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.


202410.1007/978-1-0716-3549-0_3Heinrichs, M. E., G. J. Piedade, O. Popa, P. Sommers, G. Trubl, J. Weissenbach and J. RahlffBreaking the Ice: A Review of Phages in Polar EcosystemsBacteriophages: Methods and Protocols 31–71
202410.1016/j.soilbio.2023.109253Ahkami, A. H., O. Qafoku, T. Roose, Q. Mou, Y. Lu, Z. G. Cardon, Y. Wu, C. Chou, J. B. Fisher, T. Varga, P. Handakumbura, J. A. Aufrecht, A. Bhattacharjee and J. J. MoranEmerging sensing, imaging, and computational technologies to scale nano-to macroscale rhizosphere dynamics – Review and research perspectivesSoil Biology and Biochemistry189 109253
202410.1016/j.ymben.2023.11.006Boob, A. G., J. Chen and H. ZhaoEnabling pathway design by multiplex experimentation and machine learningMetabolic Engineering81 70–87
202410.1002/csc2.21131Lee, M. S., R. A. Boyd, C. Jang, J. W. Lee and D. K. LeeIdentifying biomass yield potential of tetra-, hexa-, and octoploid prairie cordgrass populations grown on marginal landsCrop Science64(1) 523–33
202410.1111/ele.14331Ridgeway, J., J. Kane, E. Morrissey, H. Starcher and E. BrzostekRoots selectively decompose litter to mine nitrogen and build new soil carbonEcology Letters27(1) e14331
202410.1016/j.apsoil.2023.105156Da Silva, C. G. N., M. S. Vidal, F. d. S. Dourado, E. S. Dias, A. C. Howe and E. d. C. JesusSpecific primers for the rapid detection and quantitation of Rhizobium elite strains of common beans in the plant and environmentApplied Soil Ecology193 105156
202410.1128/spectrum.02536-23Dubinkina, V., S. Bhogale, P. H. Hsieh, P. Dibaeinia, A. Nambiar, S. Maslov, Y. Yoshikuni and S. SinhaA transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strainsMicrobiology Spectrum12(1) e0253623
2023Suzuki, Y. and J. C. Venter20 Years of the Minimal Cell’s Rise from Theory to PracticeKeiko SFC Journal22(2) 42–53
202310.1111/gcbb.13056Blanc-Betes, E., N. Gomez-Casanovas, W. H. Yang, J. Chandrasoma, T. J. Clark, et al.Accelerating the development of a sustainable bioenergy portfolio through stable isotopesGCB Bioenergy15(7) 840–66
202310.1039/D2GC04425KMohan, M., O. Demerdash, B. A. Simmons, J. C. Smith, M. K. Kidder and S. SinghAccurate prediction of carbon dioxide capture by deep eutectic solvents using quantum chemistry and a neural networkGreen Chemistry25(9) 3475–92
202310.1016/j.soilbio.2022.108886Foley, M. M., S. J. Blazewicz, K. J. McFarlane, A. Greenlon, M. Hayer, J. A. Kimbrel, B. J. Koch, V. L. Monsaint-Queeney, K. Morrison, E. Morrissey, B. A. Hungate and J. Pett-RidgeActive populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslandsSoil Biology and Biochemistry177 108886
202310.1002/bbb.2427Singh, R., S. S. Bhagwat, M. B. Viswanathan, Y. R. Cortés-Peña, K. K. Eilts, G. McDonough, M. Cao, J. S. Guest, H. Zhao and V. SinghAdsorptive separation and recovery of triacetic acid lactone from fermentation brothBiofuels, Bioproducts and Biorefining17(1) 109–20
202310.1371/journal.pone.0288102Chen, Y., J. W. Gin, Y. Wang, M. de Raad, S. Tan, N. J. Hillson, T. R. Northen, P. D. Adams and C. J. PetzoldAlkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate formatPLOS ONE18(7) e0288102
202310.1021/acs.analchem.3c00957Rodríguez, E. P., Y. Li, A. Vaniya, P. M. Shih and O. FiehnAlternative Identification of Glycosides Using MS/MS Matching with an In Silico-Modified Aglycone Mass Spectra LibraryAnalytical Chemistry95(28) 10618–24
202310.1021/acssuschemeng.2c06876Tan, L., H. L. Scott, M. D. Smith, S. V. Pingali, H. M. O’Neill, J. L. Morrell-Falvey, J. Katsaras, J. C. Smith, B. H. Davison, J. G. Elkins and J. D. NickelsAmphiphilic Co-Solvents Modulate the Structure of Membrane DomainsACS Sustainable Chemistry & Engineering11(4) 1598–609
202310.1089/ind.2022.0039Maitra, S. and V. SinghApplication of Time-Domain 1H NMR for Investigating Dynamics of Vegetative Lipids in Bioenergy Crops at Different Developmental StagesIndustrial Biotechnology19(2) 86–93
202310.1016/j.biortech.2022.128280Meng, X., Y. Wang, A. J. Conte, S. Zhang, J. Ryu, J. J. Wie, Y. Pu, B. H. Davison, C. G. Yoo and A. J. RagauskasApplications of biomass-derived solvents in biomass pretreatment – Strategies, challenges, and prospectsBioresource Technology368 128280
202310.1002/mlf2.12076Wu, L., Y. Yang, D. Ning, Q. Gao, H. Yin, N. Xiao, B. Y. Zhou, S. Chen, Q. He and J. ZhouAssessing mechanisms for microbial taxa and community dynamics using process modelsmLife2(3) 239–52
202310.1017/S1473550423000058Trubl, G., K. M. Stedman, K. F. Bywaters, E. E. Matula, P. Sommers, et al.Astrovirology: how viruses enhance our understanding of life in the UniverseInternational Journal of Astrobiology1–25
202310.1021/acs.biomac.3c00047Annamraju, A., K. Rajan, X. Zuo, B. K. Long, S. V. Pingali, T. J. Elder and N. LabbéAtomic Level Interactions and Suprastructural Configuration of Plant Cell Wall Polymers in Dialkylimidazolium Ionic LiquidsBiomacromolecules24(5) 2164–72
202310.1021/acscentsci.3c00813Gu, N. X., C. T. Palumbo, A. C. Bleem, K. P. Sullivan, S. J. Haugen, S. P. Woodworth, K. J. Ramirez, J. K. Kenny, L. D. Stanley, R. Katahira, S. S. Stahl and G. T. BeckhamAutoxidation Catalysis for Carbon–Carbon Bond Cleavage in LigninACS Central Science9(12) 2277–85
202310.1111/mec.16893Braga, L. P. P. and R. I. SchumacherAwaking the dormant virome in the rhizosphereMolecular Ecology32(11) 2985–99
202310.1007/s11274-023-03631-2Das, S., I. N. Najar, M. T. Sherpa, S. Kumar, P. Sharma, K. Mondal, S. Tamang and N. ThakurBaseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activityWorld Journal of Microbiology and Biotechnology39(7) 179
2023Sebesta, J., C. Pastore, H. Hou and J. YuBiocontainment of genetically modified Synechocystis sp. PCC 6803The 2023 Alabama State University STEM Research Symposium
202310.1016/j.biortech.2022.128216Walls, L. E., P. Otoupal, R. Ledesma-Amaro, S. B. Velasquez-Orta, J. M. Gladden and L. Rios-SolisBioconversion of cellulose into bisabolene using Ruminococcus flavefaciens and Rhodosporidium toruloidesBioresource Technology368 128216
202310.1021/acs.biomac.3c00288Zhao, Z.-M., X. Meng, Y. Pu, M. Li, Y. Li, Y. Zhang, F. Chen and A. J. RagauskasBioconversion of Homogeneous Linear C-Lignin to PolyhydroxyalkanoatesBiomacromolecules24(9) 3996–4004
202310.1016/j.eti.2022.102977Banerjee, S., R. Singh and V. SinghBioenergy crops as alternative feedstocks for recovery of anthocyanins: A reviewEnvironmental Technology & Innovation29 102977
202310.1021/acs.est.2c05683Yang, Y., H. Jin, X. Li and J. YanBiohydrogenation of 1,3-Butadiene to 1-Butene under Acetogenic Conditions by Acetobacterium wieringaeEnvironmental Science & Technology57(4) 1637–45
202310.3390/horticulturae9090964Montoya-Martínez, A. C., K. M. Figueroa-Brambila, A. Escalante-Beltrán, N. D. López-Montoya, V. Valenzuela-Ruíz, F. I. Parra-Cota, M. I. Estrada Alvarado and S. de los Santos-VillalobosBiological Control Mechanisms of Bacillus cabrialesii subsp. tritici TSO2T against Fusarium languescens, the Causal Agent of Wilt in Jalapeño PeppersHorticulturae9(9) 964
202310.1007/s12155-022-10513-2Casler, M. D., D. Lee, R. B. Mitchell, K. J. Moore, P. R. Adler, et al.Biomass Quality Responses to Selection for Increased Biomass Yield in Perennial Energy GrassesBioEnergy Research16(2) 877–85
202310.1038/s41893-023-01160-2Demarteau, J., B. Cousineau, Z. Wang, B. Bose, S. Cheong, G. Lan, N. R. Baral, S. J. Teat, C. D. Scown, J. D. Keasling and B. A. HelmsBiorenewable and circular polydiketoenamine plasticsNature Sustainability6(11) 1426–35
202310.1038/s41467-023-40464-xEnglund, E., M. Schmidt, A. A. Nava, S. Klass, L. Keiser, Q. Dan, L. Katz, S. Yuzawa and J. D. KeaslingBiosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange BoundariesNature Communications14(1) 4871
202310.1016/j.copbio.2022.102870Zha, J., Z. Zhao, Z. Xiao, T. Eng, A. Mukhopadhyay, M. A. G. Koffas and Y. J. TangBiosystem design of Corynebacterium glutamicum for bioproductionCurrent Opinion in Biotechnology79 102870
202310.1038/s41598-023-40496-9Harwood, T. V., D. G. C. Treen, M. Wang, W. de Jong, T. R. Northen and B. P. BowenBLINK enables ultrafast tandem mass spectrometry cosine similarity scoringScientific Reports13(1) 13462
202310.1002/yea.3837Barros, K. O., F. B. M. Alvarenga, G. Magni, G. F. L. Souza, M. A. Abegg, F. Palladino, S. S. da Silva, R. C. L. B. Rodrigues, T. K. Sato, C. T. Hittinger and C. A. RosaThe Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast speciesYeast40(2) 84–101
202310.1089/ast.2023.0072Prescott, R. D., Y. L. Chan, E. J. Tong, F. Bunn, C. T. Onouye, et al.Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural RelevanceAstrobiology23(12) 1348–67
202310.1016/j.jbc.2022.102782Hall, B. W., C. A. Bingman, B. G. Fox, D. R. Noguera and T. J. DonohueA broad specificity β-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including γ-valerolactoneJournal of Biological Chemistry299(1) 102782
202310.1016/j.agrformet.2023.109532Wu, G., K. Guan, C. Jiang, H. Kimm, G. Miao, X. Yang, C. J. Bernacchi, X. Sun, A. E. Suyker and C. E. MooreCan upscaling ground nadir SIF to eddy covariance footprint improve the relationship between SIF and GPP in croplands?Agricultural and Forest Meteorology338 109532
202310.1039/D3SE00353AKubis, M. R. and L. R. LyndCarbon capture from corn stover ethanol production via mature consolidated bioprocessing enables large negative biorefinery GHG emissions and fossil fuel-competitive economicsSustainable Energy & Fuels7(16) 3842–52
2023Hou, H. J. M., J. Sebesta, A. Deshpande, C. Pastore, L. Laurens and J. YuCarbon metabolism of a polyphosphate synthase mutant in cyanobacteriaGorden Conference Photosynthesis
202310.1002/jaa2.52Majeed, F., M. Khanna, R. Miao, E. Blanc-Betes, T. Hudiburg and E. DeLuciaCarbon mitigation payments can reduce the riskiness of bioenergy crop productionJournal of the Agricultural and Applied Economics Association2(2) 181–97
202310.1021/acscatal.3c02775Kim, M. S., D. Choi, J. Ha, K. Choi, J.-H. Yu, J. A. Dumesic and G. W. HuberCatalytic Strategy for Conversion of Triacetic Acid Lactone to Potassium SorbateACS Catalysis13(21) 14031–41
202310.3389/fpls.2023.1089011Bryant, N., W. Muchero, R. A. Weber, J. Barros, J.-G. Chen, T. J. Tschaplinski, Y. Pu and A. J. RagauskasCell wall response of field grown Populus to Septoria infectionFrontiers in Plant Science14
202310.1007/s10482-023-01840-1Roldán, D. M. and R. J. MenesCharacterisation of ‘Candidatus Methylobacter titanis’ sp. nov., a putative novel species of Methylobacter clade 2 and their distribution in sediments of freshwater lakes in maritime AntarcticaAntonie van Leeuwenhoek116(7) 721–38
202310.1128/aem.00406-23Sharma, B. D., D. G. Olson, R. J. Giannone, R. L. Hettich and L. R. LyndCharacterization and Amelioration of Filtration Difficulties Encountered in Metabolomic Studies of Clostridium thermocellum at Elevated Sugar ConcentrationsApplied and Environmental Microbiology89(4) e00406-23
202310.1094/phytofr-10-23-0136-rSubedi, N., T. Cowell, M. L. Cope-Arguello, P. A. Paul, G. Cellier, et al.Characterization of Ralstonia pseudosolanacearum diversity and screening tomato, pepper, and eggplant resistance to manage bacterial wilt in South AsiaPhytoFrontiers™
202310.1089/phage.2023.0004Bryan, D. W., L. K. Hudson, J. Wang and T. G. DenesCharacterization of a Diverse Collection of Salmonella Phages Isolated from Tennessee WastewaterPHAGE4(2) 90–98
202310.1111/jfs.13084Quintela, I. A., D. C. Valentine, A. Hwang, T. Vasse, K.-J. Ho and V. C. H. WuCharacterization of Shiga toxin-producing Escherichia coli bacteriophages isolated from agricultural environments and examination of their prevalence with bacterial hostsJournal of Food Safety43(6) e13084
202310.1016/j.virusres.2023.199049Ali, S., A. Karaynir, H. Salih, S. Öncü and B. BozdoğanCharacterization, genome analysis and antibiofilm efficacy of lytic Proteus phages RP6 and RP7 isolated from university hospital sewageVirus Research326 199049
202310.3390/fermentation9010005Deshavath, N. N., B. S. Dien, P. J. Slininger, Y.-S. Jin and V. SinghA Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery ApproachFermentation9(1) 5
202310.1016/j.biortech.2023.128630Jia, Y., S. Maitra and V. SinghChemical-free production of multiple high-value bioproducts from metabolically engineered transgenic sugarcane ‘oilcane’ bagasse and their recovery using nanofiltrationBioresource Technology371 128630
202310.1002/chem.202203941Álvarez-Martínez, I., C. Ruprecht, D. Senf, H.-t. Wang, B. R. Urbanowicz and F. PfrengleChemo-Enzymatic Synthesis of Long-Chain Oligosaccharides for Studying Xylan-Modifying EnzymesChemistry – A European Journal29(26) e202203941
202310.1016/j.plantsci.2023.111874Chang, E., W. Guo, J. Chen, J. Zhang, Z. Jia, T. J. Tschaplinski, X. Yang, Z. Jiang and J. LiuChromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thicknessPlant Science337 111874
202310.1021/acs.est.3c05240Blanc-Betes, E., N. Gomez-Casanovas, M. D. Hartman, T. W. Hudiburg, M. Khanna, W. J. Parton and E. H. DeLuciaClimate vs Energy Security: Quantifying the Trade-offs of BECCS Deployment and Overcoming Opportunity Costs on Set-Aside LandEnvironmental Science & Technology57(48) 19732–48
202310.1094/Pbiomes-02-22-0007-RLagergren, J., M. Cashman, V. G. M. Vergara, P. R. Eller, J. G. F. M. Gazolla, H. B. Chhetri, J. Streich, S. Climer, P. Thornton, W. Joubert and D. JacobsonClimatic Clustering and Longitudinal Analysis with Impacts on Food, Bioenergy, and PandemicsPhytobiomes Journal7(1) 65–77
202310.1021/acs.est.2c06674Wang, Y., N. R. Baral, M. Yang and C. D. ScownCo-Processing Agricultural Residues and Wet Organic Waste Can Produce Lower-Cost Carbon-Negative Fuels and BioplasticsEnvironmental Science & Technology57(7) 2958–69
202310.1007/978-1-0716-2784-6_27Ko, D. K. and F. BrandizziCoexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress ResponsesPlant Proteostasis: Methods and Protocols2581 385–401
202310.1038/s41564-023-01361-7Kelliher, J. M., M. Rudolph, P. Vangay, A. Abbas, M. A. Borton, et al.Cohort-based learning for microbiome research community standardsNature Microbiology8(5) 751–3
202310.1039/D2LC00980CHa, N. S., J. R. Onley, K. Deng, P. Andeer, B. P. Bowen, et al.A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screeningLab on a Chip23(15) 3361–69
202310.3390/foods12030599Apostolakos, I., S. Paramithiotis and M. MataragasComparative Genomic Analysis Reveals the Functional Traits and Safety Status of Lactic Acid Bacteria Retrieved from Artisanal Cheeses and Raw Sheep MilkFoods12(3) 599
202310.1038/s41598-023-48788-wMontso, P. K., A. M. Kropinski, F. Mokoena, R. E. Pierneef, V. Mlambo and C. N. AtebaComparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faecesScientific Reports13(1) 21426
202310.1038/s42003-023-05299-8Longley, R., A. Robinson, J. A. Liber, A. E. Bryson, D. P. Morales, et al.Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungiCommunications Biology6(1) 948
202310.1016/j.ymben.2023.01.001Hu, M., H. V. Dinh, Y. Shen, P. F. Suthers, C. J. Foster, C. M. Call, X. Ye, J. Pratas, Z. Fatma, H. Zhao, J. D. Rabinowitz and C. D. MaranasComparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scaleMetabolic Engineering76 1–17
202310.1093/femspd/ftad009Yadav, A., M. N. Brewer, M. S. Elshahed and E. I. ShawComparative transcriptomics and genomics from continuous axenic media growth identifies Coxiella burnetii intracellular survival strategiesPathogens and Disease81 ftad009
202310.1128/spectrum.03176-23Kalb, M. J., A. W. Grenfell, A. Jain, J. Fenske-Newbart and J. A. GralnickComparison of phage-derived recombinases for genetic manipulation of Pseudomonas speciesMicrobiology Spectrum11(6) e03176-23
202310.3390/microorganisms11020265Sánchez-Hidalgo, M., M. J. García, I. González, D. Oves-Costales and O. GenilloudComplete Genome Sequence Analysis of Kribbella sp. CA-293567 and Identification of the Kribbellichelins A & B and Sandramycin Biosynthetic Gene ClustersMicroorganisms11(2) 265
202310.1128/MRA.00607-23Sullivan, B., C. E. Kitzmiller, W. C. Tran, M. Choudoir, R. Simoes, N. Dayarathne and K. M. DeAngelisComplete genome sequence of Bacillus thuringiensis strain RC340, isolated from a temperate forest soil sample in New EnglandMicrobiology Resource Announcements12(11) e00607-23
202310.1128/MRA.00585-23Fisher, T., F. Durmazolu, K. M. DeAngelis and M. A. MorrowComplete genome sequence of Bradyrhizobium NP1, isolated from forest soilMicrobiology Resource Announcements12(10) e00585-23
202310.1128/mra.00145-23Mulay, S. A., W. G. Alexander, C. R. Hahn, D. M. Klingeman, M. S. Elshahed, N. H. Youssef and M. PodarComplete Genome Sequence of Desulfomicrobium sp. Strain ZS1 from Zodletone Spring in Oklahoma, USAMicrobiology Resource Announcements12(5) e00145-23
202310.1128/MRA.00508-23Alibaglouei, M., L. R. Trutschel, A. R. Rowe and J. D. SackettComplete genome sequence of Halomonas sp. strain M1, a thiosulfate-oxidizing bacterium isolated from a hyperalkaline serpentinizing system, Ney SpringsMicrobiology Resource Announcements12(11) e00508-23
202310.1128/MRA.00583-23Martínez-López, N. A., B. A. Peña-Ocaña, R. García-Contreras, T. Maeda, R. Rincón-Rosales, A. Cazares, Y. Hoshiko and V. M. Ruíz-ValdiviezoComplete genome sequence of Paenibacillus sp. VCA1 isolated from crater lake of the El Chichón VolcanoMicrobiology Resource Announcements12(11) e00583-23
202310.1128/MRA.00288-23Trutschel, L. R., A. R. Rowe and J. D. SackettComplete genome sequence of Roseinatronobacter sp. strain S2, a chemolithoheterotroph isolated from a pH 12 serpentinizing systemMicrobiology Resource Announcements12(9) e00288-23
202310.1128/mra.00824-22Fraccascia, D., R. M. Chanyi, E. Altermann, N. C. Roy, S. H. Flint and W. C. McNabbComplete Genome Sequences of Eight Faecalibacterium sp. Strains Isolated from Healthy Human StoolMicrobiology Resource Announcements12(1) e00824-22
202310.1016/j.crmicr.2023.100193Valenzuela Ruiz, V., G. Santoyo, L. J. Gómez Godínez, L. A. Cira Chávez, F. I. Parra Cota and S. de los Santos VillalobosComplete genome sequencing of Bacillus cabrialesii TE3T: A plant growth-promoting and biological control agent isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui ValleyCurrent Research in Microbial Sciences4 100193
202310.1038/s41586-023-06027-2Huang, J., A. Quest, P. Cruz-Morales, K. Deng, J. H. Pereira, et al.Complete integration of carbene-transfer chemistry into biosynthesisNature617(7960) 403–8
202310.3390/md21030165Elvheim, A. I., C. Li and B. LandfaldConservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine InvertebratesMarine Drugs21(3) 165
202310.1111/1462-2920.16299Parada, A. E., X. Mayali, P. K. Weber, J. Wollard, A. E. Santoro, J. A. Fuhrman, J. Pett-Ridge and A. E. DekasConstraining the composition and quantity of organic matter used by abundant marine ThaumarchaeotaEnvironmental Microbiology25(3) 689–704
202310.1128/msystems.00017-21Jo, C., D. B. Bernstein, N. Vaisman, H. M. Frydman and D. SegrèConstruction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial InteractionsmSystems8(2) e00017-21
202310.1021/acssynbio.3c00443Koh, H. G., J. Kim, C. V. Rao, S.-J. Park and Y.-S. JinConstruction of a Compact Array of Microplasma Jet Devices and Its Application for Random Mutagenesis of Rhodosporidium toruloidesACS Synthetic Biology12(11) 3406-3413
202310.1016/j.polymdegradstab.2023.110466Suzuki, M., Y. Tachibana, P. Soulenthone, T. Suzuki, H. Takeno and K.-i. KasuyaControl of marine biodegradation of an aliphatic polyester using endosporesPolymer Degradation and Stability215 110466
202310.1016/j.ymben.2023.09.013Nguyen, V., P. Xue, Y. Li, H. Zhao and T. LuControlling circuitry underlies the growth optimization of Saccharomyces cerevisiaeMetabolic Engineering80 173–83
2023Tibocha-Bonilla, J. D., R. Santibáñez-Palominos and K. ZenglerCoralME - An automated tool for next-generation metabolic model design and optimizationMetabolic Engineering 15
202310.1038/s41467-023-37164-xMcLaughlin, S., K. Zhalnina, S. Kosina, T. R. Northen and J. SasseThe core metabolome and root exudation dynamics of three phylogenetically distinct plant speciesNature Communications14(1) 1649
202310.1038/s41598-023-32078-6George, N. A. and L. A. HugCRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflictsScientific Reports13(1) 5611
202310.1093/hr/uhad085Yao, T., G. Yuan, H. Lu, Y. Liu, J. Zhang, G. A. Tuskan, W. Muchero, J.-G. Chen and X. YangCRISPR/Cas9-based gene activation and base editing in PopulusHorticulture Research10(6) uhad085
202310.2489/jswc.2023.00069Bell, S. L., A. E. Zimmerman and K. S. HofmockelCropping system drives microbial community response to simulated climate change and plant inputsJournal of Soil and Water Conservation78(2) 178–92
202310.1128/mbio.03189-22Wang, D., K. A. Hunt, P. Candry, X. Tao, N. Q. Wofford, J. Zhou, M. J. McInerney, D. A. Stahl, R. S. Tanner, A. Zhou, M. Winkler and C. PanCross-Feedings, Competition, and Positive and Negative Synergies in a Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to MethanemBio14(2) e03189-22
202310.1093/nar/gkad328Zheng, J., Q. Ge, Y. Yan, X. Zhang, L. Huang and Y. YindbCAN3: automated carbohydrate-active enzyme and substrate annotationNucleic Acids Research51(W1) W115–W121
202310.1007/s00299-023-03062-1Hooghvorst, I. and F. AltpeterdCas9-3xSRDX-mediated transcriptional repression in sugarcanePlant Cell Reports42(11) 1837–40
202310.1002/prot.26422Boorla, V. S., R. Chowdhury, R. Ramasubramanian, B. Ameglio, R. Frick, J. J. Gray and C. D. MaranasDe novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)Proteins: Structure, Function, and Bioinformatics91(2) 196–208
202310.1073/pnas.2303335120Davenport, R., B. P. Bowen, L. M. Lynch, S. M. Kosina, I. Shabtai, T. R. Northen and J. LehmannDecomposition decreases molecular diversity and ecosystem similarity of soil organic matterProceedings of the National Academy of Sciences120(25) e2303335120
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202110.1016/j.copbio.2021.01.005Candry, P. and R. GaniguéChain elongators, friends, and foesCurrent Opinion in Biotechnology67 99-110
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202110.3389/fmicb.2021.687971Saldierna Guzmán, J. P., M. Reyes-Prieto and S. C. HartCharacterization of Erwinia gerundensis A4, an Almond-Derived Plant Growth-Promoting EndophyteFrontiers in Microbiology12
202110.1007/s10482-021-01633-4Fasusi, O. A., A. E. Amoo and O. O. BabalolaCharacterization of plant growth-promoting rhizobacterial isolates associated with food plants in South AfricaAntonie van Leeuwenhoek114(10) 1683–708
202110.1002/pei3.10056Hsieh, J.-F., S. T. Krause, D. Kainer, J. Degenhardt, W. J. Foley and C. KülheimCharacterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infectionPlant-Environment Interactions2(4) 177–93
202110.3390/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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202110.1099/ijsem.0.004912Nde, A. L., G. Charimba, A. Hitzeroth, L. Oosthuizen, L. Steyn, J. D. Newman and C. HugoChryseobacterium pennae sp. nov., isolated from poultry feather wasteInternational Journal of Systematic and Evolutionary Microbiology71(7)
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202110.1038/s42003-021-02244-5Ware, I. M., M. E. Van Nuland, Z. K. Yang, C. W. Schadt, J. A. Schweitzer and J. K. BaileyClimate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenologyCommunications Biology4(1) 748
202110.1021/acs.jproteome.0c00952Lantz, C., M. A. Zenaidee, B. Wei, Z. Hemminger, R. R. Ogorzalek Loo and J. A. LooClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass SpectrometryJournal of Proteome Research20(4) 1928-1935
202110.1002/bit.27896Dong, C., Z. Shi, L. Huang, H. Zhao, Z. Xu and J. LianCloning and characterization of a panel of mitochondrial targeting sequences for compartmentalization engineering in Saccharomyces cerevisiaeBiotechnology and Bioengineering118(11) 4269–77
202110.1093/plcell/koab042Salomé, P. A. and S. S. MerchantCo-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discoveryPlant Cell33(4) 1058-1082
202110.1073/pnas.2022982118Busta, L., E. Schmitz, D. K. Kosma, J. C. Schnable and E. B. CahoonA co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistryProceedings of the National Academy of Sciences of the United States of America118(12)
202110.1186/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/mBio.01442-21Swift, C. L., K. B. Louie, B. P. Bowen, C. A. Hooker, K. V. Solomon, V. Singan, C. Daum, C. P. Pennacchio, K. Barry, V. Shutthanandan, J. E. Evans, I. V. Grigoriev, T. R. Northen and M. A. O’malleyCocultivation of anaerobic fungi with rumen bacteria establishes an antagonistic relationshipmBio12(4)
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202110.1128/AEM.00524-21Kim, S.-K., J. Russell, M. Cha, M. E. Himmel, Y. J. Bomble and J. WestphelingCoexpression of a β-d-Xylosidase from Thermotoga maritima and a Family 10 Xylanase from Acidothermus cellulolyticus Significantly Improves the Xylan Degradation Activity of the Caldicellulosiruptor bescii ExoproteomeApplied and Environmental Microbiology87(14) e0052421
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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
202110.1128/AEM.02541-20Fracchia, F., L. Mangeot-Peter, L. Jacquot, F. Martin, C. Veneault-Fourrey and A. DeveauColonization of Naive Roots from Populus tremula x alba Involves Successive Waves of Fungi and Bacteria with Different Trophic AbilitiesApplied and Environmental Microbiology87(6) e02541-20
202110.1002/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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202110.1002/agj2.20832von Haden, A. C., M. B. Burnham, W. H. Yang and E. H. DeLuciaComparative establishment and yield of bioenergy sorghum and maize following pre-emergence waterloggingAgronomy Journal113(6) 5602–11
202110.1038/s41598-020-79733-wLiu, J., A. Cheng, M. Wang, M. Liu, D. Zhu, et al.Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2Scientific Reports11(1) 616
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202110.1016/j.hal.2021.102037Dreher, T. W., E. W. Davis, R. S. Mueller and T. G. OttenComparative genomics of the ADA clade within the NostocalesHarmful Algae104 102037
202110.1016/j.bbrc.2021.02.046Abdelhamid, A. G. and N. K. El-DougdougComparative genomics of the gut commensal Bifidobacterium bifidum reveals adaptation to carbohydrate utilizationBiochemical and Biophysical Research Communications547 155–61
202110.1128/Spectrum.01414-21Wu, X., A. E. Kazakov, S. Gushgari-Doyle, X. Yu, V. Trotter, R. K. Stuart and R. ChakrabortyComparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in JanthinobacteriumMicrobiology Spectrum9(3) e01414-21
202110.1021/acs.est.1c00802Wu, X., A. Chauhan, A. C. Layton, M. C. Y. Lau Vetter, B. T. Stackhouse, D. E. Williams, L. Whyte, S. M. Pfiffner, T. C. Onstott and T. A. VishnivetskayaComparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High ArcticEnvironmental Science and Technology55(18) 12683-12693
202110.1186/s13068-021-01897-yHapps, R. M., B. Addison, C. Doeppke, B. S. Donohoe, M. F. Davis and A. E. Harman-WareComparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomassBiotechnology for Biofuels14(1) 58
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202110.3390/microorganisms9112249Ramesh, C., M. Anwesh, N. V. Vinithkumar, R. Kirubagaran and L. DufosséComplete Genome Analysis of Undecylprodigiosin Pigment Biosynthesizing Marine Streptomyces Species Displaying Potential Bioactive ApplicationsMicroorganisms9(11) 2249
202110.1128/MRA.00002-21Podar, P. T., K. Peyton, A. Soren, R. L. Wilpiszeski, C. C. Gilmour, D. A. Elias and M. PodarComplete Genome Sequence of Desulfobulbus oligotrophicus Prop6, an Anaerobic Deltabacterota Strain That Lacks Mercury Methylation CapabilityMicrobiology Resource Announcements10(5) e00002-21
202110.1128/MRA.00412-21Joshi, S., P. T. Podar, F. E. Dewhirst and M. PodarComplete Genome Sequence of Human Oral Actinomyces sp. HMT175 Strain ORNL0102, a Host of the Saccharibacterium (TM7) HMT957Microbiology Resource Announcements10(23) e00412-21
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202110.1038/s41589-020-00729-8Dolberg, T. B., A. T. Meger, J. D. Boucher, W. K. Corcoran, E. E. Schauer, A. N. Prybutok, S. Raman and J. N. LeonardComputation-guided optimization of split protein systemsNature Chemical Biology17(5) 531–9
202110.1002/cssc.202101137Zhou, P., K. L. Sánchez-Rivera, G. W. Huber and R. C. Van LehnComputational Approach for Rapidly Predicting Temperature-Dependent Polymer Solubilities Using Molecular-Scale ModelsChemSusChem14(19) 4307–16
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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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202110.1016/j.cub.2021.03.089Mohammadi, S., L. Yang, A. Harpak, S. Herrera-Álvarez, M. del Pilar Rodríguez-Ordoñez, J. Peng, K. Zhang, J. F. Storz, S. Dobler, A. J. Crawford and P. AndolfattoConcerted evolution reveals co-adapted amino acid substitutions in Na+K+-ATPase of frogs that prey on toxic toadsCurrent Biology31(12) 2530-2538.e10
202110.1038/s41396-021-00920-2Emmett, B. D., V. Lévesque-Tremblay and M. J. HarrisonConserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungiISME Journal15(8) 2276-2288
202110.1038/s41598-021-91394-xBenedict, A. B., P. Ghosh, S. M. Scott and J. S. GriffittsA conserved rhizobial peptidase that interacts with host-derived symbiotic peptidesScientific Reports11(1) 11779
202110.1093/bioinformatics/btab347Liber, J. A., G. Bonito and G. M. N. BenucciCONSTAX2: improved taxonomic classification of environmental DNA markersBioinformatics37(21) 3941–3
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
202110.1111/mec.15767Smith, G. R., L. C. Edy and K. G. PeayContrasting fungal responses to wildfire across different ecosystem typesMolecular Ecology30(3) 844–54
202110.1038/s41467-021-21763-7Basso, B., R. A. Martinez-Feria, L. Rill and J. T. RitchieContrasting long-term temperature trends reveal minor changes in projected potential evapotranspiration in the US MidwestNature Communications12(1) 1476
202110.1093/plcell/koaa021Baetsen-Young, A., H. Chen, S. H. Shiu and B. DayContrasting transcriptional responses to Fusarium virguliforme colonization in symptomatic and asymptomatic hostsThe Plant Cell33(2) 224–47
202110.1098/rspb.2021.0621Bell-Dereske, L. P. and S. E. EvansContributions of environmental and maternal transmission to the assembly of leaf fungal endophyte communitiesProceedings of the Royal Society B: Biological Sciences288(1956) 20210621
202110.1128/mBio.03620-20He, X., G. L. Chadwick, C. P. Kempes, V. J. Orphan and C. MeileControls on interspecies electron transport and size limitation of anaerobically methane-oxidizing microbial consortiamBio12(3)
202110.1021/acssuschemeng.1c01629Cheng, M.-H., B. S. Dien, Y.-S. Jin, S. Thompson, J. Shin, P. J. Watson Slininger, N. Qureshi and V. SinghConversion of High-Solids Hydrothermally Pretreated Bioenergy Sorghum to Lipids and Ethanol Using Yeast CulturesACS Sustainable Chemistry & Engineering9(25) 8515–25
202110.1002/csc2.20609Casto, A. L., K. M. Murphy and M. A. GehanCoping with cold: Sorghum cold stress from germination to maturityCrop Science61(6) 3894-3907
202110.1007/s40789-020-00394-1Zhu, T., R. Wang, N. Yi, W. Niu, L. Wang and Z. XueCorrection to: CO2 and SO2 emission characteristics of the whole process industry chain of coal processing and utilization in China (International Journal of Coal Science & Technology, (2020), 7, 1, (19-25), 10.1007/s40789-020-00297-1)International Journal of Coal Science and Technology8(1) 176
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202110.1016/j.ymben.2021.09.008Lee, S.-B., M. Tremaine, M. Place, L. Liu, A. Pier, D. J. Krause, D. Xie, Y. Zhang, R. Landick, A. P. Gasch, C. T. Hittinger and T. K. SatoCrabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiaeMetabolic Engineering68 119–30
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202110.1111/pbi.13651de Vries, L., M. Brouckaert, A. Chanoca, H. Kim, M. R. Regner, et al.CRISPR-Cas9 editing of CAFFEOYL SHIKIMATE ESTERASE 1 and 2 shows their importance and partial redundancy in lignification in Populus tremula × P. albaPlant Biotechnology Journal19(11) 2221–34
202110.1186/s13068-020-01852-3Li, M., X. Lang, M. Moran Cabrera, S. De Keyser, X. Sun, N. Da Silva and I. WheeldonCRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianusBiotechnology for Biofuels14(1)
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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
202110.3389/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
202110.3389/fgeed.2021.673566Oz, M. T., A. Altpeter, R. Karan, A. Merotto and F. AltpeterCRISPR/Cas9-Mediated Multi-Allelic Gene Targeting in Sugarcane Confers Herbicide ToleranceFrontiers in Genome Editing3
202110.1111/nph.17713Irving, T. B., B. Alptekin, B. Kleven and J. M. AnéA critical review of 25 years of glomalin research: a better mechanical understanding and robust quantification techniques are requiredNew Phytologist232(4) 1572-1581
202110.3390/microorganisms9020321Lee, J. A., A. C. Baugh, N. J. Shevalier, B. Strand, S. Stolyar and C. J. MarxCross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial CommunityMicroorganisms9(2)
202110.1007/s12571-021-01156-wAllee, A., L. R. Lynd and V. VazeCross-national analysis of food security drivers: comparing results based on the Food Insecurity Experience Scale and Global Food Security IndexFood Security13(5) 1245–61
202110.1038/s41594-021-00646-xCao, Q., D. R. Boyer, M. R. Sawaya, R. Abskharon, L. Saelices, B. A. Nguyen, J. Lu, K. A. Murray, F. Kandeel and D. S. EisenbergCryo-EM structures of hIAPP fibrils seeded by patient-extracted fibrils reveal new polymorphs and conserved fibril coresNature Structural and Molecular Biology28(9) 724-730
202110.1128/mSystems.01306-20Carper, D. L., D. J. Weston, A. Barde, C. M. Timm, T.-Y. Lu, et al.Cultivating the Bacterial Microbiota of Populus RootsmSystems6(3) e01306-20
202110.1016/j.ymben.2021.02.006Ni, Z., A. E. Stine, K. E. J. Tyo and L. J. BroadbeltCurating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway designMetabolic Engineering65 79-87
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202110.1073/pnas.2100281118Blaby-Haas, C. E.Cyanobacteria provide a new paradigm in the regulation of cofactor dependenceProceedings of the National Academy of Sciences118(7) e2100281118
202110.1111/tpj.15492Muchlinski, A., M. Jia, K. Tiedge, J. S. Fell, K. A. Pelot, L. Chew, D. Davisson, Y. Chen, J. Siegel, J. T. Lovell and P. ZerbeCytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.)Plant Journal108(4) 1053-1068
202110.5194/essd-13-281-2021Jiang, C., K. Guan, G. Wu, B. Peng and S. WangA daily, 250M and real-time gross primary productivity product (2000–present) covering the contiguous United StatesEarth System Science Data13(2) 281–98
202110.1093/nar/gkab765Dibaeinia, P. and S. SinhaDeciphering enhancer sequence using thermodynamics-based models and convolutional neural networksNucleic Acids Research49(18) 10309–27
202110.1128/AEM.01037-21Thorgersen, M. P., J. Xue, E. L. W. Majumder, V. V. Trotter, X. Ge, F. L. Poole, T. K. Owens, L. M. Lui, T. N. Nielsen, A. P. Arkin, A. M. Deutschbauer, G. Siuzdak and M. W. W. AdamsDeciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based MetabolomicsApplied and Environmental Microbiology87(21) e01037-21
202110.1021/acssuschemeng.0c07925Das, L., E. C. Achinivu, C. A. Barcelos, E. Sundstrom, B. Amer, E. E. K. Baidoo, B. A. Simmons, N. Sun and J. M. GladdenDeconstruction of Woody Biomass via Protic and Aprotic Ionic Liquid Pretreatment for Ethanol ProductionACS Sustainable Chemistry & Engineering9(12) 4422–32
202110.1038/s41467-021-22765-1McGivern, B. B., M. M. Tfaily, M. A. Borton, S. M. Kosina, R. A. Daly, C. D. Nicora, S. O. Purvine, A. R. Wong, M. S. Lipton, D. W. Hoyt, T. R. Northen, A. E. Hagerman and K. C. WrightonDecrypting bacterial polyphenol metabolism in an anoxic wetland soilNature Communications12(1)
202110.1073/pnas.2022838118Garruss, A. S., K. M. Collins and G. M. ChurchDeep representation learning improves prediction of LacI-mediated transcriptional repressionProceedings of the National Academy of Sciences of the United States of America118(27)
202110.3389/fmolb.2021.716973Quadir, F., R. S. Roy, E. Soltanikazemi and J. ChengDeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based ModellingFrontiers in Molecular Biosciences8
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202110.1073/pnas.2105739118Staquicini, D. I., F. H. F. Tang, C. Markosian, V. J. Yao, F. I. Staquicini, et al.Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chainProceedings of the National Academy of Sciences of the United States of America118(30)
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202110.1016/j.watres.2020.116571Shabtai, I. A., L. M. Lynch and Y. G. MishaelDesigning clay-polymer nanocomposite sorbents for water treatment: A review and meta-analysis of the past decadeWater Research188 116571
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202110.1111/1751-7915.13832Gauttam, R., A. Mukhopadhyay, B. A. Simmons and S. W. SingerDevelopment of dual-inducible duet-expression vectors for tunable gene expression control and CRISPR interference-based gene repression in Pseudomonas  putida KT2440Microbial Biotechnology14(6) 2659–78
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202110.1371/journal.pcbi.1009448Wang, L., V. Upadhyay and C. D. MaranasdGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway designPLoS Computational Biology17(9) e1009448
202110.1094/MPMI-11-20-0316-FISilva Pankievicz, V. C., F. P. do Amaral, J. M. Ané and G. StaceyDiazotrophic bacteria and their mechanisms to interact and benefit cerealsMolecular Plant-Microbe Interactions34(5) 491-498
202110.1111/nph.17287Sonawane, B. V., N. K. Koteyeva, D. M. Johnson and A. B. CousinsDifferences in leaf anatomy determines temperature response of leaf hydraulic and mesophyll CO2 conductance in phylogenetically related C4 and C3 grass speciesNew Phytologist230(5) 1802-1814
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202110.1093/sysbio/syaa066Morales-Briones, D. F., G. Kadereit, D. T. Tefarikis, M. J. Moore, S. A. Smith, S. F. Brockington, A. Timoneda, W. C. Yim, J. C. Cushman and Y. YangDisentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.lSystematic Biology70(2) 219-235
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202110.1073/pnas.2020024118Ewens, S. D., A. F. S. Gomberg, T. P. Barnum, M. A. Borton, H. K. Carlson, K. C. Wrighton and J. D. CoatesThe diversity and evolution of microbial dissimilatory phosphite oxidationProceedings of the National Academy of Sciences of the United States of America118(11)
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202110.1128/mSystems.00614-21Sorensen, J. W., L. A. Zinke, A. M. ter Horst, C. Santos-Medellín, A. Schroeder and J. B. EmersonDnase treatment improves viral enrichment in agricultural soil viromesmSystems6(5)
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202110.1002/bit.27576Kuanyshev, N., C. V. Rao, B. Dien and Y. S. JinDomesticating a food spoilage yeast into an organic acid-tolerant metabolic engineering host: Lactic acid production by engineered Zygosaccharomyces bailiiBiotechnology and Bioengineering118(1) 372–82
202110.1039/D0GC03855EGong, C., N. Bryant, X. Meng, S. Bhagia, Y. Pu, D. Xin, C. Bender Koch, C. Felby, L. G. Thygesen, A. Ragauskas and S. T. ThomsenDouble bonus: surfactant-assisted biomass pelleting benefits both the pelleting process and subsequent enzymatic saccharification of the pretreated pelletsGreen Chemistry23(2) 1050–61
202110.29303/jbt.v21i2.2802Viersanova, A. and H. PurwantoDraft Genome of Lysinibacillus sphaericus Isolate 229C Pathogenic to Vector MosquitoesJurnal Biologi Tropis21(2) 576–86
202110.1128/MRA.00884-20Bhattacharjee, A., L. N. Anderson, T. Alfaro, A. Porras-Alfaro, A. Jumpponen, K. S. Hofmockel, J. K. Jansson, C. R. Anderton and W. C. NelsonDraft Genome Sequence of Fusarium sp. Strain DS 682, a Novel Fungal Isolate from the Grass RhizosphereMicrobiology Resource Announcements10(1) e00884-20
202110.1128/MRA.00150-21Thompson, M. G., C. B. Eiben, A. N. Pearson and P. M. ShihDraft Genome Sequence of Mycobacterium sp. Strain JC1 DSM 3803Microbiology Resource Announcements10(19) e00150-21
202110.1128/MRA.00212-21Rosario, M. E., J. Camm, D. Cavanagh, D. C. Rowley and D. R. NelsonDraft Genome Sequence of Pseudoalteromonas sp. Strain JC3Microbiology Resource Announcements10(36) e00212-21
202110.1128/MRA.00628-21McDermith, E. J., A. R. Sterling, M. J. Bertin and B. D. JenkinsDraft Genome Sequence of Salegentibacter sp. Strain BDJ18, a Plankton-Associated Bacterium in the Northeast Atlantic OceanMicrobiology Resource Announcements10(36) e00628-21
202110.1128/MRA.00793-21Podar, N. A., D. Klingeman, F. Miranda-Sanchez, F. E. Dewhirst and M. PodarDraft Genome Sequence of Schaalia odontolytica Strain ORNL0103, a Basibiont of “Candidatus Saccharibacteria” HMT352Microbiology Resource Announcements10(44) e00793-21
202110.1128/MRA.00580-21Nickolson, G. P., N. M. Balasjin and C. W. MarshallDraft Genome Sequence of Staphylococcus succinus Strain GN1, Isolated from a Basement Floor in Milwaukee, WIMicrobiology Resource Announcements10(27) e00580-21
202110.1016/j.crmicr.2021.100055Sergio, d. l. S.-V., K. James Michael, P.-C. Fannie Isela, V.-R. Valeria, H.-K. Corina, G.-O. Luis Fernando, T. James Michael, H. Sheng Yang and P.-C. Juan JoseDraft genome sequence of Paraburkholderia sp. strain XV isolated from the rhizosphere of mango (Mangifera indica L.)Current Research in Microbial Sciences2 100055
202110.1128/MRA.00652-21Villarreal, A. R., D. E. Campbell, S. S. Webster and R. C. HunterDraft genome sequence of scheffersomyces spartinae ARV011, a marine yeast isolateMicrobiology Resource Announcements10(45)
202110.1128/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
202110.1128/MRA.00531-21Mok, S., P. R. Flanagan, E. Roycroft, T. R. Rogers and M. M. FitzgibbonDraft Genome Sequences of Clinical Respiratory Isolates of Mycobacterium goodii Recovered in IrelandMicrobiology Resource Announcements10(31) e00531-21
202110.1128/MRA.01485-20Borre, I. and E. C. SonnenscheinDraft Genome Sequences of Nine Environmental Bacterial Isolates Colonizing PlasticMicrobiology Resource Announcements10(11) e01485-20
202110.1128/MRA.00482-21Babalola, O. O., B. S. Adeleke and A. S. AyangbenroDraft Genome Sequencing of Stenotrophomonas indicatrix BOVIS40 and Stenotrophomonas maltophilia JVB5, Two Strains with Identifiable Genes Involved in Plant Growth PromotionMicrobiology Resource Announcements10(28) e00482-21
202110.1128/MRA.00029-21Babalola, O. O., O. A. Fasusi, A. E. Amoo and A. S. AyangbenroDraft Genomic Analysis of Pseudomonas sp. Strain OA3, a Potential Plant Growth-Promoting Rhizospheric BacteriumMicrobiology Resource Announcements10(11) e00029-21
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202110.1038/s41467-021-21449-0Azeez, A., Y. C. Zhao, R. K. Singh, Y. S. Yordanov, M. Dash, P. Miskolczi, K. Stojkovič, S. H. Strauss, R. P. Bhalerao and V. B. BusovEARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancyNature Communications12(1)
202110.1016/j.scitotenv.2020.144498Villa, J. A., Y. Ju, T. Yazbeck, S. Waldo, K. C. Wrighton and G. BohrerEbullition dominates methane fluxes from the water surface across different ecohydrological patches in a temperate freshwater marsh at the end of the growing seasonScience of the Total Environment767
202110.1038/s41467-021-25976-8Luo, Y., G. Jiang, T. Yu, Y. Liu, L. Vo, H. Ding, Y. Su, W. W. Qian, H. Zhao and J. PengECNet is an evolutionary context-integrated deep learning framework for protein engineeringNature Communications12(1) 5743
202110.1128/mSystems.00537-21Kothari, A., S. Roux, H. Zhang, A. Prieto, D. Soneja, et al.Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental TolerancemSystems6(3) e00537-21
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202110.1088/1748-9326/abd7afChen, L., D. Debnath, J. Zhong, K. Ferin, A. VanLoocke and M. KhannaThe economic and environmental costs and benefits of the renewable fuel standardEnvironmental Research Letters16(3) 034021
202110.1002/bbb.2148Happs, R. M., A. W. Bartling, C. Doeppke, A. E. Harman-Ware, R. Clark, E. G. Webb, M. J. Biddy, J.-G. Chen, G. A. Tuskan, M. F. Davis, W. Muchero and B. H. DavisonEconomic impact of yield and composition variation in bioenergy crops: Populus trichocarpaBiofuels, Bioproducts and Biorefining15(1) 176–88
202110.1016/j.jclepro.2021.126875Viswanathan, M. B., M.-H. Cheng, T. E. Clemente, I. Dweikat and V. SinghEconomic perspective of ethanol and biodiesel coproduction from industrial hempJournal of Cleaner Production299 126875
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202110.3390/plants10030513Zhai, Z., H. Liu and J. ShanklinEctopic Expression of OLEOSIN 1 and Inactivation of GBSS1 Have a Synergistic Effect on Oil Accumulation in Plant LeavesPlants10(3) 513
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202110.1038/s41561-021-00725-0Fullerton, K. M., M. O. Schrenk, M. Yücel, E. Manini, M. Basili, et al.Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent marginNature Geoscience14(5) 301-306
202110.3389/fpls.2021.669064Kates, H. R., J. R. Doby, C. M. Siniscalchi, R. LaFrance, D. E. Soltis, P. S. Soltis, R. P. Guralnick and R. A. FolkThe Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing SuccessFrontiers in Plant Science12
202110.1016/j.micres.2020.126640Igiehon, N. O., O. O. Babalola, X. Cheseto and B. TortoEffects of rhizobia and arbuscular mycorrhizal fungi on yield, size distribution and fatty acid of soybean seeds grown under drought stressMicrobiological Research242 126640
202110.1016/j.jcat.2021.03.013Demir, B., T. Kropp, E. B. Gilcher, M. Mavrikakis and J. A. DumesicEffects of water on the kinetics of acetone hydrogenation over Pt and Ru catalystsJournal of Catalysis403 215–27
202110.1111/mmi.14717Monge, E. C. and J. G. GardnerEfficient chito-oligosaccharide utilization requires two TonB-dependent transporters and one hexosaminidase in Cellvibrio japonicusMolecular Microbiology116(2) 366-380
202110.1016/j.ymben.2021.01.004Wang, X., J. H. Pereira, S. Tsutakawa, X. Fang, P. D. Adams, A. Mukhopadhyay and T. S. LeeEfficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450Metabolic Engineering64 41–51
202110.3389/fenrg.2021.640337Yue, F., W. Lan, L. Zhang, F. Lu, R. Sun and J. RalphEfficient Synthesis of Pinoresinol, an Important Lignin Dimeric Model CompoundFrontiers in Energy Research9
202110.1128/AEM.00972-21Sipes, K., A. Almatari, A. Eddie, D. Williams, E. Spirina, E. Rivkina, R. Liang, T. C. Onstott, T. A. Vishnivetskaya and K. G. LloydEight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian PermafrostApplied and Environmental Microbiology87(19) e00972-21
202110.1099/ijsem.0.004977Hering, S., M. K. Jansson and M. E. J. BuhlEikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic speciesInternational Journal of Systematic and Evolutionary Microbiology71(9)
202110.1016/j.electacta.2020.137326Rago, L., D. Popp, J. T. Heiker and F. HarnischElectroactive microorganisms in mouse fecesElectrochimica Acta365
202110.1016/j.mec.2021.e00176Stephens, K., F. R. Zakaria, E. VanArsdale, G. F. Payne and W. E. BentleyElectronic signals are electrogenetically relayed to control cell growth and co-culture compositionMetabolic Engineering Communications13 e00176
202110.1039/D1GC00911GZhao, Z.-M., S. Zhang, X. Meng, Y. Pu, Z.-H. Liu, W. K. Ledford, S. M. Kilbey, B.-Z. Li and A. J. RagauskasElucidating the mechanisms of enhanced lignin bioconversion by an alkali sterilization strategyGreen Chemistry23(13) 4697–709
202110.1002/anie.202012213Samkian, A. E., G. R. Kiel, C. G. Jones, H. M. Bergman, J. Oktawiec, H. M. Nelson and T. D. TilleyElucidation of Diverse Solid-State Packing in a Family of Electron-Deficient Expanded Helicenes via Microcrystal Electron Diffraction (MicroED)**Angewandte Chemie - International Edition60(5) 2493-2499
202110.1371/journal.pcbi.1008983Sarkar, D., M. Landa, A. Bandyopadhyay, H. B. Pakrasi, J. P. Zehr and C. D. MaranasElucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modelingPLoS Computational Biology17(5) e1008983
202110.1007/s10664-021-09940-0Cashman, M., J. Firestone, M. B. Cohen, T. Thianniwet and W. NiuAn empirical investigation of organic software product linesEmpirical Software Engineering26(3) 44
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202110.1016/j.ymben.2021.04.015Eng, T., D. Banerjee, A. K. Lau, E. Bowden, R. A. Herbert, J. Trinh, J.-P. Prahl, A. Deutschbauer, D. Tanjore and A. MukhopadhyayEngineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactorMetabolic Engineering66 229–38
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202110.1021/jacsau.0c00103Ellis, E. S., D. J. Hinchen, A. Bleem, L. Bu, S. J. B. Mallinson, et al.Engineering a Cytochrome P450 for Demethylation of Lignin-Derived Aromatic AldehydesJACS Au1(3) 252–61
202110.1002/9783527815128.ch8Harnden, K. A., Y. Wang, L. Vo, H. Zhao and Y. LuEngineering Artificial MetalloenzymesProtein Engineering: Tools and Applications 177–205
202110.1016/j.copbio.2020.09.011Liu, D., M. Liberton, J. I. Hendry, J. Aminian-Dehkordi, C. D. Maranas and H. B. PakrasiEngineering biology approaches for food and nutrient production by cyanobacteriaCurrent Opinion in Biotechnology67 1–6
202110.1016/j.ymben.2021.04.005Seo, H., J.-W. Lee, R. J. Giannone, N. J. Dunlap and C. T. TrinhEngineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesisMetabolic Engineering66 179–90
202110.1093/jimb/kuab067Tran, V. G. and H. ZhaoEngineering robust microorganisms for organic acid productionJournal of Industrial Microbiology and Biotechnology49(2)
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202110.1021/jacs.1c01885Jellen, M. J., I. Liepuoniute, M. Jin, C. G. Jones, S. Yang, X. Jiang, H. M. Nelson, K. N. Houk and M. A. Garcia-GaribayEnhanced Gearing Fidelity Achieved through Macrocyclization of a Solvated Molecular Spur GearJournal of the American Chemical Society143(20) 7740-7747
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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
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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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202110.1515/hf-2021-0015Ikeda, T., N. Takata, S. Sakamoto, S. Hu, Nuoendagula, S. Hishiyama, N. Mitsuda, W. Boerjan, J. Ralph and S. KajitaImproved chemical pulping and saccharification of a natural mulberry mutant deficient in cinnamyl alcohol dehydrogenaseHolzforschung75(10) 968–77
202110.1021/acssynbio.0c00591Delorenzo, D. M., J. Diao, R. Carr, Y. Hu and T. S. MoonAn Improved CRISPR Interference Tool to Engineer Rhodococcus opacusACS Synthetic Biology10(4) 786-798
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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
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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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202110.1093/jxb/erab437Griffiths, M., X. Wang, K. Dhakal, H. Guo, A. Seethepalli, Y. Kang and L. M. YorkInteractions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.)Journal of Experimental Botany73(3) 967–79
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202110.1021/acs.orglett.0c03966Nelson, H. M., J. C. Siu, A. Saha, D. Cascio, S. N. MacMillan, S. B. Wu, C. Lu, J. A. Rodríguez, K. N. Houk and S. LinIsolation and X-ray Crystal Structure of an Electrogenerated TEMPO-N3Charge-Transfer ComplexOrganic Letters23(2) 454-458
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202110.1093/sysbio/syaa038Neumann, J. S., R. Desalle, A. Narechania, B. Schierwater and M. TesslerMorphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data SetsSystematic Biology70(2) 360–75
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