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Jonathan A Eisen

Title(s)Professor, Evolution and Ecology
SchoolUniversity of California, Davis
Phone530-752-3498
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Garner E, Brown CL, Schwake DO, Rhoads WJ, Arango-Argoty G, Zhang L, Jospin G, Coil DA, Eisen JA, Edwards MA, Pruden A. Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016. Emerg Infect Dis. 2019 Nov; 25(11):2013-2020. PMID: 31625848.
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    2. Yamaguchi MS, Ganz HH, Cho AW, Zaw TH, Jospin G, McCartney MM, Davis CE, Eisen JA, Coil DA. Bacteria isolated from Bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds potentially associated with animal signaling. PLoS One. 2019; 14(9):e0216846. PMID: 31518350.
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    3. Hicks DJ, Coil DA, Stahmer CG, Eisen JA. Network analysis to evaluate the impact of research funding on research community consolidation. PLoS One. 2019; 14(6):e0218273. PMID: 31211808.
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    4. Coil DA, Jospin G, Darling AE, Wallis C, Davis IJ, Harris S, Eisen JA, Holcombe LJ, O'Flynn C. Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment. PLoS One. 2019; 14(6):e0214354. PMID: 31181071.
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    5. Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. Early-Career Scientists Shaping the World. mSystems. 2019 May 07; 4(3). PMID: 31219787.
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    6. Wilkins LGE, Ettinger CL, Jospin G, Eisen JA. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Sci Rep. 2019 Feb 28; 9(1):3059. PMID: 30816235.
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    7. Bik HM, Alexiev A, Aulakh SK, Bharadwaj L, Flanagan J, Haggerty JM, Hird SM, Jospin G, Lang JM, Sauder LA, Neufeld JD, Shaver A, Sethi A, Eisen JA, Coil DA. Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria. mSphere. 2019 02 20; 4(1). PMID: 30787117.
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    8. Rosado PM, Leite DCA, Duarte GAS, Chaloub RM, Jospin G, Nunes da Rocha U, P Saraiva J, Dini-Andreote F, Eisen JA, Bourne DG, Peixoto RS. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J. 2019 04; 13(4):921-936. PMID: 30518818.
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    9. Hird SM, Ganz H, Eisen JA, Boyce WM. The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status. mSphere. 2018 10 24; 3(5). PMID: 30355662.
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    10. Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biol. 2018 08; 16(8):e2006352. PMID: 30086128.
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    11. DeFrancesco L. Erratum: California voters and CIRM-will lightning strike twice? Nat Biotechnol. 2018 07 06; 36(7):660. PMID: 29979647.
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    12. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 07 06; 36(7):660. PMID: 29979671.
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    13. Horng KR, Ganz HH, Eisen JA, Marks SL. Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ. 2018; 6:e4827. PMID: 29844978.
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    14. Dahlhausen KE, Doroud L, Firl AJ, Polkinghorne A, Eisen JA. Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJ. 2018; 6:e4452. PMID: 29576947.
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    15. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. Correction: A microbial survey of the International Space Station (ISS). PeerJ. 2018; 5. PMID: 29498380.
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    16. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 02 06; 36(2):196. PMID: 29406516.
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    17. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. A microbial survey of the International Space Station (ISS). PeerJ. 2017; 5:e4029. PMID: 29492330.
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    18. Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R. Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol. 2017; 8:2264. PMID: 29234309.
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    19. Wilbanks EG, Salman-Carvalho V, Jaekel U, Humphrey PT, Eisen JA, Buckley DH, Zinder SH. The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria. Front Microbiol. 2017; 8:1623. PMID: 28928719.
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    20. Ettinger CL, Williams SL, Abbott JM, Stachowicz JJ, Eisen JA. Microbiome succession during ammonification in eelgrass bed sediments. PeerJ. 2017; 5:e3674. PMID: 28828269.
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    21. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017 Aug 08; 35(8):725-731. PMID: 28787424.
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    22. Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat Biotechnol. 2017 Jul; 35(7):676-683. PMID: 28604660.
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    23. Fahimipour AK, Kardish MR, Lang JM, Green JL, Eisen JA, Stachowicz JJ. Global-Scale Structure of the Eelgrass Microbiome. Appl Environ Microbiol. 2017 06 15; 83(12). PMID: 28411219.
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    24. Mukhopadhyay R, Joaquin J, Hogue R, Fitzgerald S, Jospin G, Mars K, Eisen JA, Chaturvedi V. Complete Genome Sequence of Dolosigranulum pigrum from a Patient with Interstitial Lung Disease Using Single-Molecule Real-Time Sequencing Technology. Genome Announc. 2017 May 04; 5(18). PMID: 28473398.
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    25. Coil DA, Ettinger CL, Eisen JA. Gut Check: The evolution of an educational board game. PLoS Biol. 2017 04; 15(4):e2001984. PMID: 28453514.
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    26. Ettinger CL, Voerman SE, Lang JM, Stachowicz JJ, Eisen JA. Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge. PeerJ. 2017; 5:e3246. PMID: 28462046.
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    27. Mukhopadhyay R, Joaquin J, Hogue R, Kilaru A, Jospin G, Mars K, Eisen JA, Chaturvedi V. Complete Genome Sequence of a Paenalcaligenes hominis Strain Isolated from a Paraplegic Patient with Neurogenic Bladder Using Single-Molecule Real-Time Sequencing Technology. Genome Announc. 2017 Apr 27; 5(17). PMID: 28450518.
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    28. Lujan KM, Eisen JA, Coil DA. Draft Genome Sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. Strain UCD-KL20, Shewanella sp. Strain UCD-KL12, and Shewanella sp. Strain UCD-KL21, Isolated from Seagrass. Genome Announc. 2017 Mar 30; 5(13). PMID: 28360178.
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    29. Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 2017 03; 15(3):e2001793. PMID: 28350798.
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    30. Dahms PA, Martin AL, Ganz HH, Eisen JA, Coil DA. Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a Feline Anal Sac. Genome Announc. 2017 Mar 23; 5(12). PMID: 28336587.
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    31. Ganz HH, Doroud L, Firl AJ, Hird SM, Eisen JA, Boyce WM. Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses. mSystems. 2017 Jan-Feb; 2(1). PMID: 28293681.
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    32. Tokajian S, Salloum T, Eisen JA, Jospin G, Farra A, Mokhbat JE, Coil DA. Genomic attributes of extended-spectrum ß-lactamase-producing Escherichia coli isolated from patients in Lebanon. Future Microbiol. 2017 03; 12:213-226. PMID: 28262042.
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    33. Klein BA, Lemon KP, Gajare P, Jospin G, Eisen JA, Coil DA. Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility. Genome Announc. 2017 Feb 23; 5(8). PMID: 28232444.
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    34. Kincheloe GN, Eisen JA, Coil DA. Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria). Genome Announc. 2017 Feb 09; 5(6). PMID: 28183767.
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    35. Jiao JY, Carro L, Liu L, Gao XY, Zhang XT, Hozzein WN, Lapidus A, Huntemann M, Reddy TBK, Varghese N, Hadjithomas M, Ivanova NN, Göker M, Pillay M, Eisen JA, Woyke T, Klenk HP, Kyrpides NC, Li WJ. Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds. Stand Genomic Sci. 2017; 12:21. PMID: 28174619.
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    36. Lymperopoulou DS, Coil DA, Schichnes D, Lindow SE, Jospin G, Eisen JA, Adams RI. Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72. Stand Genomic Sci. 2017; 12:17. PMID: 28163826.
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    37. Kozyreva VK, Jospin G, Greninger AL, Watt JP, Eisen JA, Chaturvedi V. Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance. mSphere. 2016 Nov-Dec; 1(6). PMID: 28028547.
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    38. Ibrahim J, Eisen JA, Jospin G, Coil DA, Khazen G, Tokajian S. Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections. PLoS One. 2016; 11(12):e0168177. PMID: 27977735.
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    39. De Vries DR, Martin AL, Ganz HH, Eisen JA, Coil DA. Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3. Genome Announc. 2016 Dec 15; 4(6). PMID: 27979940.
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    40. Koenigsaecker TM, Eisen JA, Coil DA. Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria). Genome Announc. 2016 Oct 13; 4(5). PMID: 27738036.
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    41. Lujan KM, Eisen JA, Coil DA. Draft Genome Sequence of Tenacibaculum soleae UCD-KL19. Genome Announc. 2016 Oct 13; 4(5). PMID: 27738035.
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    42. Klein BA, Lemon KP, Faller LL, Jospin G, Eisen JA, Coil DA. Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria). Genome Announc. 2016 Oct 06; 4(5). PMID: 27795241.
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    43. Shehata HR, Ettinger CL, Eisen JA, Raizada MN. Genes Required for the Anti-fungal Activity of a Bacterial Endophyte Isolated from a Corn Landrace Grown Continuously by Subsistence Farmers Since 1000 BC. Front Microbiol. 2016; 7:1548. PMID: 27757101.
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    44. Nelson RL, Castro MA, Katti M, Eisen JA, Van Laar TA. Genome Sequence of a Multidrug-Resistant Strain of Bacillus pumilus, CB01, Isolated from the Feces of an American Crow, Corvus brachyrhynchos. Genome Announc. 2016 Aug 18; 4(4). PMID: 27540060.
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    45. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome. 2016 Jun 03; 4(1):24. PMID: 27255532.
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    46. Alexiev A, Coil DA, Jospin G, Eisen JA, Adams JY. Draft Genome Sequence of Klebsiella pneumoniae UCD-JA29 Isolated from a Patient with Sepsis. Genome Announc. 2016 May 05; 4(3). PMID: 27151785.
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    47. Coil DA, Neches RY, Lang JM, Brown WE, Severance M, Cavalier D, Eisen JA. Growth of 48 built environment bacterial isolates on board the International Space Station (ISS). PeerJ. 2016; 4:e1842. PMID: 27019789.
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    48. Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. Draft Genome Sequences of Two Pseudoalteromonas porphyrae Strains Isolated from Seagrass Sediment. Genome Announc. 2016 Mar 17; 4(2). PMID: 26988038.
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    49. Alexiev A, Krusor ML, Jospin G, Lang JM, Eisen JA, Coil DA. Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina. Genome Announc. 2016 Mar 10; 4(2). PMID: 26966219.
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    50. Alexiev A, Krusor ML, Jospin G, Lang JM, Eisen JA, Coil DA. Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina. Genome Announc. 2016 Feb 18; 4(1). PMID: 26893412.
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    51. Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment. Genome Announc. 2016 Feb 18; 4(1). PMID: 26893436.
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    52. Tokajian S, Eisen JA, Jospin G, Matar G, Araj GF, Coil DA. Draft Genome Sequence of Klebsiella pneumoniae KGM-IMP216 Harboring blaCTX-M-15, blaDHA-1, blaTEM-1B, blaNDM-1, blaSHV-28, and blaOXA-1, Isolated from a Patient in Lebanon. Genome Announc. 2016 Jan 28; 4(1). PMID: 26823584.
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    53. Tokajian S, Eisen JA, Jospin G, Hamze M, Rafei R, Salloum T, Ibrahim J, Coil DA. Draft Genome Sequences of Acinetobacter baumannii Strains Harboring the blaNDM-1 Gene Isolated in Lebanon from Civilians Wounded during the Syrian Civil War. Genome Announc. 2016 Jan 28; 4(1). PMID: 26823599.
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    54. Coil DA, Jospin G, Eisen JA, Adams JY. Additional Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients. Genome Announc. 2016 Jan 21; 4(1). PMID: 26798108.
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    55. Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes). Genome Announc. 2015 Nov 19; 3(6). PMID: 26586901.
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    56. Coil DA, Benardini JN, Eisen JA. Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft. Genome Announc. 2015 Nov 19; 3(6). PMID: 26586895.
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    57. Coil DA, Eisen JA. Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado. Genome Announc. 2015 Nov 19; 3(6). PMID: 26586867.
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    58. Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput Biol. 2015 Nov; 11(11):e1004573. PMID: 26565399.
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    59. O'Flynn C, Deusch O, Darling AE, Eisen JA, Wallis C, Davis IJ, Harris SJ. Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis. Genome Biol Evol. 2015 Nov 13; 7(12):3397-413. PMID: 26568374.
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    60. Jungblut AD, Hawes I, Mackey TJ, Krusor M, Doran PT, Sumner DY, Eisen JA, Hillman C, Goroncy AK. Microbial Mat Communities along an Oxygen Gradient in a Perennially Ice-Covered Antarctic Lake. Appl Environ Microbiol. 2016 01 15; 82(2):620-30. PMID: 26567300.
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    61. Coil DA, Flanagan JC, Stump A, Alexiev A, Lang JM, Eisen JA. Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter. PeerJ. 2015; 3:e1400. PMID: 26587357.
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    62. Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain UCD-SED8 (Phylum Gammaproteobacteria). Genome Announc. 2015 Nov 05; 3(6). PMID: 26543114.
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    63. Betts MN, Jospin G, Eisen JA, Coil DA. Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes). Genome Announc. 2015 Oct 15; 3(5). PMID: 26472846.
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    64. Boundy-Mills K, Hess M, Bennett AR, Ryan M, Kang S, Nobles D, Eisen JA, Inderbitzin P, Sitepu IR, Torok T, Brown DR, Cho J, Wertz JE, Mukherjee S, Cady SL, McCluskey K. The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections. Appl Environ Microbiol. 2015 Sep 01; 81(17):5671-4. PMID: 26092453.
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    65. Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P, Vandamme P, Eisen JA, Garrity G, Hugenholtz P, Kyrpides NC. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci. 2015; 10:26. PMID: 26203337.
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    66. Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. Swabs to genomes: a comprehensive workflow. PeerJ. 2015; 3:e960. PMID: 26020012.
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    67. Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, Gilbert JA. Forensic analysis of the microbiome of phones and shoes. Microbiome. 2015; 3:21. PMID: 25969737.
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    68. Hasan NA, Grim CJ, Lipp EK, Rivera IN, Chun J, Haley BJ, Taviani E, Choi SY, Hoq M, Munk AC, Brettin TS, Bruce D, Challacombe JF, Detter JC, Han CS, Eisen JA, Huq A, Colwell RR. Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species. Proc Natl Acad Sci U S A. 2015 May 26; 112(21):E2813-9. PMID: 25964331.
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    69. Coil DA, Alexiev A, Wallis C, O'Flynn C, Deusch O, Davis I, Horsfall A, Kirkwood N, Jospin G, Eisen JA, Harris S, Darling AE. Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome. Genome Announc. 2015 Apr 09; 3(2). PMID: 25858832.
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    70. Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. Whole genome sequencing of extended-spectrum ß-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon. Front Cell Infect Microbiol. 2015; 5:32. PMID: 25905047.
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    71. Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA. Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae). Genome Announc. 2015 Jan 29; 3(1). PMID: 25635016.
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    72. Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA. Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria). Genome Announc. 2015 Jan 29; 3(1). PMID: 25635017.
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    73. Ettinger CL, Shehata HR, Johnston-Monje D, Raizada MN, Eisen JA. Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria). Genome Announc. 2015 Jan 22; 3(1). PMID: 25614570.
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    74. Ettinger CL, Mousa WM, Raizada MN, Eisen JA. Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria). Genome Announc. 2015 Jan 22; 3(1). PMID: 25614569.
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    75. Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A. 2015 Feb 24; 112(8):E911-20. PMID: 25605935.
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    76. Dunitz MI, Coil DA, Jospin G, Eisen JA, Adams JY. Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients. Genome Announc. 2014 Dec 18; 2(6). PMID: 25523766.
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    77. Lang JM, Eisen JA, Zivkovic AM. The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types. PeerJ. 2014; 2:e659. PMID: 25538865.
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    78. Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci. 2014; 9:10. PMID: 25780503.
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    79. Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT. Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLoS Genet. 2014 Nov; 10(11):e1004784. PMID: 25393412.
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    80. Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton IL, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics. 2014 Oct 23; 15:924. PMID: 25342549.
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    81. Holland-Moritz HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA. Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1. Genome Announc. 2014 Aug 21; 2(4). PMID: 25146141.
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    82. 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, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 2014 Aug; 12(8):e1001920. PMID: 25093819.
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    83. Lee RD, Jospin G, Coil DA, Eisen JA. Draft Genome Sequence of the Endosymbiont "Candidatus Ruthia magnifica" UCD-CM (Phylum Proteobacteria). Genome Announc. 2014 Jul 17; 2(4). PMID: 25035337.
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    84. Bik HM, Coil DA, Eisen JA. microBEnet: lessons learned from building an interdisciplinary scientific community in the online sphere. PLoS Biol. 2014 Jun; 12(6):e1001884. PMID: 24937755.
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    85. Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ. 2014; 2:e415. PMID: 24918035.
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    86. Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA. Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announc. 2014 May 15; 2(3). PMID: 24831154.
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    87. Tokajian S, Eisen JA, Jospin G, Coil DA. Draft Genome Sequences of Streptococcus pyogenes Strains Associated with Throat and Skin Infections in Lebanon. Genome Announc. 2014 May 15; 2(3). PMID: 24831139.
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    88. Göker M, Spring S, Scheuner C, Anderson I, Zeytun A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Stand Genomic Sci. 2014 Jun 15; 9(3):1105-17. PMID: 25197486.
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    89. Dunitz MI, James PM, Jospin G, Eisen JA, Coil DA, Chandler JA. Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae. Genome Announc. 2014 Apr 24; 2(2). PMID: 24762940.
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    90. Göker M, Lu M, Fiebig A, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Mayilraj S, Rohde M, Detter JC, Bunk B, Spring S, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci. 2014 Jun 15; 9(3):1076-88. PMID: 25197484.
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    91. Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environ Microbiol. 2014 Nov; 16(11):3398-415. PMID: 24428801.
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    92. Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12. Genome Announc. 2014 Feb 20; 2(1). PMID: 24558247.
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    93. Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. Draft Genome Sequence of Extended-Spectrum ß-Lactamase-Producing Klebsiella pneumoniae Isolated from a Patient in Lebanon. Genome Announc. 2014 Feb 20; 2(1). PMID: 24558251.
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    94. Tokajian S, Eisen JA, Jospin G, Farra A, Coil DA. Draft Genome Sequences of Extended-Spectrum ß-Lactamase-Producing Escherichia coli Strains Isolated from Patients in Lebanon. Genome Announc. 2014 Feb 20; 2(1). PMID: 24558252.
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    95. Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014; 2:e243. PMID: 24482762.
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    96. Eisen JA, Ganley E, MacCallum CJ. Open science and reporting animal studies: who's accountable? PLoS Biol. 2014 Jan; 12(1):e1001757. PMID: 24409097.
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    97. Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG, Beck BJ, Whitman WB, Hugenholtz P, Klenk HP. Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Stand Genomic Sci. 2014 Jun 15; 9(3):1278-84. PMID: 25197443.
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    98. Coil DA, Lo JR, Chen R, Ward N, Robb FT, Eisen JA. Draft Genome Sequence of the Arsenate-Respiring Bacterium Chrysiogenes arsenatis Strain DSM 11915. Genome Announc. 2013 Nov 14; 1(6). PMID: 24233593.
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    99. Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 2014 Jan; 8(1):1-3. PMID: 24152717.
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    100. Wu D, Jospin G, Eisen JA. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One. 2013; 8(10):e77033. PMID: 24146954.
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    101. Martin ME, Bhatnagar S, George MD, Paster BJ, Canfield DR, Eisen JA, Solnick JV. The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque. PLoS One. 2013; 8(10):e76375. PMID: 24116104.
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    102. Eisen JA, Maccallum CJ, Neylon C. Expert failure: re-evaluating research assessment. PLoS Biol. 2013 Oct; 11(10):e1001677. PMID: 24115910.
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    103. Palaniappan K, Meier-Kolthoff JP, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Rohde M, Mayilraj S, Spring S, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio. Stand Genomic Sci. 2013 Oct 16; 9(1):57-70. PMID: 24501645.
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    104. Anderson I, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Lang E, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of Frateuria aurantia type strain (Kondô 67(T)), a xanthomonade isolated from Lilium auratium Lindl. Stand Genomic Sci. 2013 Oct 16; 9(1):83-92. PMID: 24501647.
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    105. Garrity GM, Banfield J, Eisen J, van der Lelie N, McMahon T, Rusch D, Delong E, Moran MA, Currie C, Furhman J, Hallam S, Hugenholtz P, Moran N, Nelson K, Roberts R, Stepanauskas R. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013. Stand Genomic Sci. 2013 Jul 30; 8(3):561-70. PMID: 24501639.
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    106. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013 Jul 25; 499(7459):431-7. PMID: 23851394.
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    107. Holland-Moritz HE, Bevans DR, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria). Genome Announc. 2013 Jun 27; 1(3). PMID: 23792744.
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    108. Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Pan C, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Kyrpides NC, Klenk HP. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. Stand Genomic Sci. 2013; 8(2):228-38. PMID: 23991255.
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    109. Huntemann M, Stackebrandt E, Held B, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Woyke T, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Stand Genomic Sci. 2013; 8(2):177-87. PMID: 23991250.
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    110. Liolos K, Abt B, Scheuner C, Teshima H, Held B, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Klenk HP, Kyrpides NC. Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Stand Genomic Sci. 2013; 8(2):165-76. PMID: 23991249.
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    111. Flanagan JC, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announc. 2013 May 16; 1(3). PMID: 23682147.
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    112. Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announc. 2013 May 09; 1(3). PMID: 23661474.
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    113. Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announc. 2013 May 09; 1(3). PMID: 23661480.
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    114. Lang JM, Darling AE, Eisen JA. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One. 2013; 8(4):e62510. PMID: 23638103.
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    115. Stackebrandt E, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Stand Genomic Sci. 2013 Apr 15; 8(1):15-25. PMID: 23961308.
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    116. Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Han C, Cheng JF, Tapia R, Goodwin LA, Bruce D, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Rohde M, Tindall BJ, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Stand Genomic Sci. 2013 Apr 15; 8(1):37-46. PMID: 23961310.
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    117. Abt B, Göker M, Scheuner C, Han C, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Rohde M, Spring S, Gronow S, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Woyke T, Klenk HP. Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. Stand Genomic Sci. 2013 Apr 15; 8(1):88-105. PMID: 23961314.
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    118. Mavromatis K, Stackebrandt E, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Stand Genomic Sci. 2013 Apr 15; 8(1):26-36. PMID: 23961309.
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    119. Mavromatis K, Stackebrandt E, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Spring S, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Stand Genomic Sci. 2013 Apr 15; 8(1):47-57. PMID: 23961311.
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    120. Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria). Genome Announc. 2013 Mar 21; 1(2):e0012013. PMID: 23516225.
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    121. Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4. Genome Announc. 2013 Mar 21; 1(2):e0008613. PMID: 23516213.
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    122. Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP. Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics. 2013 Feb 12; 14:95. PMID: 23402223.
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    123. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013; 4:2120. PMID: 23979677.
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    124. Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A. 2013 Jan 15; 110(3):1053-8. PMID: 23277585.
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    125. Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Stand Genomic Sci. 2012 Dec 19; 7(2):210-20. PMID: 23408178.
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    126. Traag BA, Pugliese A, Eisen JA, Losick R. Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis. J Bacteriol. 2013 Jan; 195(2):253-60. PMID: 23123912.
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    127. Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012; 8(10):e1002743. PMID: 23133348.
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    128. Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics. 2012 Oct 13; 13:264. PMID: 23061897.
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    129. Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Stand Genomic Sci. 2012 Oct 10; 7(1):107-19. PMID: 23450183.
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    130. Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Rohde M, Tindall BJ, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Stand Genomic Sci. 2012 Oct 10; 7(1):120-30. PMID: 23450211.
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    131. Jiang X, Langille MG, Neches RY, Elliot M, Levin SA, Eisen JA, Weitz JS, Dushoff J. Functional biogeography of ocean microbes revealed through non-negative matrix factorization. PLoS One. 2012; 7(9):e43866. PMID: 23049741.
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    132. Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One. 2012; 7(9):e42304. PMID: 23028432.
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    133. Chandler JA, Eisen JA, Kopp A. Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hosts. Appl Environ Microbiol. 2012 Oct; 78(20):7327-36. PMID: 22885750.
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    134. Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One. 2012; 7(7):e41389. PMID: 22848480.
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    135. Anderson I, Chertkov O, Chen A, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Palaniappan K, Land M, Pan C, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand Genomic Sci. 2012 Jul 30; 6(3):1-13. PMID: 23407703.
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    136. Eisen JA. Badomics words and the power and peril of the ome-meme. Gigascience. 2012 Jul 12; 1(1):6. PMID: 23587201.
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    137. Langille MG, Laird MR, Hsiao WW, Chiu TA, Eisen JA, Brinkman FS. MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics. 2012 Jul 15; 28(14):1947-8. PMID: 22576174.
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    138. Mavromatis K, Chertkov O, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Bruce D, Goodwin LA, Pitluck S, Huntemann M, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Stand Genomic Sci. 2012 May 25; 6(2):210-9. PMID: 22768364.
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    139. Huntemann M, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Stand Genomic Sci. 2012 May 25; 6(2):185-93. PMID: 22768362.
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    140. Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao OD, Göker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci. 2012 May 25; 6(2):145-54. PMID: 22768358.
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    141. Göker M, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Stand Genomic Sci. 2012 May 25; 6(2):230-9. PMID: 22768366.
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    142. Abt B, Han C, Scheuner C, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Gronow S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci. 2012 May 25; 6(2):194-209. PMID: 22768363.
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    143. Anderson I, Saunders E, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Chang YJ, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Stand Genomic Sci. 2012 May 25; 6(2):155-64. PMID: 22768359.
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    144. Anderson I, Held B, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Stand Genomic Sci. 2012 May 25; 6(2):174-84. PMID: 22768361.
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    145. Copeland A, Zeytun A, Yassawong M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Mavromatis K, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Sikorski J, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). Stand Genomic Sci. 2012 May 25; 6(2):240-50. PMID: 22768367.
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    146. Copeland A, Gu W, Yasawong M, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng JF, Goodwin LA, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Pan C, Brambilla EM, Rohde M, Tindall BJ, Sikorski J, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Stand Genomic Sci. 2012 Mar 19; 6(1):21-30. PMID: 22675595.
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    147. Han C, Kotsyurbenko O, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Stand Genomic Sci. 2012 Mar 19; 6(1):94-103. PMID: 22675602.
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    148. Wu M, Chatterji S, Eisen JA. Accounting for alignment uncertainty in phylogenomics. PLoS One. 2012; 7(1):e30288. PMID: 22272325.
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    149. Göker M, Daligault H, Mwirichia R, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Han C, Land M, Hauser L, Pan C, Brambilla EM, Rohde M, Spring S, Sikorski J, Wirth R, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent. Stand Genomic Sci. 2011 Dec 31; 5(3):407-15. PMID: 22675590.
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    150. Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Abt B, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)). Stand Genomic Sci. 2011 Dec 31; 5(3):398-406. PMID: 22675589.
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    151. Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K. Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. G3 (Bethesda). 2011 Nov; 1(6):515-22. PMID: 22384362.
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    152. Chang YJ, Land M, Hauser L, Chertkov O, Del Rio TG, Nolan M, Copeland A, Tice H, Cheng JF, Lucas S, Han C, Goodwin L, Pitluck S, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Mavromatis K, Liolios K, Brettin T, Fiebig A, Rohde M, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci. 2011 Oct 15; 5(1):97-111. PMID: 22180814.
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    153. Pati A, Gronow S, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Mikhailova N, Huntemann M, Chen A, Palaniappan K, Land M, Hauser L, Detter JC, Brambilla EM, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20). Stand Genomic Sci. 2011 Oct 15; 5(1):41-9. PMID: 22180809.
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    154. Liolios K, Sikorski J, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Kotsyurbenko O, Rohde M, Tindall BJ, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113). Stand Genomic Sci. 2011 Oct 15; 5(1):30-40. PMID: 22180808.
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    155. Woyke T, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Mwirichia R, Sikorski J, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262). Stand Genomic Sci. 2011 Oct 15; 5(1):21-9. PMID: 22180807.
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    156. Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Mavromatis K, Daum C, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Jeffries CD, Detter JC, Rohde M, Abt B, Pukall R, Göker M, Bristow J, Markowitz V, Hugenholtz P, Eisen JA. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Stand Genomic Sci. 2011 Oct 15; 5(1):121-34. PMID: 22180816.
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    157. Lapidus A, Chertkov O, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Abt B, Spring S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10). Stand Genomic Sci. 2011 Oct 15; 5(1):86-96. PMID: 22180813.
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    158. Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system. PLoS Genet. 2011 Sep; 7(9):e1002272. PMID: 21966276.
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    159. Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environ Microbiol. 2012 Jan; 14(1):162-76. PMID: 21914098.
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    160. Kembel SW, Eisen JA, Pollard KS, Green JL. The phylogenetic diversity of metagenomes. PLoS One. 2011; 6(8):e23214. PMID: 21912589.
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    161. Darling AE, Tritt A, Eisen JA, Facciotti MT. Mauve assembly metrics. Bioinformatics. 2011 Oct 01; 27(19):2756-7. PMID: 21810901.
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    162. Mindell DP, Fisher BL, Roopnarine P, Eisen J, Mace GM, Page RD, Pyle RL. Aggregating, tagging and integrating biodiversity research. PLoS One. 2011; 6(8):e19491. PMID: 21829594.
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    163. Anderson I, Göker M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Huber H, Yasawong M, Rohde M, Spring S, Abt B, Sikorski J, Wirth R, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A). Stand Genomic Sci. 2011 Jul 01; 4(3):381-92. PMID: 21886865.
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    164. Anderson I, Sikorski J, Zeytun A, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Ngatchou-Djao OD, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1). Stand Genomic Sci. 2011 Jul 01; 4(3):322-30. PMID: 21886859.
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    165. Han C, Mwirichia R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR). Stand Genomic Sci. 2011 Jul 01; 4(3):371-80. PMID: 21886864.
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    166. Huntemann M, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). Stand Genomic Sci. 2011 Jul 01; 4(3):303-11. PMID: 21886857.
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    167. Daligault H, Lapidus A, Zeytun A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Complete genome sequence of Haliscomenobacter hydrossis type strain (O). Stand Genomic Sci. 2011 Jul 01; 4(3):352-60. PMID: 21886862.
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    168. Han C, Gronow S, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Zeytun A, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Treponema succinifaciens type strain (6091). Stand Genomic Sci. 2011 Jul 01; 4(3):361-70. PMID: 21886863.
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    169. Sikorski J, Teshima H, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Ngatchou-Djao OD, Rohde M, Pukall R, Spring S, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Mahella australiensis type strain (50-1 BON). Stand Genomic Sci. 2011 Jul 01; 4(3):331-41. PMID: 21886860.
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    170. Göker M, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2). Stand Genomic Sci. 2011 Jul 01; 4(3):393-401. PMID: 21886866.
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    171. Munk AC, Lapidus A, Lucas S, Nolan M, Tice H, Cheng JF, Del Rio TG, Goodwin L, Pitluck S, Liolios K, Huntemann M, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Tapia R, Han C, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Yasawong M, Brambilla EM, Rohde M, Sikorski J, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Tsukamurella paurometabola type strain (no. 33). Stand Genomic Sci. 2011 Jul 01; 4(3):342-51. PMID: 21886861.
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    172. Ivanova N, Sikorski J, Chertkov O, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Kannan KP, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL). Stand Genomic Sci. 2011 Jul 01; 4(3):312-21. PMID: 21886858.
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    173. Gronow S, Held B, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA. Complete genome sequence of Bacteroides salanitronis type strain (BL78). Stand Genomic Sci. 2011 Apr 29; 4(2):191-9. PMID: 21677856.
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    174. Göker M, Gronow S, Zeytun A, Nolan M, Lucas S, Lapidus A, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP. Complete genome sequence of Odoribacter splanchnicus type strain (1651/6). Stand Genomic Sci. 2011 Apr 29; 4(2):200-9. PMID: 21677857.
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    175. Land M, Held B, Gronow S, Abt B, Lucas S, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Hauser L, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139). Stand Genomic Sci. 2011 Apr 29; 4(2):233-43. PMID: 21677860.
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    176. Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ioanna P, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bilek Y, Hader T, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Stand Genomic Sci. 2011 Apr 29; 4(2):173-82. PMID: 21677854.
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    177. Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Stand Genomic Sci. 2011 Apr 29; 4(2):131-43. PMID: 21677850.
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    178. Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Göker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Marivirga tractuosa type strain (H-43). Stand Genomic Sci. 2011 Apr 29; 4(2):154-62. PMID: 21677852.
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    179. Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Jeffries CD, Brambilla EM, Röhl A, Mwirichia R, Rohde M, Tindall BJ, Sikorski J, Wirth R, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. Complete genome sequence of Oceanithermus profundus type strain (506). Stand Genomic Sci. 2011 Apr 29; 4(2):210-20. PMID: 21677858.
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    180. Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Kannan KP, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Stand Genomic Sci. 2011 Apr 29; 4(2):221-32. PMID: 21677859.
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    181. Mavromatis K, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Göker M, Gronow S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Stand Genomic Sci. 2011 Apr 29; 4(2):144-53. PMID: 21677851.
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    182. Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC. Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci U S A. 2011 May 10; 108(19):7850-4. PMID: 21518859.
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    183. Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Stand Genomic Sci. 2011 Apr 29; 4(2):163-72. PMID: 21677853.
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    184. Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One. 2011 Mar 18; 6(3):e18011. PMID: 21437252.
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    185. Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Leadbetterella byssophila type strain (4M15). Stand Genomic Sci. 2011 Mar 04; 4(1):2-12. PMID: 21475582.
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    186. Lang E, Teshima H, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Kopitz M, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Weeksella virosa type strain (9751). Stand Genomic Sci. 2011 Feb 22; 4(1):81-90. PMID: 21475590.
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    187. Abt B, Lu M, Misra M, Han C, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Cellulophaga algicola type strain (IC166). Stand Genomic Sci. 2011 Feb 22; 4(1):72-80. PMID: 21475589.
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    188. Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Stand Genomic Sci. 2011 Feb 22; 4(1):45-53. PMID: 21475586.
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    189. Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Del Rio TG, Tice H, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Truepera radiovictrix type strain (RQ-24). Stand Genomic Sci. 2011 Feb 22; 4(1):91-9. PMID: 21475591.
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    190. Pagani I, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Chertkov O, Davenport K, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Kannan KP, Djao OD, Rohde M, Pukall R, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Stand Genomic Sci. 2011 Feb 20; 4(1):100-10. PMID: 21475592.
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    191. Pitluck S, Sikorski J, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Djao OD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). Stand Genomic Sci. 2011 Feb 20; 4(1):54-62. PMID: 21475587.
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    192. Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Stand Genomic Sci. 2011 Feb 20; 4(1):36-44. PMID: 21475585.
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    193. Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Beck B, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Isosphaera pallida type strain (IS1B). Stand Genomic Sci. 2011 Feb 20; 4(1):63-71. PMID: 21475588.
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    194. Chertkov O, Sikorski J, Nolan M, Lapidus A, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Djao OD, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Han C, Detter JC, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Thermomonospora curvata type strain (B9). Stand Genomic Sci. 2011 Feb 20; 4(1):13-22. PMID: 21475583.
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    195. Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol. 2011 Jan 20; 7(1):e1001061. PMID: 21283775.
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    196. Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010 Dec 25; 3(3):243-8. PMID: 21304727.
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    197. Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea. 2010 Dec 23; 2010:690737. PMID: 21234345.
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    198. Sikorski J, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Yasawong M, Rohde M, Pukall R, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). Stand Genomic Sci. 2010 Dec 15; 3(3):304-14. PMID: 21304735.
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    199. Djao OD, Zhang X, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1). Stand Genomic Sci. 2010 Dec 15; 3(3):268-75. PMID: 21304731.
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    200. Han C, Gu W, Zhang X, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Schneider S, Rohde M, Göker M, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). Stand Genomic Sci. 2010 Dec 15; 3(3):337-45. PMID: 21304738.
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    201. Sun H, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Djao OD, Rohde M, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509). Stand Genomic Sci. 2010 Nov 30; 3(3):325-36. PMID: 21304737.
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    202. Anderson I, Djao OD, Misra M, Chertkov O, Nolan M, Lucas S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Sikorski J, Spring S, Rohde M, Eichinger K, Huber H, Wirth R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Methanothermus fervidus type strain (V24S). Stand Genomic Sci. 2010 Nov 20; 3(3):315-24. PMID: 21304736.
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    203. Pitluck S, Yasawong M, Held B, Lapidus A, Nolan M, Copeland A, Lucas S, Del Rio TG, Tice H, Cheng JF, Chertkov O, Goodwin L, Tapia R, Han C, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Pukall R, Spring S, Rohde M, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3). Stand Genomic Sci. 2010 Nov 20; 3(3):285-93. PMID: 21304733.
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    204. Sun H, Spring S, Lapidus A, Davenport K, Del Rio TG, Tice H, Nolan M, Copeland A, Cheng JF, Lucas S, Tapia R, Goodwin L, Pitluck S, Ivanova N, Pagani I, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Han C, Rohde M, Brambilla E, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. Complete genome sequence of Desulfarculus baarsii type strain (2st14). Stand Genomic Sci. 2010 Nov 20; 3(3):276-84. PMID: 21304732.
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    205. Del Rio TG, Chertkov O, Yasawong M, Lucas S, Deshpande S, Cheng JF, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Pukall R, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Intrasporangium calvum type strain (7 KIP). Stand Genomic Sci. 2010 Nov 16; 3(3):294-303. PMID: 21304734.
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    206. Brambilla E, Djao OD, Daligault H, Lapidus A, Lucas S, Hammon N, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Stand Genomic Sci. 2010 Oct 27; 3(2):203-11. PMID: 21304750.
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    207. Kiss H, Cleland D, Lapidus A, Lucas S, Del Rio TG, Nolan M, Tice H, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Lu M, Brettin T, Detter JC, Göker M, Tindall BJ, Beck B, McDermott TR, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Cheng JF. Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1). Stand Genomic Sci. 2010 Oct 27; 3(2):153-62. PMID: 21304745.
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    208. Sikorski J, Munk C, Lapidus A, Ngatchou Djao OD, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Han C, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Sims D, Meincke L, Brettin T, Detter JC, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Lang E, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). Stand Genomic Sci. 2010 Oct 27; 3(2):194-202. PMID: 21304749.
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    209. Roeselers G, Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. Complete genome sequence of Candidatus Ruthia magnifica. Stand Genomic Sci. 2010 Oct 27; 3(2):163-73. PMID: 21304746.
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    210. Nolan M, Sikorski J, Davenport K, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Tapia R, Brettin T, Detter JC, Han C, Yasawong M, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Ferrimonas balearica type strain (PAT). Stand Genomic Sci. 2010 Oct 27; 3(2):174-82. PMID: 21304747.
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    211. Mavromatis K, Yasawong M, Chertkov O, Lapidus A, Lucas S, Nolan M, Del Rio TG, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Tapia R, Han C, Bruce D, Goodwin L, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Brambilla E, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). Stand Genomic Sci. 2010 Oct 18; 3(2):136-44. PMID: 21304743.
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    212. Mavromatis K, Sikorski J, Pabst E, Teshima H, Lapidus A, Lucas S, Nolan M, Glavina Del Rio T, Cheng JF, Bruce D, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). Stand Genomic Sci. 2010 Sep 28; 3(2):117-25. PMID: 21304741.
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    213. Pitluck S, Yasawong M, Munk C, Nolan M, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P). Stand Genomic Sci. 2010 Sep 28; 3(2):108-16. PMID: 21304740.
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    214. Yasawong M, Teshima H, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018). Stand Genomic Sci. 2010 Sep 28; 3(2):126-35. PMID: 21304742.
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    215. Göker M, Held B, Lucas S, Nolan M, Yasawong M, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter JC, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Olsenella uli type strain (VPI D76D-27C). Stand Genomic Sci. 2010 Aug 20; 3(1):76-84. PMID: 21304694.
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    216. Sikorski J, Lapidus A, Chertkov O, Lucas S, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Han C, Brambilla E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Bruce D, Detter C, Tapia R, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Spring S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288). Stand Genomic Sci. 2010 Aug 20; 3(1):57-65. PMID: 21304692.
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    217. Labutti K, Mayilraj S, Clum A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). Stand Genomic Sci. 2010 Aug 20; 3(1):85-92. PMID: 21304695.
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    218. Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Stand Genomic Sci. 2010 Aug 20; 3(1):66-75. PMID: 21304693.
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    219. Sikorski J, Tindall BJ, Lowry S, Lucas S, Nolan M, Copeland A, Glavina Del Rio T, Tice H, Cheng JF, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Meiothermus silvanus type strain (VI-R2). Stand Genomic Sci. 2010 Jul 29; 3(1):37-46. PMID: 21304690.
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    220. Abt B, Foster B, Lapidus A, Clum A, Sun H, Pukall R, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Cellulomonas flavigena type strain (134). Stand Genomic Sci. 2010 Jul 29; 3(1):15-25. PMID: 21304688.
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    221. Chang YJ, Pukall R, Saunders E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Acidaminococcus fermentans type strain (VR4). Stand Genomic Sci. 2010 Jul 29; 3(1):1-14. PMID: 21304687.
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    222. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Fähnrich R, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci. 2010 Jul 29; 3(1):26-36. PMID: 21304689.
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    223. Labutti K, Sikorski J, Schneider S, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Tindall BJ, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290). Stand Genomic Sci. 2010 Jul 29; 3(1):47-56. PMID: 21304691.
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    224. Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Brettin T, Detter JC, Tapia R, Han C, Heimerl T, Weikl F, Brambilla E, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Stand Genomic Sci. 2010 Jun 15; 2(3):245-59. PMID: 21304709.
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    225. Pati A, Sikorski J, Gronow S, Munk C, Lapidus A, Copeland A, Glavina Del Tio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Brachyspira murdochii type strain (56-150). Stand Genomic Sci. 2010 Jun 15; 2(3):260-9. PMID: 21304710.
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    226. Kiss H, Lang E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Cheng JF, Han C, Goodwin L, Pitluck S, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Spring S, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460). Stand Genomic Sci. 2010 Jun 15; 2(3):270-9. PMID: 21304711.
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    227. 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, Ovchinnikova G, Chertkov O, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Saunders E, Brettin T, Detter JC, Chain P, Eichinger K, Huber H, Spring S, Rohde M, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Archaeoglobus profundus type strain (AV18). Stand Genomic Sci. 2010 Jun 15; 2(3):327-46. PMID: 21304717.
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    228. Pati A, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Chertkov O, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Stand Genomic Sci. 2010 Jun 15; 2(3):300-8. PMID: 21304714.
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    229. Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Woyke T, Goodwin L, Pitluck S, Held B, Brettin T, Tapia R, Ivanova N, Mikhailova N, Pati A, Liolios K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24). Stand Genomic Sci. 2010 Jun 15; 2(3):290-9. PMID: 21304713.
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    230. Liolios K, Sikorski J, Jando M, Lapidus A, Copeland A, Glavina T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Woyke T, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Chertkov O, Kuske C, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Thermobispora bispora type strain (R51). Stand Genomic Sci. 2010 Jun 15; 2(3):318-26. PMID: 21304716.
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    231. Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Stand Genomic Sci. 2010 Jun 15; 2(3):280-9. PMID: 21304712.
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    232. Copeland A, Sikorski J, Lapidus A, Nolan M, Glavina T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Pukall R, Chertkov O, Brettin T, Han C, Kuske C, Bruce D, Goodwin L, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Erratum to: Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Stand Genomic Sci. 2010 Jun 15; 2(3):361-2. PMID: 21304720.
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    233. Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics. 2010 Jun 12; 11:317. PMID: 20540779.
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    234. 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, Detter JC, Kuske C, Bruce D, Goodwin L, Ovchinikova G, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Stand Genomic Sci. 2010 May 15; 2(2):228-88. PMID: 21304706.
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    235. Morgan JL, Darling AE, Eisen JA. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One. 2010 Apr 16; 5(4):e10209. PMID: 20419134.
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    236. Langille MG, Eisen JA. BioTorrents: a file sharing service for scientific data. PLoS One. 2010 Apr 14; 5(4):e10071. PMID: 20418944.
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    237. Ivanova N, Sikorski J, Jando M, Munk C, 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, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Meincke L, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Geodermatophilus obscurus type strain (G-20). Stand Genomic Sci. 2010 Mar 30; 2(2):158-67. PMID: 21304698.
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    238. 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, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Brettin T, Detter JC, Schütze A, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen F. Complete genome sequence of Spirosoma linguale type strain (1). Stand Genomic Sci. 2010 Mar 30; 2(2):176-85. PMID: 21304700.
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    239. Sikorski J, Lapidus A, Copeland A, Misra M, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Jando M, Schneider S, Bruce D, Goodwin L, Pitluck S, Liolios K, Mikhailova N, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chertkov O, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). Stand Genomic Sci. 2010 Mar 30; 2(2):203-11. PMID: 21304703.
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    240. 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, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Brettin T. Complete genome sequence of Kribbella flavida type strain (IFO 14399). Stand Genomic Sci. 2010 Mar 30; 2(2):186-93. PMID: 21304701.
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    241. Harmon-Smith M, Celia L, Chertkov O, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Pitluck S, Pati A, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Göker M, Beck B, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen F. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300). Stand Genomic Sci. 2010 Mar 30; 2(2):220-7. PMID: 21304705.
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    242. Wirth R, Sikorski J, Brambilla E, Misra M, Lapidus A, Copeland A, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Tapia R, Bruce D, Goodwin L, Pitluck S, Pati A, Anderson I, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Bilek Y, Hader T, Land M, Hauser L, Chang YJ, Jeffries CD, Tindall BJ, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Thermocrinis albus type strain (HI 11/12). Stand Genomic Sci. 2010 Mar 30; 2(2):194-202. PMID: 21304702.
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    243. Tice H, Mayilraj S, Sims D, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Copeland A, Cheng JF, Meincke L, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen F. Complete genome sequence of Nakamurella multipartita type strain (Y-104). Stand Genomic Sci. 2010 Mar 30; 2(2):168-75. PMID: 21304699.
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    244. 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, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. Complete genome sequence of Conexibacter woesei type strain (ID131577). Stand Genomic Sci. 2010 Mar 30; 2(2):212-9. PMID: 21304704.
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    245. 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, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Lang E, Spring S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175). Stand Genomic Sci. 2010 Mar 24; 2(2):149-57. PMID: 21304697.
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    246. Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One. 2010 Mar 19; 5(3):e9605. PMID: 20333302.
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    247. Tu Q, Eisen J, Chang C. Surface-enhanced Raman spectroscopy study of indolic molecules adsorbed on gold colloids. J Biomed Opt. 2010 Mar-Apr; 15(2):020512. PMID: 20459221.
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    248. 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, Pitluck S, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci. 2010 Feb 28; 2(1):107-16. PMID: 21304683.
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    249. 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, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci. 2010 Feb 28; 2(1):87-95. PMID: 21304681.
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    250. 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, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Chertkov O, Han C, Brettin T, Detter JC, Wahrenburg C, Rohde M, Pukall R, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). Stand Genomic Sci. 2010 Jan 28; 2(1):9-18. PMID: 21304673.
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    251. 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, Detter JC, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Stand Genomic Sci. 2010 Jan 28; 2(1):29-37. PMID: 21304675.
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    252. 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, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Han C, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Gordonia bronchialis type strain (3410). Stand Genomic Sci. 2010 Jan 28; 2(1):19-28. PMID: 21304674.
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    253. 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, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci. 2010 Jan 28; 2(1):49-56. PMID: 21304677.
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    254. 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, Mikhailova N, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Munk C, Kiss H, Chain P, Han C, Brettin T, Detter JC, Schüler E, Göker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)). Stand Genomic Sci. 2010 Jan 28; 2(1):38-48. PMID: 21304676.
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    255. 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, Goodwin L, Ivanova N, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07). Stand Genomic Sci. 2010 Jan 28; 2(1):1-8. PMID: 21304672.
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    256. Ivanova N, Daum C, Lang E, Abt B, Kopitz M, Saunders E, Lapidus A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Markowitz V, Eisen JA, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Haliangium ochraceum type strain (SMP-2). Stand Genomic Sci. 2010 Jan 28; 2(1):96-106. PMID: 21304682.
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    257. 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, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Pati A, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. Complete genome sequence of Veillonella parvula type strain (Te3). Stand Genomic Sci. 2010 Jan 28; 2(1):57-65. PMID: 21304678.
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    258. 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, Brettin T, Han C, Detter JC, Ovchinikova G, Pati A, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spröer C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chain P. Complete genome sequence of Streptobacillus moniliformis type strain (9901). Stand Genomic Sci. 2009 Dec 30; 1(3):300-7. PMID: 21304670.
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    259. Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T, Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Ovchinikova G, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Stand Genomic Sci. 2009 Dec 30; 1(3):308-16. PMID: 21304671.
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    260. 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, Pitluck S, Göker M, Ovchinikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21). Stand Genomic Sci. 2009 Dec 30; 1(3):234-41. PMID: 21304662.
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    261. 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, Pitluck S, Ovchinikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Rhodothermus marinus type strain (R-10). Stand Genomic Sci. 2009 Dec 29; 1(3):283-90. PMID: 21304669.
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    262. 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, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24; 462(7276):1056-60. PMID: 20033048.
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    263. 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, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Göker M, Spring S, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883). Stand Genomic Sci. 2009 Nov 22; 1(3):254-61. PMID: 21304665.
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    264. 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, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Han C, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC, Detter JC. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2). Stand Genomic Sci. 2009 Nov 22; 1(3):270-7. PMID: 21304667.
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    265. 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, Han C, Pitluck S, Pati A, Mavrommatis K, Ivanova N, Ovchinnikova G, Chen A, Palaniappan K, Schneider S, Rohde M, Chain P, D'haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1). Stand Genomic Sci. 2009 Nov 22; 1(3):234-41. PMID: 21304663.
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    266. 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, Detter JC, Han C, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Pitluck S, Pati A, Mavromatis K, Ivanova N, Ovchinnikova G, Chen A, Palaniappan K, Chain P, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Halorhabdus utahensis type strain (AX-2). Stand Genomic Sci. 2009 Nov 22; 1(3):218-25. PMID: 21304660.
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    267. 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, Goodwin L, Pati A, Ivanova N, Mavromatis K, Ovchinnikova G, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C. Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134). Stand Genomic Sci. 2009 Nov 22; 1(3):262-9. PMID: 21304666.
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    268. 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, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Stand Genomic Sci. 2009 Nov 22; 1(3):242-53. PMID: 21304664.
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    269. 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, Goodwin L, Pitluck S, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Göker M, Tindall BJ, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Kangiella koreensis type strain (SW-125). Stand Genomic Sci. 2009 Nov 22; 1(3):226-33. PMID: 21304661.
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    270. Eisen JA, MacCallum CJ. Genomics of emerging infectious disease: A PLoS collection. PLoS Biol. 2009 Oct; 7(10):e1000224. PMID: 19855830.
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    271. 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, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). Stand Genomic Sci. 2009 Sep 28; 1(2):174-82. PMID: 21304654.
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    272. 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, Goodwin L, Pitluck S, Pati A, Mavromatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Pukall R, Klenk HP, Kyrpides NC. Complete genome sequence of Sanguibacter keddieii type strain (ST-74). Stand Genomic Sci. 2009 Sep 24; 1(2):110-8. PMID: 21304646.
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    273. 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, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Detter JC, Han C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Anaerococcus prevotii type strain (PC1). Stand Genomic Sci. 2009 Sep 24; 1(2):159-65. PMID: 21304652.
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    274. 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, Chang YJ, Jeffries CD, Kopitz M, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Rohde M, Kyrpides NC, Klenk HP. Complete genome sequence of Dyadobacter fermentans type strain (NS114). Stand Genomic Sci. 2009 Sep 24; 1(2):133-40. PMID: 21304649.
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    275. 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, Cheng JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, D'haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Rohde M, Klenk HP, Kyrpides NC. Complete genome sequence of Cryptobacterium curtum type strain (12-3). Stand Genomic Sci. 2009 Sep 24; 1(2):93-100. PMID: 21304644.
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    276. 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, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Bristow J, Göker M, Rohde M, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845). Stand Genomic Sci. 2009 Sep 24; 1(2):101-9. PMID: 21304645.
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    277. 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, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang YJ, Jeffries CD, Chertkov O, Brettin T, Detter JC, Han C, Ali Z, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Catenulispora acidiphila type strain (ID 139908). Stand Genomic Sci. 2009 Sep 24; 1(2):119-25. PMID: 21304647.
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    278. 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, Han C, Pitluck S, Mikhailova N, Pati A, Mavrommatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b). Stand Genomic Sci. 2009 Sep 24; 1(2):126-32. PMID: 21304648.
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    279. 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, Kuske C, Bruce D, Goodwin L, Chain P, D'haeseleer P, Chen A, Palaniappan K, Ivanova N, Mavromatis K, Mikhailova N, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Saccharomonospora viridis type strain (P101). Stand Genomic Sci. 2009 Sep 24; 1(2):141-9. PMID: 21304650.
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    280. 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, Pitluck S, Anderson I, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, D'haeseleer P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chain P. Complete genome sequence of Halogeometricum borinquense type strain (PR3). Stand Genomic Sci. 2009 Sep 24; 1(2):150-9. PMID: 21304651.
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    281. 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, Kuske C, Bruce D, Goodwin L, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Stand Genomic Sci. 2009 Sep 23; 1(2):166-73. PMID: 21304653.
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    282. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A. 2009 Oct 06; 106(40):17187-92. PMID: 19805153.
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    283. 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, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Meincke L, Sims D, Brettin T, Detter JC, Han C, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. Complete genome sequence of Desulfomicrobium baculatum type strain (X). Stand Genomic Sci. 2009 Jul 20; 1(1):29-37. PMID: 21304634.
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    284. 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, Göker M, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CC, Brettin T, Detter JC, Han C, Chain P, Tindall BJ, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Actinosynnema mirum type strain (101). Stand Genomic Sci. 2009 Jul 20; 1(1):46-53. PMID: 21304636.
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    285. 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, Pati A, Chen A, Palaniappan K, Göker M, Spring S, Land M, Hauser L, Chang YJ, Jeffries CC, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP). Stand Genomic Sci. 2009 Jul 20; 1(1):38-45. PMID: 21304635.
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    286. 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, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jefferies CC, Saunders E, Brettin T, Detter JC, Han C, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122). Stand Genomic Sci. 2009 Jul 20; 1(1):21-8. PMID: 21304633.
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    287. 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, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Stand Genomic Sci. 2009 Jul 20; 1(1):3-11. PMID: 21304631.
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    288. 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, Ovchinnikova G, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Schneider S, Göker M, Pukall R, Kyrpides NC, Klenk HP. Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci. 2009 Jul 20; 1(1):12-20. PMID: 21304632.
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    289. Han C, Spring S, Lapidus A, Del Rio TG, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Saunders E, Chertkov O, Brettin T, Göker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci. 2009 Jul 20; 1(1):54-62. PMID: 21304637.
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    290. Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One. 2009 Jul 01; 4(7):e6085. PMID: 19568419.
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    291. Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. Assembling the marine metagenome, one cell at a time. PLoS One. 2009; 4(4):e5299. PMID: 19390573.
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    292. Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet. 2009 Feb; 5(2):e1000362. PMID: 19197347.
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    293. Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One. 2009; 4(1):e4207. PMID: 19148287.
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    294. Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics. 2008 Dec 11; 9:597. PMID: 19077236.
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    295. Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methé BA. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics. 2008 Nov 26; 9:562. PMID: 19036158.
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    296. Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol. 2008; 9(11):R158. PMID: 19000309.
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    297. Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008 Oct 13; 9(10):R151. PMID: 18851752.
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    298. Wu D, Hartman A, Ward N, Eisen JA. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One. 2008 Jul 02; 3(7):e2566. PMID: 18596968.
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    299. Eisen JA. PLoS Biology 2.0. PLoS Biol. 2008 Feb; 6(2):e48. PMID: 18303952.
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    300. Hazen TH, Wu D, Eisen JA, Sobecky PA. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Appl Environ Microbiol. 2007 Dec; 73(23):7703-10. PMID: 17921277.
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    301. Pfarr K, Foster J, Slatko B, Hoerauf A, Eisen JA. On the taxonomic status of the intracellular bacterium Wolbachia pipientis: should this species name include the intracellular bacteria of filarial nematodes? Int J Syst Evol Microbiol. 2007 Aug; 57(Pt 8):1677-8. PMID: 17684235.
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    302. Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A. 2007 Jul 10; 104(28):11784-9. PMID: 17606904.
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    303. Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, Allers T. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet. 2007 May 18; 3(5):e77. PMID: 17511521.
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    304. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16. PMID: 17355171.
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    305. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007 Mar; 5(3):e77. PMID: 17355176.
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    306. Eisen JA. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol. 2007 Mar; 5(3):e82. PMID: 17355177.
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    307. Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. The Calyptogena magnifica chemoautotrophic symbiont genome. Science. 2007 Feb 16; 315(5814):998-1000. PMID: 17303757.
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    308. Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Eisen J, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci U S A. 2006 Oct 10; 103(41):15200-5. PMID: 17015832.
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    309. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol. 2006 Sep; 4(9):e286. PMID: 16933976.
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    310. Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics. 2006 Oct; 88(4):443-51. PMID: 16782302.
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    316. Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, Ravel J. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proc Natl Acad Sci U S A. 2005 May 17; 102(20):7315-20. PMID: 15883371.
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    317. Badger JH, Eisen JA, Ward NL. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. Int J Syst Evol Microbiol. 2005 May; 55(Pt 3):1021-6. PMID: 15879228.
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    322. Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics. 2004 Sep; 168(1):21-33. PMID: 15454524.
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    323. Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol. 2004 May; 22(5):554-9. PMID: 15077118.
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    324. Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A. 2004 Apr 13; 101(15):5646-51. PMID: 15064399.
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    325. Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen J, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg S, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NM. Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol. 2004 Apr; 134(2):183-91. PMID: 15003838.
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    326. Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2004 Mar; 2(3):E69. PMID: 15024419.
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    327. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004 Apr 02; 304(5667):66-74. PMID: 15001713.
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    328. Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science. 2003 Dec 12; 302(5652):1967-9. PMID: 14671304.
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    329. Yang RZ, Huang Q, Xu A, McLenithan JC, Eisen JA, Shuldiner AR, Alkan S, Gong DW, Eison JA. Comparative studies of resistin expression and phylogenomics in human and mouse. Biochem Biophys Res Commun. 2003 Oct 24; 310(3):927-35. PMID: 14550293.
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    331. Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, Fraser CM. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol. 2003 Sep; 185(17):5220-33. PMID: 12923095.
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    336. Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol. 2003 Apr; 51(6):859-66. PMID: 12777046.
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    342. Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR, Venter JC, Fraser CM. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. 2002 10; 184(19):5479-90. PMID: 12218036.
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    350. Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, Eisen J, Slatko B. Sequencing and analysis of a 63 kb bacterial artificial chromosome insert from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi. Int J Parasitol. 2002 Feb; 32(2):159-66. PMID: 11812492.
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    362. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14; 408(6814):796-815. PMID: 11130711.
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    370. Nierman WC, Eisen JA, Fleischmann RD, Fraser CM. Genome data: what do we learn? Curr Opin Struct Biol. 2000 Jun; 10(3):343-8. PMID: 10851186.
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    371. Coleman MA, Eisen JA, Mohrenweiser HW. Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse. Genomics. 2000 May 01; 65(3):274-82. PMID: 10857751.
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    372. Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 2000 Mar 15; 28(6):1397-406. PMID: 10684935.
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    373. Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000 Mar 10; 287(5459):1809-15. PMID: 10710307.
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    374. Nierman W, Eisen JA, Fraser CM. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis. Res Microbiol. 2000 Mar; 151(2):79-84. PMID: 10865951.
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    375. Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature. 1999 Dec 16; 402(6763):761-8. PMID: 10617197.
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    376. Eisen JA, Hanawalt PC. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res. 1999 Dec 07; 435(3):171-213. PMID: 10606811.
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    377. White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. 1999 Nov 19; 286(5444):1571-7. PMID: 10567266.
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    378. Eisen JA. Going to extremes. Archaea: bridging the gap between bacteria and eukarya (A Keystone Symposia), Taos, NM, USA, 9-14 January 1999. Trends Genet. 1999 Jun; 15(6):218-9. PMID: 10419407.
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    379. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 1999 May 27; 399(6734):323-9. PMID: 10360571.
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    380. Eisen JA. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 1998 Sep 15; 26(18):4291-300. PMID: 9722651.
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    381. Wei MH, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA, Lerman MI. In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. Hum Genet. 1998 Sep; 103(3):355-64. PMID: 9799093.
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    382. Gruber TM, Eisen JA, Gish K, Bryant DA. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS Microbiol Lett. 1998 May 01; 162(1):53-60. PMID: 9595663.
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    383. Eisen JA. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 1998 Mar; 8(3):163-7. PMID: 9521918.
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    384. White RB, Eisen JA, Kasten TL, Fernald RD. Second gene for gonadotropin-releasing hormone in humans. Proc Natl Acad Sci U S A. 1998 Jan 06; 95(1):305-9. PMID: 9419371.
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    385. Eisen JA, Kaiser D, Myers RM. Gastrogenomic delights: a movable feast. Nat Med. 1997 Oct; 3(10):1076-8. PMID: 9334711.
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    386. Shafer RW, Eisen JA, Merigan TC, Katzenstein DA. Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe. J Virol. 1997 Jul; 71(7):5441-8. PMID: 9188616.
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    387. Eisen JA. The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package. Methods Mol Biol. 1997; 70:13-38. PMID: 9089600.
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    388. Eisen JA. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol. 1995 Dec; 41(6):1105-23. PMID: 8587109.
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    389. Eisen JA, Sweder KS, Hanawalt PC. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 1995 Jul 25; 23(14):2715-23. PMID: 7651832.
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    390. Eisen JA, Benito MI, Walbot V. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Res. 1994 Jul 11; 22(13):2634-6. PMID: 8041625.
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    391. Liu SK, Eisen JA, Hanawalt PC, Tessman I. recA mutations that reduce the constitutive coprotease activity of the RecA1202(Prtc) protein: possible involvement of interfilament association in proteolytic and recombination activities. J Bacteriol. 1993 Oct; 175(20):6518-29. PMID: 8407828.
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    392. Eisen JA, Smith SW, Cavanaugh CM. Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. J Bacteriol. 1992 May; 174(10):3416-21. PMID: 1577710.
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