. Y., Zhou, J. Z. and Firestone, M. K. 2018 Plant roots alter microbial functional genes supporting root litter decomposition Soil Biology & Biochemistry 10.1016/j.soilbio.2018.09.013
Sul, W. J., Asuming-Brempong, S., Wang, Q., Tourlousse, D. M., Penton, C. R., Deng, Y., Rodrigues, J. L. M., Adiku, S. G. K., Jones, J. W., Zhou, J. Z., Cole, J. R. and Tiedje, J. M. 2013 Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon Soil Biology & Biochemistry 10.1016/j.soilbio.2013.05.007
Swenson, Tami L., Bowen, Benjamin P., Nico, Peter S. and Northen, Trent R. 2015 Competitive sorption of microbial metabolites on an iron oxide mineral Soil Biology & Biochemistry 10.1016/j.soilbio.2015.07.022
Swenson, Tami L., Jenkins, Stefan, Bowen, Benjamin P. and Northen, Trent R. 2015 Untargeted soil metabolomics methods for analysis of extractable organic matter Soil Biology & Biochemistry 10.1016/j.soilbio.2014.10.007
Szymanski, L. M., Sanford, G. R., Heckman, K. A., Jackson, R. D. and Marin-Spiotta, E. 2019 Conversion to bioenergy crops alters the amount and age of microbially-respired soil carbon Soil Biology & Biochemistry 10.1016/j.soilbio.2018.08.025
Tu, Q. C., He, Z. L., Wu, L. Y., Xue, K., Xie, G., Chain, P., Reich, P. B., Hobbie, S. E. and Zhou, J. Z. 2017 Metagenomic reconstruction of nitrogen cycling pathways in a CO2- enriched grassland ecosystem Soil Biology & Biochemistry 10.1016/j.soilbio.2016.12.017
Whitman, T., Whitman, E., Woolet, J., Flannigan, M. D., Thompson, D. K. and Parisien, M. A. 2019 Soil bacterial and fungal response to wildfires in the Canadian boreal forest across a burn severity gradient Soil Biology & Biochemistry 10.1016/j.soilbio.2019.107571
Williamson, K. E., Kan, J., Polson, S. W. and Williamson, S. J. 2011 Optimizing the indirect extraction of prokaryotic DNA from soils Soil Biology & Biochemistry 10.1016/j.soilbio.2010.04.017
Xu, X., Luo, Y. Q. and Zhou, J. Z. 2012 Carbon quality and the temperature sensitivity of soil organic carbon decomposition in a tallgrass prairie Soil Biology & Biochemistry 10.1016/j.soilbio.2012.03.007
Myrold, D. D., Zeglin, L. H. and Jansson, J. K. 2014 The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes Soil Science Society of America Journal 10.2136/sssaj2013.07.0287dgs
D’haeseleer, Patrik, Lee, Jackson Z., Prufert-Bebout, Leslie, Burow, Luke C., Detweiler, Angela M., Weber, Peter K., Karaoz, Ulas, Brodie, Eoin L., Glavina del Rio, Tijana, Tringe, Susannah G., Bebout, Brad M. and Pett-Ridge, Jennifer 2017 Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate Standards in Genomic Sciences 10.1186/s40793-017-0279-6
Everroad, R. Craig, Stuart, Rhona K., Bebout, Brad M., Detweiler, Angela M., Lee, Jackson Z., Woebken, Dagmar, Prufert-Bebout, Leslie and Pett-Ridge, Jennifer 2016 Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria Standards in Genomic Sciences 10.1186/s40793-016-0174-6
Land, M. L., Hyatt, D., Jun, S. R., Kora, G. H., Hauser, L. J., Lukjancenko, O. and Ussery, D. W. 2014 Quality scores for 32,000 genomes Standards in Genomic Sciences 10.1186/1944-3277-9-20
Lorenzi, H. A., Hoover, J., Inman, J., Safford, T., Murphy, S., Kagan, L. and Williamson, S. J. 2011 TheViral MetaGenome Annotation Pipeline (VMGAP): An automated tool for the functional annotation of viral Metagenomic shotgun sequencing data Standards in Genomic Sciences 10.4056/sigs.1694706
Klempin, F., Marr, R. A. and Peterson, D. A. 2012 Modification of Pax6 and Olig2 Expression in Adult Hippocampal Neurogenesis Selectively Induces Stem Cell Fate and Alters Both Neuronal and Glial Populations Stem Cells 10.1002/stem.1005
Das, A., Gerlits, O., Parks, J. M., Langan, P., Kovalevsky, A. and Heller, W. T. 2015 Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation Structure 10.1016/j.str.2015.10.005
Das A, Gerlits O, Parks JM, Langan P, Kovalevsky A, and Heller WT 2016 Protein Kinase A Catalytic Subunit Primed for Action Time-Lapse Crystallography of Michaelis Complex Formation Structure 10.1016/j.str.2015.10.005
Goodsell, D. S., Autin, L. and Olson, A. J. 2019 Illustrate: Software for Biomolecular Illustration Structure 10.1016/j.str.2019.08.011
Koppole S, Smith JC, and Fischer S 2007 The Structural Coupling between ATPase Activation and Recovery Stroke in the Myosin II Motor Structure 10.1016/j.str.2007.06.008
Kovalevsky A, Aggarwal M, Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R 2018 "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation Structure 10.1016/j.str.2018.01.006
Langan, P., Sangha, A. K., Wymore, T., Parks, J. M., Yang, Z. K., Hanson, B. L., Fisher, Z., Mason, S. A., Blakeley, M. P., Forsyth, V. T., Glusker, J. P., Carrell, H. L., Smith, J. C., Keen, D. A., Graham, D. E. and Kovalevsky, A. 2014 L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study Structure 10.1016/j.str.2014.07.002
Smith, J. C. 2006 Tight in Titin Structure 10.1016/j.str.2006.02.001
Smith, J. C. and Roux, B. 2013 Eppur si muove! The 2013 Nobel Prize in Chemistry Structure 10.1016/j.str.2013.11.005
Satari, B., Karimi, K., Kumar, R. 2018 Cellulose solvents-based pretreatment for enhanced second-generation biofuels production: A review Sustainable Energy and Fuels 10.1039/C8SE00287H
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 2018 Overexpression of a serine hydroxymethyltransferase increases biomass production and reduces recalcitrance in the bioenergy crop Populus Sustainable Energy and Fuels 10.1039/C8SE00471D
Goodsell, D. S. 2019 Symmetry at the Cellular Mesoscale Symmetry-Basel 10.3390/sym11091170
Garcia, David C., Mohr, Benjamin P., Dovgan, Jakob T., Hurst, Gregory B., Standaert, Robert F. and Doktycz, Mitchel J. 2018 Elucidating the potential of crude cell extracts for producing pyruvate from glucose Synthetic Biology 10.1093/synbio/ysy006
McLaughlin, David J., Kumar, T. K. Arun, Blackwell, Meredith, Letcher, Peter M. and Roberson, Robert W. 2015 9 Subcellular Structure and Biochemical Characters in Fungal Phylogeny Systematics and Evolution: Part B 10.1007/978-3-662-46011-5_9
King, K., Li, H., Kang, J. L. and Lu, C. F. 2019 Mapping quantitative trait loci for seed traits in Camelina sativa Theoretical and Applied Genetics 10.1007/s00122-019-03371-8
Zhang, X. Y., Valdes-Lopez, O., Arellano, C., Stacey, G. and Balint-Kurti, P. 2017 Genetic dissection of the maize (Zea mays L.) MAMP response Theoretical and Applied Genetics 10.1007/s00122-017-2876-6
Bondar AN, Knapp-Mohammady M, Suhai S, Fischer S, and Smith JC 2011 Ground-State Properties of the Retinal Molecule from Quantum Mechanical to Classical Mechanical Computations of Retinal Proteins Theoretical Chemistry Accounts 10.1007/s00214-011-1054-1
Bondar AN, Smith JC, and Elstner M 2010 Mechanism of a Proton Pump Analyzed with Computer Simulations Theoretical Chemistry Accounts 10.1007/s00214-009-0565-5
Krishnan M, Schulz R, and Smith JC 2009 Protein Dynamical Transition Role of Methyl Dynamics and Local Diffusion Theory and Applications of Computational Chemistry 2008 AIP Conference Proceedings 10.1063/1.3108363
Bdeir, R., Muchero, W., Yordanov, Y., Tuskan, G.A., Busov, V., and Gailing, O. 2019 Genome-wide association studies of bark texture in Populus trichocarpa Tree Genetics & Genomes 10.1007/s11295-019-1399-5
Labbé, Jessy, Jorge, Véronique, Kohler, Annegret, Vion, Patrice, Marçais, Benoît, Bastien, Catherine, Tuskan, Gerald A., Martin, Francis and Le Tacon, François 2011 Identification of quantitative trait loci affecting ectomycorrhizal symbiosis in an interspecific F1 poplar cross and differential expression of genes in ectomycorrhizas of the two parents: Populus deltoides and Populus trichocarpa Tree Genetics & Genomes 10.1007/s11295-010-0361-3
Xue, L. J., Alabady, M. S., Mohebbi, M. and Tsai, C. J. 2015 Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremulaxalba 717-1B4 Tree Genetics & Genomes 10.1007/s11295-015-0907-5
Ye X, Yuan S, Guo H, Chen F, Tuskan GA, and Cheng ZM 2012 Evolution and Divergence in the Coding and Promoter Regions of the Populus Gene Family Encoding Xyloglucan Endotransglycosylase/Hydrolases Tree Genetics & Genomes 10.1007/s11295-011-0431-1
Harfouche, A. L., Jacobson, D. A., Kainer, D., Romero, J. C., Harfouche, A. H., Scarascia Mugnozza, G., Moshelion, M., Tuskan, G. A., Keurentjes, J. J. B. and Altman, A. 2019 Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence Trends in Biotechnology 10.1016/j.tibtech.2019.05.007
Lazar, Z., Liu, N. and Stephanopoulos, G. 2018 Holistic Approaches in Lipid Production by Yarrowia lipolytica Trends in Biotechnology 10.1016/j.tibtech.2018.06.007
Peers, G. 2014 Increasing algal photosynthetic productivity by integrating ecophysiology with systems biology Trends in Biotechnology 10.1016/j.tibtech.2014.09.007
Juhas, M., Eberl, L. and Glass, J. I. 2011 Essence of life: essential genes of minimal genomes Trends in Cell Biology 10.1016/j.tcb.2011.07.005
Shade, A., Dunn, R. R., Blowes, S. A., Keil, P., Bohannan, B. J. M., Herrmann, M., Kusel, K., Lennon, J. T., Sanders, N. J., Storch, D. and Chase, J. 2018 Macroecology to Unite All Life, Large and Small Trends in Ecology & Evolution 10.1016/j.tree.2018.08.005
Plett, J. M. and Martin, F. 2011 Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes Trends in Genetics 10.1016/j.tig.2010.10.005
Raman, S., Taylor, N., Genuth, N., Fields, S. and Church, G. M. 2014 Engineering allostery Trends in Genetics 10.1016/j.tig.2014.09.004
Long, P. E., Williams, K. H., Hubbard, S. S. and Banfield, J. F. 2016 Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes Trends in Microbiology 10.1016/j.tim.2016.04.006
Wehrs, M., Tanjore, D., Eng, T., Lievense, J., Pray, T. R., and Mukhopadhyay, A. 2019 Engineering Robust Production Microbes for Large-Scale Cultivation Trends in Microbiology 10.1016/j.tim.2019.01.006
Borland, A. M., Hartwell, J., Weston, D. J., Schlauch, K. A., Tschaplinski, T. J., Tuskan, G. A., Yang, X. H. and Cushman, J. C. 2014 Engineering crassulacean acid metabolism to improve water-use efficiency Trends in Plant Science 10.1016/j.tplants.2014.01.006
Fernie, A. R., Obata, T., Allen, A. E., Araujo, W. L. and Bowler, C. 2012 Leveraging metabolomics for functional investigations in sequenced marine diatoms Trends in Plant Science 10.1016/j.tplants.2012.02.005
Libault, M., Pingault, L., Zogli, P. and Schiefelbein, J. 2017 Plant Systems Biology at the Single-Cell Level Trends in Plant Science 10.1016/j.tplants.2017.08.006
Rhee, S. Y., Birnbaum, K. D. and Ehrhardt, D. W. 2019 Towards Building a Plant Cell Atlas Trends in Plant Science 10.1016/j.tplants.2019.01.006
Widhalm, J. R., Jaini, R., Morgan, J. A. and Dudareva, N. 2015 Rethinking how volatiles are released from plant cells Trends in Plant Science 10.1016/j.tplants.2015.06.009
Lin, J. S., Zhu, M. T., Cai, M. X., Zhang, W. P., Fatima, M., Jia, H. F., Li, F. F. and Ming, R. 2019 Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L Tropical Plant Biology 10.1007/s12042-019-09238-y
Wang, J., Li, Y. X., Zhu, F., Ming, R. and Chen, L. Q. 2019 Genome-Wide Analysis of Nitrate Transporter (NRT/NPF) Family in Sugarcane Saccharum spontaneum L Tropical Plant Biology 10.1007/s12042-019-09220-8
Zhang, W. P., Lin, J. S., Dong, F., Ma, Q., Wu, S. L., Ma, X. Y., Fatima, M., Jia, H. F. and Ming, R. 2019 Genomic and Allelic Analyses of Laccase Genes in Sugarcane (Saccharum spontaneum L.) Tropical Plant Biology 10.1007/s12042-019-09239-x
Evans, Barbara R., Pingali, Sai Venkatesh, Bhagia, Samarthya, O’Neill, Hugh M. and Ragauskas, Arthur J. 2019 Structural Studies of Deuterium-Labeled Switchgrass Biomass Understanding Lignocellulose: Synergistic Computational and Analytic Methods 10.1021/bk-2019-1338.ch002
Dale, J. B., Smeesters, P. R., Courtney, H. S., Penfound, T. A., Hohn, C. M., Smith, J. C. and Baudry, J. Y. 2017 Structure-based design of broadly protective group a streptococcal M protein-based vaccines Vaccine 10.1016/j.vaccine.2016.11.065
Lynch RM, Rong R, Li B, Shen T, Honnen W, Mulenga J, Allen S, Pinter A, Gnanakaran S, and Derdeyn CA 2010 Subtype-Specific Conservation of Isoleucine 309 in the Envelope V3 Domain is Linked to Immune Evasion in Subtype C HIV-1 Infection Virology 10.1016/j.virol.2010.04.010
Zelaya, A. J., Parker, A. E., Bailey, K. L., Zhang, P., Van Nostrand, J., Ning, D., Elias, D. A., Zhou, J., Hazen, T. C., Arkin, A. P. and Fields, M. W. 2019 High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer Water Research 10.1016/j.watres.2019.114917S
Yang, P., Ng, T. L. and Cai, X. M. 2019 Reward-Based Participant Management for Crowdsourcing Rainfall Monitoring: An Agent-Based Model Simulation Water Resources Research 10.1029/2018wr024447
Meirelles, M. L., Bracho, R. and Ferreira, E. A. B. 2015 Carbon dioxide exchange in a tropical wet grassland Wetlands Ecology and Management 10.1007/s11273-015-9421-7
Babele, P. K. and Young, J. D. 2019 Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria Wiley Interdisciplinary Reviews-Systems Biology and Medicine 10.1002/wsbm.1472
Brooks, A. N., Turkarslan, S., Beer, K. D., Lo, F. Y. and Baliga, N. S. 2011 Adaptation of cells to new environments Wiley Interdisciplinary Reviews-Systems Biology and Medicine 10.1002/wsbm.136
Gardner, J. G. 2016 Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus World Journal of Microbiology & Biotechnology 10.1007/s11274-016-2068-6