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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 (millsmd@ornl.gov) 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
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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
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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
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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
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