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

Research Publications

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

 

YearDOIAuthorsTitleJournalVolume/Pages
10.1002/9781119312994.apr0348Ding, L., J.-G. Chen, A. M. Jones and S. M. AssmannHeterotrimeric G-Protein-Coupled Signaling in Higher PlantsAnnual Plant Reviews online30–63
200010.1128/AEM.66.8.3616-3620.2000Marsh, T. L., P. Saxman, J. Cole and J. TiedjeTerminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysisApplied and Environmental Microbiology66(8) 3616–20
200410.1126/science.1093857Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, et al.Environmental genome shotgun sequencing of the Sargasso SeaScience304(5667) 66–74
200410.1073/pnas.0401526101Lindell, D., M. B. Sullivan, Z. I. Johnson, A. C. Tolonen, F. Rohwer and S. W. ChisholmTransfer of photosynthesis genes to and from Prochlorococcus virusesProceedings of the National Academy of Sciences of the United States of America101(30) 11013–8
200410.1128/JB.186.14.4457-4465.2004Friedman, L. and R. KolterTwo genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrixJournal of Bacteriology186(14) 4457–65
200410.1046/j.1365-2958.2003.03877.xFriedman, L. and R. KolterGenes involved in matrix formation in Pseudomonas aeruginosa PA14 biofilmsMolecular Microbiology51(3) 675–90
200510.1093/bioinformatics/bti613Xing, Y. and C. LeeAssessing the application of Ka/Ks ratio test to alternatively spliced exonsBioinformatics21(19) 3701-3703
200510.1371/journal.pbio.0030144Sullivan, M. B., M. L. Coleman, P. Weigele, F. Rohwer and S. W. ChisholmThree Prochlorococcus cyanophage genomes: signature features and ecological interpretationsPLoS Biology3(5) e144
200510.1128/JB.187.3.940-948.2005Romano, J. D. and R. KolterPseudomonas-Saccharomyces interactions: influence of fungal metabolism on bacterial physiology and survivalJournal of Bacteriology187(3) 940–8
200510.1128/JB.187.10.3551-3555.2005Reguera, G. and R. KolterVirulence and the environment: a novel role for Vibrio cholerae toxin-coregulated pili in biofilm formation on chitinJournal of Bacteriology187(10) 3551–5
200510.1016/j.str.2005.01.019Johnson, E., D. Cascio, M. R. Sawaya, M. Gingery and I. SchröderCrystal structures of a tetrahedral open pore ferritin from the hyperthermophilic Archaeon Archaeoglobus fulgidusStructure13(4) 637-648
200510.1093/bioinformatics/bti346Garrity, G. M. and T. G. LilburnSelf-organizing and self-correcting classifications of biological dataBioinformatics21(10) 2309-2314
200510.1093/nar/gki038Cole, J. R., B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity and J. M. TiedjeThe Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysisNucleic Acids Research33(Suppl_1) D294–6
200610.1021/ja058831yXu, Q., H. Guo, A. Wlodawer and H. GuoThe importance of dynamics in substrate-assisted catalysis and specificityJournal of the American Chemical Society128(18) 5994–5
200610.1093/nar/gkl396Xing, Y., T. Yu, Y. N. Wu, M. Roy, J. Kim and C. LeeAn expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphsNucleic Acids Research34(10) 3150-3160
200610.1002/qua.20810Walewski, Ł., D. Krachtus, S. Fischer, J. C. Smith, P. Bała and B. LesyngSCC-DFTB energy barriers for single and double proton transfer processes in the model molecular systems malonaldehyde and porphyceneInternational Journal of Quantum Chemistry106(3) 636–40
200610.1371/journal.pbio.0040234Sullivan, M. B., D. Lindell, J. A. Lee, L. R. Thompson, J. P. Bielawski and S. W. ChisholmPrevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hostsPLoS Biology4(8) e234
200610.1016/j.str.2006.02.001Smith, J. C.Tight in titinStructure14(3) 389–90
200610.1021/bi052433qSchwarzl, S. M., J. C. Smith and S. FischerInsights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanismBiochemistry45(18) 5830–47
200610.1021/jp055314tMoritsugu, K. and J. C. SmithTemperature-dependent protein dynamics: a simulation-based probabilistic diffusion-vibration Langevin descriptionJournal of Physical Chemistry B110(11) 5807–16
200610.1155/JAMDS/2006/16018Moffat, J.Mathematical modelling of information age conflictJournal of Applied Mathematics and Decision Sciences2006
200610.1002/prot.20981Mesentean, S., S. Fischer and J. C. SmithAnalyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mappingProteins64(1) 210–8
200610.1021/ja055962qKurkal-Siebert, V. and J. C. SmithLow-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 kJournal of the American Chemical Society128(7) 2356–64
200610.1016/j.jnoncrysol.2006.01.115Kurkal-Siebert, V., R. M. Daniel, J. L. Finney, M. Tehei, R. V. Dunn and J. C. SmithEnzyme hydration, activity and flexibility: A neutron scattering approachJournal of Non-Crystalline Solids352(42–49) 4387–93
200610.1016/j.jmb.2006.06.022Koppole, S., J. C. Smith and S. FischerSimulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery strokeJournal of Molecular Biology361(3) 604–16
200610.1021/ct600092cImhof, P., F. Noe, S. Fischer and J. C. SmithAM1/d Parameters for Magnesium in MetalloenzymesJournal of Chemical Theory and Computation2(4) 1050–6
200610.1021/bi060461iGuo, H., A. Wlodawer, T. Nakayama, Q. Xu and H. GuoCatalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidaseBiochemistry45(30) 9129–37
200610.1073/pnas.0510013103Glass, J. I., N. Assad-Garcia, N. Alperovich, S. Yooseph, M. R. Lewis, M. Maruf, C. A. Hutchison, 3rd, H. O. Smith and J. C. VenterEssential genes of a minimal bacteriumProceedings of the National Academy of Sciences of the United States of America103(2) 425–30
200610.1038/sj.cdd.4401807Efferth, T., S. M. Schwarzl, J. Smith and R. OsiekaRole of glucose-6-phosphate dehydrogenase for oxidative stress and apoptosisCell Death and Differentiation13(3) 527–8
200610.1039/b516451fBondar, A. N., J. C. Smith and S. FischerStructural and energetic determinants of primary proton transfer in bacteriorhodopsinPhotochemical and Photobiological Sciences5(6) 547–52
200610.1021/ja060731kBaudry, J.Van der waals interactions and decrease of the rotational barrier of methyl-sized rotators: a theoretical studyJournal of the American Chemical Society128(34) 11088–93
200610.1039/b610075aBalog, E., J. C. Smith and D. PerahiaConformational heterogeneity and low-frequency vibrational modes of proteinsPhysical Chemistry Chemical Physics8(47) 5543–8
200710.1016/j.inffus.2005.04.003Zheng, Y., E. A. Essock, B. C. Hansen and A. M. HaunA new metric based on extended spatial frequency and its application to DWT based fusion algorithmsInformation Fusion8(2 SPEC. ISS.) 177-192
200710.1021/bi061737pXu, Q., H. B. Guo, A. Wlodawer, T. Nakayama and H. GuoThe QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-AsBiochemistry46(12) 3784–92
200710.1021/jp0670743Xu, Q., H. Guo, A. Gorin and H. GuoStabilization of a transition-state analogue at the active site of yeast cytosine deaminase: importance of proton transfersJournal of Physical Chemistry B111(23) 6501–6
200710.1529/biophysj.105.079723Topham, C. M. and J. C. SmithOrientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-formBiophysical Journal92(3) 769–86
2007Smith, J. C., A. N. Bondar, S. Suhai and P. T. FrangopolComputer Simulations of Local Anesthetic Mechanisms Quantum Chemical Investigation of ProcaineRomanian Reports in Physics59(2) 289–99
200710.1117/12.727781Privitera, G., S. Tudisco, L. Lanzanò, F. Musumeci, S. Privitera, A. Scordino, D. Tudisco, M. Mazzillo and G. CondorelliSingle photon spectrometer for biomedical application: New developmentsProgress in Biomedical Optics and Imaging - Proceedings of SPIE6628
200710.1039/9781847557773-00099Nutt, D. R. and J. C. SmithChoosing an Appropriate Water Model for Use in Biomolecular SimulationsPhysics and Chemistry of Ice451–8
200710.1021/ct700053uNutt, D. R. and J. C. SmithMolecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?Journal of Chemical Theory and Computation3(4) 1550–60
200710.1093/bioinformatics/btm241Newberg, L. A., W. A. Thompson, S. Conlan, T. M. Smith, L. A. McCue and C. E. LawrenceA phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site predictionBioinformatics23(14) 1718-1727
200710.1529/biophysj.107.111898Moritsugu, K. and J. C. SmithCoarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance HessianBiophysical Journal93(10) 3460–9
200710.1016/j.jmb.2006.12.058Mesentean, S., S. Koppole, J. C. Smith and S. FischerThe principal motions involved in the coupling mechanism of the recovery stroke of the myosin motorJournal of Molecular Biology367(2) 591–602
200710.1073/pnas.0708199104Meinhold, L., J. C. Smith, A. Kitao and A. H. ZewailPicosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulationProceedings of the National Academy of Sciences of the United States of America104(44) 17261–5
200710.1002/prot.21246Meinhold, L. and J. C. SmithProtein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patternsProteins66(4) 941–53
200710.1103/PhysRevLett.99.138101Meinhold, L., F. Merzel and J. C. SmithLattice dynamics of a protein crystalPhysical Review Letters99(13) 138101
2007Mazzotti, A., E. Stucchi, G. L. Fradelizio, L. Zanzi and P. ScandoneRe-processing of the CROP-04 seismic dataBollettino della Societa Geologica Italiana, Supplemento7 141-153
200710.1016/j.str.2007.06.008Koppole, S., J. C. Smith and S. FischerThe structural coupling between ATPase activation and recovery stroke in the myosin II motorStructure15(7) 825–37
200710.1093/bioinformatics/btm343Kim, N. and C. LeeQPRIMER: A quick web-based application for designing conserved PCR primers from multigenome alignmentsBioinformatics23(17) 2331-2333
200710.1093/nar/gkl884Kim, N., A. V. Alekseyenko, M. Roy and C. LeeThe ASAP II database: Analysis and comparative genomics of alternative splicing in 15 animal speciesNucleic Acids Research35(SUPPL. 1) D93-D98
200710.1186/gb-2007-8-12-r264Kannan, N., J. Wu, G. S. Anand, S. Yooseph, A. F. Neuwald, J. C. Venter and S. S. TaylorEvolution of allostery in the cyclic nucleotide binding moduleGenome Biology8(12) R264
200710.1371/journal.pbio.0050017Kannan, N., S. S. Taylor, Y. Zhai, J. C. Venter and G. ManningStructural and functional diversity of the microbial kinomePLoS Biology5(3) e17
200710.1073/pnas.0702981104Guo, H. B. and H. GuoMechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificityProceedings of the National Academy of Sciences of the United States of America104(21) 8797–802
200710.1016/B978-012374212-4.50049-3Fantini, S. and P. TaroniOptical MammographyCancer Imaging445-453
200710.1128/JB.01343-06Earl, A. M., R. Losick and R. KolterBacillus subtilis genome diversityJournal of Bacteriology189(3) 1163–70
200710.1002/chem.200700358de Hatten, X., Z. Cournia, I. Huc, J. C. Smith and N. Metzler-NolteForce-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimicsChemistry13(29) 8139–52
200710.1073/pnas.0701401104Daidone, I., M. B. Ulmschneider, A. Di Nola, A. Amadei and J. C. SmithDehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide foldingProceedings of the National Academy of Sciences of the United States of America104(39) 15230–5
200710.1021/jp065172iCournia, Z., G. M. Ullmann and J. C. SmithDifferential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation studyJournal of Physical Chemistry B111(7) 1786–801
200710.1093/nar/gkl889Cole, J. R., B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity and J. M. TiedjeThe ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public dataNucleic Acids Research35(SUPPL. 1) D169-D172
200710.1080/02770900701595568Cicutto, L. and M. AshbyThe importance of a community-based asthma helplineJournal of Asthma44(9) 705-710
200710.1038/nbt1316Chen, F. and R. A. DixonLignin modification improves fermentable sugar yields for biofuel productionNature Biotechnology25(7) 759–61
200710.1016/j.cell.2007.10.053Bonneau, R., M. T. Facciotti, D. J. Reiss, A. K. Schmid, M. Pan, et al.A predictive model for transcriptional control of physiology in a free living cellCell131(7) 1354–65
200710.1016/j.jsb.2006.10.007Bondar, A. N., S. Suhai, S. Fischer, J. C. Smith and M. ElstnerSuppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elementsJournal of Structural Biology157(3) 454–69
200710.1186/1471-2105-8-456Bare, J. C., P. T. Shannon, A. K. Schmid and N. S. BaligaThe Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applicationsBMC Bioinformatics8 456
200710.1093/bioinformatics/btl647Alekseyenko, A. V. and C. J. LeeNested Containment List (NCList): A new algorithm for accelerating interval query of genome alignment and interval databasesBioinformatics23(11) 1386-1393
200810.1002/mrc.2201Yelle, D. J., J. Ralph and C. R. FrihartCharacterization of nonderivatized plant cell walls using high-resolution solution-state NMR spectroscopyMagnetic Resonance in Chemistry46(6) 508–17
200810.1371/journal.pone.0001456Williamson, S. J., D. B. Rusch, S. Yooseph, A. L. Halpern, K. B. Heidelberg, J. I. Glass, C. Andrews-Pfannkoch, D. Fadrosh, C. S. Miller, G. Sutton, M. Frazier and J. C. VenterThe Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samplesPLoS One3(1) e1456
200810.1016/j.copbio.2008.02.014Weng, J. K., X. Li, N. D. Bonawitz and C. ChappleEmerging strategies of lignin engineering and degradation for cellulosic biofuel productionCurrent Opinion in Biotechnology19(2) 166–72
200810.1002/jcc.20902Voltz, K., J. Trylska, V. Tozzini, V. Kurkal-Siebert, J. Langowski and J. SmithCoarse-grained force field for the nucleosome from self-consistent multiscalingJournal of Computational Chemistry29(9) 1429–39
200810.1021/pr800031fVan, P. T., A. K. Schmid, N. L. King, A. Kaur, M. Pan, K. Whitehead, T. Koide, M. T. Facciotti, Y. A. Goo, E. W. Deutsch, D. J. Reiss, P. Mallick and N. S. BaligaHalobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverageJournal of Proteome Research7(9) 3755–64
200810.1529/biophysj.108.135442Tran, L. M., M. L. Rizk and J. C. LiaoEnsemble modeling of metabolic networksBiophysical Journal95(12) 5606–17
2008Shealy, P., R. Mukhopadhyay, S. Smith and H. ValafarAutomated assignment of backbone resonances using residual dipolar couplings acquired from a protein with known structureProceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008646-652
200810.1111/j.1462-2920.2008.01626.xShaw, A. K., A. L. Halpern, K. Beeson, B. Tran, J. C. Venter and J. B. MartinyIt's all relative: ranking the diversity of aquatic bacterial communitiesEnvironmental Microbiology10(9) 2200–10
200810.2993/0278-0771(2008)28[110:HEOMSF]2.0.CO;2Sepez, J.Historical ecology of Makah subsistence foraging patternsJournal of Ethnobiology28(1) 110-133
200810.1016/j.bbamem.2008.06.014Sengupta, D., J. C. Smith and G. M. UllmannPartitioning of amino-acid analogues in a five-slab membrane modelBiochimica et Biophysica Acta (BBA) - Biomembranes1778(10) 2234–43
200810.1007/s12155-008-9025-7Saballos, A., W. Vermerris, L. Rivera and G. EjetaAllelic Association, Chemical Characterization and Saccharification Properties of brown midrib Mutants of Sorghum (Sorghum bicolor (L.) Moench)BioEnergy Research1(3–4) 193–204
200810.1093/bioinformatics/btm592Reiss, D. J., M. T. Facciotti and N. S. BaligaModel-based deconvolution of genome-wide DNA bindingBioinformatics24(3) 396–403
200810.1088/1742-6596/125/1/012055Petridis, L. and J. C. SmithCellulosic ethanol: progress towards a simulation model of lignocellulosic biomassJournal of Physics: Conference Series125
200810.1073/pnas.0809160105Oda, Y., F. W. Larimer, P. S. Chain, S. Malfatti, M. V. Shin, L. M. Vergez, L. Hauser, M. L. Land, S. Braatsch, J. T. Beatty, D. A. Pelletier, A. L. Schaefer and C. S. HarwoodMultiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironmentsProceedings of the National Academy of Sciences of the United States of America105(47) 18543–8
200810.1021/ja8034027Nutt, D. R. and J. C. SmithDual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulationsJournal of the American Chemical Society130(39) 13066–73
200810.1103/PhysRevLett.100.188103Neusius, T., I. Daidone, I. M. Sokolov and J. C. SmithSubdiffusion in peptides originates from the fractal-like structure of configuration spacePhysical Review Letters100(18) 188103
200810.1529/biophysj.108.131714Moritsugu, K. and J. C. SmithREACH coarse-grained biomolecular simulation: transferability between different protein structural classesBiophysical Journal95(4) 1639–48
200810.1529/biophysj.107.121418Meinhold, L., D. Clement, M. Tehei, R. Daniel, J. L. Finney and J. C. SmithProtein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scatteringBiophysical Journal94(12) 4812–8
200810.1002/anie.200802679McLain, S. E., A. K. Soper, I. Daidone, J. C. Smith and A. WattsCharge-based interactions between peptides observed as the dominant force for association in aqueous solutionAngewandte Chemie International Edition47(47) 9059–62
2008Mahrooz, A., M. Nouri, M. R. Rashidi, N. Aslanabadi, D. Qujeq and A. AzariParaoxonase and Arylesterase activities of human serum paraoxonase in coronary artery diseaseKoomesh10(1) 1-6+1
200810.1111/j.1365-313X.2008.03457.xLi, X., J. K. Weng and C. ChappleImprovement of biomass through lignin modificationThe Plant Journal54(4) 569–81
200810.1103/PhysRevLett.100.138102Kurkal-Siebert, V., R. Agarwal and J. C. SmithHydration-dependent dynamical transition in protein: protein interactions at ≈ 240 KPhysical Review Letters100(13) 138102
200810.1021/jp076641zKrishnan, M., V. Kurkal-Siebert and J. C. SmithMethyl group dynamics and the onset of anharmonicity in myoglobinJournal of Physical Chemistry B112(17) 5522–33
200810.1007/s12155-008-9004-zKim, H., J. Ralph and T. AkiyamaSolution-state 2D NMR of Ball-milled Plant Cell Wall Gels in DMSO-d6BioEnergy Research1(1) 56–66
200810.1007/s12155-008-9020-zJackson, L. A., G. L. Shadle, R. Zhou, J. Nakashima, F. Chen and R. A. DixonImproving Saccharification Efficiency of Alfalfa Stems Through Modification of the Terminal Stages of Monolignol BiosynthesisBioEnergy Research1(3–4) 180–92
200810.1021/bi801685fImker, H. J., J. Singh, B. P. Warlick, F. R. Tabita and J. A. GerltMechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrumBiochemistry47(43) 11171–3
200810.1016/j.jmb.2007.12.073Grintsevich, E. E., S. A. Benchaar, D. Warshaviak, P. Boontheung, F. Halgand, J. P. Whitelegge, K. F. Faull, R. R. Ogorzalek Loo, D. Sept, J. A. Loo and E. ReislerMapping the Cofilin Binding Site on Yeast G-Actin by Chemical Cross-LinkingJournal of Molecular Biology377(2) 395-409
200810.1093/nar/gkm815Faith, J. J., M. E. Driscoll, V. A. Fusaro, E. J. Cosgrove, B. Hayete, F. S. Juhn, S. J. Schneider and T. S. GardnerMany Microbe Microarrays Database: Uniformly normalized Affymetrix compendia with structured experimental metadataNucleic Acids Research36(SUPPL. 1) D866-D870
200810.1016/j.copbio.2008.10.010Cardenas, E. and J. M. TiedjeNew tools for discovering and characterizing microbial diversityCurrent Opinion in Biotechnology19(6) 544–9
200810.1016/j.ijhydene.2008.07.102Burrows, E., F. Chaplen and R. ElyOptimization of media nutrient composition for increased photofermentative hydrogen production by Synechocystis sp. PCC 6803International Journal of Hydrogen Energy33(21) 6092–9
200810.1021/jp801916fBondar, A. N., J. Baudry, S. Suhai, S. Fischer and J. C. SmithKey role of active-site water molecules in bacteriorhodopsin proton-transfer reactionsJournal of Physical Chemistry B112(47) 14729–41
200810.1016/j.ymben.2008.02.001Bernstein, J. R., T. Bulter and J. C. LiaoTransfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotinMetabolic Engineering10(45720) 131-140
200810.1021/ac800795fBenton, H. P., D. M. Wong, S. A. Trauger and G. SiuzdakXCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterizationAnalytical Chemistry80(16) 6382–9
200810.1021/bi801425eBecker, V., D. Sengupta, R. Ketteler, G. M. Ullmann, J. C. Smith and U. KlingmullerPacking density of the erythropoietin receptor transmembrane domain correlates with amplification of biological responsesBiochemistry47(45) 11771–82
200810.1080/10635150802434394Alekseyenko, A. V., C. J. Lee and M. A. SuchardWagner and Dollo: A stochastic duet by composing two parsimonious solosSystematic Biology57(5) 772-784
200910.1088/0031-9155/54/17/008Zhou, J. and J. QiTheoretical analysis and simulation study of a high-resolution zoom-in PET systemPhysics in Medicine and Biology54(17) 5193–208
200910.1007/978-3-642-02498-6_3Zhou, J. and J. QiHigh-resolution adaptive PET imagingInternational Conference on Information Processing in Medical Imaging21 26–37
200910.1038/hdy.2009.26Zakharov, E. V., N. F. Lobo, C. Nowak and J. J. HellmannIntrogression as a likely cause of mtDNA paraphyly in two allopatric skippers (Lepidoptera: Hesperiidae)Heredity102(6) 590–9
200910.1111/j.1469-8137.2008.02663.xYin, T. M., X. Y. Zhang, L. E. Gunter, S. X. Li, S. D. Wullschleger, M. R. Huang and G. A. TuskanMicrosatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genomeNew Phytologist181(2) 498–503
200910.1002/chem.200902297Xu, Q., Y. Z. Chu, H. B. Guo, J. C. Smith and H. GuoEnergy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferasesChemistry15(46) 12596–9
200910.1002/pro.105Xu, J., M. F. Crowley and J. C. SmithBuilding a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulationProtein Science18(5) 949–59
200910.1186/1471-2180-9-149Xia, Q., T. Wang, E. L. Hendrickson, T. J. Lie, M. Hackett and J. A. LeighQuantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludisBMC Microbiology9
200910.1016/j.ymben.2009.08.004Wong, W. W. and J. C. LiaoMicrobial maximal specific growth rate as a square-root function of biomass yield and two kinetic parametersMetabolic Engineering11(6) 409–14
200910.1073/pnas.0812874106Wikoff, W. R., A. T. Anfora, J. Liu, P. G. Schultz, S. A. Lesley, E. C. Peters and G. SiuzdakMetabolomics analysis reveals large effects of gut microflora on mammalian blood metabolitesProceedings of the National Academy of Sciences of the United States of America106(10) 3698–703
2009Widya, I., R. G. A. Bults, M. H. A. Huis In't Veld and M. M. R. Vollenbroek-HuttenScenario-based requirements elicitation in a pain-teletreatment applicationICSOFT 2009 - 4th International Conference on Software and Data Technologies, Proceedings2 406-413
200910.1371/journal.pone.0005485Whitehead, K., M. Pan, K. Masumura, R. Bonneau and N. S. BaligaDiurnally entrained anticipatory behavior in archaeaPLoS One4(5) e5485
200910.1186/1471-2229-9-88Vogel, J. P., M. Tuna, H. Budak, N. Huo, Y. Q. Gu and M. A. SteinwandDevelopment of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyonBMC Plant Biology9 88
200910.1021/ct900256kUlmschneider, J. P., J. P. Doux, J. A. Killian, J. C. Smith and M. B. UlmschneiderPeptide Partitioning and Folding into Lipid BilayersJournal of Chemical Theory and Computation5(9) 2202–5
200910.1021/ja9064365Thukral, L., J. C. Smith and I. DaidoneCommon folding mechanism of a β-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulationsJournal of the American Chemical Society131(50) 18147–52
200910.1007/s10933-008-9266-7Swindles, G. T., D. J. Charman, H. M. Roe and P. A. SansumEnvironmental controls on peatland testate amoebae (Protozoa: Rhizopoda) in the North of Ireland: Implications for Holocene palaeoclimate studiesJournal of Paleolimnology42(1) 123-140
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200910.1021/ja809660gSpies, M. A., J. G. Reese, D. Dodd, K. L. Pankow, S. R. Blanke and J. BaudryDeterminants of catalytic power and ligand binding in glutamate racemaseJournal of the American Chemical Society131(14) 5274–84
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200910.1021/ct900292rSchulz, R., B. Lindner, L. Petridis and J. C. SmithScaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale SupercomputerJournal of Chemical Theory and Computation5(10) 2798–808
200910.1016/j.bpj.2008.10.007Schulz, R., M. Krishnan, I. Daidone and J. C. SmithInstantaneous normal modes and the protein glass transitionBiophysical Journal96(2) 476–84
200910.1126/science.1178534Schnable, P. S., D. Ware, R. S. Fulton, J. C. Stein, F. Wei, et al.The B73 maize genome: complexity, diversity, and dynamicsScience326(5956) 1112–5
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200910.1021/ja809767vPhatak, P., J. S. Frahmcke, M. Wanko, M. Hoffmann, P. Strodel, J. C. Smith, S. Suhai, A. N. Bondar and M. ElstnerLong-distance proton transfer with a break in the bacteriorhodopsin active siteJournal of the American Chemical Society131(20) 7064–78
200910.1002/jcc.21075Petridis, L. and J. C. SmithA molecular mechanics force field for ligninJournal of Computational Chemistry30(3) 457–67
200910.1080/08927010902995564Pérez-Roa, R. E., M. A. Anderson, D. Rittschof, C. G. Hunt and D. R. NogueraInvolvement of reactive oxygen species in the electrochemical inhibition of barnacle (Amphibalanus amphitrite) settlementBiofouling25(6) 563-571
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200910.1111/j.1755-0998.2008.02203.xNowak, C., C. M. Brown and J. J. HellmannMicrosatellite markers for the hybridizing tiger swallowtails, Papilio glaucus and P. canadensis, and their applicability to historic specimens and congeneric speciesMolecular Ecology Resources9(3) 800–3
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200910.1007/s00239-009-9290-xMontague, M., C. Barnes, H. O. Smith, R. Y. Chuang and S. VasheeThe evolution of RecD outside of the RecBCD complexJournal of Molecular Evolution69(4) 360–71
200910.1002/cphc.200800502Min, W., S. Lu, G. R. Holtom and X. S. XieTriple-resonance coherent anti-stokes Raman scattering microspectroscopyChemPhysChem10(2) 344–7
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200910.1063/1.3108363Krishnan, M., R. Schulz and J. C. SmithProtein Dynamical Transition Role of Methyl Dynamics and Local DiffusionAIP Conference Proceedings1102(1)
200910.1109/NSSMIC.2009.5401623Komarov, S., Y. Yin, H. Wu and Y.-C. TaiSimulation study of charge collection in highly pixilated CdZnTe detector for PET imaging2009 IEEE Nuclear Science Symposium Conference Record (NSS/MIC)2892–95
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200910.1093/mp/ssp047Hedenstrom, M., S. Wiklund-Lindstrom, T. Oman, F. Lu, L. Gerber, P. Schatz, B. Sundberg and J. RalphIdentification of lignin and polysaccharide modifications in Populus wood by chemometric analysis of 2D NMR spectra from dissolved cell wallsMolecular Plant2(5) 933–42
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200910.1560/ijc.49.2.155Bondar, A.-N. and J. C. SmithWater Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton PumpingIsrael Journal of Chemistry49(2) 155–61
200910.1038/nbt.1586Atsumi, S., W. Higashide and J. C. LiaoDirect photosynthetic recycling of carbon dioxide to isobutyraldehydeNature Biotechnology27(12) 1177–80
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201010.1128/mBio.00169-10Zhou, J., Y. Deng, F. Luo, Z. He, Q. Tu and X. ZhiFunctional molecular ecological networksmBio1(4)
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201010.1016/j.jmb.2010.06.026Zahran, M., I. Daidone, J. C. Smith and P. ImhofMechanism of DNA recognition by the restriction enzyme EcoRVJournal of Molecular Biology401(3) 415–32
201010.1038/nature09530Yooseph, S., K. H. Nealson, D. B. Rusch, J. P. McCrow, C. L. Dupont, et al.Genomic and functional adaptation in surface ocean planktonic prokaryotesNature468(7320) 60–6
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201010.1073/pnas.0914506107Yang, S., M. L. Land, D. M. Klingeman, D. A. Pelletier, T. Y. Lu, S. L. Martin, H. B. Guo, J. C. Smith and S. D. BrownParadigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiaeProceedings of the National Academy of Sciences of the United States of America107(23) 10395–400
201010.1007/s12539-010-0070-5Xu, Q., X. Ye, L. Y. Li, Z. M. Cheng and H. GuoStructural basis for the action of xyloglucan endotransglycosylases/hydrolases: insights from homology modelingInterdisciplinary Sciences: Computational Life Sciences2(2) 133–9
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201010.1093/protein/gzq049Xu, J. and J. C. SmithProbing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variantsProtein Engineering, Design and Selection23(10) 759–68
2010Xu, J., G. R. Bao, H. Wang, P. Zhu, F. S. Li, Y. Z. Li, S. Luo and S. Y. LiExperimental study on hydrolysis of rubber seed oil in sub-critical waterHuaxue Gongcheng/Chemical Engineering (China)38(1) 46-49
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201010.1371/journal.pone.0012947Saharay, M., H. Guo and J. C. SmithCatalytic mechanism of cellulose degradation by a cellobiohydrolase, CelSPLoS One5(10) e12947
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201010.1534/genetics.110.113910Okada, M., C. Lanzatella, M. C. Saha, J. Bouton, R. Wu and C. M. TobiasComplete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactionsGenetics185(3) 745–60
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201010.1073/pnas.1006175107McKinlay, J. B. and C. S. HarwoodCarbon dioxide fixation as a central redox cofactor recycling mechanism in bacteriaProceedings of the National Academy of Sciences of the United States of America107(26) 11669–75
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202110.3389/fpls.2021.652319Jarvis, B. A., T. B. Romsdahl, M. G. McGinn, T. J. Nazarenus, E. B. Cahoon, K. D. Chapman and J. C. SedbrookCRISPR/Cas9-Induced fad2 and rod1 Mutations Stacked With fae1 Confer High Oleic Acid Seed Oil in Pennycress (Thlaspi arvense L.)Frontiers in Plant Science12
202110.1099/ijsem.0.005100Jansson, M. K., S. Hering and M. E. J. BuhlParvimonas parva sp. nov., derived from a human genito-urinary lesionInternational Journal of Systematic and Evolutionary Microbiology71(12)
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202110.1073/pnas.2009501118Huberman, L. B., V. W. Wu, D. J. Kowbel, J. Lee, C. Daum, I. V. Grigoriev, R. C. O’Malley and N. L. GlassDNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungusProceedings of the National Academy of Sciences118(13) e2009501118
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202110.1039/D1GC01727FHuang, K., M. Mohan, A. George, B. A. Simmons, Y. Xu and J. M. GladdenIntegration of acetic acid catalysis with one-pot protic ionic liquid configuration to achieve high-efficient biorefinery of poplar biomassGreen Chemistry23(16) 6036–49
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202110.3390/cells10061526Hu, Z., Z. Nie, C. Yan, H. Huang, X. Ma, Y. Wang, N. Ye, G. A. Tuskan, X. Yang and H. YinTranscriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnierianaCells10(6) 1526
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202110.1002/pei3.10056Hsieh, J.-F., S. T. Krause, D. Kainer, J. Degenhardt, W. J. Foley and C. KülheimCharacterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infectionPlant-Environment Interactions2(4) 177–93
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202110.48550/arXiv.2107.08046Holman, H.-Y. N., W. Zhao, J. D. Nill, L. Chen, S. R. Narayanasamy and T. JeohAn Open-channel Microfluidic Membrane Device for In situ Hyperspectral mapping of enzymatic cellulose hydrolysisarXiv:2107.08046v1
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202110.1002/btpr.3172Hillman, E. T., M. Li, C. A. Hooker, J. A. Englaender, I. Wheeldon and K. V. SolomonHydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianusBiotechnology Progress37(5)
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202110.1111/nph.17527Hestrin, R., P. K. Weber, J. Pett-Ridge and J. LehmannPlants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transportNew Phytologist231(5) 1746–57
202110.1094/pbiomes-04-20-0029-fiHestrin, R., M. R. Lee, B. K. Whitaker and J. Pett-RidgeThe Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic DistributionPhytobiomes Journal5(1) 14–28
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202110.1099/ijsem.0.004977Hering, S., M. K. Jansson and M. E. J. BuhlEikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic speciesInternational Journal of Systematic and Evolutionary Microbiology71(9)
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202110.1111/1365-2656.13407Helms, J. A., IV, K. A. Roeder, S. E. Ijelu, I. Ratcliff and N. M. HaddadBioenergy landscapes drive trophic shifts in generalist antsJournal of Animal Ecology90(3) 738–50
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202110.1016/j.jbc.2021.101029Haviland, Z. K., D. Nong, K. L. Vasquez Kuntz, T. J. Starr, D. Ma, M. Tien, C. T. Anderson and W. O. HancockNanoscale dynamics of cellulose digestion by the cellobiohydrolase TrCel7AJournal of Biological Chemistry297(3) 101029
202110.1016/j.tplants.2021.06.015Hassan, M. M., Y. Zhang, G. Yuan, K. De, J.-G. Chen, W. Muchero, G. A. Tuskan, Y. Qi and X. YangConstruct design for CRISPR/Cas-based genome editing in plantsTrends in Plant Science26(11) 1133–52
202110.1128/mra.01035-19Harris, C. R., D. M. Akob, M. Fabisch, F. Beulig, T. Woyke, N. Shapiro, A. Lapidus, H.-P. Klenk and K. KüselDraft Genome Sequence of Bordetella sp. Strain FB-8, Isolated from a Former Uranium Mining Area in GermanyMicrobiology Resource Announcements10(14)
202110.1002/9783527815128.ch8Harnden, K. A., Y. Wang, L. Vo, H. Zhao and Y. LuEngineering Artificial MetalloenzymesProtein Engineering: Tools and Applications177–205
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202110.1039/D1GC02744AHaridevan, H., D. A. C. Evans, A. J. Ragauskas, D. J. Martin and P. K. AnnamalaiValorisation of technical lignin in rigid polyurethane foam: a critical evaluation on trends, guidelines and future perspectivesGreen Chemistry23(22) 8725–53
202110.1002/bbb.2185Happs, R. M., A. W. Bartling, C. Doeppke, A. E. Harman-Ware, R. Clark, E. G. Webb, M. J. Biddy, J.-G. Chen, G. A. Tuskan, M. F. Davis, W. Muchero and B. H. DavisonCover Image, Volume 15, Issue 1Biofuels, Bioproducts and Biorefining15(1) i-i
202110.1002/bbb.2148Happs, R. M., A. W. Bartling, C. Doeppke, A. E. Harman-Ware, R. Clark, E. G. Webb, M. J. Biddy, J.-G. Chen, G. A. Tuskan, M. F. Davis, W. Muchero and B. H. DavisonEconomic impact of yield and composition variation in bioenergy crops: Populus trichocarpaBiofuels, Bioproducts and Biorefining15(1) 176–88
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202110.1101/gr.270033.120Hao, Y., M. E. Mabry, P. P. Edger, M. Freeling, C. Zheng, et al.The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatibleGenome Research31(5) 799-810
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202110.1016/bs.aecr.2021.01.003Haan, N. L., B. G. Iuliano, C. Gratton and D. A. LandisDesigning agricultural landscapes for arthropod-based ecosystem services in North AmericaAdvances in Ecological Research64 191–250
202110.1039/D1CB00112DHa, N. S., M. de Raad, L. Z. Han, A. Golini, C. J. Petzold and T. R. NorthenFaster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnologyRSC Chemical Biology2(5) 1331–51
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202110.3390/genes12020288Guo, Z., M. Xu, H. Nagano, L. V. Clark, E. J. Sacks and T. YamadaCharacterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensisGenes12(2) 288
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202110.1111/ejss.13005Guber, A., T. Kutlu, M. Rivers and A. KravchenkoMass-balance approach to quantify water distribution in soils based on X-ray computed tomography imagesEuropean Journal of Soil Science72(2) 578–92
202110.1016/j.soilbio.2021.108225Guber, A., E. Blagodatskaya, A. Juyal, B. S. Razavi, Y. Kuzyakov and A. KravchenkoTime-lapse approach to correct deficiencies of 2D soil zymographySoil Biology and Biochemistry157 108225
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202110.1002/saj2.20273Grace, P. and G. P. RobertsonSoil carbon sequestration potential and the identification of hotspots in the eastern Corn Belt of the United StatesSoil Science Society of America Journal85(5) 1410–24
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202110.1007/s00425-021-03774-2Gleadow, R. M., B. A. McKinley, C. K. Blomstedt, A. C. Lamb, B. L. Møller and J. E. MulletRegulation of dhurrin pathway gene expression during Sorghum bicolor developmentPlanta254(6) 119
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202110.1128/AEM.02541-20Fracchia, F., L. Mangeot-Peter, L. Jacquot, F. Martin, C. Veneault-Fourrey and A. DeveauColonization of Naive Roots from Populus tremula x alba Involves Successive Waves of Fungi and Bacteria with Different Trophic AbilitiesApplied and Environmental Microbiology87(6) e02541-20
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202110.1093/molbev/msaa221Foflonker, F. and C. E. Blaby-HaasColocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function DiscoveryMolecular Biology and Evolution38(2) 650–62
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202110.3389/fmicb.2021.628308Fenton, C. A., Q. Tang, D. G. Olson, M. I. Maloney, J. L. Bose, L. R. Lynd and A. W. FentonInhibition of Pyruvate Kinase From Thermoanaerobacterium saccharolyticum by IMP Is Independent of the Extra-C DomainFrontiers in Microbiology12
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202110.1111/1751-7915.13790Chroumpi, T., M. Peng, M. V. Aguilar-Pontes, A. Müller, M. Wang, J. Yan, A. Lipzen, V. Ng, I. V. Grigoriev, M. R. Mäkelä and R. P. de VriesRevisiting a ‘simple’ fungal metabolic pathway reveals redundancy, complexity and diversityMicrobial Biotechnology14(6) 2525-2537
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202110.1111/jpy.13132Chorazyczewski, A. M., I.-S. Huang, H. Abdulla, X. Mayali and P. V. ZimbaThe Influence of Bacteria on the Growth, Lipid Production, and Extracellular Metabolite Accumulation by Phaeodactylum tricornutum (Bacillariophyceae)Journal of Phycology57(3) 931–40
202110.1021/jasms.1c00013Choe, K., P. Xue, H. Zhao and J. V. SweedlermacroMS: Image-Guided Analysis of Random Objects by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass SpectrometryJournal of the American Society for Mass Spectrometry32(5) 1180–8
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202110.3389/fmicb.2021.598180Chiniquy, D., E. M. Barnes, J. Zhou, K. Hartman, X. Li, A. Sheflin, A. Pella, E. Marsh, J. Prenni, A. M. Deutschbauer, D. P. Schachtman and S. G. TringeMicrobial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related PhylotypesFrontiers in Microbiology12
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202110.1016/j.mib.2021.08.006Chiappino-Pepe, A., V. Pandey and O. BillkerGenome reconstructions of metabolism of Plasmodium RBC and liver stagesCurrent Opinion in Microbiology63 259-266
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202110.1111/mec.15773Cheng, J., Y. Yang, M. M. Yuan, Q. Gao, L. Wu, Z. Qin, Z. J. Shi, E. A. G. Schuur, J. R. Cole, J. M. Tiedje and J. ZhouWinter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stabilityMolecular Ecology30(4) 926-937
202110.1038/s41467-021-25678-1Chen, Y., Y. Wang, D. Paez-Espino, M. F. Polz and T. ZhangProkaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plantsNature Communications12(1) 5398
202110.1038/s41598-021-90303-6Chen, X., J. Liu, Z. Guo, T. Wu, J. Hou and J. ChengProtein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14Scientific Reports11(1)
202110.1016/j.xplc.2021.100215Chen, T.-C., M. Chern, M. Steinwand, D. Ruan, Y. Wang, A. Isharani and P. RonaldPaladin, a tyrosine phosphatase-like protein, is required for XA21-mediated immunity in ricePlant Communications2(4) 100215
202110.1099/ijsem.0.004801Chen, S., S. Zheng, D. Zhang, B. Hetharua, J. Gui, X. An and H. XuIsolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sedimentInternational Journal of Systematic and Evolutionary Microbiology71(5)
202110.1029/2020MS002284Chen, P., Y. Yuan, W. Li, S. D. LeDuc, T. J. Lark, X. Zhang and C. ClarkAssessing the Impacts of Recent Crop Expansion on Water Quality in the Missouri River Basin Using the Soil and Water Assessment ToolJournal of Advances in Modeling Earth Systems13(6) e2020MS002284
202110.1021/acs.nanolett.0c05038Chen, P., Y. Li, Y. Nishiyama, S. V. Pingali, H. M. O’Neill, Q. Zhang and L. A. BerglundSmall Angle Neutron Scattering Shows Nanoscale PMMA Distribution in Transparent Wood BiocompositesNano Letters21(7) 2883–90
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202110.1021/acs.est.0c06133Chen, L., E. Blanc-Betes, T. W. Hudiburg, D. Hellerstein, S. Wallander, E. H. DeLucia and M. KhannaAssessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program LandEnvironmental Science & Technology55(2) 1301–9
202110.3868/11-00559-001Chen, J.Biophysical Models and Applications in Ecosystem AnalysisMichigan State University Press
202110.1093/nar/gkaa939Chen, I. A., K. Chu, K. Palaniappan, A. Ratner, J. Huang, et al.The IMG/M data management and analysis system v.6.0: new tools and advanced capabilitiesNucleic Acids Research49(D1) D751–63
202110.1186/s13068-020-01865-yChen, F., C. Zhuo, X. Xiao, T. H. Pendergast and K. M. DevosA rapid thioacidolysis method for biomass lignin composition and tricin analysisBiotechnology for Biofuels14(1) 18
202110.1002/prot.26052Chen, C., T. Wu, Z. Guo and J. ChengCombination of deep neural network with attention mechanism enhances the explainability of protein contact predictionProteins: Structure, Function and Bioinformatics89(6) 697-707
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202110.1073/pnas.2106480118Chen, C., V. S. Boorla, D. Banerjee, R. Chowdhury, V. S. Cavener, R. H. Nissly, A. Gontu, N. R. Boyle, K. Vandegrift, M. S. Nair, S. V. Kuchipudi and C. D. MaranasComputational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2Proceedings of the National Academy of Sciences118(42) e2106480118
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202110.1073/pnas.2101254118Chase, A. B., C. Weihe and J. B. H. MartinyAdaptive differentiation and rapid evolution of a soil bacterium along a climate gradientProceedings of the National Academy of Sciences of the United States of America118(18)
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202110.1128/AEM.02301-20Chang, J., D. D. Kim, J. D. Semrau, J. Y. Lee, H. Heo, W. Gu and S. YoonEnhancement of Nitrous Oxide Emissions in Soil Microbial Consortia via Copper Competition between Proteobacterial Methanotrophs and DenitrifiersApplied and Environmental Microbiology87(5) 45672
202110.1039/d1gc02865kChang, H., M. S. Kim, G. W. Huber and J. A. DumesicDesign of closed-loop recycling production of a Diels-Alder polymer from a biomass-derived difuran as a functional additive for polyurethanesGreen Chemistry23(23) 9479-9488
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202110.1186/s13068-021-02033-6Chandrasekar, M., L. Joshi, K. Krieg, S. Chipkar, E. Burke, D. J. Debrauske, K. D. Thelen, T. K. Sato and R. G. OngA high solids field-to-fuel research pipeline to identify interactions between feedstocks and biofuel productionBiotechnology for Biofuels14(1) 179
202110.1111/pce.14004Chai, Y. N., Y. Ge, V. Stoerger and D. P. SchachtmanHigh-resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communitiesPlant, Cell & Environment44(5) 1611-1626
202110.3390/cryst11101227Chai, L., P. Zhu, J. Chai, C. Pang, B. Andi, S. McSweeney, J. Shanklin and Q. LiuAlphaFold Protein Structure Database for Sequence-Independent Molecular ReplacementCrystals11(10) 1227
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202110.1002/csc2.20609Casto, A. L., K. M. Murphy and M. A. GehanCoping with cold: Sorghum cold stress from germination to maturityCrop Science61(6) 3894-3907
202110.1128/MRA.00759-21Castillo, D. J., M. W. V. Goethem and T. P. MakhalanyaneThree Draft Single-Cell Genome Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern OceanMicrobiology Resource Announcements10(39) e00759-21
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202110.1126/sciadv.abh2488Carey, S. B., J. Jenkins, J. T. Lovell, F. Maumus, A. Sreedasyam, et al.Gene-rich UV sex chromosomes harbor conserved regulators of sexual developmentScience Advances7(27) eabh2488
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202110.3389/fmicb.2021.679894Čadež, N., N. Bellora, R. Ulloa, M. Tome, H. Petković, M. Groenewald, C. T. Hittinger and D. LibkindHanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative EnvironmentsFrontiers in Microbiology12
202110.1073/pnas.2022982118Busta, L., E. Schmitz, D. K. Kosma, J. C. Schnable and E. B. CahoonA co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistryProceedings of the National Academy of Sciences of the United States of America118(12)
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202110.3390/ijms22062845Burjoski, V. and A. S. N. ReddyThe landscape of rna-protein interactions in plants: Approaches and current statusInternational Journal of Molecular Sciences22(6) 45683
202110.3390/genes12101609Bueno de Mesquita, C. P., J. Zhou, S. M. Theroux and S. G. TringeMethanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar SalternGenes12(10) 1609
202110.1021/acssuschemeng.0c08829Brunner, M., S. Imberti, B. A. Simmons, G. G. Warr and R. AtkinLiquid Nanostructure of Cholinium Argininate Biomass SolventsACS Sustainable Chemistry & Engineering9(7) 2880–90
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202110.1186/s13068-021-02083-wBrown, J. L., C. L. Swift, S. J. Mondo, S. Seppala, A. Salamov, et al.Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substratesBiotechnology for Biofuels14(1)
202110.1128/mra.00495-21Brown, I., S. G. Tringe, N. Ivanova, L. Goodwin, N. Shapiro, J. Alcorta, D. Pan, A. Chistoserdov, S. Sarkisova and T. WoykeHigh-Quality Draft Genome Sequence of the Siderophilic and Thermophilic Leptolyngbyaceae Cyanobacterium JSC-12Microbiology Resource Announcements10(25) 10.1128/mra.00495-21
202110.1128/mSystems.00835-21Brisson, V., X. Mayali, B. Bowen, A. Golini, M. Thelen, R. K. Stuart and T. R. NorthenIdentification of Effector Metabolites Using Exometabolite Profiling of Diverse MicroalgaemSystems6(6) e00835-21
202110.1128/MRA.01427-20Bridges, C. M., M. C. Nelson, J. Graf and D. J. GageDraft Genome Sequences of Dysgonomonas sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower TermiteMicrobiology Resource Announcements10(4) e01427-20
202110.1128/MRA.00079-21Bridges, C. M. and D. J. GageDraft Genome Sequences of Dysgonomonas sp. Strains GY75 and GY617, Isolated from the Hindgut of Reticulitermes flavipesMicrobiology Resource Announcements10(12) e00079-21
202110.1097/ebp.0000000000001228Brewington, J., J. Cloud, C. Johansson, D. Olson and J. SmileyIn patients with Clostridium difficile infection, is fecal microbiota transplant better than vancomycin for resolving diarrhea?Evidence-Based Practice24(10) 39–40
202110.1002/biot.202100237Brant, E. J., M. C. Baloglu, A. Parikh and F. AltpeterCRISPR/Cas9 mediated targeted mutagenesis of LIGULELESS-1 in sorghum provides a rapidly scorable phenotype by altering leaf inclination angleBiotechnology Journal16(11) 2100237
202110.1039/D1GC01591EBrandner, D. G., J. S. Kruger, N. E. Thornburg, G. G. Facas, J. K. Kenny, et al.Flow-through solvolysis enables production of native-like lignin from biomassGreen Chemistry23(15) 5437–41
202110.1186/s12864-021-07957-9Braga, L. P. P., R. V. Pereira, L. F. Martins, L. M. S. Moura, F. B. Sanchez, J. S. L. Patané, A. M. da Silva and J. C. SetubalGenome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactionsBMC Genomics22(1) 652
202110.1007/s10533-021-00789-5Bradford, M. A., S. A. Wood, E. T. Addicott, E. P. Fenichel, N. Fields, J. González-Rivero, F. V. Jevon, D. S. Maynard, E. E. Oldfield, A. Polussa, E. B. Ward and W. R. WiederQuantifying microbial control of soil organic matter dynamics at macrosystem scalesBiogeochemistry156(1) 19-40
202110.1094/pbiomes-07-20-0051-rBowsher, A. W., G. M. N. Benucci, G. Bonito and A. ShadeSeasonal Dynamics of Core Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf BacteriaPhytobiomes Journal5(1) 60–68
202110.3389/fmars.2021.593566Bowman, J. S., B. A. S. Van Mooy, D. P. Lowenstein, H. F. Fredricks, C. M. Hansel, R. Gast, J. R. Collins, N. Couto and H. W. DucklowWhole Community Metatranscriptomes and Lipidomes Reveal Diverse Responses Among Antarctic Phytoplankton to Changing Ice ConditionsFrontiers in Marine Science8
202110.1073/pnas.2106818118Bowman, E. K., J. M. Wagner, S.-F. Yuan, M. Deaner, C. M. Palmer, S. D’Oelsnitz, L. Cordova, X. Li, F. F. Craig and H. S. AlperSorting for secreted molecule production using a biosensor-in-microdroplet approachProceedings of the National Academy of Sciences118(36) e2106818118
202110.1038/s41396-021-01178-4Bowers, R. M., S. Nayfach, F. Schulz, S. P. Jungbluth, I. A. Ruhl, A. Sheremet, J. Lee, D. Goudeau, E. A. Eloe-Fadrosh, R. Stepanauskas, R. R. Malmstrom, N. C. Kyrpides, P. F. Dunfield and T. WoykeDissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolutionThe ISME Journal16(5) 1337-1347
202110.3389/fmars.2021.611937Bourbonnais, A., C. Frey, X. Sun, L. A. Bristow, A. Jayakumar, N. E. Ostrom, K. L. Casciotti and B. B. WardProtocols for Assessing Transformation Rates of Nitrous Oxide in the Water ColumnFrontiers in Marine Science8
202110.1128/MRA.01485-20Borre, I. and E. C. SonnenscheinDraft Genome Sequences of Nine Environmental Bacterial Isolates Colonizing PlasticMicrobiology Resource Announcements10(11) e01485-20
202110.1002/tpg2.20114Bornowski, N., K. J. Michel, J. P. Hamilton, S. Ou, A. S. Seetharam, et al.Genomic variation within the maize stiff-stalk heterotic germplasm poolPlant Genome14(3)
202110.3389/fenrg.2021.781552Bomble, Y. J. and M. C. JewettEditorial: Cell Free Biocatalysis for the Production of BioproductsFrontiers in Energy Research9
202110.1038/s43705-021-00083-3Bolduc, B., O. Zablocki, J. Guo, A. A. Zayed, D. Vik, P. Dehal, E. M. Wood-Charlson, A. Arkin, N. Merchant, J. Pett-Ridge, S. Roux, M. Vaughn and M. B. SullivaniVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecologyISME Communications1(1) 77
202110.1002/cbic.202000452Bogart, J. W., M. D. Cabezas, B. Vögeli, D. A. Wong, A. S. Karim and M. C. JewettCell-Free Exploration of the Natural Product Chemical SpaceChemBioChem22(1) 84-91
202110.1186/s40168-021-01119-5Boeuf, D., J. M. Eppley, D. R. Mende, R. R. Malmstrom, T. Woyke and E. F. DeLongMetapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineageMicrobiome9(1) 172
202110.1186/s40168-020-00983-xBlaustein, R. A., L. M. Michelitsch, A. J. Glawe, H. Lee, S. Huttelmaier, N. Hellgeth, S. Ben Maamar and E. M. HartmannToothbrush microbiomes feature a meeting ground for human oral and environmental microbiotaMicrobiome9(1) 32
202110.1111/gcbb.12757Blanc-Betes, E., I. B. Kantola, N. Gomez-Casanovas, M. D. Hartman, W. J. Parton, A. L. Lewis, D. J. Beerling and E. H. DeLuciaIn silico assessment of the potential of basalt amendments to reduce N2O emissions from bioenergy cropsGCB Bioenergy13(1) 224–41
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