Jonathan Eisen Full CV

BIOGRAPHICAL SKETCH

JONATHAN A. EISEN

Professor

UC Davis Genome Center

Dept. of Evolution and Ecology

Dept. of Medical Microbiology and Immunology

University of California, Davis

Twitter: @phylogenomics

Lab: phylogenomics.wordpress.com

Blog: phylogenomics.blogspot.com

EDUCATION

1991-1998 Stanford University, Ph.D., Biological Sciences, 1998

1986-1990 Harvard College, A.B., Biology, Cum Laude, 1990

PROFESSIONAL EXPERIENCE

EMPLOYMENT

  • 2006-current Full Professor, University of California, Davis
    U. C. Davis Genome Center, Department of Medical Microbiology and Immunology in the School of Medicine, Department of Evolution and Ecology in the College of Biological Sciences
  • 2006-current Adjunct Scientist, Lawrence Berkeley National Laboratory, DOE-Joint Genome Institute
  • 2000-2008 Adjunct Faculty, Department of Biology , Johns Hopkins University
  • 2002-2006 Full Investigator, Department of Microbial Genomics, The Institute for Genomic Research (TIGR)
  • 1998-2002 Assistant Investigator, Department of Microbial Genomics, The Institute for Genomic Research (TIGR)
  • 1991-1998 PhD Student, Stanford University Department of Biological Sciences
    Research in the lab of Prof. Philip C. Hanawalt on the phylogenomics of DNA repair genes, proteins and processes.
  • 1991 Summer Field Assistant, Rocky Mountain Biological Laboratory .
    Worked with Prof. Ward Watt on molecular studies of isozyme polymorphisms in Colias butterflies.
  • 1989-1990 Research Assistant, Harvard University.
    Research in the lab of Prof. Colleen A. Cavanaugh . Applied molecular techniques to characterize the chemoautotrophic sulfur-utilizing endosymbionts of the marine invertebrate Solemya velum (Bivalvia:Mollusca).
  • 1988-1989 Research Assistant, Harvard University.
    Research in the lab of Prof. Fakhri A. Bazzaz . Helped design and conduct study on the effects of variation in light and water quality and quantity on the physiology of four species of birch (Betula). Also conducted independent experiment on circadian rhythms in Abutilon theophrasti.
  • 1988 Summer Field Assistant, Rocky Mountain Biological Laboratory .
    Worked with Prof. William A. Calder III from the University of Arizona. Monitored weight and temperature rhythms, dive energetics, foraging strategies, nesting success, and behavior of alpine hummingbirds.
  • 1987 Summer Intern InvestigatorPublic Defender Service of the District of Columbia .
    Interviewed and evaluated witnesses, law enforcement agents, and defendents; obtained signed witness statements; researched case histories; investigated and photographed crime scenes; delivered subpoenas, etc.

HONORS, AWARDS, and RECOGNITION

  • 2012 Talk on “Meet your microbes” featured on TED : >500,000 views as of 1/25/2014
  • 2012 Elected Fellow, American Academy of Microbiology
  • 2011 Benjamin Franklin Award for Open Access in the Life Sciences
  • 2010-2014 Member, Institute of Medicine Forum on Microbial Threats
  • 2010 Chair, Division R, American Society for Microbiology
  • 2008 Blog posting selected for “The Open Laboratory 2008” a collection of the best science blog posts of the year
  • 2004-2006 Member, Defense Science Studies Group (DSSG) Class of 2004-2005.
  • 2002-2009 Member, Faculty of 1000
  • 2002 Selected one of Esquire Magazine’s “ Best and Brightest Innovators ”
  • 1999 “Martin Rodbell Fellowship”, The Institute for Genomic Research
  • 1997 “ Walter J. Gores Award for Excellence in Teaching”, Stanford University
  • 1997 Stanford University Centennial TA Award
  • 1993 Stanford University Centennial TA Award
  • 1991-1994 National Science Foundation Predoctoral Fellowship

ADVISORY BOARDS and COMMITTEES

  • 2014-present Scientific Advisory Board, Symbiota
  • 2013-present Scientific Advisory Board, uBiome
  • 2012-2014 Scientific Advisory Board, ICBG Indonesia Biodiversity Project
  • 2011-present Scientific Advisory Board, The Earth Microbiome Project
  • 2010-2012 Member, Communications Committee, American Society for Microbiology
  • 2009-current Program Advisory Committee, Joint Genome Institute’s Microbial Genome & Metagenome Programs
  • 2008-2009 Committee on Life Sciences, National Academy of Sciences.
  • 2007-2014 Advisory Group, UC Davis Genome Center Nucleic Acids Core Facility
  • 2007-2009 Sci/Tech Advisory Board on Biosecurity, Lawrence Livermore National Laboratory
  • 2004-2007 Scientific Advisory Board, National Evolutionary Synthesis Center, North Carolina
  • 2003-2007 Scientific Advisory Board, Saccharomyces Genome Database , Stanford University
  • 2000-2002 Scientific Advisory Board, Geneformatics Inc.

EDITORIAL BOARDS and JOURNAL ROLES

TEACHING and CURRICULAR DEVELOPMENT

  • 2008-present. Co-Instructor, Biological Sciences 2C: Biodiversity and the Tree of Life, UC Davis.
  • 2007-2014. Guest Lecturer, Workshop in Applied Phylogenetics, Bodega Marine Lab.
  • 2008-2014. Instructor, EVE161-Microbial Phylogenomics, UC Davis. Taught every other year.
  • 2010-current. Advisor, UC Davis Collaborative Learning at the Interface of Mathematics and Biology (CLIMB) program.
  • 2002-2004. Lecturer and Co-Designer, Genome Sequencing and Analysis Course, Marine Biological Laboratory
  • 2003. Visiting Fellow. Comparative Genomics IGERT, University of Arizona.
  • 1999-2003. Guest Lecturer. Short Course on Molecular Evolution, Marine Biological Laboratory.
  • 1999-2001. Guest Lecturer. Cold Spring Harbor Laboratory Genomics Course.
  • 1999-2003. Guest Lecturer. Jackson Lab Genome Sequence Analysis Course.
  • 1996-1998. Head Teaching Assistant and Co-Course Designer. Stanford University “SME Core: The Heart” with Profs. David Botstein, Rick Myers, David Cox, et al.
  • 1995-1998 Stanford Science Design Committee (one of two graduate students on the committee). Responsible to redesigning the Science, Math and Engineering requirements for non-science majors at Stanford.
  • 1991-1998. Teaching Assistantships at Stanford University for Evolution and Ecology (taught by Prof. Carol Boggs), Genetics and Molecular Biology (taught by Robert Simoni), and DNA Replication (taught by Prof. Philip C. Hanawalt).
  • 1988-1990. Biology Undergraduate Group Committee, Harvard College
  • 1989. Prepared invited proposed for the creation of Environmental Science and Policy Major at Harvard
  • 1989-1990. Teaching Assistant. Organismal and Evolutionary Biology, Harvard University (taught by Karel Liem).
  • Ongoing Guest lectures on “Genomics” or “Phylogenomics” in a diversity of courses at UC Davis, UMD, and JHU over the last 14 years.

GRADUATE GROUP AFFILIATIONS

  • Population Biology Graduate Group (PBGG)
  • Graduate Group in Ecology (GGE)
  • Microbiology Graduate Group (GMIC)
  • Graduate Group in Computer Science (GGCS)
  • Integrative Genetics and Genomics (GIGG)
  • Biophysics Graduate Group (GBPH)

CRUISES and FIELD STATIONS

  • 2002 Atlantis/Alvin Research Cruise (Galápagos Rift Hydrothermal Vents Expedition 6: May 24-June 4, 2002). See Cruise Web Site.
  • 1992 Atlantis/Alvin Research Cruise (Cruise 125, Leg43, Dives 2541, 2542).
  • 1991, 1988 Summer Research Assistant, Rocky Mountain Biology Lab.
  • 1989 Tropical Ecology Field Course (Harvard University with field research in Venezuela).

PUBLICATIONS


25 HIGHLIGHTED PUBLICATIONS (people in the Eisen lab when work was done are in bold).

  1. Darling AEJospin GLowe E, Matsen FA 4th, Bik HMEisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2:e243. PMID: 24482762. PMC3897386.
  2. Sharpton TJ, Jospin GWu DLangille MGI, Pollard KS, Eisen JA. 2012. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resourceBMC Bioinformatics 13: 264. PMID: 23061897. PDF.
  3. Chandler JA, Lang JMBhatnagar SEisen JA, Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model systemPLoS Genetics 7(9): e1002272. PMID: 21966276. PDF.
  4. 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. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462(7276): 1056-1060. PMID: 20033048. PDF. Supplemental Information PDF.
  5. Hartman A, Lough D, Fiehn O, Barupal D, Fishbein T, Zasloff M, Eisen JA. 2009. Human gut microbiome adopts an alternative state following small bowel transplantationProceedings of the National Academy of Sciences USA 106(40): 17187-17192. PMID: 19805153. PDF.
  6. Wu MEisen JA. 2008. A simple, fast, and accurate method of phylogenomic inferenceGenome Biology 9: R151. PMID: 18851752. PDF.
  7. Newton ILG, 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 DEisen JA, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genomeScience 315: 998-1000. PMID: 17303757. PDF. Supplement PDF
  8. 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. 2006. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryotePLoS Biology 4: e286. PMID: 16933976. PDF.
  9. Wu D, Daugherty SC, van Aken S, Pai G, Watkins K, Khouri H, Tallon L, Zaborsky J, Dunbar H, Tran P, Moran NA, Eisen JA. 2006. Metabolic complementarity and genomics of the dual symbiosis of sharpshooters. PLoS Biology 4: e188. PMID: 16729848. PDF.
  10. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson JD, Hoffman J, Parsons R, Baden-Tillson H, Pfannkock C, Rogers Y-H, and Smith HO. 2004. Environmental whole genome shotgun sequencing: the Sargasso Sea. Science 304: 66-74. PMID: 15001713. PDF. Supplement.PDF.
  11. Wu M, Sun L, Vamathevan J, Riegler M, Deboy R, Brownlie J, McGraw E, Mohamoud Y, Lee P, Berry K, Khouri HM, Paulsen IT, Nelson KE, Martin W, Esser C, Ahmadinejad N, Wiegand C, Durkin AS, Nelson WC, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Gwinn M, Kolonay JF, Madupu R, Craven MB, Utterback T, Weidman J, Nierman WC, Aken SV, Tettelin H, O’Neill S, Eisen JA. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome massively infected with mobile genetic elements. PLoS Biology 2: 327-341. PMID: 15024419. PDF.
  12. Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. PMID: 12805538. PDF.
  13. 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 JA, 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. 2002. Genome sequence of the human malaria parasite Plasmodium falciparumNature 419: 498-511. PMID: 12368864. PDF.
  14. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF. 2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633. PMID: 11832943. PDF.
  15. Ward N, Eisen JA, Fraser CM, Stackebrandt E. 2001. Sequenced strains must be saved from extinction. Nature 414: 148. PMID: 11700527. PDF.
  16. Salzberg SL, White O, Peterson J, Eisen JA. 2001. Microbial genes in the human genome: lateral transfer or gene loss? Science 292: 1903-1906. PMID: 11358996PDF.
  17. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature 408: 796-815. PMID: 11130711. PDF.
  18. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM. 2000. The genome sequence of Vibrio cholerae, the etiologic agent of choleraNature 406: 477-483. PMID: 10952301.
  19. Eisen JA, Heidelberg JF, White O, Salzberg SL. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1: research 0011.1-0011.9. PMID: 11178265.
  20. Fraser CM, Eisen JA, Salzberg SL. 2000. Microbial genome sequencing. Nature 406: 799-803. PMID: 10963611.
  21. Eisen JA, Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutation Research 435: 171-213. PMID: 10606811.
  22. 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 SL, Smith HO, Venter JC, Fraser CM. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1Science 286: 1571-1577. PMID: 10567266.
  23. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysisGenome Research 8: 163-167. PMID: 9521918.
  24. Eisen JA. 1995. 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. Journal of Molecular Evolution 41: 1105-1123. PMID: 8587109. PDF.
  25. Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Research 23: 2715-2723. PMID: 7651832. PDF.

FULL LIST OF PUBLICATIONS (genome data reports listed separately at the end)

  1. Edwards J, Johnson C, Santos-Medellin C, Lurie E, Podishetty NK, Bhatnagar SEisen JA, Sundaresan V. Structure, variation, and assembly of the root-associated microbiomes of rice. In press. Proceedings of the National Academy of Sciences USA.
  2. Lang JMEisen JA, Zivcovik A. 2014. The microbes we eat: abundance and taxonomy of microbes consumed in a days worth of model mealsPeer J 2: e659.
  3. Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JADarling AE, Facciotti MT. 2014. Phylogenetically driven sequencing of extremely halophilic Archaea reveals strategies for static and dynamic osmo-response. PLOS Genetics 10: e1004784. doi: 10.1371/journal.pgen.1004784. PMID: 25393412.
  4. Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton IL, Woyke T, Wu DLang JMEisen JA, Cavanaugh CM. 2014. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 15: 924. PMID: 25342549.
  5. 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. 2014. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLOS Biology 12: ee1001920. PMID: 25093819. PMCID: PMC4122341.
  6. Bik HMCoil DA, Eisen JA. 2014. microBEnet: lessons learned from building an interdisciplinary scientific community in the online sphere. PLOS Biology 12: e1001884. PMID: 24937755. PMCID: PMC4060986.
  7. Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. 2014. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415. PMID: 24918035. PMCID: PMC4045339.
  8. Darling AEJospin GLowe E, Matsen FA 4th, Bik HMEisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243. PMID: 24482762. PMC3897386.
  9. Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Faccioti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. 2014. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt MarshEnvironmental Microbiology doi: 10.1111/1462-2920.12388. PMID: 24428801.
  10. Eisen JA, Ganley E, Maccallum CJ. 2014. Open science and reporting animal studies: Who’s accountable? PLOS Biology 12: e1001757. PMID: 24409097. PMC3883631.
  11. 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. 2013. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME Journal 8: 1-3. PMCID: PMC3869023.
  12. Wu D, Jospin GEisen JA. 2013. 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 8(10): e77033. doi:10.1371/journal.pone.0077033. PMCID: PMC3798382.
  13. Eisen JA, MacCallum CJ, Neylon C. 2013. Expert failure: re-evaluating research assessment. PLOS Biology 11(10): e1001677.  PMCID: PMC3792859.
  14. Martin ME, Bhatnagar S, George MD, Paster BJ, Canfield DR, Eisen JA, Solnick JS. 2013. The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque. PLOS ONE 8(10): e76375. PMCID: PMC3792980.
  15. Castelle C, Hug LA, Wrighton KC, Thgomas, BC, Williams KH, Wu D, Tringe SG, Singer S, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4: 2120. PMCID: PMC3903129.
  16. Garrity G, Banfield J, Eisen JA, van der Lelie N, McMahon T, Rusch D, DeLong E, Moran M, Currie C, Fuhrman 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, 2012. Standards in Genomic Sciences, 8: 561-570. PMCID: PMC3910701.
  17. 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. 2013. Insights into the phylogeny and coding potential of microbial dark matter.  Nature 499(7459): 431-7. doi: 10.1038/nature12352.
  18. Wu D, Jospin GEisen JA. 2013. Systematic identification of gene families for use as markers for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroupsPLOS One 8: e77033. PMCID: PMC3798382.
  19. Lang JM, Darling AEEisen JA. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS ONE 8: e62510. PMCID: PMC3636077.
  20. Rands C, Darling AE, 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. 2013. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 14: 95.
  21. 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. 2013. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences USA 110: 1053-1058. PDF.
  22. Eisen JA. 2012. Phylogenetic and phylogenomic approaches to analysis of microbial communities. In “The Social Biology of Microbial Communities – A Report from the National Academy of Sciences Forum on Microbial Threats.” PDF.
  23. Traag B, Pugliese A, Eisen JA, Losick R. 2012. Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis. Journal of Bacteriology 195: 253-260. PMID: 23123912. PDF.
  24. Kembel SW, Wu MEisen JA, Green JL. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Computational Biology 8: e1002743. PMID: 23133348. PDF.
  25. Sharpton TJ, Jospin G, Wu D, Langille MGI, Pollard KS, Eisen JA. 2012. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics 13: 264. PMID: 23061897. PMCID: PMC3481395. PDF.
      • More information and data links available here.
  26. Jiang X, Langille MGINeches RY, Elliot MA, Levin SA, Eisen JA, Weitz JS, Dushoff J. 2012. Functional biogeography of ocean microbes: dimension reduction of metagenomic data identifies biological patterns across scalesPLoS ONE 7: e43866. PMID: 23049741. PMCID: PMC3445553 PDF.
  27. Tritt AEisen JA, Facciotti M, Darling A. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7: e42304 . PMID: 23028432. PMCID: PMC3441570 PDF.
  28. Chandler JA, Eisen JA, Kopp A. 2012. Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hostsApplied and Environmental Microbiology 78: 7327-7336. PMID: 22885750. PDF.
  29. Lynch EA, Langille MGIDarling AEWilbanks EGHaltiner C, Shao KSY, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. 2012. Sequencing of seven haloarchaeal genomes reveals patterns of genomic fluxPLoS ONE 7: e41389. PMID: 22848480. PDF.
  30. Eisen JA. 2012. Badomics words and the power and peril of the ome-memeGigascience 1:6. PDF. PMCID: PMC3617454.
  31. Langille MGI, Laird M, Hsiao W, Chiu T, Eisen JA, Brinkman F. 2012. MicrobeDB: a locally maintainable database of microbial genomic sequence. Bioinformatics 28: 1947-1948. PMID: 22576174. PDF.
  32. Wu M, Chatterji SEisen JA. 2012. Accounting for alignment uncertainty in phylogenomicsPLoS ONE 7: e30288. PMID: 22272325. PMCID: PMC3260272. PDF.
  33. Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. 2012. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14: 162-176. PMID: 21914098. PMCID: PMC3429862. PDF.
  34. 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. 2011. Genome-scale analysis of programmed DNA elimination sites in Tetrahymena thermophila. G3 1: 515-522. PMID: 22384362. PDF.
  35. Chandler JA, Lang JMBhatnagar SEisen JA, Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system. PLoS Genetics 7: e1002272. PMID: 21966276. PDF. Data at Figshare.
  36. Darling ATritt AEisen JA, Facciotti M. 2011. Mauve assembly metrics. Bioinformatics 27: 2756-2757. PMID: 21810901. PDF.
  37. Kembel S, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomesPLoS ONE 6: e23214. PMID: 21912589. PDF.
  38. Mindell DP, Fisher BL, Roopnarine P, Eisen JA, Mace GM, Page RDM, Pyle RL. 2011. Aggregating, tagging and integrating biodiversity research. PLoS ONE 6: e19491. PMCID: PMC3148223. PDF.
  39. Martiny JBH, Eisen JAPenn K, Allison SD, Horner-Devine MC. 2011. Drivers of bacterial β-diversity depend on spatial scale. Proceedings of the National Academy of Sciences USA 108: 7850-7854. PMID: 21518859. PDF.
  40. Wu DWu M, Halpern A, Rusch D, Yooseph S, Frazier M, Venter JC, Eisen JA. 2011. Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic treesPLoS ONE 6: e18011. PMID: 21437252. PDF.
  41. Sharpton TJ, Risenfeld S, Kembel SW, Ladau J, O’Dwyer J, Green JL, Eisen JA, Pollard KS. 2011. PhylOTU: A high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology 7: e1001061. PMID: 21283775. PMCID: PMC3024254. PDF.
  42. 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. 2010The genome sequence of Methanohalophilus mahii SLP reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010: 690737. PMID: 21234345. PDF.
  43. Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA. 2010. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics 11: 317. PMID: 20540779. PDF.
  44. 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. 2010. Meeting Report. The Terabase Metagenomics workshop and the vision of an Earth Microbiome Project. Standards in Genomic Sciences 3: 243-248. PMID: 21304727. PDF.
  45. Morgan JLDarling AEisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial communityPLoS ONE 5: e10209. PMID: 20419134. PDF. Data available here.
  46. Langille MGIEisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5: e10071. PMID: 20418944. PDF.
  47. 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. 2010. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS ONE 5: e9605. PMID: 20333302. PDF.
  48. 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. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaNature 462: 1056-1060. PMID: 20033048. PDF.Supplemental Information PDF.
  49. Hartman A, Lough D, Fiehn O, Barupal D, Fishbein T, Zasloff M, Eisen JA. 2009. Human gut microbiome adopts an alternative state following small bowel transplantationProceedings of the National Academy of Sciences USA 106: 17187-17192. PMID: 19805153. PDF.
  50. Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collection. PLoS Biology 7: e1000224. PMID: 19855830. PDF.
  51. 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 JABadger JH, Distel DL. 2009. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS ONE 4: e6085. PMID: 19568419. PDF.
  52. Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. 2009. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genetics 5: e1000362. PMID: 19197347. PDF.
  53. 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. 2009. Assembling the marine metagenome, one cell at a timePLoS ONE 4: e5299. PMID: 19390573. PDF.
  54. Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb FT Colman AS, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 4: e4207. PMID: 19148287. PDF.
  55. Eisen JA. 2009. Genomic evolvability and the origin of novelty: studying the past, interpreting the present, and predicting the future. In Relman DA, Hamburg MA, Choffness ER, Mack A (ed), Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. The National Academies Press, Washington, DC. PDF.
  56. Eisen JA. 2009. What is so bad about brain doping? Apparently, NIH thinks something is. In Rohn J, (ed), The Open Laboratory 2008. Lulu.Com.
  57. Eisen JA. 2008. PLoS Biology 2.0. PLoS Biology 6: e48. PMID: 18303952.
  58. Valdes J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. 2008. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applicationsBMC Genomics 9: 597. PMID: 19077236. PDF.
  59. 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, Methe BA. 2008. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics 9: 562. PMID: 19036158. PDF.
  60. 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. 2008. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitansGenome Biology 9: R158. PMID: 19000309. PDF.
  61. Wu MEisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9: R151. PMID: 18851752. PDF.
  62. Wu DHartman A, Ward N, Eisen JA. 2008. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 3: e2566. PMID: 18596968. PDF.
  63. Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. RECOMB 2008. PDF.
  64. Hazen TH, Wu D, Eisen JA, Sobecky PA. 2007. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Applied and Environmental Microbiology 73: 7703-7710. PMID: 17921277. PDF.
  65. Pfarr K, Foster J, Slatko B, Hoerauf A, Eisen JA. 2007. On the taxonomic status of the intracellular bacteria Wolbachia pipientis: should this species naming include the intracellular bacteria of filarial nematodes? International Journal of Systematic and Evolutionary Microbiology 57: 1677-1678. PMID: 17684235. PDF.
  66. Maresca JA, Graham JE, Wu MEisen JA, Bryant DA. 2007. Identification of a new family of lycopene cyclases in photosynthetic bacteriaProceedings of the National Academy of Sciences USA 104: 11784-11789. PMID: 1760690. PDF.
  67. Norais C, Hawkins M, Eisen JAHartman A, Myllkallio H, Allers T. 2007. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genetics 3: e77. PMID: 17511521. PDF.
  68. Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5: e82. PMID: 17355177. PDF.
  69. 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. 2007. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biology 5: e16 . PMID: 17355171. PDF.
  70. 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, Falcon 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. 2007. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern tropical pacific. PLoS Biology 5: e77. PMID: 17355176. PDF.
  71. Newton ILG, 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 DEisen JA, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998-1000. PMID: 17303757. PDF. Supplement PDF.
  72. Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Lartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. 2006. Evolution of sensory complexity recorded in a myxobacterial genome. Proceedings of the National Academy of Sciences USA 103: 15200-5. PMID: 17015832. PDF.
  73. Eisen JA, Coyne RS, Wu MWu 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. 2006. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology 4: e286. PMID: 16933976. PDF.
  74. Wu D, Daugherty SC, van Aken S, Pai G, Watkins K, Khouri H, Tallon L, Zaborsky J, Dunbar H, Tran P, Moran NA, Eisen JA. 2006. Metabolic complementarity and genomics of the dual symbiosis of sharpshooters. PLoS Biology 4: e188. PMID: 16729848. PDF.
  75. Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, 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. 2006. Comparative genomics of emerging human ehrlichiosis agentsPLoS Genetics 2: e21. PMID: 16482227. PDF.
  76. Leebens-Mac J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, DePamphilis C, DeSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin, EV, Mishler BD, Philippe H, Pirer JC, Qiu Y-L, Rheee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. 2006. Taking the first steps towards a phylogenetic reporting standard: minimal information about a phylogenetic analysis (MIAPA). OMICS 10: 231-238PDF.
  77. Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E. 2006. The use of HAPPY mapping for the higher order assembly of the Tetrahymena genomeGenomics 88: 443-451PDF.
  78. Penn KWu DEisen JA, Ward N. 2006. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72: 1680-1683. PMID: 16461727. PDF.
  79. Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA. 2005. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genetics 1: e65. PMID: 16729848. PDF.
  80. Schmidt EW, Nelson JT, Rakso D, Sudek S, Eisen JA, Haygood MG, Ravel J. 2005. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the obligate cyanobacterial symbiont of Lissoclinum patella (ascidia). Proceedings of the National Academy of Sciences USA 102: 7315-7320. PMID: 15883371. PDF.
  81. Badger JHEisen JA, Ward N. 2005. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA-based phylogenetic analysis; implications for the taxonomy of the orders Rhodobacterales and Caulobacterales. International Journal of Systematic and Evolutionary Microbiology 55: 1021-1026. PMID: 15879228. PDF.
  82. Desjardins CEisen JA, Nene V. 2005. New evolutionary frontiers from unusual virus genomesGenome Biology 6: 212-213. PMID: 15774035. PDF.
  83. Seshadri R, Adrian L, Fouts DE, Phillippy AM, Eisen JA, Methe BM, Deboy RT, Ward NL, Nelson WC, Khouri HM, Kang KH, Tran K, Forberger HA, Robinson JM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Fraser CM, Zinder SH, Heidelberg JF. 2005. Genome sequence of the anaerobic PCE-bioremediating bacterium, Dehalococcoides ethenogenes strain 195Science 307: 105-108. PMID: 15637277. PDF.
  84. Robb FT, Gonzalez JM, Sokolova T, Chernyh N, Lebedinski A, Tallon LJ, Jones K, Wu MEisen JA. 2005. Primary energy metabolism in geothermal environments: the role of carbon monoxideIn Inskeep WP, McDermott TR, (ed), Geothermal Biology and Geochemistry in Yellowstone National Park. Montana State University Thermal Biology Institute, Bozeman, MT. pp. 163-170. PDF.
  85. Eisen JA. 2005. Coordinating efforts to understand microbes in the environment. Letter to the Editor in Microbe 71: 157. PDF.
  86. Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RB, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, 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. 2004. Genome sequence of Silicibacter pomeroyi reveals unique adaptations to the marine environmentNature 432: 910-913. PMID: 15602564. PDF.
  87. Tanaka M, Earl AM, Howell HA, Park M-J, Eisen JA, Peterson SN, Battista JR. 2004. Analysis of Deinococcus radiodurans’ transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics 168: 21-33. PMID: 15454524. PDF. Supplement.PDF
  88. Ward NM, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy R, Seshadria R, Salzberg SL, Jensen HB, Birkeland NK, Nelson W, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Feldblyum TV, Fraser CM, Lillehaug J, Eisen JA. 2004. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)PLoS Biology 2: 1616-1628. PMID: 15383840. PDF.
  89. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson JD, Hoffman J, Parsons R, Baden-Tillson H, Pfannkock C, Rogers Y-H, and Smith HO. 2004. Environmental whole genome shotgun sequencing: the Sargasso Sea. Science 304: 66-74. PMID: 15001713. PDF. Supplement.PDF.
  90. Wu M, Sun L, Vamathevan J, Riegler M, Deboy R, Brownlie J, McGraw E, Mohamoud Y, Lee P, Berry K, Khouri HM, Paulsen IT, Nelson KE, Martin W, Esser C, Ahmadinejad N, Wiegand C, Durkin AS, Nelson WC, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Gwinn M, Kolonay JF, Madupu R, Craven MB, Utterback T, Weidman J, Nierman WC, Aken SV, Tettelin H, O’Neill S, Eisen JA. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome massively infected with mobile genetic elements. PLoS Biology 2: 327-341. PMID: 15024419. PDF.
  91. Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen JA, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg SL, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NM. 2004. Gene synteny and evolution of genome architecture in trypanosomatids. Molecular and Biochemical Parasitology 134: 183-191. PMID: 15003838. PDF.
  92. 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. 2004. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proceedings of the National Academy of Sciences USA 101: 5646-5651. PMID: 15064399. PDF.
  93. 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. 2004. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature Biotechnology 22: 554-559. PMID: 15077118. PDF
  94. 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. 2003. The genome of Geobacter sulfurreducens: insights into metal reduction in subsurface environments. Science 302: 1967-1969. PMID: 14671304. PDF.
  95. Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, 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. 2003. Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83. Journal of Bacteriology 185: 5591-5601. PMID: 12949112. PDF.
  96. 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. 2003. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophageJournal of Bacteriology 185: 5220-5233. PMID: 12923095. PDF.
  97. Yang R-Z, Huang Q, Xu A, McLenithan JC, Eisen JA, Shuldiner AR, Alkan S, Gong D-W. 2003. Comparative studies of resistin expression and phylogenomics in human and mouse. Biochemical and Biophysical Research Communications 310: 927–935. PMID: 14550293. PDF.
  98. Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD. 2003. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. Journal of Bacteriology 185: 3392-3399. PMID: 12754238. PDF.
  99. Seshadri R, Paulsen IT, Eisen JA, 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. 2003. Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proceedings of the National Academy of Sciences USA 100: 5455-5460. PMID: 12704232. PDF.
  100. Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. PMID: 12805538. PDF.
  101. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071-2074. PMID: 12663927. PDF.
  102. Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. 2003. The age of the Arabidopsis thaliana genome duplication. Plant Molecular Biology 51: 859-866. PMID: 12777046. PDF.
  103. Shank T, Fornari D, Yoerger S, Humphries S, Bradley A, Hammond S, Lupton J, Schierer D, Collier R, Reysenbach A-L, Ding K, Seyfried W, Butterfield D, Olson E, Lilley M, Ward N, Eisen JA. 2003. Deep submergence synergy: Alvin and ABE explore the Galápagos Rift at 86°W. EOS 84: 425, 432-433. PDF.
  104. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, 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, Kolsto AB, Fraser CM. 2003. The complete genome sequence of Bacillus anthracis Ames and comparison to closely-related B. cereus group bacteria. Nature 423: 81-86. PMID: 12721629. PDF.
  105. Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Dusterhoft A, Tummler B, Fraser CM. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental Microbiology 4: 799-808. PMID: 12534463. PDF.
  106. Eisen JA, Wu M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theoretical and Population Biology 61: 481-487. PMID: 12167367. PDF.
  107. Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, 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. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nature Biotechnology 20: 1118-1123. PMID: 12368813. PDF.
  108. Van Houten B, Eisen JA, Hanawalt PC. 2002. A cut above: discovery of an alternative excision repair pathway in bacteria. Proceedings of the National Academy of Sciences USA 99: 2581-2583. PMID: 11880612. PMCID: PMC122389. PDF.
  109. 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 JA, 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. 2002. Genome sequence of the human malaria parasite Plasmodium falciparumNature 419: 498-511. PMID: 12368864. PDF.
  110. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, 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. 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbiontsProceedings of the National Academy of Sciences USA 99: 13148-13153. PMID: 12271122. PDF.
  111. Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. 2002. The value of complete microbial genome sequencing (You get what you pay for). Journal of Bacteriology 184: 6403-6405. PMID: 12426324. PDF.
  112. 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 Jr, Venter JC, Fraser CM. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strainsJournal of Bacteriology 184: 5479-5490. PMID: 12218036. PDF.
  113. Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, 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. 2002. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiaeProceedings of the National Academy of Sciences USA 99: 12391-12396. PMID: 12200547. PDF.
  114. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF. 2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633. PMID: 11832943. PDF.
  115. Eisen JA, 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, Venter JC, Gruber TM, Ketchum KA, Tettelin H, Bryant DA, Fraser CM. 2002. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proceedings of the National Academy of Sciences USA 99: 9509-9514. PMID: 12093901. PDF.
  116. DasSarma S, Kennedy SP, Berquist B, Ng WV, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L. 2002. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeonPhotosynthesis Research 70: 3-17. PMID: 16228359. PDF.
  117. Eisen JA. 2002. Brouhaha over the other yeast. Nature 415: 845-848. PMID: 11859347. PDF.
  118. Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, Eisen JA, Slatko B. 2002. Sequencing and analysis of a 63 kb BAC from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi. International Journal of Parasitology 32: 159-166. PMID: 11812492. PDF.
  119. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida Jr NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee Sr D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li M-J, McClelland R, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao Z-Y, Dolan M, Chumley F, Tingey SC, Tomb J-F, Gordon MP, Olson MV, Nester EW. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294: 2317-2323. PMID: 11743193. PDF.
  120. Eisen JA. 2001. Response to Mackiewicz et al. Genome Biology 2: interactions1004.1-1004.4. PDF.
  121. Tettelin H, Nelson KE, Paulsen I, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin S, Gwinn M, Kolonoay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CK, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM. 2001. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293: 498-506. PMID: 11463916. PDF. Supplemental information
  122. Ward N, Eisen JA, Fraser CM, Stackebrandt E. 2001. Sequenced strains must be saved from extinction. Nature 414: 148. PMID: 11700527. PDF.
  123. Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM. 2001. Complete genome sequence of Caulobacter crescentusProceedings of the National Academy of Sciences USA 98: 4136-4141. PMID: 11259647. PDF.
  124. Salzberg SL, Eisen JA. 2001. Lateral gene transfer or viral colonization? Science 293: 1048. PMID: 11503638. PDF.
  125. Salzberg SL, White O, Peterson J, Eisen JA. 2001. Microbial genes in the human genome: lateral transfer or gene loss? Science 292: 1903-1906. PMID: 11358996PDF.
  126. Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes H-W. 2001. Sequence and analysis of the Arabidopsis genome. Current Opinion in Plant Biology 4: 105-110. PMID: 11228431. PDF.
  127. Nelson KE, Eisen JA, Fraser CM. 2001. The genome of Thermotoga maritima MSB8. Methods in Enzymology 330: 169-180. PMID: 11210497. PDF.
  128. Eisen JA. 2001. GastrogenomicsNature 409: 463-465. PMID: 11206526. PDF.
  129. Haft DH, Loftus, BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O. 2001. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Research 29: 41-43. PMID: 11125044. PMCID: PMC29844. PDF.
  130. Eisen JA. 2000. Microbial and plant genomics. Journal of Biolaw and Business, Spec Supp 21-24. PDF.
  131. 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 JA, Fraser CM. 2000. Genome sequences of Chlamydia trachomatis MoPn and C. pneumoniae AR39Nucleic Acids Research 28: 1397-1406. PMID: 10684935. PDF.
  132. Quetier F, Brennicke A, Eisen JA. 2000. Integration of the three genomes in the plant cell: the extent of protein and nucleic acid traffic between nucleus, plastids and mitochondria, In Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815. PMID: 11130711. PDF.
  133. Britt AB, Eisen JA. 2000. DNA repair and recombination, In Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815. PMID: 11130711. PDF.
  134. Nierman W, Eisen JA, Fleischmann RD, Fraser CM. 2000. Genome data: what do we learn? Current Opinion in Structural Biology 10: 343-348. PMID: 10851186. PDF.
  135. 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. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287: 1809-1815. PMID: 10710307. PDF.
  136. Coleman MA, Eisen JA, Mohrenweiser HW. 2000. Cloning and characterization of HARP: A prokaryotic HepA related SNF2 helicase protein from human and mouse. Genomics 65: 274-282. PMID: 10857751. PDF.
  137. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM. 2000. The genome sequence of Vibrio cholerae, the etiologic agent of choleraNature 406: 477-483. PMID: 10952301. PDF. Supplemental information.
  138. Eisen JA, Heidelberg JF, White O, Salzberg SL. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1: research 0011.1-0011.9. PMID: 11178265. PDF.
  139. Pollock DD, Eisen JA, Doggett NA, Cummings MP. 2000. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Molecular Biology and Evolution 7: 1776-1788. PMID: 11110893. PDF.
  140. Eisen JA. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Current Opinion in Genetics and Development 10: 606-611. PMID: 11088009. PDF.
  141. Eisen JA. 2000. Assessing evolutionary relationships among microbes from whole genome analysis. Current Opinion in Microbiology 3: 475-480. PMID: 11050445. PDF.
  142. Fraser CM, Eisen JA, Fleischmann RD, Ketchum KA, Peterson S. 2000. Comparative genomics and understanding of microbial biology. Emerging Infectious Diseases 6: 505-512. PMID: 10998382. PDF.
  143. Fraser CM, Eisen JA, Salzberg SL. 2000. Microbial genome sequencingNature 406: 799-803. PMID: 10963611. PDF.
  144. Nierman W, Eisen JA, Fraser CM. 2000. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis. Research in Microbiology 151: 79-84. PMID: 10865951. PDF.
  145. Lin X, Kaul S, Rounsley S, Shea TP, Benito M-I, 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, Aken SV, 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. 1999. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761-768. PMID: 10617197. PDF.
  146. Eisen JA, Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutation Research 435: 171-213. PMID: 10606811. PDF.
  147. Eisen JA. 1999. Going to extremes. Trends in Genetics 15: 218-219. PMID: 10419407. PDF.
  148. Eisen JA. 1999. Mechanistic basis of microsatellite instability. In Microsatellites: Evolution and Applications (DB Goldstein and C Schlotterer, eds). Oxford University Press, Oxford. PDF.
  149. 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 SL, Smith HO, Venter JC, Fraser CM. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1Science 286: 1571-1577. PMID: 10567266. PDF.
  150. 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. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-329. PMID: 10360571. PDF.
  151. Eisen JA. 1998. Evolution of DNA repair genes, proteins and processes. PhD Thesis. Stanford University. PDF.
  152. Wei M-H, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA, Lerman MI. 1998. In-silico initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. Human Genetics 103: 355-364. PMID: 9799093. PDF.
  153. Eisen JA. 1998. A phylogenomic study of the MutS family of proteins. Nucleic Acids Research 26: 4291-4300. PMID: 9722651. PMCID: PMC147835. PDF.
  154. Gruber TM, Eisen JA, Gish K, Bryant DA. 1998. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS Microbiology Letters 162: 53-60. PMID: 9595663. PMCID: PMC3182672. PDF.
  155. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysisGenome Research 8: 163-167. PMID: 9521918. PDF.
  156. White RB, Eisen JA, Kasten TW, Fernald RD. 1998. Second gene for gonadotropin-releasing hormone in humans. Proceedings of the National Academy of Sciences USA 95: 305-309. PMID: 941937. PMCID: PMC18209. PDF.
  157. Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feastNature Medicine 3: 1076-1078. PMID: 9334711. PMCID: PMC315595. PDF.
  158. Eisen JA. 1997. The genetic data environment: a user modifiable and expandable multiple sequence analysis package, In Methods in Molecular Biology vol 70: Sequence Data Analysis Guidebook (SR Swindell, ed), Humana, Totowa, NJ, pp. 13-38. PMID: 90896. PDF.
  159. Shafer RW, Eisen JA, Merigan TC, Katzenstein DA. 1997. Sequence and drug susceptibility of subtype C reverse transcriptase from HIV-1-seroconverters in ZimbabweJournal of Virology 71: 5441-5448. PMID: 9188616. PMCID: PMC191784. PDF.
  160. Eisen JA. 1995. 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. Journal of Molecular Evolution 41: 1105-1123. PMID: 8587109. PMCID: PMC3188426. PDF.
  161. Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Research 23: 2715-2723. PMID: 7651832. PMCID: PMC307096. PDF.
  162. Eisen JA, Benito M-I, Walbot V. 1994. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Research 22: 2634-2636. PMID: 8041625. PMCID: PMC308220. PDF. Prosite motif
  163. Liu SK, Eisen JA, Hanawalt PC, Tessman IW. 1993. recA mutations that reduce the constitutive coprotease activity of the RecA1202(PrtC) protein: possible involvement of interfilament association in proteolytic and recombination activitiesJournal of Bacteriology 175: 6518-6529. PMID: 8407828. PMCID: PMC206762. PDF.
  164. Eisen JA, Smith SW, Cavanaugh CM. 1992. Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum Say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysisJournal of Bacteriology 174: 3416-3421. PMID: 1577710. PMCID: PMC206016. PDF.

Genome report publications. We have been publishing “report” papers for genomes sequenced as part of multiple projects. I am listing them separately because of the large number of reports.

Genomes of Plant and Animal Microbes

  1. Ettinger CL, Shehata HR, Johnston-Monje D, Raizada MN, Eisen JA. Draft Genome Sequence of Enterobacter sp. str. UCD-UG_FMILLET (Phylum Proteobacteria). Genome Announcements
  2. Ettinger CL, Shehata HR, Johnston-Monje D, Raizada MN, Eisen JADraft Genome Sequence of Burkholderia gladioli str. UCD-UG_CHAPALOTE (Phylum Proteobacteria). Genome Announc 3(1):e01462-14. doi:10.1128/genomeA.01462-14.
  3. Lee RDJospin GCoil DAEisen JA. 2014. Draft genome sequence of the endosymbiont “Candidatus Ruthia magnifica” UCD-CM (Phylum Proteobacteria). Genome Announcements 2: e00717-14. PMID: 25035337. PMCID: PMC4102874.
  4. 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. 2010. Complete genome sequence of Candidatus Ruthia magnificaStandards in Genomic Sciences 3: 163-173.
  5. Dunitz MI, James PM, Jospin GEisen JACoil DA, Chandler JA. 2014. Draft genome sequence of Tatumella sp. strain UCD-D_suzukii (Phylum Proteobacteria) isolated from Drosophila suzukii larvaeGenome Announcements 2: e00349-14. PMID: 24762940. PMCID: PMC3999497.

Genomics of Sepsis

  1. Dunitz MICoil DAJospin GEisen JA, Adams JY. 2014. Draft genome sequences of Escherichia coli strains isolated from septic patients. Genome Announcements 2:e01278-14; doi:10.1128/genomeA.01278-14

Collaboration with Sima Tokajian who was on sabbatical in the Eisen lab in 2013

  1. Tokajian S, Eisen JAJospin GCoil DA. 2014. Draft genome sequences of Streptococcus pyogenes strains associated with throat and skin infections in LebanonGenome Announcements 2: e00358-14. PMCID: PMC4022803.
  2. Tokajian S, Eisen JAJospin G, Farra A, Coil DA. 2014. Draft genome sequences of extended-spectrum β-lactamase-producing Escherchia coli strains isolated from patients in LebanonGenome Announcements 2: e00123-14. PMCID: PMC3931373.
  3. Tokajian S, Eisen JAJospin G, Farra A, Coil DA. 2014. Draft genome sequence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from a patient in LebanonGenome Announcements 2: e00121-14. PMCID: PMC3931372.

NSF Tree of Life Project

  1. Bhatnagar S, Badger JH, Madupu R, Khouri HM, O’Connor EM, Robb FT, Ward NL, Eisen JA. In press. Genome sequence of the sulfate-reducing thermophilic bacterium Thermodesulfovibrio yellowstonii DSM 11347T (Phylum Nitrospirae). Genome Announcements 3: e01489-14. doi:10.1128/genomeA.01489-14.
  2. Bhatnagar S, Badger JH, Madupu R, Khouri HM, O’Connor EM, Robb FT, Ward NL, Eisen JA. 2014. Genome sequence of a sulfate-reducing thermophilic bacterium, Thermodesulfobacterium commune DSM 2178T (phylum Thermodesulfobacteria). Genome Announcements 3: e01490-14. doi:10.1128/genomeA.01490-14.
  3. Holland-Moritz HECoil DABadger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA. 2014. Draft genome sequence of the pyridinediol-fermenting bacterium Synergistes jonesii 78-1Genome Announcements 2: e00833-14.
  4. Alexiev ACoil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA. 2014. Complete genome sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announcements 2: e00470-14. PMID: 24831154. PMCID: PMC4022818.
  5. Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA. 2014. Complete genome sequence of the extreme thermophile Dictyoglomus thermophilum H-6-12. Genome Announcements 2: e00109-14. PMCID: PMC3931368.
  6. Coil DALo JRChen R, Ward N, Robb FT, Eisen JA. 2013. Draft genome sequence of the arsenate respiring bacterium Chrysiogenes arsenatis DSM11915. Genome Announcements 1: e00953-13. PMCID: PMC3828317.

Microbiology of the Built Environment undergraduate project on “swabs to genomes”.

  1. Holland-Moritz HEBevans DRLang JMDarling AEEisen JA, Coil DA. 2013. Draft genome Sequence of Leucobacter sp. strain UCD-THU (Phylum Actinobacteria). Genome Announcements 1: e00325-13. PMCID: PMC3675516.
  2. Coil DADoctor JILang JMDarling AEEisen JA. 2013. Draft genome sequence of Kocuria sp. strain UCD-OTCP (Phylum Actinobacteria). Genome Announcements 1: e00172-13. PMCID: PMC3650433.
  3. Flanagan JCLang JMDarling AEEisen JACoil DA. 2013. Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announcements 1: e00244-13. PMCID: PMC3656209.
  4. Diep ALLang JMDarling AEEisen JACoil DA. 2013. Draft genome sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announcements 1: e00197-13. PMCID: PMC3650439.
  5. Bendiks ZALang JMDarling AEEisen JACoil DA. 2013. Draft genome sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria). Genome Announcements 1: e00120-13. PMCID: PMC3622984.
  6. Lo JRLang JMDarling AE, Eisen JACoil DA. 2013. Draft genome sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4Genome Announcements 1: e00086-13. PMCID: PMC3622973.

DOE-JGI Genomic Encyclopedia of Bacteria and Archaea

  1. 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. 2014. Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Standards in Genomic Sciences 9: 1105-17.
  2. 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. 2014. 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. Standards in Genomic Sciences 9: 1076-88.
  3. 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. 2013. Genome sequence of Frateuria aurantia type strain (Kondô 67(T)), a xanthomonade isolated from Lilium auratium Lindl. Standards in Genomic Sciences 9: 83-92.
  4. 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. 2013. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences 9: 57-70. PMID: 24501645.
  5. Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, 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, Pan C, Rohde M, Gronow S, Göker M, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Kyrpides N, Klenk HP. 2013. Complete genome sequence of the free-living aerobic spirochete Turneriella parva type strain (HT. Standards in Genomic Sciences 8: 228-238.
  6. Huntemann M, Stackebrandt E, Held B, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Tapia L, 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 J, Bristow J, Eisen JA, Markowitz V, Woyke T, Hugenholtz P, Kyrpides N, Klenk HP, Lapidus A. 2013. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T). Standards in Genomic Sciences 8: 177-187.
  7. Liolios K, Abt B, Scheuner C, Chertkov O, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng J, Tapia R, Goodwin L, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall B, Detter J, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Klenk H, Klenk H-P, Kyrpides N. 2013. Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692T) from the alkaline Lake Magadi in the East African Rift. Standards in Genomic Sciences 8: 165-176.
  8. Abt B, Göker M, Scheuner C, Han C, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Chang J, 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 E, Rohde M, Spring S, Gronow S, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Woyke T, Klenk H. 2013. Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria and Spirochaeta stenostrepta in the genus Treponema as Treponema caldaria comb. nov; Treponema stenostrepta comb. nov; and Treponema zuelzerae comb. nov; and emendation of the genus Treponema. Standards In Genomic Sciences, 8: 88-105.
  9. Mavromatis K, Stackebrandt E, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Goodwin L, 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 J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides N. 2013. Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT). Standards in Genomic Sciences 8: 47-57.
  10. Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Han C, Cheng J, Tapia R, Goodwin L, 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 B, Göker M, Woyke T, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides N. 2013. High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5T). Standards in Genomic Sciences 8: 37-46.
  11. Stackebrandt E, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Rohde M, Gronow S, Göker M, Detter J, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk HP, & Woyke T. 2013. Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437T). Standards in Genomic Sciences 8: 26-36.
  12. Stackebrandt E, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng J, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Chang Y, Land M, Hauser L, Rohde M, Pukall R, Göker M, Detter J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P. 2013. Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Standards in Genomic Sciences 8: 15-25.
  13. 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. 2012. Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8 T). Standards in Genomic Sciences 7: 210-220.
  14. 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. 2012. Genome sequence of the orange-pigmented sea-water bacterium Owenweeksia hongkongensis type strain (UST20020801 T)Standards in Genomic Sciences 7: 120-130.
  15. 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. 2012. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea. Standards in Genomic Sciences 7: 107-119.
  16. 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. 2012. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT). Standards in Genomic Sciences 6: 1-13. doi: 10.4056/sigs.2736042.
  17. 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. 2012. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). Standards in Genomic Sciences 6: 240-250. PMID: 22768367.
  18. 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. 2012. Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences 6: 230-239. PMID: 22768366.
  19. 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. 2012. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Standards in Genomic Sciences 6: 210-219. PMID: 22768364.
  20. 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. 2012. 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. Standards in Genomic Sciences 6: 194-209. PMID: 22768363.
  21. 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. 2012. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T))Standards in Genomic Sciences 6: 185-193. PMID: 22768362.
  22. 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. 2012. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences 6: 174-184. PMID: 22768361.
  23. 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. 2012. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))Standards in Genomic Sciences 6: 155-164. PMID: 22768359.
  24. 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. 2012. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences 6: 145-154. PMID: 22768358.
  25. 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. 2012. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1T). Standards in Genomic Sciences 6: 94-103. PDF. PMID: 22675602
  26. 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. 2012. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimneyStandards in Genomic Sciences 6: 21-30. PMID: 22675595.
  27. Göker M, Daligault H, Mwirichia R, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng J, 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 E, Rohde M, Spring S, Sikorski J, Wirth R, Detter J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P. 2011. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent. Standards in Genomic Sciences 5: 407-415. 
  28. Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng J, Tapia R, Han C, Goodwin L, Pitluck S, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla E, Rohde M, Abt B, Verbag S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides N, Klenk H-P, & Woyke T. 2011. Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T). Standards in Genomic Sciences 5: 398-406.
  29. 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. 2011. 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. Standards in Genomic Sciences 5: 121-134.
  30. 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. 2011. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Standards in Genomic Sciences 5: 97-111.
  31. 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. 2011. Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10). Standards in Genomic Sciences 5: 86-96.
  32. 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. 2011. Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20). Standards in Genomic Sciences 5: 41-49.
  33. 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. 2011. Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113)Standards in Genomic Sciences 5: 30-40.
  34. 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. 2011. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262). Standards in Genomic Sciences 5: 21-29.
  35. 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. 2011. Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2). Standards in Genomic Sciences 4: 393-401.
  36. 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. 2011. Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A)Standards in Genomic Sciences 4: 381-392.
  37. 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. 2011. Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR). Standards in Genomic Sciences 4: 371-380.
  38. 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. 2011. Complete genome sequence of Treponema succinifaciens type strain (6091). Standards in Genomic Sciences 4: 361-370.
  39. 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. 2011. Complete genome sequence of Haliscomenobacter hydrossis type strain (O). Standards in Genomic Sciences 4: 352-360.
  40. 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. 2011. Complete genome sequence of Tsukamurella paurometabola type strain (no. 33). Standards in Genomic Sciences 4: 342-351.
  41. 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. 2011. Complete genome sequence of Mahella australiensis type strain (50-1 BON). Standards in Genomic Sciences 4: 331-341.
  42. 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. 2011. Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1). Standards in Genomic Sciences 4: 322-330.
  43. 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. 2011. Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL)Standards in Genomic Sciences 4: 312-321.
  44. 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. 2011. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2))Standards in Genomic Sciences 4: 303-311.
  45. 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. 2011. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139). Standards in Genomic Sciences 4: 233-243. PMID: 21677860
  46. 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. 2011. Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Standards in Genomic Sciences 4: 221-232. PMID: 21677859
  47. 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. 2011. Complete genome sequence of Oceanithermus profundus type strain (506). Standards in Genomic Sciences 4: 210-220. PMID: 21677858
  48. 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. 2011. Complete genome sequence of Bacteroides salanitronis type strain (BL78). Standards in Genomic Sciences 4: 200-209. PMID: 21677857
  49. 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. 2011. Complete genome sequence of Bacteroides salanitronis type strain (BL78). Standards in Genomic Sciences 4: 191-199. PMID: 21677856
  50. 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. 2011. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Standards in Genomic Sciences 4: 173-182. PMID: 21677854
  51. 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. 2011. Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Standards in Genomic Science 4: 163-172. PMID: 21677853
  52. 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. 2011. Complete genome sequence of Marivirga tractuosa type strain (H-43). Standards in Genomic Sciences 4: 154-162. PMID: 21677852
  53. 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. 2011. Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Standards in Genomic Sciences 4: 144-153. PMID: 21677851
  54. 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. 2011. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Standards in Genomic Sciences 4: 131–143. PMCID: PMC3111988.
  55. 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. 2011. Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Standards in Genomic Sciences 4: 100-110.
  56. 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. 2011. Complete genome sequence of Truepera radiovictrix type strain (RQ-24). Standards in Genomic Sciences 4: 91-99.
  57. 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. 2011. Complete genome sequence of Weeksella virosa type strain (9751). Standards in Genomic Sciences 4: 81-90.
  58. 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. 2011. Complete genome sequence of Cellulophaga algicola type strain (IC166). Standards in Genomic Sciences 4: 72-80.
  59. 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. 2011. Complete genome sequence of Isosphaera pallida type strain (IS1B). Standards in Genomic Sciences 4: 63-71.
  60. 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. 2011. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). Standards in Genomic Sciences 4: 54-62.
  61. 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. 2011. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Standards in Genomic Sciences 4: 45-53.
  62. 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. 2011. Complete genome sequence of Paludibacter propionicigenes type strain (WB4)Standards in Genomic Sciences 4: 36-44.
  63. 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. 2011. Complete genome sequence of Thermomonospora curvata type strain (B9). Standards in Genomic Sciences 4: 13-22.
  64. 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. 2011. Complete genome sequence of Leadbetterella byssophila type strain (4M15). Standards in Genomic Sciences 4: 2-12.
  65. 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. 2010. Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). Standards in Genomic Sciences 3: 337-345.
  66. 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). Standards in Genomic Sciences 3: 325-336.
  67. 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. 2010. Complete genome sequence of Methanothermus fervidus type strain (V24S). Standards in Genomic Sciences 3: 315-324.
  68. 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. 2010. Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). Standards in Genomic Sciences 3: 304-14.
  69. 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. 2010. Complete genome sequence of Intrasporangium calvum type strain (7 KIP). Standards in Genomic Sciences 3: 294-303.
  70. 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. 2010. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3). Standards in Genomic Sciences 3: 285-293.
  71. 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. 2010. Complete genome sequence of Desulfarculus baarsii type strain (2st14)Standards in Genomic Sciences 3: 276-284.
  72. 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. 2010. Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1). Standards in Genomic Sciences 3: 268-275.
  73. 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. 2010. Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Standards in Genomic Sciences 3: 203-211.
  74. 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. 2010. Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). Standards in Genomic Sciences 3: 194-202.
  75. 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. 2010. Complete genome sequence of Ferrimonas balearica type strain (PAT). Standards in Genomic Sciences 3: 174-182.
  76. 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. 2010. Complete genome sequence of Thermobaculum terrenum’ type strain (YNP1)Standards in Genomic Sciences, 3: 153-162.
  77. 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. 2010. Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). Standards in Genomic Sciences 3: 136-144.
  78. 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. 2010. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018). Standards in Genomic Sciences 3: 126-135.
  79. 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. 2010. Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). Standards in Genomic Sciences 3: 117-125.
  80. 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. 2010. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT)Standards in Genomic Sciences 3: 108-116.
  81. 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. 2010. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). Standards in Genomic Sciences 3: 85-92.
  82. 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. 2010. Complete genome sequence of Olsenella uli type strain (VPI D76D-27C)Standards in Genomic Sciences 3: 76-84.
  83. 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. 2010. Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Standards in Genomic Sciences 3: 66-75.
  84. 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. 2010. Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T)Standards in Genomic Sciences 3: 57-65.
  85. Labutti K, Sikorski J, Schneider S, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng J-F, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Tindall BJ, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Lapidus A. 2010. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290T)Standards in Genomic Sciences 3: 47-56.
  86. Sikorski J, Tindall BJ, Lowry S, Lucas S, Nolan M, Copeland A, Glavina Del Rio T, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Lapidus A. 2010. Complete genome sequence of Meiothermus silvanus type strain (VI-R2T)Standards in Genomic Sciences 3: 37-46.
  87. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Lapidus A. 2010. Complete genome sequence of Meiothermus ruber type strain (21T)Standards in Genomic Sciences 3: 26-36.
  88. Abt B, Foster B, Lapidus A, Clum A, Sun H, Pukall R, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng J-F, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P. 2010. Complete genome sequence of Cellulomonas flavigena type strain (134T)Standards in Genomic Sciences 3: 15-25.
  89. Chang Y-J, Pukall R, Saunders E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng J-F, 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 H-P. 2010. Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)Standards in Genomic Sciences 3: 1-14.
  90. 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. 2010. Complete genome sequence of Archaeoglobus profundus type strain (AV18). Standards in Genomic Sciences 2: 327-346.
  91. Liolios K, Sikorski J, Jando M, Lapidus A, Copeland A, Glavina T, Nolan M, Lucas S, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P, Kyrpides NC. 2010. Complete genome sequence of Thermobispora bispora type strain (R51T)Standards in Genomic Sciences 2: 318-326.
  92. Pati A, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P, Kyrpides NC. 2010. Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)Standards in Genomic Sciences 2: 300-308.
  93. Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P, Kyrpides NC. 2010. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)Standards in Genomic Sciences 2: 290-299.
  94. Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P. 2010. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T)Standards in Genomic Sciences 2: 280-289.
  95. Kiss H, Lang E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Cheng J-F, Han C, Goodwin L, Pitluck S, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, 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 H-P. 2010. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)Standards in Genomic Sciences 2: 270-279.
  96. 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 J-F, 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 Y-J, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P. 2010. Complete genome sequence of Brachyspira murdochii type strain (56-150T)Standards in Genomic Sciences 2: 260-269.
  97. Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng J-F, 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 Y-J, 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 H-P. 2010. Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)Standards in Genomic Sciences 2: 245-259.
  98. Harmon-Smith M, Celia L, Chertkov O, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Brettin T, Göker M, Beck B, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Chen F. 2010. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T)Standards in Genomic Sciences 2: 220-227.
  99. 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. 2010. Complete genome sequence of Conexibacter woesei type strain (ID131577)Standards in Genomic Sciences 2: 212-219.
  100. Sikorski J, Lapidus A, Copeland A, Misra M, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P. 2010. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T)Standards in Genomic Sciences 2: 203-211.
  101. Wirth R, Sikorski J, Brambilla E, Misra M, Lapidus A, Copeland A, Nolan M, Lucas S, Chen F, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Tindall BJ, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P. 2010. Complete genome sequence of Thermocrinis albus type strain (HI 11/12T)Standards in Genomic Sciences 2: 194-202.
  102. Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Brettin T. 2010. Complete genome sequence of Kribbella flavida type strain (IFO 14399T). Standards in Genomic Sciences 2: 186-193.
  103. Lail K, Sikorski J, Saunders E, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, 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 Y-J, 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 H-P, Chen F. 2010. Complete genome sequence of Spirosoma linguale type strain (1T)Standards in Genomic Sciences 2: 176-185.
  104. Tice H, Mayilraj S, Sims D, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Copeland A, Cheng J-F, 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 Y-J, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Chen F. 2010. Complete genome sequence of Nakamurella multipartita type strain (Y-104T)Standards in Genomic Sciences 2: 168-175.
  105. 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. 2010. Complete genome sequence of Geodermatophilus obscurus type strain (G-20T)Standards in Genomic Sciences 2: 158-167.
  106. Sikorski J, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng J-F, 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 Y-J, 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 H-P. 2010. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)Standards in Genomic Sciences 2: 149-157.
  107. Saunders E, Tindall BJ, Fähnrich R, Lapidus A, Copeland A, Del Rio TG, Lucas S, Chen F, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk H-P, Kyrpides NC. 2010. Complete genome sequence of Haloterrigena turkmenica type strain (4kT). Standards in Genomic Sciences 2: 107-116.
  108. 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. 2010. Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)Standards in Genomic Sciences 2: 96-106.
  109. Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Tice H, Copeland A, Cheng J-F, 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 Y-J, 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 H-P, Lucas S. 2010. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T)Standards in Genomic Sciences 2: 87-95.
  110. Gronow S, Welnitz S, Lapidus A, Nolan M, Ivanova N, Glavina Del Rio T, Copeland A, Chen F, Tice H, Pitluck S, Cheng J-F, Saunders E, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Land M, Hauser L, Chang Y-J, 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 H-P, Lucas S. 2010. Complete genome sequence of Veillonella parvula type strain (Te3T)Standards in Genomic Sciences 2: 57-65.
  111. Pati A, LaButti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng J-F, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang Y-J, 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 H-P, Lapidus A. 2010. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T)Standards in Genomic Sciences 2: 49-56.
  112. Spring S, Nolan M, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, 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 Y-J, 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 H-P. 2010. Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)Standards in Genomic Sciences 2: 38-48.
  113. Nolan M, Sikorski J, Jando M, Lucas S, Lapidus A, Glavina Del Rio T, Chen F, Tice H, Pitluck S, Cheng J-F, Chertkov O, Sims D, Meincke L, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Land M, Hauser L, Chang Y-J, 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 H-P. 2010. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)Standards in Genomic Sciences 2: 29-37.
  114. Ivanova N, Sikorski J, Jando M, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng J-F, Chen F, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, 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 H-P, Kyrpides NC. 2010. Complete genome sequence of Gordonia bronchialis type strain (3410T)Standards in Genomic Sciences 2: 19-28.
  115. Mavromatis K, Sikorski J, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, 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 Y-J, 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 H-P, Kyrpides NC. 2010. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)Standards in Genomic Sciences 2: 9-18.
  116. Foster B, Pukall R, Abt B, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Pitluck S, Cheng J-F, 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 Y-J, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Lapidus A. 2010. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)Standards in Genomic Sciences 2: 1-8.
  117. Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T, Del Rio , Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, 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. 2009. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Standards in Genomic Sciences 1: 308-16. See erratum in SIGS 2: 228
  118. 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. 2009. Complete genome sequence of Streptobacillus moniliformis type strain (9901T)Standards in Genomic Sciences 1: 300-307.
  119. 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. 2009. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T)Standards in Genomic Sciences 1: 292-299.
  120. 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. 2009. Complete genome sequence of Rhodothermus marinus type strain (R-10T)Standards in Genomic Sciences 1: 283-290.
  121. 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. 2009. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T)Standards in Genomic Sciences 1: 270-277.
  122. 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. 2009. Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T)Standards in Genomic Sciences 1: 262-269.
  123. 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. 2009. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T). Standards in Genomic Sciences 1: 254-261.
  124. 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. 2009. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T)Standards in Genomic Sciences 1: 242-253.
  125. Pukall R, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng J-F, 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 H-P, Hugenholtz P. 2009. Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1T)Standards in Genomic Sciences 1: 234-241.
  126. Han C, Sikorski J, Lapidus A, Nolan M, Glavina Del Rio T, Tice H, Cheng J-F, 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 Y-J, Jeffries CD, Chain P, Saunders E, Brettin T, Göker M, Tindall BJ, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Detter JC. 2009. Complete genome sequence of Kangiella koreensis type strain (SW-125T)Standards in Genomic Sciences 1: 226-233.
  127. 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. 2009. Complete genome sequence of Halorhabdus utahensis type strain (AX-2T)Standards in Genomic Sciences 1: 218-225.
  128. Saunders E, Pukall R, Abt B, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng J-F, 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 Y-J, 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 H-P, Han C. 2009. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T)Standards in Genomic Sciences 1: 174-182.
  129. Copeland A, Sikorski J, Lapidus A, Nolan M, Glavina T, Lucas S, Chen F, Tice H, Pitluck S, Cheng J-F, 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 H-P, Detter JC. 2009. Complete genome sequence of Atopobium parvulum type strain (IPP 1246T)Standards in Genomic Sciences 1: 166-173. Note erratum in Standards in Genomic Sciences 2: 361-362.
  130. 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. 2009. Complete genome sequence of Anaerococcus prevotii type strain (PC1T)Standards in Genomic Sciences 1: 159-65.
  131. 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. 2009. Complete genome sequence of Halogeometricum borinquense type strain (PR3T)Standards in Genomic Sciences 1: 150-159.
  132. 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. 2009. Complete genome sequence of Saccharomonospora viridis type strain (P101). Standards in Genomic Sciences 1: 141-149.
  133. 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. 2009. Complete genome sequence of Dyadobacter fermentans type strain (NS114T)Standards in Genomic Sciences 1: 133-140.
  134. 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. 2009. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b). Standards in Genomic Sciences, 1: 126-132.
  135. Copeland 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, Ivanov N, Mavromatis K, Chen A, Palaniappan K, Chai P, Land M, Hauser L, Chang YJ, Jeffries CD, Chertkov O, Brettin T, Detter JC, Han C, Ali Z, Tindall BJ, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP 2009. Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T)Standards in Genomic Sciences 1: 119-125.
  136. Ivanova N, 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, Mavrommatis K, Chen A, Palaniappan K, D’haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Goker M, Pukall R, Klenk HP, Kyrpides NC 2009. Complete genome sequence of Sanguibacter keddieii type strain (ST-74T)Standards in Genomic Sciences 1: 110-118.
  137. 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. 2009. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845)Standards in Genomic Sciences 1: 101-109.
  138. 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. 2009. Complete genome sequence of Cryptobacterium curtum type strain (12-3). Standards in Genomic Sciences 1: 93-100.
  139. 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. 2009. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3)Standards in Genomic Sciences 1: 54-62.
  140. Land M, Mayilraj S, Chen F, Copeland A, Glavina del Rio T, Nolan M, Lucas S, Tice H, Cheng J-F, Chertkov O, Bruce D, Goodwin L, Pitluck S, Rohde M, Goeker M, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Chang Y-J, Jeffries CC, Brettin T, Detter JC, Han C, Chain P, Tindall BJ, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, 2009. Complete genome sequence of Actinosynnema mirum type strain (101T)Standards in Genomic Sciences 1: 46-53.
  141. 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. 2009. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP)Standards in Genomic Sciences 1: 38-45.
  142. 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. 2009. Complete genome sequence of Desulfomicrobium baculatum type strain (X). Standards in Genomic Sciences 1: 29-37.
  143. 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. 2009. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T)Standards in Genomic Sciences 1: 21-28.
  144. 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. 2009. Complete genome sequence of Kytococcus sedentarius type strain (541)Standards in Genomic Sciences 1: 12-20.
  145. 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. 2009. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10)Standards in Genomic Sciences 1: 3-11.

Books

  1. Barton N, Briggs D, Eisen JA, Goldstein DB, Patel N. Evolution. 833 pages, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Other Publications

  1. Wu MEisen JA. 2011. Towards automated phylogenomic inferenceIn Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley Press. (Note – this is a slightly edited reprinting of a paper published in Genome Biology).
  2. Eisen JA. 2011. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbesIn Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley Press. (Note – this is a slightly edited reprinting of a paper published in PLOS Biology).
  3. Eisen JA, McConnell W. 2009. My View: UC Davis strike: Teaching is more than just about being paid. Sacramento Bee September 23, 2009.
  4. Schlom DG, Gall KA, Eisen JA, Joseph AD, Murphy CJ. 2007. Passive and semi-passive nanomaterial-based sensors for multi-year remote detection. Defense Science Study Group 2004-2005 Papers.
  5. Brodley C, Eisen JA. 2007. Tampering with DNA: National Security Needs for Detection and Design. Defense Science Study Group 2004-2005 Papers.
  6. Eisen JA. 2007. Toward a global field guide for microorganisms. Defense Science Study Group 2004-2005 Papers.

Meeting reports, white papers, and other documents in which I have played a role, helped write, etc.


Meetings Organized

Information Coming Soon.


RESEARCH SUPPORT

ONGOING

  • Innate Immunity and Alteration of the Oral Microbiome in SIV Infected Rhesus Macaques. NIH. 08/01/2012 – 09/02/2015. Co-Principal Investigator, Michael George (Principal Investigator).
  • Development and use of metagenomic approaches to address challenging soil borne disease problems in horticultural crops. USDA. 12/30/2012 – 11/01/2015. $128,532. Eisen PI.
  • Identification of Genomic Determinants of Virulence by Whole-Genome Sequencing of Human Septicemic E. coli and High-Throughput Electronic Patient Phenotyping. 07/01/2013 – 07/01/2015. $25,000. Eisen PI.
  • Protecting the Fragile Intestine: Integrating Microbiota and Mucosal Health. RISE – UC Davis. 04/30/2013 – 04/30/2015. $860,000. Co-Investigator, Satya Dandekar (Principal Investigator).
  • The Environmental Niche Atlas: Global Mapping of Microbial Functions. Gordon and Betty Moore Foundation, Eisen (CoPI), 6/30/12 – 5/31/15, $ 1,513,352.
  • Innovating the Communication of Scholarship. IFHA Program at UC Davis. $750,000. Eisen (CoPI), Mario Biagioli (PI). 07/31/2013 – 07/30/2016
  • microBEnet: a network for microbiology of the built environment. Alfred P. Sloan Foundation, Eisen (PI); 7/1/2010-6/30/2014, Percent Effort 20%
  • Corn Associated Microbes. MARS Corporation, Eisen (PI), 7/1/2010 – current; $500,000.

GRANTS – COMPLETED

  • Bayesian Taxonomic Assignment for the Next Generation Metagenomics. Department of Homeland Security. Eisen (PI) – 8/16/2011 – 8/16/2012 $252,362,
  • GEPR: The effects of the microbiome on the rice transcriptome. NSF DBI-0923806 (Bais, PI); 8/1/09-7/31/12. Role: CoPI
  • MRI: Acquisition of a Roche Genome Sequence Titanium System for Studies of Microbial Communities, NSF DBI-0923556, Eisen (PI); 8/15/09-7/31/13; Role: PI.
  • Canine Oral Microbiome Project. MARS Corporation. Eisen (PI), 12/1/2010 – 12/1/2013 $1,200,000.
  • The Genomic Encyclopedia of Bacteria and Archaea. DOE – 7/1/2010 – 10/1/2012 Eisen (PI), $450,000.
  • Microbial Genome Sequencing: High-Resolution Phylogenomics of Halophilic Archaea. NSF 0949453. Facciotti (PI); 10/1/09-9/30/12. Role: CoPI
  • The Phylofacts: phylogenomic encyclopedia of microbial protein families. NSF. 02/01/2008-01/30/2010. $1,900,000. Sjolander (PI), Eisen (CoPI).
  • iSEEM: Integrating statistical, evolutionary, ecological approaches to metagenomics. Gordon and Betty Moore Foundation, Eisen (PI); 12/01/2007-10/01/2011.
  • Microstates to Microdynamics: A New Mathematics of Biology. DARPA via subcontract from Princeton, Levin (PI); 04/01/2007-03/31/2011; Role: Co-PI
  • Microbial diversity in ileal transplants. Broad Medical Research Foundation, 11/01/2006 – 10/31/2007 $$35,000, Co-Investigator, Michael Zasloff (Principal Investigator).
  • Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA). Gordon and Betty Moore Foundation, 09/15/2006 – 12/14/2008 $325,253). Subcontract to Eisen. Larry Smarr (Principal Investigator).
  • Detecting Natural versus Unnatural DNA. DARPA 06/01/2006 – 05/31/2007 $74,833, Co-Investigator, Carla Brodley (Principal Investigator)
  • The Complete Genome Sequence of Teredinibacter turnerae T7902T (gamma-proteobacterium), the cultivable Intracellular endosymbiont of wood-boring marine mollusk Lyrodus pedicellatus. NSF, 05/30/2006 – 05/29/2007 $149,431, Eisen (CoPI), Dan Distel (Principal Investigator).
  • Microbial Genome Sequencing: EST Survey of Charophycean green Algae. NSF, 12/01/2005 – 11/30/2008 $270,645, Eisen (Co-Investigator). Charles Delwiche (Principal Investigator).
  • Comparative Genomics of Chemosynthetic Symbionts. Co-Investigator, (Colleen Cavanaugh, Principal Investigator). NSF, 09/15/2004 – 03/31/2009 $538,193.
  • Biodefense Resource Centers for Biodefense of Emerging/Re-emerging Infectious Diseases. NIH-HHSSN266200400038C, 06/30/2004 – 06/29/2006, $21,110,385, Eisen (CoPI), Owen White (Principal Investigator).
  • CAREER: Integrating Bacterial Diversity into Environmental Change Research and Education. NSF #MCB-0347324, 05/01/2004 – 04/30/2006, $86, 338, Eisen (CoPI), Jen Hughes (Principal Investigator).
  • NIH Biodefense Pathogen Genome Resource (BPGR). 02/02/2004 – 02/01/2009 $19,931,966, Assistant Researcher, Owen White (Principal Investigator).
  • Genome Sequence of Prochloron didemni: an obligate cyanobacterial symbiont of the ascidian Lissoclinum patella. NSF EF0412226, 01/01/2004 – 01/01/2007 $705,417, Eisen (Co-PI), Jacques Ravel (Principal Investigator).
  • Genome Sequencing: Genomic Sequencing of two Globally Ubiquitous Members of the Epsilon Proteobacteria. NSF, 01/01/2004 – 12/31/2005 $121, 500, Eisen (CoPI). Craig Cary (Principal Investigator).
  • A high speed network connection for Genomic Research. NSF-ANI-0333537, Assistant Researcher. 09/15/2003 – 08/31/2005, $164,732.
  • Interactive Studies of Wolbachia–Eukaryotic Interactions: Genomes to Communities and Back. Assistant Researcher. Jack Warren (Principal Investigator). NSF, 09/01/2003 – 08/31/2006 $211,645.
  • Microbial Genome Sequencing: Complete Genome Sequencing of the Extremely Halophilic Archaea Haloferax volcanii. NSF-EF-0243492, 08/01/2003 – 01/30/2007, $247,185, Principal Investigator.
  • Biogeochemistry of Kamchatka thermophiles. NSF, 05/01/2003 – 04/31/2007, Eisen (CoPI), $201,748. Juergen Weigel (Principal Investigator)
  • Tetrahymena Genome Sequencing Project. NIH-NIGMS 04/01/2003 – 03/31/2009 Grant #R01 GM067012, $3,873, 442, Principal Investigator.
  • Microbial Genome Sequencing: Shotgun Sequencing of Tetrahymena thermophila, NSF EF-024036 03/15/2003 – 06/30/2007, $2,567,000, Principal Investigator.
  • Phylogenomics: A Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life. NSF #DEB-022865 10/01/2002 – 09/30/2007 $2,480,000, Principal Investigator,
  • Effects of Host Environment on Bacterial Genome Evolution. NSF, 10/01/2002 – 09/30/2004 $216,458, Assistant Researcher. Nancy Moran (Principal Investigator)
  • Continuation of the Comprehensive Microbial Resource. DOE Grant #DE-FG02-01ER6320, 09/01/2001 – 08/31/, $2,047,000. Eisen (CoPI). Owen White (Principal Investigator),
  • Pathogen Functional Genomics Resource Center- Anthracis Supplement. Assistant Researcher. NIH #N01-AI-15447, 01/01/2002 – 12/31/2004 Grant, $7,381,926. Tim Read (Principal Investigator).
  • Identifying the Proteins that Mediate the Ionizing of Gene expression in the radiation resistant organism D. radiodurans strain D1. DOE, 07/15/2001 – 07/14/2004 $503,300, Assistant Researcher, John Battista (Principal Investigator)
  • The Whole Genome Sequence of Actinomyces naeslundi. NIH – 12/01/2000 – 11/30/2002 $615,483, Co-Investigator, Tim Read (Principal Investigator),
  • Environmental Genomics and Microbial Observatories: Analysis of genetic variability, gene content, and genomic potential in uncultivated marine picoplankton. NSF #MCB-0084211, 10/01/2000 – 09/30/2003 Grant, $962,208, Co-Investigator. John F. Heidelberg (Principal Investigator).
  • Complete Genome Sequence of M. capsulatus. DOE, 04/17/2000 – 04/16/2002 $658,000, Eisen Principal Investigator, University of Bergen
  • Comparative Genomics of Wolbachia. NIH – NIAID #U01 AI46517-01, 04/01/2000 – 03/31/2001, $280,383, Co-Investigator, , Scott O’ Neill (Principal Investigator).
  • Intelligent Computational Genomic Analysis. NSF #KDI-9980088, 09/01/1999 – 08/30/2002 $156,692, Assistant Researcher, , Simon Kasif (Principal Investigator).
  • Shotgun Sequencing of Plasmids from Marine Sediment Bacteria Genetic Exploration. ONR #N000149910860, 07/01/1999 – 09/30/2001, $114,592, Principal Investigator.

STUDENTS, POST DOCS, and OTHER LAB PERSONNEL

HIGH SCHOOL STUDENTS

  • Henna Hundal (Summer 2014).
  • Kevin Yang (2012-2013). Afterwards went to the University of Chicago.
  • Roger Chen. (Summer 2010). Afterwards went to Stanford University.
  • Ryan Maples. (Summer 2010 participant in the UC Davis Young Scholars Program)
  • Rohit Misra. (Summer 2010).
  • Ray Zhou (Summer 2009). Afterwards went to Stanford University.

UNDERGRADUATE STUDENTS AND INTERNS

  • Makayla Betts (2014-current)
  • Muntaha Samad (2014-current)
  • Leesa Li (2014-current)
  • Camilla Dayrit (2014-current)
  • Ruth Lee (2012-2013)
  • Andrew Stump (2013-2014). Afterwards became a research technician at Genentech.
  • Hoon San Ong (2013-2014).
  • Akshay Sethi (2012-2013)
  • Andrew Shaver (2012-2013).
  • Wan Nurul Naszeerah (2012-2013). After UC Davis went to Masters program at the Yale School of Public Health.
  • Eric Lowe (2012-2013). After UC Davis became a Customer Service Representative at 23 and me.
  • Lakshmi Bharadwaj (2012-2013). Afterwards became a Master’s student at CalPoly in Stem Cell Biology.
  • Sabreen Aulakh (2012-2014). After the lab took at position at the UC Davis Medical Center.
  • Madison Dunitz (2012-2013). After UC Davis became a research associate in the Eisen lab.
  • Jennifer Flanagan (2012-2014). After UC Davis went to work in a lab at UCSF.
  • Hannah Holland-Moritz (2012-2014). After UC Davis became a research associate in the Eisen lab.
  • Alexandra Alexiev (2012-current).
  • Zachary Bendiks (2011-2013). Afterwards continued as a UC Davis undergraduate.
  • Dakota Bevans (2011-2012).
  • Amanda Diep (2011-2013). As of 2014 a medical scribe at CEP American.
  • Jessica Doctor (2011-2012).
  • Jonathon Lo (2011-2013).
  • Carolina Bistue. Afterwards went to Masters program at UC Davis in Viticulture and Enology.
  • Clare Xu. Afterwards became an Associate Data Analyst Intern at Percepta Associates.
  • Ryan Corces-Zimmerman. Afterwards went to PhD program at Stanford University.
  • Holly Huse. (2005-2007). Summer Intern while in college and worked as a technician in the lab after graduating college. Afterwards went to PhD program at University of Texas, Austin.
  • Sarah Post (2004). Afterwards went to medical school at the University of Pennsylvania.
  • Kevin Penn (2003-2005). Worked as a technician in the lab after graduating college. Afterwards went to PhD program at Scripps Institute of Oceanography)

GRADUATE STUDENTS

  • Sonia Ghose (Population Biology)
  • Cassie Ettinger (Genetics)
  • Katherine Dahlhausen (Biophysics)
  • Ladan Daroud (Computer Science)
  • Christopher Beitel (Genetics)
  • Laura Vann (Genetics)
  • Marisano James (Population Biology)
  • Russell Neches (Microbiology)
  • Srijak Bhatnagar (Microbiology)
  • Elizabeth Wilbanks, PhD from UC Davis in Microbiology in 2014.
  • Jenna Morgan Lang. PhD from UC Davis in Microbiology in 2012. Afterwards did a post-doc at UC Davis
  • Amber Hartman. PhD from Johns Hopkins University in Biology in 2009. Afterwards went to the White House PCAST.
  • Sean Geer, Masters from UC Davis in 2009. Afterwards went to PhD program at UC Davis.
  • Caitlin Haltiner, Masters in Forensics from UC Davis in 2012. Afterwards went to USUHS Medical School.

POST-DOCS

  • Alana Firl (2014-current)
  • Sarah Hird (2013-current)
  • Jenna Lang (2012-current)
  • David Coil (2012-current)
  • Holly Bik (afterwards became Birmingham Fellow, Birmingham University)
  • Thomas Sharpton (afterwards became Asst. Professor, Oregon State University)
  • Morgan Langille (afterwards became an Assistant Professor at Dalhausie University)
  • Jonathan Badger (afterwards became an Assistant Professor, JCVI)
  • Aaron Darling (afterwards became am Assistant Professor, Sydney Technical University)
  • Dongying Wu (afterwards became a Project Scientist, UC Davis)
  • Sourav Chatterji (afterwards became a Software Engineer)
  • Chris Desjardin (afterwards became a Staff Scientist, Broad Institute)
  • Martin Wu (afterwards became an Assistant Professor at University of Virginia)
  • James Sakwa (afterwards went to work at the South Africa Genome Center).

OTHER PERSONNEL

  • Dongying Wu (current)
  • Guillaume Jospin (current)
  • John Zhang (current)
  • Marcel Huntemann (2006-2007). Afterwards became a software engineer at the DOE-JGI.
  • Andrew Tritt. Afterwards became a software engineer at the DOE-JGI.

VISITING RESEARCHERS

  • Sima Tokajian (2013) – visiting Professor from LAU.
  • Kathryn Teague (2013) – visiting undergrad from The University of the Pacific, Geology
  • J. Matthew Haggerty – visiting PhD student in 2013, currently at San Diego State
  • Lea Benedicte Skov Hansen – visiting post doc in 2012
  • Alex Yu – visiting Professor in 2011.

PRESS COVERAGE (EXAMPLES)

2014

2013

2012

2011

2010

2009

2008 and before


TALKS AND PRESENTATIONS

2014

2013

  • November 8. Phylogeny-driven approaches to genomics and metagenomics. Talk at IHU Méditerranée Infection, Marseilles, France. Video on Youtube.
  • October 3. Facilitating the Spread of Scientific Knowledge via Open Science. Invited talk for Infectious Disease Week Meeting in San Francisco, CA.
  • August 7. Bayesian Taxonomic Assignment for the Next-Generation Metagenomics. Department of Homeland Security Workshop on Microbial Forensics.
  • July 29. Phylogenetic and Phylogenomic Approaches to Studying the Dark Matter of Biology. Talk for UC Berkeley Evolution Institute.
  • May 31. All microbes, all the time. Keynote talk for UC Davis Teen Biotechnology Challenge Awards Ceremony. Slideshow with audio on Youtube. Slideshare.
  • May 24. microBEnet – the microbiology of the Built Environment network. Talk for Annual Meeting of the Sloan Foundation Program in Microbiology of the Built Environment. Slideshow w/ audio on Youtube. Slideshare
  • May 14. Microbiota & Microbiomes.
  • May 6. Phylogeny-Driven Approaches to Genomics and Metagenomics. Guest seminar at Fresno State University.
  • April 29. The Need for a Phylogeny Driven Genomic Encyclopedia of Eukaryotes. At SMBE-Eukaryotic Omics Satellite meeting at UC Davis. Slideshow on YoutubeSlideshare.
  • April 22. Publication and Its Discontents. Round table discussion sponsored by the American Cultures and Politics Research Cluster at UC Davis.
  • March 20. Phylogeny-Driven Approaches to Genomics and Metagenomics. Talk for UC Davis Genome Center Faculty Meeting.
  • March 15. Microbiomes and DNA based Studies of Microbial Diversity. Talk at Singularity University. https://www.slideshare.net/slideshow/embed_code/17245824#
  • March 8. The Human Microbiome 101. Talk for Future of Genomic Medicine 13. Slideshare.
  • March 4. Sequencing: The Now Generation. Talk for Bodega Applied Phylogenetics Course.
  • February 2.  Science Online 2013.  Session on “Wearing multiple hats” presentation with Ed Yong.
  • January 28. DNA based Studies of Microbial Diversity. Guest Lecture for MCB182 “Principles of Genomics” at UC Davis. Slideshare.
  • January 9. Open Access Explored discussion with Jorge Cham of PHD Comics. Announcement here.  Storify here.  Video here.

2012

2011

  • November 30. Getting Famous or Getting Scooped. Risks and opportunities in sharing your science and scholarship. UC Davis Center for Science and Innovation Studies Workshop.
  • November 15.  Phylogeny driven studies for metagenomics. iPAM meeting.  Video slideshow on YoutubeSlideshare.http://www.youtube.com/watch?v=33PkjPRjP9Y&feature=youtu.be
  • October 25. The dark matter of biology. At the 2011 Compass Summit, Los Angeles, CA. Video on ForaTV.
  • September 24. The Dark Matter of Biology. Pence Art Gallery, Davis, CA for “An Evening with the Genome Center.” Talk on Vimeo. Youtube.
  • September 12. DNA and the Hidden World of Microbes. CLIMB Symposium, UC Davis, Davis, CA. Slideshare Video with Audio on SciVee.  Slideshow on Youtube.
  • July 9. Phylogenomics and the Diversification of Microbes. At “Microbial Diversity Course Symposium on Microbial Genomics”, Marine Biological Lab, Woods Hole, MA. Slideshare.
  • June 29. The dark matter of the biological universe. Invited Talk at the National Institutes of Medicine Forum on Microbial Threats, Washington DC.
  • June 21. Social media and personal genomics – web conference. Next generation sequencing conference.
  • June 15. Open access and open science. Talk plus Roundtable Discussion on Education and Synthetic Biology, Synthetic Biology 5.0 Conference, Stanford, CA. Video on Vimeo. Slideshare.
  • June 9. Molecular studies of microbial ecology. Keynote talk at Indoor Air 2011 Conference workshop on “Microbiology of the Built Environment”, Austin, TX. Slideshare slidecast with audio.  Second attempt at Slidecast.
  • May 20. Bioinformatics for Microbial Forensics. Presented to the White House Working Group on Microbial Forensics, White House Conference Center, Washington DC.
  • May 9. The Deal with Carbon: How Earth’s Mighty Microbes Respond. Lesher Center for the Arts, Walnut Creek, CA. Video of talk on Youtube.
  • April 21. Phylogenomics. C-DEBI Workshop of Evolution and the Deep Subsurface.
  • April 13. Ben Franklin, Bioinformatics, Boston, Birthdays, and me.   BioIT World, Boston, MA. Video on YoutubeSlideshare.
  • March 28. Phylogenetic Approaches to Metagenomic Analysis. Talk at Keystone Symposium on ‘Microbial Communities as Drivers of Ecosystem Complexity’. Slideshare.
  • March 10. Searching for the fourth domain. Scientific seminar series at the DOE Joint Genome Institute.
  • March 7. Phylogenomics.  Talk for UC Davis Applied Phylogenetics Course at Bodega Marine Lab. Slideshare.
  • March 2. Data management workshopVideo part 1 on Vimeo.  Video part 2 on Vimeo. 
  • February 28. Phylogenomics and the Diversification of Microbes. Invited seminar speaker, Computational Biology Program, UCLA, Los Angeles, CA.
  • February 17. Phylogenomics and the Diversification of Microbes. Invited seminar for Graduate Program in Bioinformatics (Student selected speaker), UCSF Mission Bay. Slideshare with Embedded Audio Slidecast.
  • February 11. Phylogenomics and the Diversification of Microbes.  Talk at UC Davis. Slideshare.
  • February 3. Phylogenomics and the Diversification of Microbes, Guest seminar for Integrative Biology program, UC Berkeley. Slideshare with Embedded Audio Slidecasthttps://www.slideshare.net/slideshow/embed_code/6926471#
  • January 27. Phylogenomics. Guest seminar for Biochemistry and Molecular Biology Seminar Series, Genentech, SF. Slideshare.
  • January 19. A phylogeny driven genomic encyclopedia of bacteria and archaea. Guest seminar for Biology Department, UCSD, San Diego, CA.
  • January 18. A phylogeny driven genomic encyclopedia of bacteria and archaea. Invited seminar, J. Craig Venter Institute. Slideshare.

2010

  • December 16. Phylogenomics and the Diversity and Diversification of Microbes, California Academy of Sciences, San Francisco, CA. Slideshare.
  • December 16. DNA sequencing and the modern revolution in studies of microbial diversity, California Academy of Sciences, San Francisco, CA. Slideshare. https://www.slideshare.net/slideshow/embed_code/15362023#
  • October 21.  What is Open Access Publishing.  Talk at UC Davis for Open Access Week.  Available at Archive.Org.
  • September 17. A phylogeny driven genomic encyclopedia of bacteria and archaea. Lake Arrowhead Microbial Genomes Meeting. Slideshare.
  • September 1. A phylogeny driven genomic encyclopedia of bacteria and archaea. Human Microbiome Project Meeting, St. Louis, MO. Slideshare.
  • August 11. A personal perspective on Open Access publishing. Clinical and Translational Sciences Center.  Slideshare.
  • July 18. A genomic encyclopedia of bacteria and archaea, ICiS Workshop. Computational Methods and Terabase Metagenomics, Snowbird, UT.
  • June 28. Phylogenomics of microbes: the dark matter of biology, Keynote Talk, iEVOBIO, Portland Oregon. Slideshare.
  • May 25. A phylogeny driven genomic encyclopedia of bacteria and archaea.  Talk for ASM2012 meeting in Boston. Slideshare with Audio Slidecast.
  • April 25.  A phylogeny driven genomic encyclopedia of bacteria and archaea. Talk at ASBMB 2012.   Slideshare with audio Slidecast.
  • April 17. Phylogenomics of Archaea and Bacteria, Stanford University “Evolution and Genomics” Symposium. Slideshare.
  • January. Open Access. Discussion at Science Online 2012  Slideshare.

2009

  • November 4. Phylogenomics and the origin of novelty in microbes, Invited Talk, UC Irvine, Seminar Series in Evolutionary Biology, Irvine, CA.
  • October 27. A genomic encyclopedia of bacteria and archaea.  JGI All Hands Meeting. Slideshare.
  • October 3. Microbial genomes, California Academy of Sciences Bioforum, San Francisco, CA. Partial recording on ForaTV. Discussion panel video.
  • October 2. A phylogeny driven genomic encyclopedia of bacteria and archaea, National Academy of Sciences “Microbes and Health” meeting, Irvine, CA.
  • August 11. Seeking out the dark matter of the biological universe and the need for a phylogeny driven genomic encyclopedia. Keynote Talk, Computational Systems and Bioinformatics Meeting, Stanford, CA. Slideshare.
  • June 18. A phylogenomic encyclopedia of bacteria and archaea, Invited Speaker, CIFAR Integrated Microbial Biodiversity Workshop, Asilomar, CA.
  • May 21. The 1$ Bacterial Genome: Informatics, GEBA and Me, Invited talk at American Society for Microbiology 109th General Meeting, Philadelphia, PA. Slideshare.
  • May 19. Comparative genomics of halophilic archaea, a model for science and education. Invited talk at Roche Genome Sequencing Workshop at the American Society for Microbiology 109th General Meeting, Philadelphia, PA.
  • May 18. Panel Discussion on Open Science.  At American Society for Microbiology General Meeting, Philadelphia, PA.
  • March 27. A genomic encyclopedia of bacteria and archaea. Invited talk, JGI User Meeting, Walnut Creek, CA. Slideshare.
  • February 23. Evolutionary biology is a valuable and practical tool. Invited Public Lecture, Darwin Day Celebration at The Varsity Theater, Davis, CA.
  • February 5. Phylogenomics and the origin of novelty in microbes (and a bonus birthday present for Darwin. Invited Talk, UC Davis Ecology and Evolution Seminar Series.
  • February 4. Phylogenomics of host-microbe interactions. Invited talk for the UC Davis Medical School Basic Science Council Meeting.

2008

  • November 5. A genomic encyclopedia of bacteria and archaea. Keynote speaker, International Metagenomics Conference, San Diego, CA.
  • September 16. A Genomic Encyclopedia of Bacteria and Archaea. Invited talk, Small Genome Meeting, Lake Arrowhead, CA. Slideshare.
  • August 7. Open Access Publishing, Biomedical Research Integrity program for University of Washington School of Medicine. Video on Youtube.http://www.youtube.com/watch?v=PJyvbxnmDbg&feature=youtu.be
  • June 4. Genomic Evolvability and the Origin of Novelty. ASM Division R Lecture. Slideshare.
  • May 22. Phylogneomics and the origin of novelty. Invited Talk, Institute of Medicine, Forum on Microbial Threats’ Microbial Evolution workshop.
  • April 22. Phylogenomics and the origin of novelty in microbes. Invited Talk, LBL Genomic Sciences Symposium Series, Berkeley, CA.
  • February. A genomic encyclopedia of bacteria and archaea. International AGBT Meeting, Marco Island, FL.

2007

  • October. Genomics as a tool in studying the evolution and diversity of the small things that run the planet. Invited seminar, Bay Area Biosystematists, California Academy of Sciences.
  • October 9. A genomic encyclopedia of bacteria and archaea, Plenary session presentation, Genomes, Medicine and the Environment Conference, San Diego, CA. Video on Youtube.http://www.youtube.com/watch?v=vaBAkHReUhA&feature=youtu.be
  • August. The Human Microbiome. SciFoo Camp, Mountain View, CA. Slideshare.
  • July. Bioinformatics for Metagenomics. Chair of breakout session, International Metagenomics Conference III: UCSD.
  • May ??. A genomic encyclopedia of bacteria and archaea. Invited seminar, American Academy of Microbiology Workshop.
  • May 4. Phylogenomics and the diversification of microbes. Chico State University.
  • April 13. A genomic encyclopedia for bacteria and archaea. Invited seminar, California Metagenomics Meeting, Gordon and Betty Moore Foundation.
  • March 28. Phylogenomics and the origin of novelty in microbes. Invited seminar. JGI User Meeting.
  • March 27. A genomic encyclopedia for bacteria and archaea. JGI Lab Sequencing Program Meeting.
  • February 28. Phylogenomics and the diversification of microbes. Invited seminar, U. C. Berkeley Microbiology Seminar Series.
  • March 8-9. A genomic encyclopedia for bacteria and archaea. At Bergey’s Planning Meeting to discuss sequencing genomes of all described organisms. University of Georgia.
  • January. A genomic encyclopedia of bacteria and archaea. JGI Policy Board Meeting.
  • January 22. Phylogenomic studies of microbial symbioses. U. C. Davis, Plant Pathology Seminar Series.
  • January 17. The more the merrier: genomics of single, double and polysymbioses. Invited talk.  Host microbe interaction workshop at the Plant and Animal Genomics Meeting, San Diego, CA. Slideshare.

2006

2005

  • December 16. Phylogenomics and the diversification of microbesWest Coast Bacterial Physiology. John Ingram Lecture.
  • October 18. Phylogenetic analysis and environmental genomics. Genomes, Medicine and the Environment Meeting, invited talk.
  • September 26. Sweating the small stuff. Invited Talk, Sloan Foundation Synthetic Genomics Workshop,
  • September 20. Invited Talk, NIH DNA Repair Interest Group, More questions than answers: insights into DNA repair processes from genome sequencing projects. Webcast and slidesNIH VideocastVideo on Youtube.
  • April 16. Genomic Insights into Tetrahymena’s Bag of Genetic TricksInternational Conference on Microbial Genomes:

2004

  • December 14. Extremophiles, genomics and DNA repair. DARPA Radiation Protection Workshop.
  • September. The Axis of Evol and the Phylogenomics of Microbes. Talk at Lake Arrowhead Microbial Genomes Meeting. Slideshare.
  • April 17. Phylogenomics and the Axis of EvolMicrobial Sciences Symposium, Harvard.
  • February 11. Phylogenomic Analysis of DNA Repair and Recombination Processes. Keystone Meeting on Bacterial Chromosomes, Santa Fe, NM.

2002

  • September.  Phylogenomics of Microbes. Talk at Lake Arrowhead Microbial Genomes Meeting. Slideshare.
  • February 20. Feedback loops between genomics and evolutionary analysis and why every genome center needs an evolutionary biologist. Invited seminar.  Duke University.

2001

  • November, Invited talk, American Society for Space and Gravitational Biology, Alexandria, VA.
  • October, Invited talk, University of Pennsylvania Genome Center, Philadelphia, PA.
  • October, Invited talk, DNA Repair and Related Transactions, Fallen Leaf Lake, CA.
  • September, Invited talk, Systematics Association Biennial Meeting, London, UK.
  • July, Invited talk, Gordon Conference on Microbial Population Biology, Williams, MA.
  • March, Invited talk, Society of General Microbiology, General Meeting, Edinburgh, UK.
  • January, Invited talk, International Symposium on Extremophile Genomics, Tokyo, Japan.

2000

  • December, Invited talk, University of Maryland, Department of Biology, College Park, MD.
  • October, 2000, NASA Mars Sample Handling Workshop 2, Bethesda, MD
  • October, Invited talk, Canadian Institute for Advanced Research Evolution Subsection Annual Meeting, Digby, Nova Scotia.
  • September, Invited talk, TIGR Genome Sequencing and Analysis Conference, Miami, FL.
  • September. Phylogenomics of DNA repair. Invited talk, International Small Genomes Conference, Lake Arrowhead, CA. Slideshare
  • July. National Science Foundation Tree of Life Workshop, New Haven, CT.
  • July. Invited talk, Australian American Leadership Dialogue, Washington, DC.
  • June, Invited talk, Environmental Molecular Sciences Laboratory Users Symposium, Hanford, WA.
  • April, Invited talk, North Carolina State Genomic Sciences Symposium, Raleigh, NC.
  • February, Invited talk, “Biotechnology 2000: The Science and the Impact”, The Hague, The Netherlands. Transcript available here.
  • February, Invited talk, TIGR Microbial Genomes Meeting, Chantilly, VA.

1999

  • November, 1999, DOE Which Bugs Workshop on Cellulolytic Organisms, Rockville, MD
  • November, Invited talk, Beyond the Identification of Transcribed Sequences Workshop, Chantilly, VA.
  • October, Invited talk, ASM Conference on DNA Repair, Hilton Head, SC.
  • September, Invited talk, TIGR Genome Sequencing and Analysis Conference, Miami, FL.
  • August, Invited talk, IUMS Annual Meeting, Sydney Australia.
  • July, Invited talk, John Hopkins University Department of Chemical Engineering.
  • May 27. Evolutionary perspectives of genome analysis. Stanford University Genomic Sciences Seminar Series, Stanford, CA.
  • May, Invited talk, National Institutes of Health, Section on DNA Repair, Bethesda, MD.
  • April 7. Combining evolutionary analysis and genomics into a composite phylogenomic analysis: a case study of DNA repair processes. Invited Talk, Center for Marine Biotechnology, Baltimore, MD.
  • March. ASM Colloquium on Microbial Genomics, New Orleans, LA.
  • February, Invited talk, TIGR Microbial Genomes Meeting, Chantilly, VA.
  • February, Phylogenomics of DNA repair processes, Gordon Conference on Mammalian DNA Repair, Ventura, CA.
  • January, Microbial genome sequencing, Keystone Symposium on Archaea, Taos, NM.

1998 and Before

  • October 1998. Phylogenomics: Improving Functional Predictions for Genes Using Evolutionary Analysis. Beyond the Identification of Transcribed Sequences.
  • May 1998. Phylogenomics: Improving Functional Predictions for Genes using Evolutionary AnalysisAt The Biology of Genomes, Cold Spring Harbor Laboratory.
  • October 14-24 1997. NATO Advanced Study Institute on “DNA Damage and Repair”, Tekirova, Turkey.
  • November 1996, The evolution of the RecA protein in bacteria: from systematics to structure. At CALPEG.
  • July 1995. Evolution of the RecA protein: From Systematics to StructureSlideshare.
  • May 1995RecA as a model molecule for molecular systematic studies of bacteria. At the Society for the Study of Evolution (SSE) Meeting. Montreal, Canada.

Posters at Meeting (partial list)

  • Gordon Conference on Mammalian DNA Repair, 1999, Ventura, CA
  • NATO ASI DNA Repair Conference, 1997, Antalya, Turkey.
  • Gordon Conference on Microbial Population Biology, 1997, Plymouth State College, NH.
  • Gordon Conference on Molecular Evolution, 1996, Ventura, CA.
  • Gordon Conference on Mutagenesis, 1994, Plymouth State College, NH.

Meetings and Workshops Organized

  • 2013. Citizen Microbiology session at ASM Meeting, Organizer, Denver, CO, May 19, 2013.
  • 2012. The Science and Applications of Microbial Genomics, Organizer, National Academy of Sciences Keck Center, June 12-13 2012.

OTHER

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