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Jonathan Eisen

TitlePROF-AY
InstitutionUniversity of California Davis
DepartmentEVOLUTION & ECOLOGY
Address5311 GBSF
CA 95616
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. 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 J, Shapiro HY, Ané JM, Bennett AB. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biol. 2018 Aug; 16(8):e2006352. PMID: 30086128.
      View in: PubMed
    2. Horng KR, Ganz HH, Eisen J, Marks SL. Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ. 2018; 6:e4827. PMID: 29844978.
      View in: PubMed
    3. Dahlhausen KE, Doroud L, Firl AJ, Polkinghorne A, Eisen J. Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJ. 2018; 6:e4452. PMID: 29576947.
      View in: PubMed
    4. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen J. Correction: A microbial survey of the International Space Station (ISS). PeerJ. 2018; 5. PMID: 29498380.
      View in: PubMed
    5. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen J. A microbial survey of the International Space Station (ISS). PeerJ. 2017; 5:e4029. PMID: 29492330.
      View in: PubMed
    6. Wilbanks EG, Salman-Carvalho V, Jaekel U, Humphrey PT, Eisen J, 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.
      View in: PubMed
    7. Ettinger CL, Williams SL, Abbott JM, Stachowicz JJ, Eisen J. Microbiome succession during ammonification in eelgrass bed sediments. PeerJ. 2017; 5:e3674. PMID: 28828269.
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    8. Coil DA, Ettinger CL, Eisen J. Gut Check: The evolution of an educational board game. PLoS Biol. 2017 Apr; 15(4):e2001984. PMID: 28453514.
      View in: PubMed
    9. Ettinger CL, Voerman SE, Lang JM, Stachowicz JJ, Eisen J. 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.
      View in: PubMed
    10. Lujan KM, Eisen J, 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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    11. Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen J, Leach JE, Dangl JL. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 2017 Mar; 15(3):e2001793. PMID: 28350798.
      View in: PubMed
    12. Dahms PA, Martin AL, Ganz HH, Eisen J, 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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    13. Ganz HH, Doroud L, Firl AJ, Hird SM, Eisen J, 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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    14. Kincheloe GN, Eisen J, 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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    15. De Vries DR, Martin AL, Ganz HH, Eisen J, Coil DA. Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3. Genome Announc. 2016 Dec 15; 4(6). PMID: 27979940.
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    16. Lujan KM, Eisen J, Coil DA. Draft Genome Sequence of Tenacibaculum soleae UCD-KL19. Genome Announc. 2016 Oct 13; 4(5). PMID: 27738035.
      View in: PubMed
    17. Koenigsaecker TM, Eisen J, Coil DA. Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria). Genome Announc. 2016 Oct 13; 4(5). PMID: 27738036.
      View in: PubMed
    18. Alexiev A, Coil DA, Jospin G, Eisen J, 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; PMCID: PMC4859167.
    19. Coil DA, Neches RY, Lang JM, Brown WE, Severance M, Cavalier D, Eisen J. Growth of 48 built environment bacterial isolates on board the International Space Station (ISS). PeerJ. 2016; 4:e1842. PMID: 27019789; PMCID: PMC4806633.
    20. Lee RD, Jospin G, Lang JM, Eisen J, Coil DA. Draft Genome Sequences of Two Pseudoalteromonas porphyrae Strains Isolated from Seagrass Sediment. Genome Announc. 2016 Mar 17; 4(2). PMID: 26988038; PMCID: PMC4796117.
    21. Alexiev A, Krusor ML, Jospin G, Lang JM, Eisen J, 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; PMCID: PMC4786669.
    22. Lee RD, Jospin G, Lang JM, Eisen J, Coil DA. Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment. Genome Announc. 2016 Feb 18; 4(1). PMID: 26893436; PMCID: PMC4759083.
    23. Alexiev A, Krusor ML, Jospin G, Lang JM, Eisen J, 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; PMCID: PMC4759059.
    24. Coil DA, Jospin G, Eisen J, Adams JY. Additional Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients. Genome Announc. 2016 Jan 21; 4(1). PMID: 26798108; PMCID: PMC4722275.
    25. Coil DA, Benardini JN, Eisen J. 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; PMCID: PMC4653797.
    26. Lee RD, Jospin G, Lang JM, Eisen J, Coil DA. Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes). Genome Announc. 2015 Nov 19; 3(6). PMID: 26586901; PMCID: PMC4653803.
    27. Coil DA, Eisen J. Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado. Genome Announc. 2015 Nov 19; 3(6). PMID: 26586867; PMCID: PMC4653769.
    28. Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen J, 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; PMCID: PMC4643905.
    29. Coil DA, Flanagan JC, Stump A, Alexiev A, Lang JM, Eisen J. Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter. PeerJ. 2015; 3:e1400. PMID: 26587357; PMCID: PMC4647569.
    30. Lee RD, Jospin G, Lang JM, Eisen J, Coil DA. Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain UCD-SED8 (Phylum Gammaproteobacteria). Genome Announc. 2015 Nov 05; 3(6). PMID: 26543114; PMCID: PMC4645199.
    31. Betts MN, Jospin G, Eisen J, Coil DA. Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes). Genome Announc. 2015 Oct 15; 3(5). PMID: 26472846; PMCID: PMC4611698.
    32. Coil DA, Alexiev A, Wallis C, O'Flynn C, Deusch O, Davis I, Horsfall A, Kirkwood N, Jospin G, Eisen J, 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; PMCID: PMC4392144.
    33. Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen J. Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria). Genome Announc. 2015 Jan 29; 3(1). PMID: 25635017; PMCID: PMC4319511.
    34. Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen J. Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae). Genome Announc. 2015 Jan 29; 3(1). PMID: 25635016; PMCID: PMC4319510.
    35. Ettinger CL, Shehata HR, Johnston-Monje D, Raizada MN, Eisen J. Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria). Genome Announc. 2015 Jan 22; 3(1). PMID: 25614570; PMCID: PMC4319580.
    36. Ettinger CL, Mousa WM, Raizada MN, Eisen J. Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria). Genome Announc. 2015 Jan 22; 3(1). PMID: 25614569; PMCID: PMC4319590.
    37. Dunitz MI, Coil DA, Jospin G, Eisen J, Adams JY. Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients. Genome Announc. 2014 Dec 18; 2(6). PMID: 25523766; PMCID: PMC4271156.
    38. Lang JM, Eisen J, 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; PMCID: PMC4266855.
    39. Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen J, 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; PMCID: PMC4230888.
    40. 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 J, 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; PMCID: PMC4287430.
    41. Holland-Moritz HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen J. Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1. Genome Announc. 2014 Aug 21; 2(4). PMID: 25146141; PMCID: PMC4153494.
    42. Kyrpides NC, Hugenholtz P, Eisen J, 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; PMCID: PMC4122341.
    43. Lee RD, Jospin G, Coil DA, Eisen J. Draft Genome Sequence of the Endosymbiont "Candidatus Ruthia magnifica" UCD-CM (Phylum Proteobacteria). Genome Announc. 2014 Jul 17; 2(4). PMID: 25035337; PMCID: PMC4102874.
    44. Bik HM, Coil DA, Eisen J. microBEnet: lessons learned from building an interdisciplinary scientific community in the online sphere. PLoS Biol. 2014 Jun; 12(6):e1001884. PMID: 24937755; PMCID: PMC4060986.
    45. Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen J, Darling AE. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ. 2014; 2:e415. PMID: 24918035; PMCID: PMC4045339.
    46. Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen J. Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announc. 2014 May 15; 2(3). PMID: 24831154; PMCID: PMC4022818.
    47. Dunitz MI, James PM, Jospin G, Eisen J, 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; PMCID: PMC3999497.
    48. Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen J, 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; PMCID: PMC4262008.
    49. Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen J. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12. Genome Announc. 2014 Feb 20; 2(1). PMID: 24558247; PMCID: PMC3931368.
    50. Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen J. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014; 2:e243. PMID: 24482762; PMCID: PMC3897386.
    51. Eisen J, Ganley E, MacCallum CJ. Open science and reporting animal studies: who's accountable? PLoS Biol. 2014 Jan; 12(1):e1001757. PMID: 24409097; PMCID: PMC3883631.
    52. Coil DA, Lo JR, Chen R, Ward N, Robb FT, Eisen J. Draft Genome Sequence of the Arsenate-Respiring Bacterium Chrysiogenes arsenatis Strain DSM 11915. Genome Announc. 2013 Nov 14; 1(6). PMID: 24233593; PMCID: PMC3828317.
    53. Wu D, Jospin G, Eisen J. 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; PMCID: PMC3798382.
    54. Martin ME, Bhatnagar S, George MD, Paster BJ, Canfield DR, Eisen J, Solnick JV. The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque. PLoS One. 2013; 8(10):e76375. PMID: 24116104; PMCID: PMC3792980.
    55. Eisen J, Maccallum CJ, Neylon C. Expert failure: re-evaluating research assessment. PLoS Biol. 2013 Oct; 11(10):e1001677. PMID: 24115910; PMCID: PMC3792859.
    56. Holland-Moritz HE, Bevans DR, Lang JM, Darling AE, Eisen J, Coil DA. Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria). Genome Announc. 2013 Jun 27; 1(3). PMID: 23792744; PMCID: PMC3675516.
    57. Flanagan JC, Lang JM, Darling AE, Eisen J, Coil DA. Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announc. 2013 May 16; 1(3). PMID: 23682147; PMCID: PMC3656209.
    58. Coil DA, Doctor JI, Lang JM, Darling AE, Eisen J. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announc. 2013 May 09; 1(3). PMID: 23661474; PMCID: PMC3650433.
    59. Diep AL, Lang JM, Darling AE, Eisen J, Coil DA. Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announc. 2013 May 09; 1(3). PMID: 23661480; PMCID: PMC3650439.
    60. Lang JM, Darling AE, Eisen J. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One. 2013; 8(4):e62510. PMID: 23638103; PMCID: PMC3636077.
    61. Lo JR, Lang JM, Darling AE, Eisen J, Coil DA. Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4. Genome Announc. 2013 Mar 21; 1(2):e0008613. PMID: 23516213; PMCID: PMC3622973.
    62. Bendiks ZA, Lang JM, Darling AE, Eisen J, Coil DA. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria). Genome Announc. 2013 Mar 21; 1(2):e0012013. PMID: 23516225; PMCID: PMC3622984.
    63. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen J, Banfield JF. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013; 4:2120. PMID: 23979677; PMCID: PMC3903129.
    64. 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 J, 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; PMCID: PMC3549136.
    65. Kembel SW, Wu M, Eisen J, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012; 8(10):e1002743. PMID: 23133348; PMCID: PMC3486904.
    66. Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen J. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics. 2012 Oct 13; 13:264. PMID: 23061897; PMCID: PMC3481395.
    67. Tritt A, Eisen J, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One. 2012; 7(9):e42304. PMID: 23028432; PMCID: PMC3441570.
    68. Chandler JA, Eisen J, 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; PMCID: PMC3457106.
    69. Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen J, Facciotti MT. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One. 2012; 7(7):e41389. PMID: 22848480.
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    70. Eisen J. Badomics words and the power and peril of the ome-meme. Gigascience. 2012 Jul 12; 1(1):6. PMID: 23587201; PMCID: PMC3617454.
    71. Wu M, Chatterji S, Eisen J. Accounting for alignment uncertainty in phylogenomics. PLoS One. 2012; 7(1):e30288. PMID: 22272325; PMCID: PMC3260272.
    72. Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen J, 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; PMCID: PMC3276166.
    73. Chandler JA, Lang JM, Bhatnagar S, Eisen J, 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; PMCID: PMC3178584.
    74. Kembel SW, Eisen J, Pollard KS, Green JL. The phylogenetic diversity of metagenomes. PLoS One. 2011; 6(8):e23214. PMID: 21912589.
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    75. Darling AE, Tritt A, Eisen J, Facciotti MT. Mauve assembly metrics. Bioinformatics. 2011 Oct 01; 27(19):2756-7. PMID: 21810901; PMCID: PMC3179657.
    76. 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; PMCID: PMC3148223.
    77. Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen J. 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; PMCID: PMC3060911.
    78. Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen J, 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; PMCID: PMC3024254.
    79. 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 J, Cavanaugh CM. Complete genome sequence of Candidatus Ruthia magnifica. Stand Genomic Sci. 2010 Oct 27; 3(2):163-73. PMID: 21304746; PMCID: PMC3035367.
    80. Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen J. 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; PMCID: PMC2898799.
    81. Morgan JL, Darling AE, Eisen J. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One. 2010 Apr 16; 5(4):e10209. PMID: 20419134; PMCID: PMC2855710.
    82. Langille MG, Eisen J. BioTorrents: a file sharing service for scientific data. PLoS One. 2010 Apr 14; 5(4):e10071. PMID: 20418944; PMCID: PMC2854681.
    83. 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 J. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One. 2010 Mar 19; 5(3):e9605. PMID: 20333302; PMCID: PMC2841640.
    84. 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 J. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24; 462(7276):1056-60. PMID: 20033048; PMCID: PMC3073058.
    85. Eisen J, MacCallum CJ. Genomics of emerging infectious disease: A PLoS collection. PLoS Biol. 2009 Oct; 7(10):e1000224. PMID: 19855830; PMCID: PMC2757914.
    86. 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 J, 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; PMCID: PMC2699552.
    87. Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen J, Sieracki ME, Stepanauskas R. Assembling the marine metagenome, one cell at a time. PLoS One. 2009; 4(4):e5299. PMID: 19390573; PMCID: PMC2668756.
    88. Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen J, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet. 2009 Feb; 5(2):e1000362. PMID: 19197347; PMCID: PMC2628731.
    89. 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 J. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One. 2009; 4(1):e4207. PMID: 19148287; PMCID: PMC2615216.
    90. 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 J, 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; PMCID: PMC2612030.
    91. Wu M, Eisen J. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008 Oct 13; 9(10):R151. PMID: 18851752.
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    92. Wu D, Hartman A, Ward N, Eisen J. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One. 2008 Jul 02; 3(7):e2566. PMID: 18596968; PMCID: PMC2432038.
    93. Eisen J. PLoS Biology 2.0. PLoS Biol. 2008 Feb; 6(2):e48. PMID: 18303952; PMCID: PMC2253640.
    94. Hazen TH, Wu D, Eisen J, 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; PMCID: PMC2168046.
    95. Maresca JA, Graham JE, Wu M, Eisen J, 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; PMCID: PMC1905924.
    96. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen J, 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; PMCID: PMC1821060.
    97. Eisen J. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol. 2007 Mar; 5(3):e82. PMID: 17355177; PMCID: PMC1821061.
    98. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen J, 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; PMCID: PMC1821046.
    99. Eisen J, 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; PMCID: PMC1557398.
    100. Hamilton EP, Dear PH, Rowland T, Saks K, Eisen J, Orias E. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics. 2006 Oct; 88(4):443-51. PMID: 16782302; PMCID: PMC3169840.
    101. Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen J. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 2006 Jun; 4(6):e188. PMID: 16729848; PMCID: PMC1472245.
    102. Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet. 2006 Feb; 2(2):e21. PMID: 16482227; PMCID: PMC1366493.
    103. Penn K, Wu D, Eisen J, Ward N. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Appl Environ Microbiol. 2006 Feb; 72(2):1680-3. PMID: 16461727; PMCID: PMC1392894.
    104. Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen J. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet. 2005 Nov; 1(5):e65. PMID: 16311624; PMCID: PMC1287953.
    105. Badger JH, Eisen J, 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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    106. Desjardins C, Eisen J, Nene V. New evolutionary frontiers from unusual virus genomes. Genome Biol. 2005; 6(3):212. PMID: 15774035; PMCID: PMC1088936.
    107. Seshadri R, Adrian L, Fouts DE, Eisen J, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science. 2005 Jan 07; 307(5706):105-8. PMID: 15637277.
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    108. Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen J, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. 2004 Dec 16; 432(7019):910-3. PMID: 15602564.
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    109. Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen J. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol. 2004 Oct; 2(10):e303. PMID: 15383840; PMCID: PMC517821.
    110. Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen J, 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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    111. Seshadri R, Myers GS, Tettelin H, Eisen J, 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; PMCID: PMC397461.
    112. 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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    113. 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 J. 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; PMCID: PMC368164.
    114. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen J, 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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    115. Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen J, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM. Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol. 2003 Sep; 185(18):5591-601. PMID: 12949112; PMCID: PMC193775.
    116. Eisen J, Fraser CM. Phylogenomics: intersection of evolution and genomics. Science. 2003 Jun 13; 300(5626):1706-7. PMID: 12805538.
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    117. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen J, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolstø AB, Fraser CM. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 2003 May 01; 423(6935):81-6. PMID: 12721629.
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    118. Seshadri R, Paulsen IT, Eisen J, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM, Beanan MJ, Deboy RT, Daugherty SC, Brinkac LM, Madupu R, Dodson RJ, Khouri HM, Lee KH, Carty HA, Scanlan D, Heinzen RA, Thompson HA, Samuel JE, Fraser CM, Heidelberg JF. Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proc Natl Acad Sci U S A. 2003 Apr 29; 100(9):5455-60. PMID: 12704232; PMCID: PMC154366.
    119. Ermolaeva MD, Wu M, Eisen J, 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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    120. Fraser CM, Eisen J, Nelson KE, Paulsen IT, Salzberg SL. The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol. 2002 Dec; 184(23):6403-5; discusion 6405. PMID: 12426324; PMCID: PMC135419.
    121. Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen J, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol. 2002 Nov; 20(11):1118-23. PMID: 12368813.
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    122. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen J, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002 Oct 03; 419(6906):498-511. PMID: 12368864.
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    123. Paulsen IT, Seshadri R, Nelson KE, Eisen J, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A. 2002 Oct 01; 99(20):13148-53. PMID: 12271122; PMCID: PMC130601.
    124. Tettelin H, Masignani V, Cieslewicz MJ, Eisen J, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A. 2002 Sep 17; 99(19):12391-6. PMID: 12200547; PMCID: PMC129455.
    125. Eisen J, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A. 2002 Jul 09; 99(14):9509-14. PMID: 12093901; PMCID: PMC123171.
    126. Eisen J, Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol. 2002 Jun; 61(4):481-7. PMID: 12167367.
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