Publications Using KBase for Analysis

How to Cite KBase

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163


  • Contador CA, Rodríguez V, Andrews BA, Asenjo JA. Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora. BMC Systems Biology. 2019;13. doi:10.1186/s12918-019-0683-1
    Link to Publication
  • Matu A, Lum Nde A, Oosthuizen L, Hitzeroth A, Badenhorst M, Duba L, et al. Draft Genome Sequences of Seven Chryseobacterium Type Strains. Baltrus DA, editor. Microbiology Resource Announcements. 2019;8. doi:10.1128/MRA.01518-18
    Link to Publication
  • Domeignoz-Horta LA, DeAngelis KM, Pold G. Draft Genome Sequence of Acidobacteria Group 1 Acidipila sp. Strain EB88, Isolated from Forest Soil. Baltrus DA, editor. Microbiology Resource Announcements. 2019;8. doi:10.1128/MRA.01464-18
    Link to Publication


  • diCenzo G, Mengoni A, Fondi M. Tn-Core: a toolbox for integrating Tn-seq gene essentiality data and constraint-based metabolic modelling. ACS Synthetic Biology. 2018; doi:10.1021/acssynbio.8b00432
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  • Lima ARJ, Siqueira AS, Vasconcelos JM de, Pereira JS, Azevedo JSN de, Moraes PHG, et al. Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics. Frontiers in Microbiology. 2018;9. doi:10.3389/fmicb.2018.02811
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  • Adeniji AA, Aremu OS, Babalola OO. Selecting lipopeptide-producing, Fusarium- suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5. MicrobiologyOpen. 2018; e742. doi:10.1002/mbo3.742 – Link to Publication
  • Xu X, Zarecki R, Medina S, Ofaim S, Liu X, Chen C, et al. Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions. The ISME Journal. 2018; doi:10.1038/s41396-018-0288-5 – Link to Publication
  • Checcucci A, diCenzo G, Ghini V, Bazzicalupo M, Becker A, Decorosi F, et al. Creation and characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti. ACS Synthetic Biology. 2018; doi:10.1021/acssynbio.8b00158 – Link to Publication
  • Cashman M, Cohen MB, Ranjan P, Cottingham RW. Navigating the maze: the impact of configurability in bioinformatics software. Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineering  – ASE 2018. Montpellier, France: ACM Press; 2018. pp. 757–767. doi:10.1145/3238147.3240466 – Link to Publication
  • Li W, Li H, Liu Y, Zheng P, Shapleigh JP. Salinity-Aided Selection of Progressive Onset Denitrifiers as a Means of Providing Nitrite for Anammox. Environmental Science & Technology. 2018;52: 10665–10672. doi:10.1021/acs.est.8b02314 – Link to Publication
  • Dobritsa AP, Kutumbaka KK, Samadpour M. Reclassification of Eubacterium combesii and discrepancies in the nomenclature of botulinum neurotoxin-producing clostridia: Challenging Opinion 69. Request for an Opinion. International Journal of Systematic and Evolutionary Microbiology. 2018; doi:10.1099/ijsem.0.002942
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  • Kumar M, Ji B, Babaei P, Das P, Lappa D, Ramakrishnan G, et al. Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling. Metabolic Engineering. 2018;49: 128–142. doi:10.1016/j.ymben.2018.07.018
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  • diCenzo GC, Debiec K, Krzysztoforski J, Uhrynowski W, Mengoni A, Fagorzi C, et al. Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. Genes. 2018;9: 379. doi:10.3390/genes9080379
    Link to Publication
  • Faria JP, Rocha M, Rocha I, Henry CS. Methods for automated genome-scale metabolic model reconstruction. Biochemical Society Transactions. 2018; BST20170246. doi:10.1042/BST20170246
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  • Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater: “Dynamics of groundwater naphthalene biodegradation.” Environmental Microbiology. 2018; doi:10.1111/1462-2920.14309 – Link to Publication
  • Liu R, Liang L, Choudhury A, Garst AD, Eckert CA, Oh EJ, et al. Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production. Metabolic Engineering. 2018; doi:10.1016/j.ymben.2018.07.007 – Link to Publication
  • Karp PD, Weaver D, Latendresse M. How accurate is automated gap filling of metabolic models? BMC Systems Biology. 2018;12. doi:10.1186/s12918-018-0593-7 – Link to Publication
  • Metz ZP, Ding T, Baumler DJ. Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes. Suen G, editor. PLOS ONE. 2018;13: e0198584. doi:10.1371/journal.pone.0198584 – Link to Publication
  • Nickerson KP, Senger S, Zhang Y, Lima R, Patel S, Ingano L, et al. Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue. EBioMedicine. 2018; doi:10.1016/j.ebiom.2018.04.005 – Link to Publication
  • Tsementzi D, Castro Gordillo J, Mahagna M, Gottlieb Y, Konstantinidis KT. Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis: Genomic analysis of Coxiella like tick endosymbionts. Environmental Microbiology. 2018; doi:10.1111/1462-2920.14104 – Link to Publication
  • Garza DR, van Verk MC, Huynen MA, Dutilh BE. Towards predicting the environmental metabolome from metagenomics with a mechanistic model. Nature Microbiology. 2018; doi:10.1038/s41564-018-0124-8 – Link to Publication
  • Taş N, Prestat E, Wang S, Wu Y, Ulrich C, Kneafsey T, et al. Landscape topography structures the soil microbiome in arctic polygonal tundra. Nature Communications. 2018;9. doi:10.1038/s41467-018-03089-z – Link to Publication


  • Dobritsa AP, Linardopoulou EV, Samadpour M. Transfer of 13 species of the genus Burkholderia to the genus Caballeronia and reclassification of Burkholderia jirisanensis as Paraburkholderia jirisanensis comb. nov. International Journal of Systematic and Evolutionary Microbiology. 2017;67: 3846–3853. doi:10.1099/ijsem.0.002202 – Link to Publication
  • Xie Z-X, Chen F, Zhang S-F, Wang M-H, Zhang H, Kong L-F, et al. Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea: Metaproteomics of marine viral concentrates. Environmental Microbiology. 2017; doi:10.1111/1462-2920.13937
    Link to Publication
  • Hamilton JJ, Garcia SL, Brown BS, Oyserman BO, Moya-Flores F, Bertilsson S, et al. Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. Pollard KS, editor. mSystems. 2017;2: e00091-17. doi:10.1128/mSystems.00091-17 – Link to Publication
  • Gilmore SP, Henske JK, Sexton JA, Solomon KV, Seppälä S, Yoo JI, et al. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation. BMC Genomics. 2017;18. doi:10.1186/s12864-017-4036-4 – Link to Publication
  • Jensen PA, Zhu Z, van Opijnen T. Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. Cell Reports. 2017;20: 1705–1716. doi:10.1016/j.celrep.2017.07.062
    Link to Publication
  • Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, et al. Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria. Genome Announcements. 2017;5: e00653-17. doi:10.1128/genomeA.00653-17
    Link to Publication
  • Nicholls C, Kump A, Ford S, Gonser R, Cho KH. Draft Genome Sequence of Streptococcus pyogenes Strain M3KCL. Genome Announcements. 2017;5: e00610-17. doi:10.1128/genomeA.00610-17 – Link to Publication
  • Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, et al. Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announcements. 2017;5: e00582-17. doi:10.1128/genomeA.00582-17 – Link to Publication
  • Juárez-Vázquez AL, Edirisinghe JN, Verduzco-Castro EA, Michalska K, Wu C, Noda-García L, et al. Evolution of substrate specificity in a retained enzyme driven by gene loss. eLife. 2017;6. doi:10.7554/eLife.22679 – Link to Publication
  • Jewell TNM, Karaoz U, Bill M, Chakraborty R, Brodie EL, Williams KH, et al. Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer. Frontiers in Microbiology. 2017;8. doi:10.3389/fmicb.2017.00040 – Link to Publication
  • Henry CS, Rotman E, Lathem WW, Tyo KEJ, Hauser AR, Mandel MJ. Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1. The Journal of Infectious Diseases. 2017;215: S37–S43. doi:10.1093/infdis/jiw465
    Link to Publication
  • Viver T, Orellana LH, Hatt JK, Urdiain M, Díaz S, Richter M, et al. The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa: Low diverse microbiome of C. tuberculata. Environmental Microbiology. 2017; doi:10.1111/1462-2920.13763 – Link to Publication
  • Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, et al. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Standards in Genomic Sciences. 2017;12. doi:10.1186/s40793-017-0233-7
    Link to Publication
  • Pfaller S, Tokarev V, Kessler C, McLimans C, Gomez-Alvarez V, Wright J, et al. Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169. Genome Announcements. 2017;5: e01620–16. doi:10.1128/genomeA.01620-163 – Link to Publication


  • Richards MA, Lie TJ, Zhang J, Ragsdale SW, Leigh JA, Price ND. Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. Zhulin IB, editor. Journal of Bacteriology. 2016;198: 3379–3390. doi:10.1128/JB.00571-16 – Link to Publication
  • Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. 2016; doi:10.1038/nbt.3703 – Link to Publication
  • Faria, J.P., Davis, J.J., Edirisinghe, J.N., Taylor, R.C., Weisenhorn, P.B., Olson, R.D., Stevens, R., Rocha, M., Rocha, I., Best, A.A. and DeJongh, M. Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. Frontiers in Microbiology. 2016;7: 1819. doi: 10.3389/fmicb.2016.01819 – Link to Publication
  • Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. Biotechnology for Biofuels. 2016;9. doi:10.1186/s13068-016-0607-x
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  • Ormerod KL, Wood DLA, Lachner N, Gellatly SL, Daly JN, Parsons JD, et al. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome. 2016;4. doi:10.1186/s40168-016-0181-2 – Link to Publication
  • Henry CS, Bernstein HC, Weisenhorn P, Taylor RC, Lee J-Y, Zucker J, Sung H-S. Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction. Journal of Cellular Physiology. 2016;231: 2339–2345. doi:10.1002/jcp.25428 – Link to Publication
  • diCenzo GC, Checcucci A, Bazzicalupo M, Mengoni A, Viti C, Dziewit L, et al. Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti. Nature Communications. 2016;7: 12219. doi:10.1038/ncomms12219 – Link to Publication
  • White RA, Bottos EM, Roy Chowdhury T, Zucker JD, Brislawn CJ, Nicora CD, et al. Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes. Langille M, editor. mSystems. 2016;1: e00045–16. doi:10.1128/mSystems.00045-16 – Link to Publication
  • Cardona C, Weisenhorn P, Henry C, Gilbert JA. Network-based metabolic analysis and microbial community modeling. Current Opinion in Microbiology. 2016;31: 124–131. doi:10.1016/j.mib.2016.03.008 – Link to Publication
  • McLean JS, Liu Q, Bor B, Bedree JK, Cen L, Watling M, et al. Draft Genome Sequence of Actinomyces odontolyticus actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont. Genome Announcements. 2016;4: e01685–15. doi:10.1128/genomeA.01685-15 – Link to Publication
  • Faria JP, Khazaei T, Edirisinghe J, Weisenhorn PB, Seaver S, Conrad N, Harris N, DeJongh M, Henry CS. Constructing and Analyzing Metabolic Flux Models of Microbial Communities. Hydrocarbon and Lipid Microbiology Protocols, 10.1007/8623_2016_215. – Link to Publication


  • Weston DJ, Timm CM, Walker AP, Gu L, Muchero W, Schmutz J, et al. Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host-microbiome interactions on understanding ecosystem function: Sphagnum physiology and changing climate. Plant, Cell & Environment. 2015;38: 1737–1751. doi:10.1111/pce.12458
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  • Timm CM, Campbell AG, Utturkar SM, Jun S-R, Parales RE, Tan WA, et al. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Frontiers in Microbiology. 2015;6. doi:10.3389/fmicb.2015.01118 – Link to Publication
  • Yao Y, Sun T, Wang T, Ruebel O, Northen T, Bowen B. Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases. Metabolites. 2015;5: 431–442. doi:10.3390/metabo5030431 – Link to Publication
  • Noutsos C, Perera AM, Nikolau BJ, Seaver SMD, Ware DH. Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis. Motta A, editor. PLOS ONE. 2015;10: e0124501. doi:10.1371/journal.pone.0124501 – Link to Publication
  • Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, et al. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. Frontiers in Plant Science. 2015;6. doi:10.3389/fpls.2015.00142 – Link to Publication
  • Faria JP, Edirisinghe JN, Davis JJ, Disz T, Hausmann A, Henry CS, et al. Enabling comparative modeling of closely related genomes: example genus Brucella. 3 Biotech. 2015;5: 101–105. doi:10.1007/s13205-014-0202-4 – Link to Publication
  • Wilke A, Bischof J, Harrison T, Brettin T, D’Souza M, Gerlach W, et al. A RESTful API for Accessing Microbial Community Data for MG-RAST. Gardner PP, editor. PLoS Computational Biology. 2015;11: e1004008. doi:10.1371/journal.pcbi.1004008 – Link to Publication


  • Benedict MN, Mundy MB, Henry CS, Chia N, Price ND. Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models. Maranas CD, editor. PLoS Computational Biology. 2014;10: e1003882. doi:10.1371/journal.pcbi.1003882 – Link to Publication
  • Land ML, Hyatt D, Jun S-R, Kora GH, Hauser LJ, Lukjancenko O, et al. Quality scores for 32,000 genomes. Standards in Genomic Sciences. 2014;9: 20. doi:10.1186/1944-3277-9-20 – Link to Publication

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