Jonathan Eisen Full CV

This page has a CV from a few years ago.  For an updated CV see this Google Doc.

 

 

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 Investigator, Public 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

• 2012-present Advisory Board, bioRxiv
• 2013-present Editorial Board, PeerJ
• 2012-2014 Chair of the Advisory Board, PLoS Biology
• 2010-2012 Steering Committee, PLoS Hub in Biodiversity
• 2008-2012 Academic Editor in Chief, PLoS Biology
• 2006-2014 Editorial Board, Biology Direct
• 2004-present Editorial Board, PLoS Computational Biology
• 2003-present Editorial Board, PLoS Biology
• 2003-2007 Editorial Board, Molecular Biology and Evolution
• 1999-2007 Editorial Board, Genome Research
• 2004-2006 Editorial Board, Journal of Molecular Evolution
• 2001-2003 Editorial Board, Microbiology

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).

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PUBLICATIONS

• Active list here with links, news stories, data, etc.
• Google Scholar Page
• Metrics From Google Scholar: as of 12/1/14: 42,951 citations, h-index of 77, i10 index of 184.

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

1. Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2:e243. PMID: 24482762. PMC3897386.
2. 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. PDF.
3. Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system. PLoS 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 transplantation. Proceedings of the National Academy of Sciences USA 106(40): 17187-17192. PMID: 19805153. PDF.
6. Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome 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 D, Eisen JA, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 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 eukaryote. PLoS 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 falciparum. Nature 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: 11358996. PDF.
17. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 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 cholera. Nature 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 R1. Science 286: 1571-1577. PMID: 10567266.
23. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome 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.

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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 S, Eisen 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 JM, Eisen JA, Zivcovik A. 2014. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of model meals. Peer J 2: e659.
   • Blog by J. Eisen about paper
   • Maddie Stone on Motherboard: Here’s How Many Microbes You Eat in a Single Day
   • Kevin Bonham on SciAM Blogs: The Microbes in Your Kitchen (Or in your Starbucks mocha)
   • Improbable Research: What’s Eating You, and/or Vice Versa: Microbes
   • Ross Pomeroy on Real Clear Science: This Is How Many Microbes You’ll Eat Today
   • Nathan Gray:  The microbes we eat: Study investigates bacteria in different diets
3. Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling 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 D, Lang JM, Eisen 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 HM, Coil 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.
   • Preprint
   • BioIT world story
   • PeerJ interview with Chris Beitel
   • HiC metagenomics resources from Chris Beitel
8. Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243. PMID: 24482762. PMC3897386.
   • See software page here: https://github.com/gjospin/PhyloSift
   • Phylosift blog
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 Marsh. Environmental Microbiology doi: 10.1111/1462-2920.12388. PMID: 24428801.
   • Story behind the paper by 1st author EG Wilbanks: A sulfurous symbiosis: Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett salt marsh.
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 G, Eisen 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.
    • Data from the paper at Figshare.
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.
    • Nature News Story
    • PBS News Hour Story
    • Science Magazine News
18. Wu D, Jospin G, Eisen 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: e77033. PMCID: PMC3798382.
19. Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS ONE 8: e62510. PMCID: PMC3636077.
    • • Data and Figures available on Figshare
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.
    • • Data available at Figshare
      • Eisen blog post.
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 M, Eisen 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 MGI, Neches 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 scales. PLoS ONE 7: e43866. PMID: 23049741. PMCID: PMC3445553 PDF.
    • • Detailed blog post on the story behind the paper by Russell Neches
27. Tritt A, Eisen 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.
    • • Software Page
28. Chandler JA, Eisen JA, Kopp A. 2012. Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hosts. Applied and Environmental Microbiology 78: 7327-7336. PMID: 22885750. PDF.
    • • Data at Figshare.
29. Lynch EA, Langille MGI, Darling AE, Wilbanks EG, Haltiner C, Shao KSY, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. 2012. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS ONE 7: e41389. PMID: 22848480. PDF.
    • Links to data can be found here.
30. Eisen JA. 2012. Badomics words and the power and peril of the ome-meme. Gigascience 1:6. PDF. PMCID: PMC3617454.
    • Robert Lee Hotz story in the Wall Street Journal “Here’s an Omical Tale: Scientists Discover Spreading Suffix.”
    • GigaScience launches: overseeing the transition from papers to “executable research objects”
    • Gigascience PR
    • ‘Big Data’ Journal GigaScience Makes Its Debut
    • Eisen blog post about paper: My new paper in #Gigascience: #Badomics words and the power and peril of the ome-meme
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.
    • • GitHub repository
32. Wu M, Chatterji S, Eisen JA. 2012. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 7: e30288. PMID: 22272325. PMCID: PMC3260272. PDF.
    • Blog post with additional information.
    • Zorro Software page.
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 JM, Bhatnagar S, Eisen 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.
    • Data at Figshare
36. Darling A, Tritt A, Eisen JA, Facciotti M. 2011. Mauve assembly metrics. Bioinformatics 27: 2756-2757. PMID: 21810901. PDF.
    • Software Page.
37. Kembel S, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS ONE 6: e23214. PMID: 21912589. PDF.
    • Blog post by Jonathan Eisen with more detail.
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 JA, Penn 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 D, Wu 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 trees. PLoS ONE 6: e18011. PMID: 21437252. PDF.
    • Nature News article “The challenge of microbial diversity: Out on a limb.“
    • Carl Zimmer Discover article “Glimpses of a fourth domain.“
    • Carl Zimmer Discover article #2 “Trouble in the fourth domain.“
    • Newsy video post
    • Economist Story 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.
    • Blog post with additional detail.
    • Software Page.
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. 2010. The 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.
    • WATERS Software page
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 JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5: e10209. PMID: 20419134. PDF. Data available here.
46. Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5: e10071. PMID: 20418944. PDF.
    • Website: Biotorrents.Net
    • Jonathan Eisen Blog post with more detail
    • Morgan Langille self interview
    • Press Release. 
    • Examples of news stories:
      • Cheap option for file transfers launched
      • BioTorrents: An OA File Sharing Service
      • Review: BioTorrents. – Medpedia News
      • Nature News
      • GenomeWeb
      • BioTorrents: A BitTorrent Tracker Site for Scientists
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 Archaea. Nature 462: 1056-1060. PMID: 20033048. PDF.. Supplemental Information PDF.
    • New York Times article by Carl Zimmer
    • ARS Technica article by John Timmer
    • Addition information on Eisen’s Tree of Life Blog
    • Background Story on Eisen’s Tree of Life Blog
    • JGI GEBA Web Page
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 transplantation. Proceedings of the National Academy of Sciences USA 106: 17187-17192. PMID: 19805153. PDF.
    • UC Davis Press Release.
    • UPI Story.
    • GenomeWeb Article.
    • Nature News Story.
50. Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collection. PLoS Biology 7: e1000224. PMID: 19855830. PDF.
    • PLoS Collection we edited.
    • Podcast with Dr. Kiki.
    • PLoS Blog Post.
    • Press Release from PLoS.
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 JA, Badger 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.
    • Genome entry at NCBI
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.
    • Genome available in NCBI.
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 time. PLoS 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.
    • Link to original blog post.
    • Blog post by Bora about the collection.
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 applications. BMC 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 equitans. Genome Biology 9: R158. PMID: 19000309. PDF.
61. Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9: R151. PMID: 18851752. PDF.
    • AMPHORA software page
    • Faculty of 1000 reviews
    • Blogged about by Larry Moran
62. Wu D, Hartman 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.
    • STAP Software page.
    • Blog post by Mike the Mad Biologist.
    • Blogged about by Genome Technology and Jonathan Eisen and Bora
63. Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. RECOMB 2008. PDF.
    • CompostBin Software page.
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 M, Eisen JA, Bryant DA. 2007. Identification of a new family of lycopene cyclases in photosynthetic bacteria. Proceedings of the National Academy of Sciences USA 104: 11784-11789. PMID: 1760690. PDF.
67. Norais C, Hawkins M, Eisen JA, Hartman 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 D, Eisen 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 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 eukaryote. PLoS Biology 4: e286. PMID: 16933976. PDF.
    • Press Releases: NIGMS, TIGR, PLoS, Grant Award
    • Ars Technica News Story by John Timmer
    • Tetrahymena Genome Database
    • Jonathan Eisen blog post
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.
    • Synopsis from PLoS Biology
    • Science Now “Dinner for Three” Story
    • News: Central Valley Business “Sharpshooter’s secret solved “
    • UC Davis Press Release “Sharpshooter’s Secret Is Three-Way Symbiosis“
    • JCVI Press Release
    • Sequence traces
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 agents. PLoS 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: 231-238. PDF.
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 genome. Genomics 88: 443-451. PDF.
78. Penn K, Wu D, Eisen 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.
    • News: Slashdot story
    • Press release
    • Green Car Congress
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 JH, Eisen 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 C, Eisen JA, Nene V. 2005. New evolutionary frontiers from unusual virus genomes. Genome 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 195. Science 307: 105-108. PMID: 15637277. PDF.
84. Robb FT, Gonzalez JM, Sokolova T, Chernyh N, Lebedinski A, Tallon LJ, Jones K, Wu M, Eisen JA. 2005. Primary energy metabolism in geothermal environments: the role of carbon monoxide. In 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 environment. Nature 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 bacteriophage. Journal 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.
     • Cruise Web Site
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.
     • • Supplemental Figure on UvrC evolution
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 falciparum. Nature 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 symbionts. Proceedings 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 strains. Journal 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 agalactiae. Proceedings 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 haloarchaeon. Photosynthesis 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.
     • Commentary
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
     • Commentary
     • 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 crescentus. Proceedings 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: 11358996. PDF.
     • Enhanced version of the paper with detailed links.
     • Genome News Network story.
     • New York Times article by Nick Wade.
     • Wired News article.
     • Commentary
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. Gastrogenomics. Nature 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.
     • TIGRFams web site
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 AR39. Nucleic 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 cholera. Nature 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 sequencing. Nature 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.
     • Paperback at Amazon.
     • Hardback at Amazon.
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 R1. Science 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 analysis. Genome 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 feast. Nature 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 Zimbabwe. Journal 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 activities. Journal 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 analysis. Journal 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 JA. Draft 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 RD, Jospin G, Coil DA, Eisen 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 magnifica. Standards in Genomic Sciences 3: 163-173.
5. Dunitz MI, James PM, Jospin G, Eisen JA, Coil DA, Chandler JA. 2014. Draft genome sequence of Tatumella sp. strain UCD-D_suzukii (Phylum Proteobacteria) isolated from Drosophila suzukii larvae. Genome Announcements 2: e00349-14. PMID: 24762940. PMCID: PMC3999497.

Genomics of Sepsis

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

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 HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA. 2014. Draft genome sequence of the pyridinediol-fermenting bacterium Synergistes jonesii 78-1. Genome Announcements 2: e00833-14.
4. Alexiev A, Coil 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 DA, Lo JR, Chen 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 HE, Bevans DR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome Sequence of Leucobacter sp. strain UCD-THU (Phylum Actinobacteria). Genome Announcements 1: e00325-13. PMCID: PMC3675516.
2. Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. 2013. Draft genome sequence of Kocuria sp. strain UCD-OTCP (Phylum Actinobacteria). Genome Announcements 1: e00172-13. PMCID: PMC3650433.
3. Flanagan JC, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announcements 1: e00244-13. PMCID: PMC3656209.
4. Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announcements 1: e00197-13. PMCID: PMC3650439.
5. Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria). Genome Announcements 1: e00120-13. PMCID: PMC3622984.
6. Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4. Genome 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 chimney. Standards 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 M, Eisen JA. 2011. Towards automated phylogenomic inference. In 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 microbes. In 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.

• Reports from the Institute of Medicine Forum on Microbial Threats to which I contributed:
  • Improving Food Safety Through a One Health Approach: Workshop Summary. 2012. Institute of Medicine (US). Washington (DC): National Academies Press (US).
  • The Social Biology of Microbial Communities: Workshop Summary. 2012. Institute of Medicine (US). Washington (DC): National Academies Press (US).
  • Antibiotic Resistance: Implications for Global Health and Novel Intervention Strategies: Workshop Summary. 2010. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
  • The Causes and Impacts of Neglected Tropical and Zoonotic Diseases: Opportunities for Integrated Intervention Strategies. 2011. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
  • Fungal Diseases: An Emerging Threat to Human, Animal, and Plant Health: Workshop Summary. 2011. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
  • The Science and Applications of Synthetic and Systems Biology: Workshop Summary. 2011. Institute of Medicine (US) Forum on Microbial Threats. Washington (DC): National Academies Press (US).
• Sequence-Based Classification of Select Agents: A Brighter Line (2010). National Research Council (US) Committee on Scientific Milestones for the Development of a Gene Sequence-Based Classification System for the Oversight of Select Agents. Washington (DC): National Academies Press (US). (Report from Workshop in which I participated.)
• A New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. (2009). National Research Council (US) Committee on a New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. Washington (DC): National Academies Press (US). (Report from NAS Committee to which I contributed).
• DiRuggiero J, Nandakumar R, Eisen JA, Schwartz M, Thomas R, Davila J, Ofman L, Robb FT. 2002. Genomic and physiological studies on extremophiles: model systems for exobiology. In “Frontiers of Astrobiology. Proceedings of the Astrobiology Workshop”, St Petersburg, Russia. Pavlov A. PDF. Report from Workshop to which I contributed:
• MARS Sample Handling Protocol Workshops, NASA Technical Reports, 2000-2001. (Report from Workshops in which I participated.)

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Meetings Organized

Information Coming Soon.

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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.

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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.

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PRESS COVERAGE (EXAMPLES)

2014

• July 1, 2014. Carrie Arnold article about hospital microbiomes in Environmental Health Perspectives with quotes from Jonathan Eisen.
• June 24, 2014. BioIT world story on HiC metagenomics.
• June 16, 2014. Story about collaboration with Lebanese American University (LAU).
• May 22, 2014. Candice Helfand interviews Jonathan Eisen for the Story Exchange. UC Davis professor Jonathan Eisen explains how to help make science a true meritocracy.
• May 9, 2014. Kate Gammon at Popular Science: I Got It From My Momma: 4 Surprising Things To Thank Mom For.
  • “As microbiologist Jonathan Eisen wrote in his blog, “Vaginal birth and breastfeeding can be viewed largely as delivery mechanisms for microbes (and the food for the microbes).” Thanks, mom!”
• April 18, 2014. Why SpaceX Is About to Launch Dinosaur Microbes and Toilet Germs Into Space by Becky Ferreira in Vice.
• April 16, 2014. Manipulating the Unseen Microbial Ecosystem—The Future of Hospitals? by Brooke Borel in Nova Next.
• April 16, 2014. Dirty Dog: Do Pets Track Bacteria In Your Home? by Brooke Borel in Popular Science.
• March 4, 2014. Wrap up of STEM Women Google+ Chat.
• March 4, 2014. Philly.Com: A tale of cheerleaders, microbes, and orbit
• February 21, 2014. Science Magazine: Elsewhere in Science
• February 21, 2014. PLOS Blogs: fecal transplants and climate change
• Sacramento Bee on Neanderthal Testing: Neanderthal in your blood? Answer a DNA test away
• February 12, 2014. TechEmergence: Jonathan Eisen and the Wild West of the Human Microbiome.
• January 23, 2014. National Geographic Weekend interview about the Human Microbiome.
• January 10, 2014. New Yorker article on Antimicrobial phone surfaces. 
• January 7, 2014. Genome Web story about getting more female speakers at meetings.
• January 3, 2014. John Bohannon story on Google Scholar in Science magazine discusses Eisen’s use of automated searches for discovering papers.

2013

• October 9-15. Coverage of editorial by Eisen et al. on impact factor and peer review
  • The Scientists: Useless Peer Review?
• October 10, 2013. Article in Al Jazeera by Victoria Schlesinger “Scientists Threatened by Demands to Share Data” including interview of J. Eisen.
• October 2, 2013. PhD student in the lab Russell Neches in Nature regarding his shift from physics to biology: Physicist turned microbiologist advances his career with a do-it-yourself approach by Virginia Gewin.
• October 2, 2013. Jonathan Eisen quoted in Erika Hayden story in Nature on the NIH Shutdown.
• October 1, 2013. Regarding the government shutdown and science
  • How To Access Government Websites During The Shutdown by Dove Mosher in PopSci
  • Erika Check Heyden story on “NIH shutdown effects multiply” in Nature News.
• September 2, 2013. All Things Considered story by Rob Stein on “Microbe Transplants Treat Some Diseases That Drugs Can’t Fix
• August 1, 2013. Vancouver Sun article on the TED conferences and talk and gender bias. 
• June 25, 2013. “Press P to print” in Chemistry World featuring Russell Neches
• March 24, 2013. HeLa genome sequenced without consent stories
  • Rebecca Skloot in the NY Times. The Immortal Life of Henrietta Lacks, the Sequel
  • ScienceInsider. Privacy Flap Forces Withdrawal of DNA Data on Cancer Cell Line
• March 14, 2013. Steven Salzberg wins Ben Franklin award.
• March 1, 2013. Richard Grant in the Guardian on Ome words. 
• February 27, 2013. Nature Story by Monya Baker on Ome words. 
• February 18, 2013. PhD student Russell Neches featured in story on 3D Printers in Research Labs in Chemical and Engineering News
• January 14, 2013. ‘Open access’ tributes to Aaron Swartz – SFGate
• January 14, 2013. Scholars Post Free PDFs in Honor of Aaron Swartz

2012

• December 26, 2012. Bob Dunning article in the Davis Enterprise
• December 25, 2012. Laura Geggel in the New York Times on “These Were a Few of Their Favorite Things” about science toys of scientist’s
• December 13, 2012. Annalee Newitz in io9 on The Sexiest Geek Dads in the Galaxy
• December 8, 2012. UC Davis team cheers microbes into space
• December 1, 2012. Space Florida selects UC Davis / SciStarter team: Space Florida Announces ISS Research Competition Winners
• October 17, 2012. Discover Magazine “Earth’s Last Unexplored Wilderness: Your Very Own Home.” By Bruce Barcott
• August 13, 2012. Wall Street Journal article by Robert Lee Hotz on “Here’s an Omical Tale: Scientists Discover Spreading Suffix; Researchers Develop Lots of New Words That All End Alike; ‘Sounds Futuristic’“.
• July 23, 2012. Davis Bio Research Microbiologist Rocks TEDTalk: Meet Your Microbes
• July 23, 2012. Have you the guts for faecal transplants? Irish Times
• July 16, 2012. Promusa – Mobilizing banana science for sustainable livelihoods | The ‘best genomics Venn diagram ever’ deconstructed : ProMusa blog
• July 11, 2012. Virginia Gewin in Nature: Microbes en masse: The sequencing machine  (story about Rob Knight).
• July 11, 2012. Rebecca Rosen in The Atlantic The Case (Study) of Arsenic Life: How the Internet Can Make Science Better
• July 10, 2012. TED Blog on Eisen TED talk: TED Blog | 6 great things microbes do for us
• July 2, 2012. Correction algorithms extend the reach of genome sequencing
• July 1, 2012. Twitter Top 10 Healthcare Journalists
• June 19, 2012. Angre Gallo in the Sacramento Bee on Faculty urge UC Davis to apologize to disciplined professor
• June 18, 2012. ASM 2012 Is Live
• March 23, 2012. Wired – Caleb Garling Can You Really Sequence DNA With a USB Thumb Drive? …
• March 23, 2012. Ed Yong in Nature: Microbiome sequencing offers hope for diagnostics
• March 8, 2012. Wired: Birds, Poop and Roadkill: A Field Guide to Field Guides |…
• Funding Update | ProteoMonitor | Proteomics | GenomeWeb
• March 1, 2012. Wired on Book of Germs: The Quest for a Field Guide to Microbes …
• February 26, 2012. Is a Field Guide to the Microbes in Our Future? from Your Wildlife
• February 24, 2012. What’s Living on Your Smartphone? from Alan Boyle as MSNBC
• February 23, 2012. UC Davis News-Jonathan Eisen elected to the American Academy of Microbiology
• February 4, 2012. Peer Review in Scientific Journals Isn’t Perfect – So What Else Is New? from Dennis McDonald
• February 1, 2012. Thousands of Scientists Vow to Boycott Elsevier to Protest Journal Prices – from Science Magazine
• January 10, 2012, MSNBC. Nicotine buzz from 1,300 years ago
• January 6, 2012. Scientists, Fight For Access!

2011

• December 2011. How To Wow a Potential Lab Chief – Science Careers Blog
• October 2011. Australian Radio story in Indoor Environment.
• August 30, 2011. Academic Publishers: Making Murdoch Look Good by David Dobbs.
• August 28, 2011. Ecosystem sweet ecosystem. Courtney Humphries in the Boston Globe.
• August 25, 2011. Christopher Shea from the Wall Street Journal: How Many ‘Kingdoms’ of Life Are There?
• Stories about PLoS Biology paper “How many species are there on Earth”
  • August 23, 2011. Carl Zimmer in the New York Times: How Many Species on Earth? It’s Tricky
  • September 2, 2011. Science Life blog post about this.
• August 2011. Arsenic Life story, again
  • The Scientist: Arsenic-Based Life, Open to Critique
  • Nature: Open research casts doubt on arsenic life
• August 3, 2011. Nature on The challenge of microbial diversity: Out on a limb
• July 28, 2011. Get To Know A Scienceblogger: Jonathan Eisen – Science of Blogging
• July 7, 2011. Wired News: Lovers, Losses, Putts, Egypt, and Bruce – Neuron Culture’s…
• July 2011. Towards “Tera-Terra”: Terabase Sequencing of Terrestrial Metagenomes
• June 11, 2011. Gazetaweb.com – O maior e melhor conteúdo em Alagoas:…
• June 2011. Don’t know much about phylogeny. Genome Technology.
• May 11, 2011. David Dobbs on Jonathan Eisen’s attempt to free up all the papers of his father: Free Science, One Paper at a Time | Wired Science | Wired.com
• May 2011. Ben Franklin Award
• March-June 2011. Stalking the fourth domain paper.
  • Blog post about “fourth domain” paper picked as PLoS Blog Pick of the Month
  • New paper on “stalking the fourth domain” published. Some press coverage. For more detail see blog post here
  • The Economist: A new domain of life: plenty more bugs in the sea. The Economist. Economist.FourthDomain.pdf
  • Microbe Magazine: Metagenomic Analysis Suggests Fourth Domain within Tree of Life
• March 2011. Jonathan Eisen wins Benjamin Franklin Open Science award
• February 16, 2011. Ex PhD student Amber Hartman Features in LA Times Story

2010

• December 2010. Post Doc Morgan Langille featured in Genome Technology
• December 2010. Arsenic life story.
  • The Guardian: Fallout from Nasa’s ‘arsenic bacteria’
  • Ed Yong: Arsenic bacteria – a post-mortem, a review, and some navel-gazing
  • David Dobbs in Wired: Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?
  • Microbe gets toxic response: Scientific American
• November 2010.Microbiology goes digital. Microbe Magazine.
• DOE JGI Primer on GEBA Project.
• October 2010: You Aren’t Blogging Yet. The Scientist.
• October 2010. SPARC – Science in the genes … Story about the Eisen family and Open Science
• June 27, 2010. Sacramento Bee, The : UC fumes at publisher over $1 million…
• April 2010. Biotorrents Paper
  • Eisen blog
  • Langille’s blog,
  • ARS Technica
  • Nature News Blog
  • GBMF news item
  • GenomeWeb blog
  • Nature
• April 8, 2010: Chelsea Ward article in Science News on Open Science including interview with Jonathan Eisen
• February 2010: Beyond Darwin’s Wildest Dreams. Genome Technology article.

2009

• “Genomic Encyclopedia” paper in Nature.
  • Dec 29, 2009: New York Times article by Carl Zimmer
  • ¿Cuántos microbios viven en la Tierra? | TENDENCIAS |…
  • Tehran Times : Scientists start a genomic catalog of Earth’s…
  • Microbial encyclopaedia guided by evolution : Nature News
• November 2009. This month in Blogs from Genome Technology
• November 2009. Is peer review broken? Genome Technology article.
• November 2009. MTS38 – An Embarrassment of Genomes, Podcast interview from Microbe World
• November 17, 2009. Biologists rally to sequence ‘neglected’ microbes by Elie Dolgin in Nature.
• October 2009. Gregory Petsko discusses Tree of Life blog in paper in Genome Biology.
• September 23, 2009. Sacramento Bee, The : UC Davis professors ‘walkout’ debate
• September 16, 2009. UPI: Ileostomy patients: Different gut bacteria.
• September 2009. Genomic Analyses Could Lead to “Field Guide to Microbes”
• July 28, 2009. Selected by Scientific American as one of six scientists to follow on Twitter
• July 22, 2009. Amerlia Williamson in International Science Grid This Week: Computing enables identification of microbe DNA in soil.
• July 2009. Twitter: What’s All the Chirping About? By Elia Ben-Ari in Bioscience
• June 24, 2009. Geoff Brumfiel in Nature News: Science journalism: Breaking the convention?
• June 2009. The Human Terrain. Energy Times article by Claire Sykes on human associated microbes.
• May 2009. Straight from the gut. Nature Magazine: Article featuring work in the Eisen lab on intestinal transplants.
• May 2009. Genes That Fit Podcast & Radio Show. From SETI radio. Interview w/ J. Eisen and others.
• May 8, 2009. Matt Herper in Forbes: Could Bacteria Be A Throat-Cancer Culprit? – Forbes.com
• April 2009. Brain gain: The underground world of “neuroenhancing” drugs. New Yorker article
• April 2009. Genome Technology Magazine. Metagenomics on the Move. 
• April 20, 2009. Brain-Doping at the Lab Bench | Singularity Hub
• April 19, 2009. Daniel MacArthur Jonathan Eisen: Lessons learned at the Joint Genome Institute User Meeting
• January 2009. Computing evolution. ScienceNews.
• January 5, 2009. New York Daily News: Super powers: Where can I get some?

2008 and before

• November 28, 2008. Terrestrial origin mooted for more microbes : Nature News by Matt Kaplan
• October 28, 2008. Psicofármacos e investigación científica
• October 23, 2008. Vanguardia story on Brain Doping April Fools Joke
• September 2007. Forbes Article on CCD by Matt Herper.
• August 8, 2007. Venture Beat on a “Human Microbiome Project“
• March 2007. Nature “Microbes reveal extent of biodiversity” story.
• December 2006. Sacramento News and Review Life Itself
• 2006 Glassy Winged Sharpshooter Symbionts
  • September 2006: Microbe Magazine on Sharpshooter symbionts
  • June 2006 Science Now on Sharpshooter symbionts
  • June 2006: Central Valley Business Times on Sharpshooter
  • June 2006: Nature on Sharpshooter symbionts.
  • June 2006: More on sharpshooter
• May 2006. Nature News article “Synthetic Biologists Try to Calm Fears”
• 2005. Carboxydothermus hydrogenoformans genome
  • Poison + water = hydrogen. New microbial genome shows how
  • Researchers Sequence Genome of Hydrogen-Producing Bacterium
  • Supermicrobe Might Provide Solution for Ecologic Hydrogen Generation
• September 2004. East Bay Express Publisher for the People
• March 2004. Wolbachia Press Release Innovations report
• December 2002. Esquire Magazine Best and Brightest
• Novemebr 2002. New Scientist article on Tree of Life grants. 
• October 9, 2002. Label fight heats up in Oregon by Elizabeth Weise in USA Today.
• July 2002. A Theory Evolves. US News and World Report. 
• July 2002. Clues to the Evolution of Photosynthesis in the Hindu.
• April 2002. Sorting the Microbes from the Trees by Malorye A. Branca in BioIT World.
• January 21, 2002. Faculty of 1000 review highlighted in The Scientist.
• December 2011. The Big Brains are searching for solutions. But there a no easy fixes. In US News and World Report
• May 2001. Researchers Challenge Recent Claim That Humans Acquired 223
• Bacterial Genes During Evolution by Edward Winstead in Genome News Network.
• December 2000. UC Davis Press Releas on the Arabidopsis genome
• March 2000. Retroviruses by Paul Karr in the University of Georgia Research Magazine.
• May 26, 1999. Hot trail of stolen genes. By Mark Sincell in Science Now.
• June 18, 1997. Stanford News Story about Eisen winning the Walter J. Gores Award 
• April 1997. Stanford News Story #2 about the Science Core program.
• April 1995. Stanford News Story #1 about the Science Core program.

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TALKS AND PRESENTATIONS

2014

• January 28. The quest for a field guide to the microbes. Invited talk for the “Science in the River City” teacher’s education series. Slideshare. Youtube video slideshow with audio.
• January 27. Phylogeny driven approaches to genomics and metagenomics. Invited seminar for UC Davis Plant Pathology Seminar Series. Video of talk here. Youtube video of slideshow with audio. Video now on Youtube.

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 Youtube. Slideshare.
• 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

• November 16. Faculty discussion at UC Davis on YouTube in Education.  Notes here.
• October. DNA Sequencing and Microbes, the Now Generation. At UC Davis Food for Health Symposium. Slideshow on Youtube.
• September 16.  Phylogenomic approaches to the study of microbial diversity. Keynote Talk at Lake Arrowhead Microbial Genomes Meeting. Slidehsare.  Slideshow on Youtube.
• September 6. Phylogenomic approaches to the study of microbial diversity. At Bay Area Illumina Users Meeting. Slideshare.  Slideshow on Youtube.
• July 14. Phylogenomic approaches to functional prediction. At AFP “Automated functional prediction” submeeting during ISMB 2012. Slideshow on Youtube. Slideshare.
• July 13. Networks in genomics & bioinformatics: from phylogeny to Twitter. At ISCB 2012 submeeting at ISMB2012.  Slideshow on Youtube. Slideshare.
• July 13. Open science. At BOSC2012 submeeting during ISMB2012. Slideshow on Youtube. Slideshare.
• June 23. Phylogeny driven approaches to genomics & metagenomics.  At Canadian Society for Microbiology Annual Meeting in Vancouver. Slideshow on Youtube. Slideshare.
• June 17. The microbiology of the built environment network. At American Society for Microbiology 2012 Annual Meeting. Slideshow on Youtube. 
• June 1. The microbiology of the built environment network. At Sloan Foundation Meeting on their Program on Microbiology of the Built Environment. Boulder, CO.  Video slideshow on Youtube.
• April 15. DNA sequencing and the hidden world of microbes. At The Institute for Systems Biology Symposium on Systems Biology and the Microbiome.  Video on Vimeo. Slideshow on Youtube.
• April 12.  Meet Your Microbes. Talk at TEDMED 2012 at the Kennedy Center, Washington DC.  Edited TED version. Original Tedmed version.
• March 15. Next and Next Next Generation Sequencing. Talk at Bodega Bay Marine Lab Applied Phylogenetics Course.  Youtube slideshow.
• March 8. Phylogenetic approaches to analysis of genomes and metagenomes. at NAS IOM Meeting on Social Biology of Microbes. Slideshow on Youtube. Slideshare.
• February 29. Social Media and Science. Guest panel for University of Georgia course on Science Communication.
• February 17. Towards a Field Guide to the Microbes. At AAAS 2012 Meeting, Vancouver, Canada.  Video slideshow on Youtube. Slideshare.

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 Youtube. Slideshare.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 Youtube. Slideshare.
• 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 workshop. Video 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 Slidecast. https://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

• December 5. Phylogenomics and the Diversification of Microbes. For UC Davis Center for Population Biology Seminar Series.
• November 27. Phylogenomics and the diversification of microbes. Invited talk. , Joint Genome Institute, Walnut Creek, CA.
• November 4. Phylogenomics and the diversification of microbes. Biology and Mathematics in the Bay Area Day (BaMBA II). Invited talk.
• October 26. Phyogenomics of mutualistic symbioses, U. C. Davis Research Retreat on Host-Microbe Interactions.
• October 18. Phylometagenomics: combining evolutionary analysis and metagenomics.  Talk and Session Chair in We’re not in Kansas Anymore: Where Genomics and Evolutionary Biology Meet at Genomes, Medicine and the Environment in Hilton Head, SC.
• October 12. Phylogenomics and the diversification of microbes. For U. C. Davis MCB Department Seminar Series. Slideshare.
• October 6. 1st International Metagenomics Meeting at UCSD. Keynote Talk. See video from CalIT2 and on Youtube.
• September 26. Genomics of Mutualistic Symbioses and the Origin of Novelty. 14th Annual International Meeting on Microbial Genomes, Lake Arrowhead, CA. Slideshare.
• September 20. Phylogenomics and the diversification of microbial genomes. At Novozymes in Davis, CA.
• September 18. Phylometagenomics. California Metagenomics Workshop, U. C. Berkeley.
• September 11. Challenges associated with screening small oligos. FAS DNA Synthesis and Biosecurity Workshop. Program here Meeting-FAS-9-11-2006.
• August 18. Metaphylogenomics: Combining Evolutionary Reconstructions and Metagenomic Analysis. CSB 2006 Workshop on Comparative Microbial Genomics.
• August 12. Microbial diversity. At Scifoo Camp. Slideshare.  See my blogs about this meeting.
• May 25. Phylogenomics and the Diversification of Microbes. SMBE Annual Meeting entitled Genomes, Evolution and Bioinformatics.
• May 21. On Next Generation Screening Frameworks Synthetic Biology 2. Webcast [1].
• May 11. DARPA Fundamental Laws of Biology
• March 30. Phylogenetic and other approaches to binning of metagenomic sequences: Theoretical and applied issues. JGI Users Meeting.
• February. Phylogenetic Anchors and Shotgun Environmental Sequencing. Keystone Meeting on Microbial Community Genomics in Animals and in the Environment.

2005

• December 16. Phylogenomics and the diversification of microbes. West 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 slides. NIH Videocast. Video on Youtube.
• April 16. Genomic Insights into Tetrahymena’s Bag of Genetic Tricks. International 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 Evol. Microbial 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 Analysis. At 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 Structure. Slideshare.
• May 1995. RecA as a model molecule for molecular systematic studies of bacteria. At the Society for the Study of Evolution (SSE) Meeting. Montreal, Canada.

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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.

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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.

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OTHER

• List of presentations along with video, audio and notes available at https://phylogenomics.wordpress.com/people/jonathan-eisen/talks-and-presentations/
• Google Scholar Page here.
• Tree of Life Blog: http://phylogenomics.blogspot.com
• Twitter: @phylogenomics
• Lab web page: https://phylogenomics.wordpress.com
• Microbiology of the Built Environment Network: http://microbe.net
• Slideshare: http://www.slideshare.net/phylogenomics
• Youtube channel: http://www.youtube.com/user/phylogenomics
• Figshare: https://figshare.com/authors/jonathan-eisen/97599