Patrick S. Chain - Publications

Affiliations: 
2011 Microbiology and Molecular Genetics Michigan State University, East Lansing, MI 

266 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Kubicek-Sutherland JZ, Xie G, Shakya M, Dighe PK, Jacobs LL, Daligault H, Davenport K, Stromberg LR, Stromberg ZR, Cheng Q, Kempaiah P, Ong'echa JM, Otieno V, Raballah E, Anyona S, ... ... Chain PSG, et al. Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. Plos Neglected Tropical Diseases. 15: e0008991. PMID 33524010 DOI: 10.1371/journal.pntd.0008991  0.01
2021 Carter MQ, Pham A, Huynh S, Parker CT, Miller A, He X, Hu B, Chain PSG. DNA adenine methylase, not the PstI restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli. Food Microbiology. 96: 103722. PMID 33494894 DOI: 10.1016/j.fm.2020.103722  0.01
2021 Junier P, Cailleau G, Palmieri I, Valloton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, ... ... Chain PSG, et al. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. Fems Microbiology Ecology. PMID 33440006 DOI: 10.1093/femsec/fiab003  0.04
2020 LeBrun ES, Nighot M, Dharmaprakash V, Kumar A, Lo CC, Chain PSG, Ma TY. The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice. Life (Basel, Switzerland). 11. PMID 33374112 DOI: 10.3390/life11010007  0.04
2020 Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, ... ... Chain PSG, et al. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology. PMID 33184503 DOI: 10.1038/s41564-020-00827-2  1
2020 Li PE, Myers Y Gutiérrez A, Davenport K, Flynn M, Hu B, Lo CC, Player Jackson E, Shakya M, Xu Y, Gans J, Chain PSG. A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays. Bioinformatics (Oxford, England). PMID 32777813 DOI: 10.1093/Bioinformatics/Btaa710  0.01
2020 Robinson AJ, Natvig DO, Chain PSG. Genomic Analysis of Diverse Members of the Fungal Genus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate. G3 (Bethesda, Md.). PMID 32580939 DOI: 10.1534/G3.120.401489  0.01
2020 Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, ... ... Chain PSG, et al. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology. PMID 32514073 DOI: 10.1038/S41564-020-0733-X  1
2020 Murray AE, Avalon NE, Bishop L, Davenport KW, Delage E, Dichosa AEK, Eveillard D, Higham ML, Kokkaliari S, Lo CC, Riesenfeld CS, Young RM, Chain PSG, Baker BJ. Uncovering the Core Microbiome and Distribution of Palmerolide in Across the Anvers Island Archipelago Antarctica. Marine Drugs. 18. PMID 32498449 DOI: 10.3390/Md18060298  1
2020 Wood-Charlson EM, Anubhav, Auberry D, Blanco H, Borkum MI, Corilo YE, Davenport KW, Deshpande S, Devarakonda R, Drake M, Duncan WD, Flynn MC, Hays D, Hu B, Huntemann M, ... ... Chain PSG, et al. The National Microbiome Data Collaborative: enabling microbiome science. Nature Reviews. Microbiology. PMID 32350400 DOI: 10.1038/S41579-020-0377-0  1
2020 Micheva-Viteva SN, Shakya M, Adikari SH, Gleasner CD, Velappan N, Mourant JR, Chain PSG, Hong-Geller E. A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis. Msystems. 5. PMID 32047060 DOI: 10.1128/mSystems.00609-19  0.01
2020 Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Scientific Reports. 10: 1723. PMID 32015354 DOI: 10.1038/S41598-020-58356-1  1
2019 Leguia M, Vila-Sanjurjo A, Chain PSG, Berry IM, Jarman RG, Pollett S. Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing. The Journal of Infectious Diseases. PMID 31751454 DOI: 10.1093/infdis/jiz424  0.01
2019 Shakya M, Lo CC, Chain PSG. Advances and Challenges in Metatranscriptomic Analysis. Frontiers in Genetics. 10: 904. PMID 31608125 DOI: 10.3389/Fgene.2019.00904  0.04
2019 Rawat M, Kadian K, Gupta Y, Kumar A, Chain PSG, Kovbasnjuk O, Kumar S, Parasher G. MicroRNA in Pancreatic Cancer: From Biology to Therapeutic Potential. Genes. 10. PMID 31557962 DOI: 10.3390/genes10100752  0.01
2019 Domman D, Ruis C, Dorman MJ, Shakya M, Chain PSG. Novel Insights Into the Spread of Enteric Pathogens Using Genomics. The Journal of Infectious Diseases. PMID 31538189 DOI: 10.1093/Infdis/Jiz220  0.01
2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, et al. Consent insufficient for data release-Response. Science (New York, N.Y.). 364: 446. PMID 31048484 DOI: 10.1126/Science.Aax7509  1
2019 Arzt J, Fish I, Pauszek SJ, Johnson SL, Chain PS, Rai DK, Rieder E, Goldberg TL, Rodriguez LL, Stenfeldt C. The evolution of a super-swarm of foot-and-mouth disease virus in cattle. Plos One. 14: e0210847. PMID 31022193 DOI: 10.1371/Journal.Pone.0210847  0.01
2019 Kim WK, No JS, Lee D, Jung J, Park H, Yi Y, Kim JA, Lee SH, Kim Y, Park S, Cho S, Lee GY, Song DH, Gu SH, Park K, ... ... Chain PSG, et al. Active Targeted Surveillance to Identify Sites of Emergence of Hantavirus. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 30891596 DOI: 10.1093/cid/ciz234  0.01
2019 Filippidou S, Junier T, Wunderlin T, Kooli WM, Palmieri I, Al-Dourobi A, Molina V, Lienhard R, Spangenberg JE, Johnson SL, Chain PSG, Dorador C, Junier P. Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in and Resistance to Extreme Conditions. Frontiers in Microbiology. 10: 102. PMID 30804904 DOI: 10.3389/Fmicb.2019.00102  1
2019 Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P. Bacterial spores, from ecology to biotechnology. Advances in Applied Microbiology. 106: 79-111. PMID 30798805 DOI: 10.1016/bs.aambs.2018.10.002  1
2019 Palmieri F, Estoppey A, House GL, Lohberger A, Bindschedler S, Chain PSG, Junier P. Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions. Advances in Applied Microbiology. 106: 49-77. PMID 30798804 DOI: 10.1016/bs.aambs.2018.10.001  1
2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, et al. Toward unrestricted use of public genomic data. Science (New York, N.Y.). 363: 350-352. PMID 30679363 DOI: 10.1126/Science.Aaw1280  1
2019 Zhgenti E, Erkkila T, Machablishvili A, Chanturia G, Devenport K, Migun S, Chain P, Imnadze P. Whole-genome SNP-based phylogenetic analysis of Yersinia pestis isolates from Georgia and neighboring Caucasian countries International Journal of Infectious Diseases. 79: 80. DOI: 10.1016/J.Ijid.2018.11.203  0.01
2018 Kooli WM, Junier T, Shakya M, Monachon M, Davenport KW, Vaideeswaran K, Vernudachi A, Marozau I, Monrouzeau T, Gleasner CD, McMurry K, Lienhard R, Rufener L, Perret JL, Sereda O, ... Chain PS, et al. Remedial treatment of corroded iron objects by environmental isolates. Applied and Environmental Microbiology. PMID 30478230 DOI: 10.1128/Aem.02042-18  0.01
2018 Sauder LA, Engel K, Lo CC, Chain P, Neufeld JD. Cultivation and characterization of Nitrosotenuis aquariensis, an ammonia-oxidizing archaeon from a freshwater aquarium biofilter. Applied and Environmental Microbiology. PMID 29959256 DOI: 10.1128/Aem.01430-18  0.01
2018 Johnson SL, Daligault HE, Davenport KW, Jaissle J, Frey KG, Ladner JT, Broomall SM, Bishop-Lilly KA, Bruce DC, Gibbons HS, Coyne SR, Lo CC, Meincke L, Munk AC, Koroleva GI, ... ... Chain PS, et al. Correction for Johnson et al., "Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species". Genome Announcements. 6. PMID 29348328 DOI: 10.1128/Genomea.01144-17  1
2017 Wen ZT, Liao S, Bitoun JP, De A, Jorgensen A, Feng S, Xu X, Chain PSG, Caufield PW, Koo H, Li Y. Streptococcus mutans Displays Altered Stress Responses While Enhancing Biofilm Formation by Lactobacillus casei in Mixed-Species Consortium. Frontiers in Cellular and Infection Microbiology. 7: 524. PMID 29326887 DOI: 10.3389/fcimb.2017.00524  0.01
2017 Hayashi K, Busse HJ, Golke J, Anderson J, Wan X, Hou S, Chain PSG, Prescott RD, Donachie SP. Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera. International Journal of Systematic and Evolutionary Microbiology. PMID 29111971 DOI: 10.1099/Ijsem.0.002412  0.04
2017 Xie G, Johnson SL, Davenport KW, Rajavel M, Waldminghaus T, Detter JC, Chain PS, Sozhamannan S. Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome. International Journal of Genomics. 2017: 8724304. PMID 28951866 DOI: 10.1155/2017/8724304  1
2017 Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, ... ... Chain P, et al. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Standards in Genomic Sciences. 12: 46. PMID 28775794 DOI: 10.1186/S40793-017-0258-Y  1
2017 Khmaladze E, Dzavashvili G, Chanturia G, Nikolich MP, Chain PSG, Johnson SL, Imnadze P. Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia. Genome Announcements. 5. PMID 28495766 DOI: 10.1128/genomeA.00256-17  0.01
2017 Woo HL, DeAngelis KM, Teshima H, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Munk C, Scholz M, Xu Y, Chain P, Bruce D, Detter C, et al. High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp. Genome Announcements. 5. PMID 28473393 DOI: 10.1128/Genomea.00300-17  1
2017 Oliveira RC, Davenport KW, Hovde B, Silva D, Chain PS, Correa B, Rodrigues DF. Draft Genome Sequence of Sorghum Grain Mold Fungus Epicoccum sorghinum, a Producer of Tenuazonic Acid. Genome Announcements. 5. PMID 28126937 DOI: 10.1128/Genomea.01495-16  0.01
2016 Li N, Hennelly SP, Stubben CJ, Micheva-Viteva S, Hu B, Shou Y, Vuyisich M, Tung CS, Chain PS, Sanbonmatsu KY, Hong-Geller E. Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages. Plos One. 11: e0168915. PMID 28030576 DOI: 10.1371/Journal.Pone.0168915  0.01
2016 Li PE, Lo CC, Anderson JJ, Davenport KW, Bishop-Lilly KA, Xu Y, Ahmed S, Feng S, Mokashi VP, Chain PS. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Research. PMID 27899609 DOI: 10.1093/nar/gkw1027  1
2016 D'haeseleer P, Johnson SL, Davenport KW, Chain PS, Schoeniger J, Ray D, Sinha A, Williams KP, Peña J, Branda SS, El-Etr S. Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6. Genome Announcements. 4. PMID 27365360 DOI: 10.1128/Genomea.00649-16  1
2016 Doggett NA, Mukundan H, Lefkowitz EJ, Slezak TR, Chain PS, Morse S, Anderson K, Hodge DR, Pillai S. Culture-Independent Diagnostics for Health Security. Health Security. 14: 122-142. PMID 27314653 DOI: 10.1089/Hs.2015.0074  1
2016 Ramirez MS, Xie G, Traglia GM, Johnson S, Davenport K, van Duin D, Ramazani A, Perez F, Jacobs MR, Sherratt DJ, Bonomo RA, Chain P, Tolmasky ME. Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated During a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones. Genome Biology and Evolution. PMID 27289094 DOI: 10.1093/gbe/evw135  0.01
2016 Filippidou S, Jaussi M, Junier T, Wunderlin T, Jeanneret N, Palmieri F, Palmieri I, Roussel-Delif L, Vieth-Hillebrand A, Vetter A, Chain PS, Regenspurg S, Junier P. Anoxybacillus geothermalis sp. nov., a facultative anaerobic endospore-forming bacterium isolated from mineral deposits in a geothermal station. International Journal of Systematic and Evolutionary Microbiology. PMID 27126386 DOI: 10.1099/Ijsem.0.001125  1
2016 Johnson SL, Bishop-Lilly KA, Ladner JT, Daligault HE, Davenport KW, Jaissle J, Frey KG, Koroleva GI, Bruce DC, Coyne SR, Broomall SM, Ketheesan N, Mayo M, Hoffmaster A, Elrod MG, ... ... Chain PS, et al. Correction for Johnson et al., Complete Genome Sequences for 59 Burkholderia Isolates, Both Pathogenic and Near Neighbor. Genome Announcements. 4. PMID 27103731 DOI: 10.1128/Genomea.00313-16  1
2016 Feng S, Lo CC, Li PE, Chain PS. ADEPT, a dynamic next generation sequencing data error-detection program with trimming. Bmc Bioinformatics. 17: 109. PMID 26928302 DOI: 10.1186/s12859-016-0967-z  1
2016 Wang S, Zhang H, Scharadin TM, Zimmermann M, Hu B, Pan AW, Vinall R, Lin TY, Cimino G, Chain P, Vuyisich M, Gleasner C, Mcmurry K, Malfatti M, Turteltaub K, et al. Molecular Dissection of Induced Platinum Resistance through Functional and Gene Expression Analysis in a Cell Culture Model of Bladder Cancer. Plos One. 11: e0146256. PMID 26799320 DOI: 10.1371/Journal.Pone.0146256  1
2016 Daligault HE, Johnson SL, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Munk C, ... ... Chain PS, et al. Draft Genomes for Eight Burkholderia mallei Isolates from Turkey. Genome Announcements. 4. PMID 26744368 DOI: 10.1128/Genomea.01234-15  1
2015 Cui HH, Erkkila T, Chain PS, Vuyisich M. Building International Genomics Collaboration for Global Health Security. Frontiers in Public Health. 3: 264. PMID 26697418 DOI: 10.3389/fpubh.2015.00264  0.04
2015 Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, et al. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in Microbiology. 6: 1205. PMID 26583008 DOI: 10.3389/Fmicb.2015.01205  1
2015 Oulas A, Polymenakou PN, Seshadri R, Tripp HJ, Mandalakis M, Paez-Espino AD, Pati A, Chain P, Nomikou P, Carey S, Kilias S, Christakis C, Kotoulas G, Magoulas A, Ivanova NN, et al. Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Environmental Microbiology. PMID 26487573 DOI: 10.1111/1462-2920.13095  1
2015 Johnson SL, Minogue TD, Daligault HE, Wolcott MJ, Teshima H, Coyne SR, Davenport KW, Jaissle JG, Chain PS. Finished Genome Assembly of Warm Spring Isolate Francisella novicida DPG 3A-IS. Genome Announcements. 3. PMID 26383665 DOI: 10.1128/Genomea.01046-15  1
2015 Zhgenti E, Johnson SL, Davenport KW, Chanturia G, Daligault HE, Chain PS, Nikolich MP. Genome Assemblies for 11 Yersinia pestis Strains Isolated in the Caucasus Region. Genome Announcements. 3. PMID 26383663 DOI: 10.1128/Genomea.01030-15  1
2015 Johnson SL, Minogue TD, Daligault HE, Wolcott MJ, Teshima H, Coyne SR, Davenport KW, Jaissle JG, Chain PS. Finished Genome Assembly of Yersinia pestis EV76D and KIM 10v. Genome Announcements. 3. PMID 26383662 DOI: 10.1128/Genomea.01024-15  1
2015 Shetty AR, de Gannes V, Obi CC, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Han C, Tapia R, Land M, Hauser LJ, ... ... Chain PS, et al. Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Standards in Genomic Sciences. 10: 55. PMID 26380642 DOI: 10.1186/s40793-015-0041-x  1
2015 Filippidou S, Wunderlin T, Junier T, Jeanneret N, Johnson S, McMurry K, Gleasner CD, Lo CC, Li PE, Vuyisich M, Chain PS, Junier P. Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent. Genome Announcements. 3. PMID 26316638 DOI: 10.1128/Genomea.00982-15  0.01
2015 Filippidou S, Jaussi M, Junier T, Wunderlin T, Jeanneret N, Regenspurg S, Li PE, Lo CC, Johnson S, McMurry K, Gleasner CD, Vuyisich M, Chain PS, Junier P. Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir. Genome Announcements. 3. PMID 26316637 DOI: 10.1128/Genomea.00981-15  0.01
2015 Willias SP, Chauhan S, Lo CC, Chain PS, Motin VL. CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA. Plos One. 10: e0135481. PMID 26305456 DOI: 10.1371/journal.pone.0135481  1
2015 Howe A, Chain PS. Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial). Frontiers in Microbiology. 6: 678. PMID 26217314 DOI: 10.3389/fmicb.2015.00678  0.04
2015 Filippidou S, Jaussi M, Junier T, Wunderlin T, Roussel-Delif L, Jeanneret N, Vieth-Hillebrand A, Vetter A, Regenspurg S, Johnson SL, McMurry K, Gleasner CD, Lo CC, Li P, Vuyisich M, ... Chain PS, et al. Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species. Genome Announcements. 3. PMID 26067952 DOI: 10.1128/Genomea.00575-15  1
2015 Johnson SL, Khiani A, Bishop-Lilly KA, Chapman C, Patel M, Verratti K, Teshima H, Munk AC, Bruce DC, Han CS, Xie G, Davenport KW, Chain P, Sozhamannan S. Complete Genome Assemblies for Two Single-Chromosome Vibrio cholerae Isolates, Strains 1154-74 (Serogroup O49) and 10432-62 (Serogroup O27). Genome Announcements. 3. PMID 25977434 DOI: 10.1128/genomeA.00462-15  1
2015 Filippidou S, Junier T, Wunderlin T, Lo CC, Li PE, Chain PS, Junier P. Under-detection of endospore-forming Firmicutes in metagenomic data. Computational and Structural Biotechnology Journal. 13: 299-306. PMID 25973144 DOI: 10.1016/J.Csbj.2015.04.002  1
2015 Johnson SL, Bishop-Lilly KA, Ladner JT, Daligault HE, Davenport KW, Jaissle J, Frey KG, Koroleva GI, Bruce DC, Coyne SR, Broomall SM, Li PE, Teshima H, Gibbons HS, Palacios GF, ... ... Chain PS, et al. Complete genome sequences for 59 burkholderia isolates, both pathogenic and near neighbor. Genome Announcements. 3. PMID 25931592 DOI: 10.1128/Genomea.00159-15  1
2015 Johnson SL, Daligault HE, Davenport KW, Jaissle J, Frey KG, Ladner JT, Broomall SM, Bishop-Lilly KA, Bruce DC, Gibbons HS, Coyne SR, Lo CC, Meincke L, Munk AC, Koroleva GI, ... ... Chain PS, et al. Complete genome sequences for 35 biothreat assay-relevant bacillus species. Genome Announcements. 3. PMID 25931591 DOI: 10.1128/Genomea.00151-15  1
2015 Johnson SL, Daligault HE, Davenport KW, Jaissle J, Frey KG, Ladner JT, Broomall SM, Bishop-Lilly KA, Bruce DC, Coyne SR, Gibbons HS, Lo CC, Munk AC, Rosenzweig CN, Koroleva GI, ... ... Chain PS, et al. Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica. Genome Announcements. 3. PMID 25931590 DOI: 10.1128/Genomea.00148-15  1
2015 Johnson SL, Daligault HE, Davenport KW, Coyne SR, Frey KG, Koroleva GI, Broomall SM, Bishop-Lilly KA, Bruce DC, Chertkov O, Freitas T, Jaissle J, Ladner JT, Rosenzweig CN, Gibbons HS, ... ... Chain PS, et al. Genome sequencing of 18 francisella strains to aid in assay development and testing. Genome Announcements. 3. PMID 25931589 DOI: 10.1128/Genomea.00147-15  1
2015 Bergottini VM, Filippidou S, Junier T, Johnson S, Chain PS, Otegui MB, Zapata PD, Junier P. Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.). Genome Announcements. 3. PMID 25838492 DOI: 10.1128/Genomea.00239-15  0.04
2015 Chapman C, Henry M, Bishop-Lilly KA, Awosika J, Briska A, Ptashkin RN, Wagner T, Rajanna C, Tsang H, Johnson SL, Mokashi VP, Chain PS, Sozhamannan S. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. Plos One. 10: e0120311. PMID 25794000 DOI: 10.1371/journal.pone.0120311  1
2015 Dichosa AE, Davenport KW, Li PE, Ahmed SA, Daligault H, Gleasner CD, Kunde Y, McMurry K, Lo CC, Reitenga KG, Daughton AR, Shen X, Frietze S, Wang D, Johnson SL, ... ... Chain PS, et al. Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets. Genome Announcements. 3. PMID 25792053 DOI: 10.1128/Genomea.00132-15  1
2015 Freitas TA, Li PE, Scholz MB, Chain PS. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Research. 43: e69. PMID 25765641 DOI: 10.1093/nar/gkv180  0.04
2015 Johnson SL, Baker AL, Chain PS, Currie BJ, Daligault HE, Davenport KW, Davis CB, Inglis TJ, Kaestli M, Koren S, Mayo M, Merritt AJ, Price EP, Sarovich DS, Warner J, et al. Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei. Genome Announcements. 3. PMID 25676747 DOI: 10.1128/Genomea.01282-14  1
2015 Johnson SL, Minogue TD, Teshima H, Davenport KW, Shea AA, Miner HL, Wolcott MJ, Chain PS. Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes. Genome Announcements. 3. PMID 25593267 DOI: 10.1128/genomeA.01446-14  1
2015 Kruse T, van de Pas BA, Atteia A, Krab K, Hagen WR, Goodwin L, Chain P, Boeren S, Maphosa F, Schraa G, de Vos WM, van der Oost J, Smidt H, Stams AJ. Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. Journal of Bacteriology. 197: 893-904. PMID 25512312 DOI: 10.1128/Jb.02370-14  1
2015 Wang D, Dorosky RJ, Han CS, Lo CC, Dichosa AE, Chain PS, Yu JM, Pierson LS, Pierson EA. Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm. Applied and Environmental Microbiology. 81: 890-9. PMID 25416762 DOI: 10.1128/Aem.02617-14  1
2015 Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, et al. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade Standards in Genomic Sciences. DOI: 10.4056/Sigs.3927626  1
2015 Shetty AR, de Gannes V, Obi CC, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Han C, Tapia R, Land M, Hauser LJ, ... ... Chain PSG, et al. Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4 Standards in Genomic Sciences. DOI: 10.1186/s40793-015-0041-x  1
2014 Kelly S, Sullivan J, Ronson C, Tian R, Bräu L, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woyke T, et al. Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037. Standards in Genomic Sciences. 9: 7. PMID 25780500 DOI: 10.1186/1944-3277-9-7  1
2014 Reeve W, Sullivan J, Ronson C, Tian R, Bräu L, Davenport K, Goodwin L, Chain P, Woyke T, Lobos E, Huntemann M, Pati A, Mavromatis K, Markowitz V, Ivanova N, et al. Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B. Standards in Genomic Sciences. 9: 3. PMID 25780496 DOI: 10.1186/1944-3277-9-3  1
2014 Vuyisich M, Arefin A, Davenport K, Feng S, Gleasner C, McMurry K, Parson-Quintana B, Price J, Scholz M, Chain P. Facile, high quality sequencing of bacterial genomes from small amounts of DNA. International Journal of Genomics. 2014: 434575. PMID 25478564 DOI: 10.1155/2014/434575  0.01
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Munk C, et al. Whole-genome assemblies of 56 burkholderia species. Genome Announcements. 2. PMID 25414490 DOI: 10.1128/Genomea.01106-14  1
2014 Lo CC, Chain PS. Rapid evaluation and quality control of next generation sequencing data with FaQCs. Bmc Bioinformatics. 15: 366. PMID 25408143 DOI: 10.1186/s12859-014-0366-2  0.01
2014 Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Redden CL, Rosenzweig CN, Scholz MB, Teshima H, et al. Complete Genome Assembly of Staphylococcus epidermidis AmMS 205. Genome Announcements. 2. PMID 25377697 DOI: 10.1128/Genomea.01059-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Freitas T, Frey KG, Gibbons HS, Jaissle J, Lo CC, Meincke L, Munk AC, et al. Genome Assembly of Shigella flexneri ATCC 12022, a Quality Control Reference Strain. Genome Announcements. 2. PMID 25359907 DOI: 10.1128/Genomea.01052-14  1
2014 Bishop-Lilly KA, Frey KG, Daligault HE, Davenport KW, Bruce DC, Chain PS, Coyne SR, Chertkov O, Freitas T, Jaissle J, Koroleva GI, Ladner JT, Minogue TD, Palacios GF, Redden CL, et al. Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Strain SEJ. Genome Announcements. 2. PMID 25342692 DOI: 10.1128/Genomea.01084-14  1
2014 Frey KG, Bishop-Lilly KA, Daligault HE, Davenport KW, Bruce DC, Chain PS, Coyne SR, Chertkov O, Freitas T, Jaissle J, Koroleva GI, Ladner JT, Minogue TD, Palacios GF, Redden CL, et al. Full-Genome Assembly of Reference Strain Providencia stuartii ATCC 33672. Genome Announcements. 2. PMID 25342690 DOI: 10.1128/Genomea.01082-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Li PE, Meincke L, Munk AC, Palacios GF, et al. Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931. Genome Announcements. 2. PMID 25342684 DOI: 10.1128/Genomea.01074-14  1
2014 Minogue TD, Daligault HE, Davenport KW, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Chertkov O, Freitas T, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Redden CL, et al. Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01. Genome Announcements. 2. PMID 25342683 DOI: 10.1128/Genomea.01073-14  1
2014 Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Palacios GF, Redden CL, Scholz MB, et al. Complete Genome Sequence of Type Strain Pasteurella multocida subsp. multocida ATCC 43137. Genome Announcements. 2. PMID 25342682 DOI: 10.1128/Genomea.01070-14  1
2014 Minogue TD, Daligault HE, Davenport KW, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Chertkov O, Freitas T, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Redden CL, et al. Draft Genome Assemblies of Proteus mirabilis ATCC 7002 and Proteus vulgaris ATCC 49132. Genome Announcements. 2. PMID 25342681 DOI: 10.1128/Genomea.01064-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Munk C, et al. Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains. Genome Announcements. 2. PMID 25342679 DOI: 10.1128/Genomea.01055-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Munk C, et al. Twenty Whole-Genome Bacillus sp. Assemblies. Genome Announcements. 2. PMID 25301645 DOI: 10.1128/Genomea.00958-14  1
2014 Minogue TD, Daligault HA, Davenport KW, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Chertkov O, Coyne SR, Freitas T, Frey KG, Gibbons HS, Jaissle J, Redden CL, Rosenzweig CN, et al. Complete Genome Assembly of Escherichia coli ATCC 25922, a Serotype O6 Reference Strain. Genome Announcements. 2. PMID 25291776 DOI: 10.1128/Genomea.00969-14  1
2014 Minogue TD, Daligault HE, Davenport KW, Broomall SM, Bruce DC, Chain PS, Coyne SR, Chertkov O, Freitas T, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Rosenzweig CN, et al. Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain. Genome Announcements. 2. PMID 25291775 DOI: 10.1128/Genomea.00968-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Broomall SM, Bruce DC, Chain PS, Coyne SR, Gibbons HS, Jaissle J, Rosenzweig CN, Scholz M, Teshima H, Johnson SL. Genome Assembly of Serratia marcescens Type Strain ATCC 13880. Genome Announcements. 2. PMID 25291774 DOI: 10.1128/Genomea.00967-14  1
2014 Minogue TD, Daligault HA, Davenport KW, Bishop-Lilly KA, Bruce DC, Chain PS, Chertkov O, Coyne SR, Freitas T, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Redden CL, et al. Complete Genome Assembly of Reference Strain Ochrobactrum anthropi ATCC 49687. Genome Announcements. 2. PMID 25291772 DOI: 10.1128/Genomea.00962-14  1
2014 Minogue TD, Daligault HA, Davenport KW, Bishop-Lilly KA, Bruce DC, Chain PS, Chertkov O, Coyne SR, Freitas T, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Redden CL, et al. Draft Genome Assembly of Neisseria lactamica Type Strain A7515. Genome Announcements. 2. PMID 25291770 DOI: 10.1128/Genomea.00951-14  1
2014 Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Redden CL, et al. Whole-genome sequences of nine francisella isolates. Genome Announcements. 2. PMID 25291764 DOI: 10.1128/Genomea.00941-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Meincke L, Munk AC, Palacios GF, et al. Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883. Genome Announcements. 2. PMID 25291763 DOI: 10.1128/Genomea.00939-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Freitas T, Frey KG, Gibbons HS, Jaissle J, Lo CC, Meincke L, Munk AC, et al. Genome Assembly of Methicillin-Resistant Quality Control Strain Staphylococcus aureus CDC73-57501 (ATCC 29247). Genome Announcements. 2. PMID 25278527 DOI: 10.1128/Genomea.00961-14  1
2014 Minogue TD, Daligault HE, Davenport KW, Broomall SM, Bruce DC, Chain PS, Coyne SR, Gibbons HS, Jaissle J, Chertkov O, Freitas T, Rosenzweig CN, Xu Y, Johnson SL. Draft Genome Assembly of Pseudomonas aeruginosa Quality Control Reference Strain Boston 41501. Genome Announcements. 2. PMID 25278526 DOI: 10.1128/Genomea.00960-14  1
2014 Scholz M, Lo CC, Chain PS. Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Scientific Reports. 4: 6480. PMID 25270300 DOI: 10.1038/srep06480  0.01
2014 Minogue TD, Daligault HA, Davenport KW, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Chertkov O, Coyne SR, Freitas T, Frey KG, Gibbons HS, Jaissle J, Redden CL, Rosenzweig CN, et al. Complete Genome Assembly of Streptococcus pyogenes ATCC 19615, a Group A β-Hemolytic Reference Strain. Genome Announcements. 2. PMID 25258274 DOI: 10.1128/Genomea.00976-14  1
2014 Davenport KW, Daligault HE, Minogue TD, Broomall SM, Bruce DC, Chain PS, Coyne SR, Gibbons HS, Jaissle J, Li PE, Rosenzweig CN, Scholz MB, Johnson SL. Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC 13637). Genome Announcements. 2. PMID 25258273 DOI: 10.1128/Genomea.00974-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Broomall SM, Bruce DC, Chain PS, Coyne SR, Gibbons HS, Jaissle J, Lo CC, Meincke L, Munk AC, Rosenzweig CN, Johnson SL. Draft Genome Assembly of Ralstonia pickettii Type Strain K-288 (ATCC 27853). Genome Announcements. 2. PMID 25258272 DOI: 10.1128/Genomea.00973-14  1
2014 Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Li PE, Palacios GF, Redden CL, Scholz MB, et al. Whole-Genome Sequence of Listeria monocytogenes Type Strain 53 XXIII. Genome Announcements. 2. PMID 25258271 DOI: 10.1128/Genomea.00970-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Meincke L, Munk C, Palacios GF, et al. Complete Genome Assembly of a Quality Control Reference Isolate, Moraxella catarrhalis Strain ATCC 25240. Genome Announcements. 2. PMID 25237030 DOI: 10.1128/Genomea.00938-14  1
2014 Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Redden CL, Scholz MB, Teshima H, et al. Draft Genome Assembly of Delftia acidovorans Type Strain 2167. Genome Announcements. 2. PMID 25237026 DOI: 10.1128/Genomea.00917-14  1
2014 Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Meincke L, Munk C, Palacios GF, et al. Draft Genome Assembly of Bordetella bronchiseptica ATCC 10580, a Historical Canine Clinical Isolate. Genome Announcements. 2. PMID 25237025 DOI: 10.1128/Genomea.00916-14  1
2014 Minogue TD, Daligault HA, Davenport KW, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Chertkov O, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, et al. Whole-genome sequences of 24 Brucella strains. Genome Announcements. 2. PMID 25237024 DOI: 10.1128/Genomea.00915-14  1
2014 Bishop-Lilly KA, Johnson SL, Verratti K, Luu T, Khiani A, Awosika J, Mokashi VP, Chain PS, Sozhamannan S. Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains. Genome Announcements. 2. PMID 25212618 DOI: 10.1128/genomeA.00893-14  1
2014 Kuever J, Visser M, Loeffler C, Boll M, Worm P, Sousa DZ, Plugge CM, Schaap PJ, Muyzer G, Pereira IA, Parshina SN, Goodwin LA, Kyrpides NC, Detter J, Woyke T, ... Chain P, et al. Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Standards in Genomic Sciences. 9: 821-39. PMID 25197466 DOI: 10.4056/Sigs.5209235  1
2014 Moulin L, Klonowska A, Caroline B, Booth K, Vriezen JA, Melkonian R, James EK, Young JP, Bena G, Hauser L, Land M, Kyrpides N, Bruce D, Chain P, Copeland A, et al. Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species. Standards in Genomic Sciences. 9: 763-74. PMID 25197461 DOI: 10.4056/Sigs.4861021  1
2014 Breider S, Teshima H, Petersen J, Chertkov O, Dalingault H, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Tindall BJ, Kyrpides NC, et al. Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Standards in Genomic Sciences. 9: 687-703. PMID 25197454 DOI: 10.4056/Sigs.3828824  1
2014 Visser M, Parshina SN, Alves JI, Sousa DZ, Pereira IA, Muyzer G, Kuever J, Lebedinsky AV, Koehorst JJ, Worm P, Plugge CM, Schaap PJ, Goodwin LA, Lapidus A, Kyrpides NC, ... ... Chain P, et al. Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. Standards in Genomic Sciences. 9: 655-75. PMID 25197452 DOI: 10.4056/Sigs.4718645  1
2014 Reeve W, Ballard R, Howieson J, Drew E, Tian R, Bräu L, Munk C, Davenport K, Chain P, Goodwin L, Pagani I, Huntemann M, Mavrommatis K, Pati A, Markowitz V, et al. Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece. Standards in Genomic Sciences. 9: 514-26. PMID 25197437 DOI: 10.4056/sigs.4938652  1
2014 Davenport KW, Daligault HE, Minogue TD, Bruce DC, Chain PS, Coyne SR, Jaissle JG, Koroleva GI, Ladner JT, Li PE, Palacios GF, Scholz MB, Teshima H, Johnson SL. Draft Genome Assembly of Acinetobacter baumannii ATCC 19606. Genome Announcements. 2. PMID 25146140 DOI: 10.1128/Genomea.00832-14  1
2014 Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. Plos Biology. 12: e1001920. PMID 25093819 DOI: 10.1371/Journal.Pbio.1001920  1
2014 Ramirez MS, Xie G, Johnson S, Davenport K, van Duin D, Perez F, Bonomo RA, Chain P, Tolmasky ME. Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates. Genome Announcements. 2. PMID 24948759 DOI: 10.1128/Genomea.00558-14  0.01
2014 Ladner JT, Beitzel B, Chain PS, Davenport MG, Donaldson EF, Frieman M, Kugelman JR, Kuhn JH, O'Rear J, Sabeti PC, Wentworth DE, Wiley MR, Yu GY, Sozhamannan S, et al. Standards for sequencing viral genomes in the era of high-throughput sequencing. Mbio. 5: e01360-14. PMID 24939889 DOI: 10.1128/Mbio.01360-14  1
2014 Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ. Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin. Genome Announcements. 2. PMID 24855308 DOI: 10.1128/Genomea.00482-14  0.01
2014 Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland ED, Harris CC, Sczyrba A, Chain PS, Koren S, Woyke T, Stepanauskas R. Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. Plos One. 9: e95380. PMID 24743558 DOI: 10.1371/Journal.Pone.0095380  1
2014 Xie G, Lo CC, Scholz M, Chain PS. Recruiting human microbiome shotgun data to site-specific reference genomes. Plos One. 9: e84963. PMID 24454771 DOI: 10.1371/journal.pone.0084963  0.01
2014 Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ. Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. Bmc Genomics. 15: 17. PMID 24410921 DOI: 10.1186/1471-2164-15-17  1
2014 Luo C, Rodriguez-R LM, Johnston ER, Wu L, Cheng L, Xue K, Tu Q, Deng Y, He Z, Shi JZ, Yuan MM, Sherry RA, Li D, Luo Y, Schuur EA, ... Chain P, et al. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Applied and Environmental Microbiology. 80: 1777-86. PMID 24375144 DOI: 10.1128/Aem.03712-13  1
2014 Breider S, Teshima H, Petersen J, Chertkov O, Dalingault H, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Tindall BJ, Kyrpides NC, et al. Genome sequence of Leisingera nanhaiensis strain DSM 24252 T isolated from marine sediment Standards in Genomic Sciences. 9: 687-703. DOI: 10.4056/Sigs.3823642  1
2014 Shen C, Liang W, Shi Y, Lin X, Zhang H, Wu X, Xie G, Chain P, Grogan P, Chu H. Contrasting elevational diversity patterns between eukaryotic soil microbes and plants Ecology. 95: 3190-3202. DOI: 10.1890/14-0310.1  0.08
2014 Detter JC, Johnson SL, Bishop-Lilly KA, Chain PS, Gibbons HS, Minogue TD, Sozhamannan S, Van Gieson EJ, Resnick IG. Nucleic acid sequencing for characterizing infectious and/or novel agents in complex samples Biological Identification: Dna Amplification and Sequencing, Optical Sensing, Lab-On-Chip and Portable Systems. 3-53. DOI: 10.1533/9780857099167.1.3  1
2013 Khanna N, Ghosh AK, Huntemann M, Deshpande S, Han J, Chen A, Kyrpides N, Mavrommatis K, Szeto E, Markowitz V, Ivanova N, Pagani I, Pati A, Pitluck S, Nolan M, ... ... Chain P, et al. Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production. Standards in Genomic Sciences. 9: 359-69. PMID 24976892 DOI: 10.4056/Sigs.4348035  1
2013 Dogs M, Voget S, Teshima H, Petersen J, Davenport K, Dalingault H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Standfest S, Rohde M, Gronow S, et al. Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Standards in Genomic Sciences. 9: 334-50. PMID 24976890 DOI: 10.4056/Sigs.4448212  1
2013 Galardini M, Bazzicalupo M, Biondi E, Brambilla E, Brilli M, Bruce D, Chain P, Chen A, Daligault H, Davenport KW, Deshpande S, Detter JC, Goodwin LA, Han C, Han J, et al. Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58. Standards in Genomic Sciences. 9: 325-33. PMID 24976889 DOI: 10.4056/Sigs.3797438  1
2013 Reeve W, Drew E, Ballard R, Melino V, Tian R, De Meyer S, Brau L, Ninawi M, Daligault H, Davenport K, Erkkila T, Goodwin L, Gu W, Munk C, Teshima H, ... ... Chain P, et al. Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943. Standards in Genomic Sciences. 9: 232-42. PMID 24976880 DOI: 10.4056/sigs.4478252  1
2013 Reeve W, Drew E, Ballard R, Melino V, Tian R, De Meyer S, Brau L, Ninawi M, Teshima H, Goodwin L, Chain P, Liolios K, Pati A, Mavromatis K, Ivanova N, et al. Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565. Standards in Genomic Sciences. 9: 220-31. PMID 24976879 DOI: 10.4056/sigs.4468250  1
2013 Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, et al. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Standards in Genomic Sciences. 9: 142-59. PMID 24501652 DOI: 10.4056/sigs.4287962  1
2013 Buddruhs N, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Gronow S, Kyrpides NC, Woyke T, Göker M, et al. Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the Roseobacter clade. Standards in Genomic Sciences. 9: 128-41. PMID 24501651 DOI: 10.4056/Sigs.4297965  1
2013 Freese HM, Dalingault H, Petersen J, Pradella S, Davenport K, Teshima H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, et al. Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.). Standards in Genomic Sciences. 8: 450-64. PMID 24501630 DOI: 10.4056/sigs.383362  1
2013 Neupane S, Goodwin LA, Högberg N, Kyrpides NC, Alström S, Bruce D, Quintana B, Munk C, Daligault H, Teshima H, Davenport K, Reitenga K, Green L, Chain P, Erkkila T, et al. Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4. Standards in Genomic Sciences. 8: 441-9. PMID 24501629 DOI: 10.4056/Sigs.4027757  1
2013 Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, et al. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade. Standards in Genomic Sciences. 8: 403-19. PMID 24501626 DOI: 10.4056/sigs.3927623  1
2013 Riedel T, Teshima H, Petersen J, Fiebig A, Davenport K, Daligault H, Erkkila T, Gu W, Munk C, Xu Y, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, et al. Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements. Standards in Genomic Sciences. 8: 389-402. PMID 24501625 DOI: 10.4056/Sigs.3858183  1
2013 Smith H, Akiyama T, Foreman C, Franklin M, Woyke T, Teshima H, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Xu Y, Chain P. Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium. Genome Announcements. 1. PMID 24265494 DOI: 10.1128/Genomea.00960-13  1
2013 Boscaro V, Felletti M, Vannini C, Ackerman MS, Chain PS, Malfatti S, Vergez LM, Shin M, Doak TG, Lynch M, Petroni G. Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proceedings of the National Academy of Sciences of the United States of America. 110: 18590-5. PMID 24167248 DOI: 10.1073/Pnas.1316687110  1
2013 D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, PaÅ¡a-Tolić L, Hugenholtz P, Simmons BA, Singer SW. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. Plos One. 8: e68465. PMID 23894306 DOI: 10.1371/Journal.Pone.0068465  1
2013 Venkatramanan R, Prakash O, Woyke T, Chain P, Goodwin LA, Watson D, Brooks S, Kostka JE, Green SJ. Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment. Genome Announcements. 1. PMID 23833140 DOI: 10.1128/Genomea.00449-13  0.01
2013 Khmelenina VN, Beck DA, Munk C, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Scholz M, Teshima H, Xu Y, Chain P, Bringel F, Vuilleumier S, et al. Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium. Genome Announcements. 1. PMID 23814105 DOI: 10.1128/Genomea.00053-13  1
2013 Oh S, Tandukar M, Pavlostathis SG, Chain PS, Konstantinidis KT. Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics. Environmental Microbiology. 15: 2850-64. PMID 23731340 DOI: 10.1111/1462-2920.12154  1
2013 Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature Communications. 4: 1854. PMID 23673639 DOI: 10.1038/Ncomms2884  1
2013 Mitter B, Petric A, Shin MW, Chain PS, Hauberg-Lotte L, Reinhold-Hurek B, Nowak J, Sessitsch A. Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Frontiers in Plant Science. 4: 120. PMID 23641251 DOI: 10.3389/fpls.2013.00120  1
2013 Xie G, Ramirez MS, Marshall SH, Hujer KM, Lo CC, Johnson S, Li PE, Davenport K, Endimiani A, Bonomo RA, Tolmasky ME, Chain PS. Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360). Genome Announcements. 1. PMID 23640195 DOI: 10.1128/genomeA.00168-13  0.01
2013 Sharma PK, Fu J, Zhang X, Fristensky BW, Davenport K, Chain PS, Sparling R, Levin DB. Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46. Genome Announcements. 1: e0015113. PMID 23599293 DOI: 10.1128/genomeA.00151-13  0.01
2013 Aylward FO, Tremmel DM, Starrett GJ, Bruce DC, Chain P, Chen A, Davenport KW, Detter C, Han CS, Han J, Huntemann M, Ivanova NN, Kyrpides NC, Markowitz V, Mavrommatis K, et al. Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens. Genome Announcements. 1: e0023912. PMID 23516234 DOI: 10.1128/Genomea.00239-12  1
2013 Sen A, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Ghodbhane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, et al. Draft genome sequence of Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus nitida. Genome Announcements. 1: e0010313. PMID 23516220 DOI: 10.1128/Genomea.00103-13  1
2013 Ghodhbane-Gtari F, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Ivanova N, et al. Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (Nod-) ineffective (Fix-) isolate from Coriaria nepalensis. Genome Announcements. 1: e0008513. PMID 23516212 DOI: 10.1128/Genomea.00085-13  1
2013 Ishii S, Suzuki S, Norden-Krichmar TM, Tenney A, Chain PS, Scholz MB, Nealson KH, Bretschger O. A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. Nature Communications. 4: 1601. PMID 23511466 DOI: 10.1038/Ncomms2615  1
2013 Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, ... ... Chain PS, et al. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Research. 23: 878-88. PMID 23493677 DOI: 10.1101/Gr.142208.112  1
2013 Aylward FO, Tremmel DM, Bruce DC, Chain P, Chen A, Walston Davenport K, Detter C, Han CS, Han J, Huntemann M, Ivanova NN, Kyrpides NC, Markowitz V, Mavrommatis K, Nolan M, et al. Complete Genome of Enterobacteriaceae Bacterium Strain FGI 57, a Strain Associated with Leaf-Cutter Ant Fungus Gardens. Genome Announcements. 1. PMID 23469353 DOI: 10.1128/Genomea.00238-12  1
2013 Visser M, Worm P, Muyzer G, Pereira IAC, Schaap PJ, Plugge CM, Kuever J, Parshina SN, Nazina TN, Ivanova AE, Bernier-Latmani R, Goodwin LA, Kyrpides NC, Woyke T, Chain P, et al. Genome analysis of desulfotomaculum kuznetsovii strain 17t reveals a physiological similarity with pelotomaculum thermopropionicum strain sit Standards in Genomic Sciences. 8: 69-87. DOI: 10.4056/Sigs.3627141  1
2012 Steven B, Gallegos-Graves LV, Starkenburg SR, Chain PS, Kuske CR. Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environmental Microbiology Reports. 4: 248-56. PMID 23757280 DOI: 10.1111/J.1758-2229.2012.00328.X  1
2012 Ahmed SA, Awosika J, Baldwin C, Bishop-Lilly KA, Biswas B, Broomall S, Chain PS, Chertkov O, Chokoshvili O, Coyne S, Davenport K, Detter JC, Dorman W, Erkkila TH, Folster JP, et al. Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2. Plos One. 7: e48228. PMID 23133618 DOI: 10.1371/Journal.Pone.0048228  1
2012 Pester M, Brambilla E, Alazard D, Rattei T, Weinmaier T, Han J, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Ovchinnikova G, Teshima H, Detter JC, ... ... Chain PS, et al. Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. Journal of Bacteriology. 194: 6300-1. PMID 23105050 DOI: 10.1128/Jb.01392-12  1
2012 Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, et al. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. The Isme Journal. 6: 1715-27. PMID 22717885 DOI: 10.1038/Ismej.2012.59  1
2012 Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, Fitzgerald MG, Fulton RS, Hallsworth-Pepin K, ... ... Chain PS, et al. A framework for human microbiome research Nature. 486: 215-221. PMID 22699610 DOI: 10.1038/Nature11209  1
2012 Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, ... ... Chain PSG, et al. Structure, function and diversity of the healthy human microbiome Nature. 486: 207-214. PMID 22699609 DOI: 10.1038/Nature11234  1
2012 Dichosa AE, Fitzsimons MS, Lo CC, Weston LL, Preteska LG, Snook JP, Zhang X, Gu W, McMurry K, Green LD, Chain PS, Detter JC, Han CS. Artificial polyploidy improves bacterial single cell genome recovery. Plos One. 7: e37387. PMID 22666352 DOI: 10.1371/Journal.Pone.0037387  1
2012 Beckloff N, Starkenburg S, Freitas T, Chain P. Bacterial genome annotation Methods in Molecular Biology. 881: 471-503. PMID 22639223 DOI: 10.1007/978-1-61779-827-6_16  1
2012 Zeytun A, Malfatti SA, Vergez LM, Shin M, Garcia E, Chain PS. Complete genome sequence of Francisella philomiragia ATCC 25017. Journal of Bacteriology. 194: 3266. PMID 22628499 DOI: 10.1128/Jb.00413-12  0.16
2012 Kaplan JB, Lo C, Xie G, Johnson SL, Chain PS, Donnelly R, Kachlany SC, Balashova NV. Genome sequence of Kingella kingae septic arthritis isolate PYKK081. Journal of Bacteriology. 194: 3017. PMID 22582375 DOI: 10.1128/JB.00421-12  1
2012 Ramirez MS, Xie G, Marshall SH, Hujer KM, Chain PS, Bonomo RA, Tolmasky ME. Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. 18: E254-8. PMID 22551038 DOI: 10.1111/j.1469-0691.2012.03886.x  1
2012 Leung K, Zahn H, Leaver T, Konwar KM, Hanson NW, Pagé AP, Lo CC, Chain PS, Hallam SJ, Hansen CL. A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proceedings of the National Academy of Sciences of the United States of America. 109: 7665-70. PMID 22547789 DOI: 10.1073/Pnas.1106752109  1
2012 Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PS, Reitenga KG, Xie G, Poulton NJ, Lluesma Gomez M, Masland DE, Thompson B, Bellows WK, Ziervogel K, Lo CC, Ahmed S, et al. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. Plos One. 7: e35314. PMID 22536372 DOI: 10.1371/journal.pone.0035314  1
2012 Scholz MB, Lo CC, Chain PS. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Current Opinion in Biotechnology. 23: 9-15. PMID 22154470 DOI: 10.1016/j.copbio.2011.11.013  1
2012 Yang F, Zeng X, Ning K, Liu KL, Lo CC, Wang W, Chen J, Wang D, Huang R, Chang X, Chain PS, Xie G, Ling J, Xu J. Saliva microbiomes distinguish caries-active from healthy human populations. The Isme Journal. 6: 1-10. PMID 21716312 DOI: 10.1038/Ismej.2011.71  1
2011 Hu B, Xie G, Lo CC, Starkenburg SR, Chain PS. Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Briefings in Functional Genomics. 10: 322-33. PMID 22199376 DOI: 10.1093/bfgp/elr042  0.01
2011 Starkenburg SR, Reitenga KG, Freitas T, Johnson S, Chain PS, Garcia-Pichel F, Kuske CR. Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide. Journal of Bacteriology. 193: 4569-70. PMID 21705610 DOI: 10.1128/Jb.05138-11  0.04
2011 Chain PS, Lang DM, Comerci DJ, Malfatti SA, Vergez LM, Shin M, Ugalde RA, Garcia E, Tolmasky ME. Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts. Journal of Bacteriology. 193: 4274-5. PMID 21685287 DOI: 10.1128/JB.05335-11  0.08
2011 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Chain PS, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/Nbt.1823  1
2011 Weilharter A, Mitter B, Shin MV, Chain PS, Nowak J, Sessitsch A. Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. Journal of Bacteriology. 193: 3383-4. PMID 21551308 DOI: 10.1128/JB.05055-11  0.01
2011 Chain PS, Xie G, Starkenburg SR, Scholz MB, Beckloff N, Lo CC, Davenport KW, Reitenga KG, Daligault HE, Detter JC, Freitas TA, Gleasner CD, Green LD, Han CS, McMurry KK, et al. Genomics for key players in the N cycle from guinea pigs to the next frontier. Methods in Enzymology. 496: 289-318. PMID 21514469 DOI: 10.1016/B978-0-12-386489-5.00012-9  1
2011 van Passel MW, Kant R, Zoetendal EG, Plugge CM, Derrien M, Malfatti SA, Chain PS, Woyke T, Palva A, de Vos WM, Smidt H. The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. Plos One. 6: e16876. PMID 21390229 DOI: 10.1371/journal.pone.0016876  0.01
2011 Campbell MA, Chain PS, Dang H, El Sheikh AF, Norton JM, Ward NL, Ward BB, Klotz MG. Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'. Fems Microbiology Ecology. 76: 39-48. PMID 21204874 DOI: 10.1111/J.1574-6941.2010.01027.X  1
2011 Unkefer CJ, Starkenburg SR, Twary SN, Park MS, Chain PS, Unkefer PJ. The national alliance for advanced biofuels and bioproducts (NAABB) Acs National Meeting Book of Abstracts 1
2010 Copeland A, Sikorski J, Lapidus A, Nolan M, Glavina T, Del Rio, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Pukall R, Chertkov O, Brettin T, Han C, ... ... Chain P, et al. Erratum to: Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Standards in Genomic Sciences. 2: 361-2. PMID 21304720 DOI: 10.4056/Sigs.992408  1
2010 Reeve W, O'Hara G, Chain P, Ardley J, Bräu L, Nandesena K, Tiwari R, Copeland A, Nolan M, Han C, Brettin T, Land M, Ovchinikova G, Ivanova N, Mavromatis K, et al. Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers. Standards in Genomic Sciences. 2: 347-56. PMID 21304718 DOI: 10.4056/Sigs.852027  1
2010 von Jan M, Lapidus A, Del Rio TG, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Goodwin L, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, ... ... Chain P, et al. Complete genome sequence of Archaeoglobus profundus type strain (AV18). Standards in Genomic Sciences. 2: 327-46. PMID 21304717 DOI: 10.4056/Sigs.942153  1
2010 Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavromatis K, Lucas S, Glavina Del Rio T, Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, ... ... Chain P, et al. Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Standards in Genomic Sciences. 2: 228-88. PMID 21304706 DOI: 10.4056/Sigs.881234  1
2010 Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ivanova N, Ovchinnikova G, ... ... Chain P, et al. Complete genome sequence of Conexibacter woesei type strain (ID131577). Standards in Genomic Sciences. 2: 212-9. PMID 21304704 DOI: 10.4056/Sigs.751339  1
2010 Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Labutti K, Pati A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, ... ... Chain P, et al. Complete genome sequence of Kribbella flavida type strain (IFO 14399). Standards in Genomic Sciences. 2: 186-93. PMID 21304701 DOI: 10.4056/Sigs.731321  1
2010 Lail K, Sikorski J, Saunders E, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, ... ... Chain P, et al. Complete genome sequence of Spirosoma linguale type strain (1). Standards in Genomic Sciences. 2: 176-85. PMID 21304700 DOI: 10.4056/Sigs.741334  1
2010 Sikorski J, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, ... ... Chain P, et al. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175). Standards in Genomic Sciences. 2: 149-57. PMID 21304697 DOI: 10.4056/Sigs.671209  1
2010 Saunders E, Tindall BJ, Fähnrich R, Lapidus A, Copeland A, Del Rio TG, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Chain P, et al. Complete genome sequence of Haloterrigena turkmenica type strain (4k). Standards in Genomic Sciences. 2: 107-16. PMID 21304683 DOI: 10.4056/Sigs.681272  1
2010 Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, ... ... Chain P, et al. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Standards in Genomic Sciences. 2: 87-95. PMID 21304681 DOI: 10.4056/Sigs.661199  1
2010 Reeve W, Chain P, O'Hara G, Ardley J, Nandesena K, Bräu L, Tiwari R, Malfatti S, Kiss H, Lapidus A, Copeland A, Nolan M, Land M, Hauser L, Chang YJ, et al. Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Standards in Genomic Sciences. 2: 77-86. PMID 21304680 DOI: 10.4056/sigs.43526  1
2010 Reeve W, O'Hara G, Chain P, Ardley J, Bräu L, Nandesena K, Tiwari R, Malfatti S, Kiss H, Lapidus A, Copeland A, Nolan M, Land M, Ivanova N, Mavromatis K, et al. Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum. Standards in Genomic Sciences. 2: 66-76. PMID 21304679 DOI: 10.4056/Sigs.44642  1
2010 Gronow S, Welnitz S, Lapidus A, Nolan M, Ivanova N, Glavina Del Rio T, Copeland A, Chen F, Tice H, Pitluck S, Cheng JF, Saunders E, Brettin T, Han C, Detter JC, ... ... Chain P, et al. Complete genome sequence of Veillonella parvula type strain (Te3). Standards in Genomic Sciences. 2: 57-65. PMID 21304678 DOI: 10.4056/Sigs.521107  1
2010 Pati A, Labutti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, ... ... Chain P, et al. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Standards in Genomic Sciences. 2: 49-56. PMID 21304677 DOI: 10.4056/Sigs.601105  1
2010 Spring S, Nolan M, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Land M, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, ... ... Chain P, et al. Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)). Standards in Genomic Sciences. 2: 38-48. PMID 21304676 DOI: 10.4056/Sigs.581048  1
2010 Nolan M, Sikorski J, Jando M, Lucas S, Lapidus A, Glavina Del Rio T, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Sims D, Meincke L, Brettin T, Han C, ... ... Chain P, et al. Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Standards in Genomic Sciences. 2: 29-37. PMID 21304675 DOI: 10.4056/Sigs.631049  1
2010 Ivanova N, Sikorski J, Jando M, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Mavromatis K, ... ... Chain P, et al. Complete genome sequence of Gordonia bronchialis type strain (3410). Standards in Genomic Sciences. 2: 19-28. PMID 21304674 DOI: 10.4056/Sigs.611106  1
2010 Mavromatis K, Sikorski J, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Ovchinnikova G, ... ... Chain P, et al. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). Standards in Genomic Sciences. 2: 9-18. PMID 21304673 DOI: 10.4056/Sigs.591104  1
2010 Foster B, Pukall R, Abt B, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Bruce D, ... ... Chain P, et al. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07). Standards in Genomic Sciences. 2: 1-8. PMID 21304672 DOI: 10.4056/Sigs.571102  1
2010 Xie G, Chain PS, Lo CC, Liu KL, Gans J, Merritt J, Qi F. Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Molecular Oral Microbiology. 25: 391-405. PMID 21040513 DOI: 10.1111/J.2041-1014.2010.00587.X  0.01
2010 Hather GJ, Haynes W, Higdon R, Kolker N, Stewart EA, Arzberger P, Chain P, Field D, Franza BR, Lin B, Meyer F, Ozdemir V, Smith CV, van Belle G, Wooley J, et al. The United States of America and scientific research. Plos One. 5: e12203. PMID 20808949 DOI: 10.1371/Journal.Pone.0012203  1
2010 Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, et al. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proceedings of the National Academy of Sciences of the United States of America. 107: 8818-23. PMID 20421470 DOI: 10.1073/Pnas.0913533107  1
2010 Ayala-del-Río HL, Chain PS, Grzymski JJ, Ponder MA, Ivanova N, Bergholz PW, Di Bartolo G, Hauser L, Land M, Bakermans C, Rodrigues D, Klappenbach J, Zarka D, Larimer F, Richardson P, et al. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Applied and Environmental Microbiology. 76: 2304-12. PMID 20154119 DOI: 10.1128/Aem.02101-09  1
2010 Kielak A, Rodrigues JL, Kuramae EE, Chain PS, van Veen JA, Kowalchuk GA. Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. Fems Microbiology Ecology. 71: 23-33. PMID 19811538 DOI: 10.1111/j.1574-6941.2009.00785.x  0.28
2010 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Chain P, et al. The “Minimum Information about an ENvironmental Sequence” (MIENS) specification Nature Precedings. 5: 1-1. DOI: 10.1038/Npre.2010.5252.1  1
2009 Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T, Del Rio, Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, ... ... Chain P, et al. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Standards in Genomic Sciences. 1: 308-16. PMID 21304671 DOI: 10.4056/Sigs.51657  1
2009 Nolan M, Gronow S, Lapidus A, Ivanova N, Copeland A, Lucas S, Del Rio TG, Chen F, Tice H, Pitluck S, Cheng JF, Sims D, Meincke L, Bruce D, Goodwin L, ... ... Chain P, et al. Complete genome sequence of Streptobacillus moniliformis type strain (9901). Standards in Genomic Sciences. 1: 300-7. PMID 21304670 DOI: 10.4056/Sigs.48727  1
2009 Nolan M, Tindall BJ, Pomrenke H, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Han C, Bruce D, Goodwin L, Chain P, et al. Complete genome sequence of Rhodothermus marinus type strain (R-10). Standards in Genomic Sciences. 1: 283-90. PMID 21304669 DOI: 10.4056/Sigs.46736  1
2009 Tindall BJ, Schneider S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Pitluck S, Mikhailova N, ... ... Chain P, et al. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2). Standards in Genomic Sciences. 1: 270-7. PMID 21304667 DOI: 10.4056/Sigs.42644  1
2009 Pukall R, Gehrich-Schröter G, Lapidus A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Copeland A, Saunders E, Brettin T, Detter JC, Bruce D, ... ... Chain P, et al. Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134). Standards in Genomic Sciences. 1: 262-9. PMID 21304666 DOI: 10.4056/Sigs.41646  1
2009 Chovatia M, Sikorski J, Schröder M, Lapidus A, Nolan M, Tice H, Glavina Del Rio T, Copeland A, Cheng JF, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, ... ... Chain P, et al. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883). Standards in Genomic Sciences. 1: 254-61. PMID 21304665 DOI: 10.4056/Sigs.40645  1
2009 Spring S, Lapidus A, Schröder M, Gleim D, Sims D, Meincke L, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, ... ... Chain P, et al. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Standards in Genomic Sciences. 1: 242-53. PMID 21304664 DOI: 10.4056/Sigs.39508  1
2009 Pukall R, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Chertkov O, Bruce D, Goodwin L, Kuske C, Brettin T, Detter JC, ... ... Chain P, et al. Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1). Standards in Genomic Sciences. 1: 234-41. PMID 21304663 DOI: 10.4056/Sigs.37633  1
2009 Munk C, Lapidus A, Copeland A, Jando M, Mayilraj S, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, ... Chain P, et al. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21). Standards in Genomic Sciences. 1: 234-41. PMID 21304662 DOI: 10.4056/Sigs.47643  1
2009 Han C, Sikorski J, Lapidus A, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Bruce D, ... ... Chain P, et al. Complete genome sequence of Kangiella koreensis type strain (SW-125). Standards in Genomic Sciences. 1: 226-33. PMID 21304661 DOI: 10.4056/Sigs.36635  1
2009 Anderson I, Tindall BJ, Pomrenke H, Göker M, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Chen F, Tice H, Cheng JF, Lucas S, Chertkov O, Bruce D, Brettin T, ... ... Chain P, et al. Complete genome sequence of Halorhabdus utahensis type strain (AX-2). Standards in Genomic Sciences. 1: 218-25. PMID 21304660 DOI: 10.4056/Sigs.31864  1
2009 Saunders E, Pukall R, Abt B, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, ... ... Chain P, et al. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). Standards in Genomic Sciences. 1: 174-82. PMID 21304654 DOI: 10.4056/Sigs.33592  1
2009 Copeland A, Sikorski J, Lapidus A, Nolan M, Del Rio TG, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Pukall R, Chertkov O, Brettin T, Han C, Detter JC, ... ... Chain P, et al. Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Standards in Genomic Sciences. 1: 166-73. PMID 21304653 DOI: 10.4056/Sigs.29547  1
2009 Labutti K, Pukall R, Steenblock K, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, ... ... Chain P, et al. Complete genome sequence of Anaerococcus prevotii type strain (PC1). Standards in Genomic Sciences. 1: 159-65. PMID 21304652 DOI: 10.4056/Sigs.24194  1
2009 Malfatti S, Tindall BJ, Schneider S, Fähnrich R, Lapidus A, Labuttii K, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, ... ... Chain P, et al. Complete genome sequence of Halogeometricum borinquense type strain (PR3). Standards in Genomic Sciences. 1: 150-9. PMID 21304651 DOI: 10.4056/Sigs.23264  1
2009 Pati A, Sikorski J, Nolan M, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, ... ... Chain P, et al. Complete genome sequence of Saccharomonospora viridis type strain (P101). Standards in Genomic Sciences. 1: 141-9. PMID 21304650 DOI: 10.4056/Sigs.20263  1
2009 Lang E, Lapidus A, Chertkov O, Brettin T, Detter JC, Han C, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Land M, Hauser L, ... ... Chain P, et al. Complete genome sequence of Dyadobacter fermentans type strain (NS114). Standards in Genomic Sciences. 1: 133-40. PMID 21304649 DOI: 10.4056/Sigs.19262  1
2009 Ivanova N, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Brettin T, Detter JC, ... ... Chain P, et al. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b). Standards in Genomic Sciences. 1: 126-32. PMID 21304648 DOI: 10.4056/Sigs.1854  1
2009 Copeland A, Lapidus A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Pati A, Ivanova N, Mavromatis K, ... ... Chain P, et al. Complete genome sequence of Catenulispora acidiphila type strain (ID 139908). Standards in Genomic Sciences. 1: 119-25. PMID 21304647 DOI: 10.4056/Sigs.17259  1
2009 Ivanova N, Sikorski J, Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, ... ... Chain P, et al. Complete genome sequence of Sanguibacter keddieii type strain (ST-74). Standards in Genomic Sciences. 1: 110-8. PMID 21304646 DOI: 10.4056/Sigs.16197  1
2009 Mavrommatis K, Gronow S, Saunders E, Land M, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, ... ... Chain P, et al. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845). Standards in Genomic Sciences. 1: 101-9. PMID 21304645 DOI: 10.4056/Sigs.15195  1
2009 Mavrommatis K, Pukall R, Rohde C, Chen F, Sims D, Brettin T, Kuske C, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, ... ... Chain P, et al. Complete genome sequence of Cryptobacterium curtum type strain (12-3). Standards in Genomic Sciences. 1: 93-100. PMID 21304644 DOI: 10.4056/Sigs.12260  1
2009 Land M, Lapidus A, Mayilraj S, Chen F, Copeland A, Del Rio TG, Nolan M, Lucas S, Tice H, Cheng JF, Chertkov O, Bruce D, Goodwin L, Pitluck S, Rohde M, ... ... Chain P, et al. Complete genome sequence of Actinosynnema mirum type strain (101). Standards in Genomic Sciences. 1: 46-53. PMID 21304636 DOI: 10.4056/Sigs.21137  1
2009 Clum A, Nolan M, Lang E, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavrommatis K, Mikhailova N, ... ... Chain P, et al. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP). Standards in Genomic Sciences. 1: 38-45. PMID 21304635 DOI: 10.4056/Sigs.1463  1
2009 Copeland A, Spring S, Göker M, Schneider S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavrommatis K, ... ... Chain P, et al. Complete genome sequence of Desulfomicrobium baculatum type strain (X). Standards in Genomic Sciences. 1: 29-37. PMID 21304634 DOI: 10.4056/Sigs.13134  1
2009 Land M, Pukall R, Abt B, Göker M, Rohde M, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, ... ... Chain P, et al. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122). Standards in Genomic Sciences. 1: 21-8. PMID 21304633 DOI: 10.4056/Sigs.1162  1
2009 Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, ... ... Chain P, et al. Complete genome sequence of Kytococcus sedentarius type strain (541). Standards in Genomic Sciences. 1: 12-20. PMID 21304632 DOI: 10.4056/Sigs.761  1
2009 Lapidus A, Pukall R, Labuttii K, Copeland A, Del Rio TG, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Rohde M, Göker M, ... ... Chain P, et al. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Standards in Genomic Sciences. 1: 3-11. PMID 21304631 DOI: 10.4056/Sigs.492  1
2009 Donaher N, Tanifuji G, Onodera NT, Malfatti SA, Chain PS, Hara Y, Archibald JM. The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biology and Evolution. 1: 439-48. PMID 20333213 DOI: 10.1093/Gbe/Evp047  0.04
2009 Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, ... ... Chain P, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 462: 1056-60. PMID 20033048 DOI: 10.1038/Nature08656  1
2009 Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, et al. Genomics. Genome project standards in a new era of sequencing. Science (New York, N.Y.). 326: 236-7. PMID 19815760 DOI: 10.1126/Science.1180614  1
2009 Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America. 106: 3976-81. PMID 19234113 DOI: 10.1073/Pnas.0813403106  1
2009 Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PS, Roberto FF, Hnath J, Brettin T, Keim P. Whole-genome-based phylogeny and divergence of the genus Brucella. Journal of Bacteriology. 191: 2864-70. PMID 19201792 DOI: 10.1128/Jb.01581-08  1
2009 Malfatti S, Tindall BJ, Schneider S, Fähnrich R, Lapidus A, Labuttii K, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, ... ... Chain P, et al. Complete genome sequence of Halogeometricum borinquense type strain (PR 3) Standards in Genomic Sciences. 1: 150-158. DOI: 10.4056/23264  1
2008 Oda Y, Larimer FW, Chain PS, Malfatti S, Shin MV, Vergez LM, Hauser L, Land ML, Braatsch S, Beatty JT, Pelletier DA, Schaefer AL, Harwood CS. Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proceedings of the National Academy of Sciences of the United States of America. 105: 18543-8. PMID 19020098 DOI: 10.1073/Pnas.0809160105  1
2008 Isabel S, Leblanc E, Boissinot M, Boudreau DK, Grondin M, Picard FJ, Martel EA, Parham NJ, Chain PS, Bader DE, Mulvey MR, Bryden L, Roy PH, Ouellette M, Bergeron MG. Divergence among genes encoding the elongation factor Tu of Yersinia Species. Journal of Bacteriology. 190: 7548-58. PMID 18790860 DOI: 10.1128/Jb.01067-08  1
2008 Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PS, Hauser LJ, Land ML, Larimer FW, Shin MW, Starkenburg SR. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Applied and Environmental Microbiology. 74: 3559-72. PMID 18390676 DOI: 10.1128/Aem.02722-07  1
2008 Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PS, Sayavedra-Soto LA, Poret-Peterson AT, Gentry ME, Arp DJ, Ward B, Bottomley PJ. Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Applied and Environmental Microbiology. 74: 2852-63. PMID 18326675 DOI: 10.1128/Aem.02311-07  1
2008 Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hügler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, et al. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Applied and Environmental Microbiology. 74: 1145-56. PMID 18065616 DOI: 10.1128/Aem.01844-07  1
2008 Garcia E, Chain P, Elliott JM, Bobrov AG, Motin VL, Kirillina O, Lao V, Calendar R, Filippov AA. Molecular characterization of L-413C, a P2-related plague diagnostic bacteriophage. Virology. 372: 85-96. PMID 18045639 DOI: 10.1016/J.Virol.2007.10.032  1
2007 Stein LY, Arp DJ, Berube PM, Chain PS, Hauser L, Jetten MS, Klotz MG, Larimer FW, Norton JM, Op den Camp HJ, Shin M, Wei X. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environmental Microbiology. 9: 2993-3007. PMID 17991028 DOI: 10.1111/J.1462-2920.2007.01409.X  1
2007 Garcia E, Worsham P, Bearden S, Malfatti S, Lang D, Larimer F, Lindler L, Chain P. Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union. Advances in Experimental Medicine and Biology. 603: 17-22. PMID 17966401 DOI: 10.1007/978-0-387-72124-8_2  0.01
2007 Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM, Kane SR. Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Applied and Environmental Microbiology. 73: 7347-57. PMID 17890343 DOI: 10.1128/Aem.01604-07  1
2007 Arp DJ, Chain PS, Klotz MG. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual Review of Microbiology. 61: 503-28. PMID 17506671 DOI: 10.1146/Annurev.Micro.61.080706.093449  1
2007 Kane SR, Chakicherla AY, Chain PS, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM, Hristova KR. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. Journal of Bacteriology. 189: 1931-45. PMID 17158667 DOI: 10.1128/Jb.01259-06  1
2006 Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, et al. The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. Plos Biology. 4: e383. PMID 17105352 DOI: 10.1371/Journal.Pbio.0040383  1
2006 Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, et al. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proceedings of the National Academy of Sciences of the United States of America. 103: 15280-7. PMID 17030797 DOI: 10.1073/Pnas.0606924103  1
2006 Brotcke A, Weiss DS, Kim CC, Chain P, Malfatti S, Garcia E, Monack DM. Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis. Infection and Immunity. 74: 6642-55. PMID 17000729 DOI: 10.1128/Iai.01250-06  1
2006 Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB. Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Applied and Environmental Microbiology. 72: 6299-315. PMID 16957257 DOI: 10.1128/Aem.00463-06  1
2006 Loots GG, Chain PS, Mabery S, Rasley A, Garcia E, Ovcharenko I. Array2BIO: from microarray expression data to functional annotation of co-regulated genes. Bmc Bioinformatics. 7: 307. PMID 16780584 DOI: 10.1186/1471-2105-7-307  1
2006 Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC, Andersen GL. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. Journal of Bacteriology. 188: 4453-63. PMID 16740952 DOI: 10.1128/JB.00124-06  1
2006 Mavromatis K, Doyle CK, Lykidis A, Ivanova N, Francino MP, Chain P, Shin M, Malfatti S, Larimer F, Copeland A, Detter JC, Land M, Richardson PM, Yu XJ, Walker DH, et al. The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. Journal of Bacteriology. 188: 4015-23. PMID 16707693 DOI: 10.1128/Jb.01837-05  0.04
2006 Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L, Land ML, Larimer FW, Malfatti SA, Klotz MG, Bottomley PJ, Arp DJ, Hickey WJ. Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied and Environmental Microbiology. 72: 2050-63. PMID 16517654 DOI: 10.1128/Aem.72.3.2050-2063.2006  1
2006 Beller HR, Chain PS, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. Journal of Bacteriology. 188: 1473-88. PMID 16452431 DOI: 10.1128/JB.188.4.1473-1488.2006  1
2005 Chain PS, Comerci DJ, Tolmasky ME, Larimer FW, Malfatti SA, Vergez LM, Aguero F, Land ML, Ugalde RA, Garcia E. Whole-genome analyses of speciation events in pathogenic Brucellae. Infection and Immunity. 73: 8353-61. PMID 16299333 DOI: 10.1128/IAI.73.12.8353-8361.2005  0.16
2005 Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E, Thiel J, Malfatti S, Loper JE, Lapidus A, Detter JC, et al. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proceedings of the National Academy of Sciences of the United States of America. 102: 11064-9. PMID 16043691 DOI: 10.1073/Pnas.0504930102  1
2005 Larsson P, Oyston PCF, Chain P, Chu MC, Duffield M, Fuxelius HH, Garcia E, Hälltorp G, Johansson D, Isherwood KE, Karp PD, Larsson E, Liu Y, Michell S, Prior J, et al. The complete genome sequence of Francisella tularensis, the causative agent of tularemia Nature Genetics. 37: 153-159. PMID 15640799 DOI: 10.1038/Ng1499  1
2004 Chain PSG, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Medigue C, et al. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis Proceedings of the National Academy of Sciences of the United States of America. 101: 13826-13831. PMID 15358858 DOI: 10.1073/pnas.0404012101  1
2003 Garcia E, Elliott JM, Ramanculov E, Chain PSG, Chu MC, Molineux IJ. The genome sequence of Yersinia pestis bacteriophage φA1122 reveals an intimate history with the coliphage T3 and T7 genomes Journal of Bacteriology. 185: 5248-5262. PMID 12923098 DOI: 10.1128/Jb.185.17.5248-5262.2003  1
2003 Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 424: 1042-7. PMID 12917642 DOI: 10.1038/Nature01947  1
2003 Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J. The genome of a motile marine Synechococcus. Nature. 424: 1037-42. PMID 12917641 DOI: 10.1038/Nature01943  1
2003 Chain P, Kurtz S, Ohlebusch E, Slezak T. An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges Briefings in Bioinformatics. 4: 105-123. PMID 12846393 DOI: 10.1093/Bib/4.2.105  0.01
2003 Chain P, Lamerdin J, Larimer F, Regala W, Lao V, Land M, Hauser L, Hooper A, Klotz M, Norton J, Sayavedra-Soto L, Arciero D, Hommes N, Whittaker M, Arp D. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. Journal of Bacteriology. 185: 2759-73. PMID 12700255 DOI: 10.1128/Jb.185.9.2759-2773.2003  1
2001 Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorhölter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Pühler A. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti Proceedings of the National Academy of Sciences of the United States of America. 98: 9889-9894. PMID 11481431 DOI: 10.1073/Pnas.161294698  1
2001 Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, ... ... Chain P, et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science (New York, N.Y.). 293: 668-72. PMID 11474104 DOI: 10.1126/Science.1060966  1
2000 Chain PSG, Hernandez-Lucas I, Golding B, Finan TM. oriT-directed cloning of defined large regions from bacterial genomes: Identification of the Sinorhizobium meliloti pExo megaplasmid replicator region Journal of Bacteriology. 182: 5486-5494. PMID 10986253 DOI: 10.1128/Jb.182.19.5486-5494.2000  1
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