Jonathan A. Eisen

Jonathan Eisen

Position Title

Director, UC Davis Microbiome Special Research Program
Dept. of Evolution and Ecology
Dept. of Medical Microbiology & Immunology
Genome Center
Center for Population Biology

GBSF 5311

Eisen Lab Research and Other Projects

Main Research Theme: Diversity of Microbes and Microbiomes

A major area of emphasis in my lab is in the study of the ecology, evolution and function of microbes and microbial communities. Our work in this area includes topics such as those listed below:

  • The genomic basis for the origin and evolution of new functions.
  • The ecology and evolution of microbial communities.
  • The co-evolution of microbes and their carrying vessels (i.e., hosts).
  • Variation in “evolvability.”
  • The development of phylogeny-driven computational tools to analyze genomic and metagenomic sequence data.
Current and Recent Lab Projects (examples)
  • Microbiology of the Built Environment My lab is interested in the microbial ecology of the "built environment" - that is, the places humans have created such as buildings, vehicles, water systems, etc. We do both research and communications activities in this area.
  • Seagrass Microbiomes. One of our major research topics is on the microbial communities that live in and on seagrasses and how they contribute to the evolution, ecology, and function of these important plants and their surrounding ecosystems. 
  • Istmobiome. We are collaborating with the Smithsonian Tropical Research Institute to study microbiomes of organisms on the two sides of the Panamanian Isthmus. 
Open Scientific and Scholarly Communication 

Another major interest in my group is in scientific and scholarly communication. I am deeply committed to the opening up of scholarly communication such as by improving access to literature, data, and tools and also by communicating more with the public outside of the "normal" scholarly literature through blogging, Twitter, and other means.  

UC Davis Graduate Group Affiliations

  • Population Biology
  • Microbiology
  • Ecology
  • Biophysics
  • Computer Science
  • Integrative Genetics and Genomics


  • BIS 002C Introduction to Biology
  • EVE 161 Microbial Phylogenomics

    Honors and Awards

    • UC Davis ADVANCE Scholar Award, 2019
    • Elected Representative to AAAS Council, 2017-2020.
    • Chair, Division R, American Society for Microbiology, 2010.
    • Elected Fellow of the American Academy of Microbiology, 2012
    • Esquire Magazine, "Best and Brightest Innovators", 2002
    • Walter J. Gores Award for Excellence in Teaching, 1998

    Past Positions and Education

    • 2000-2008. Adjunct Faculty, John Hopkins University, Department of Biology.
    • 1998-2006. Faculty, The Institute for Genomic Research, Rockville, MD. 
    • 1991-1998. Stanford University. PhD Student in the Department of Biological Sciences in the lab of Prof. Philip C. Hanawalt. Did research on phylogenomics of DNA repair processes. PhD in 1998.
    • 1986-1990. Harvard College.  Conducted research with Prof. Colleen Cavanaugh on chemosynthetic symbionts and Fakhri Bazzaz on plant physiology. AB in Biology 1990.

    Selected Publications. See Google Scholar for Full list. 

    Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. 2018. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLoS Biology 16(8):e2006352. doi: 10.1371/journal.pbio.2006352

    Ettinger C, Wilkins L, Dahlhausen K, Ghose S, Oberbauer D, Eisen JA, Coil D. 2018 Even Superheroes Need Help Sometimes: Three Incredible Tales of Microbial Symbiosis. Frontiers in Young Minds 6: 50. doi: 10.3389/frym.2018.00050

    Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. (2017. <red>A microbial survey of the International Space Station (ISS). </red>PeerJ 5:e4029.

    Fahimipour AK, Kardish MR, Lang JM, Green JL, Eisen JA, Stachowicz JJ. 2017. Global-scale structure of the eelgrass microbiome. Applied and Environmental Microbiolology 83: e03391-16.

    Coil DA, Ettinger CL, Eisen JA. 2017. Gut Check: The evolution of an educational board game. PLoS Biology 15(4): e2001984. 

    Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. 2017. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35: 676–683

    Ettinger CL, Voerman SE, Lang JM, Stachowicz JJ, Eisen JA. 2017. Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge. PeerJ 5: e3246

    Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL. 2017. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biology 15(3): e2001793.

    Ganz HH, Doroud L, Firl AJ, Hird SM, Eisen JA, Boyce WM. 2017. Community-level differences in the microbiome of healthy wild mallards and those infected by influenza A viruses. mSystems 2: e00188-16.

    Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. 2015. Swabs to genomes: a comprehensive workflow. PeerJ 3: e960.

    Edwards J, Johnson C, Santos-Medellin C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences USA 12: E911-20

    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.  

    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.  

    Darling AE; Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243.

    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

    Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4:2120. doi: 10.1038/ncomms3120. PMID: 23979677.

    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.

    Lang JM, Darling AE, Eisen JA. Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510. 

    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 sequenceBMC Genomics 2013, 14:95 doi:10.1186/1471-2164-14-95.

    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.

    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 JB.01778-12 . PMID: 23123912. PDF.

    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(10): e1002743.  doi:10.1371/journal.pcbi.1002743. PMID: 23133348. PDF.

    Sharpton TJ, Jospin G, Wu D, Langille MGI, Pollard KSEisen JA. 2012. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resourceBMC Bioinformatics 13: 264. doi:10.1186/1471-2105-13-264.  PMID: 23061897. PDF.

    Tritt A, Eisen JA, Facciotti M, Darling A. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 7(9): e42304.  doi:10.1371/journal.pone.0042304. PMID: 23028432. PDF.

    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(20): 7327-7336. PMID: 22885750. PDF.

    Eisen JA. 2012. Badomics words and the power and peril of the ome-meme. Gigascience 1:6. PDF.

    Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model systemPLoS Genetics 7(9): e1002272. PMID: 21966276. PDF. 

    Kembel S, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS ONE 6(8): e23214. PMID: 21912589. PDF.

    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.

    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(3): e18011. PMID: 21437252. PDF.

    Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4): e10209. PMID: 20419134. PDF.

    Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4): e10071. PMID: 20418944. PDF.

    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): 1056-60. PMID: 20033048. PDF.

    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.

    Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collection. PLoS Biology 7(10): e1000224. PMID: 19855830. PDF.

    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.

    Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9(1): R151. PMID: 18851752. PDF.

    Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3): e82. PMID: 17355177. PDF.

    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(3): e16 . PMID: 17355171. PDF.

    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(3): e77. PMID: 17355176. PDF.

    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.

    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.

    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.

    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.

    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.

    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.

    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.

    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.

    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.

    Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. PMID: 12805538. PDF.

    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.

    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.

    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.

    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.

    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.

    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.

    Eisen JA. 2002. Brouhaha over the other yeast. Nature 415: 845-848. PMID: 11859347. PDF.

    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.

    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.

    Ward N, Eisen JA, Fraser CM, Stackebrandt E. 2001. Sequenced strains must be saved from extinction. Nature 414: 148. PMID: 11700527. PDF.

    Salzberg SL, Eisen JA. 2001. Lateral gene transfer or viral colonization? Science 293: 1048. PMID: 11503638. PDF.

    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.

    Eisen JA. 2001. Gastrogenomics. Nature 409: 463-465. PMID: 11206526. PDF.

    The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.' Nature 408: 796-815. PMID: 11130711.  PDF.

    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.

    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.

    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.

    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.

    Eisen JA. 2000. Assessing evolutionary relationships among microbes from whole genome analysis. Current Opinion in Microbiology 3: 475-480. PMID: 11050445. PDF.

    Fraser CM, Eisen JA, Salzberg SL. 2000. Microbial genome sequencing. Nature 406: 799-803. PMID: 10963611. PDF

    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.

    Eisen JA, Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutation Research 435: 171-213. PMID: 10606811. PDF.

    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.

    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.

    Eisen JA. 1998. A phylogenomic study of the MutS family of proteins. Nucleic Acids Research 26: 4291-4300. PMID: 9722651. PDF.

    Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research 8: 163-167. PMID: 9521918. PDF

    Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nature Medicine 3: 1076-1078. PMID: 9334711. PDF.

    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

    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.

    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. PDF.