My CV




BIOGRAPHICAL SKETCH

JONATHAN A. EISEN
---
Professor                                                                             Phone: 530-752-3498
UC Davis Genome Center                                                  Email: jaeisen@ucdavis.edu
Dept. of Evolution and Ecology                                           Lab: http://bobcat.genomecenter.ucdavis.edu/
University of California, Davis                                            Twitter: http://twitter.com/phylogenomics
---


A.      Education

Harvard College, AB Biology, 1990

Stanford University, PhD Biological Sciences, 1998


B.       Positions and Honors

PROFESSIONAL EXPERIENCE

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 and the Joint Genome Institute
2000-current   Adjunct Faculty, Biology Department, Johns Hopkins University, Baltimore, MD
2002-2006       Full Investigator, Dept. of Microbial Genomics, The Institute for Genomic Research
1998-2002       Asst. Investigator, Dept. of Microbial Genomics, The Institute for Genomic Research
1991-1998       PhD Student, Stanford University Dept. of Biological Sciences
1991                Field Assistant, Rocky Mountain Biological Laboratory with Prof. Ward Watt
1989-1990       Research Assistant, Lab of Prof. Colleen A. Cavanaugh, Harvard University
1988                Research Assistant, Lab of Prof. Fakhri A. Bazzaz, Harvard University
1988                Field Assistant, Rocky Mountain Biological Laboratory with Prof. William A Calder III

HONORS/AWARDS

2011                Winner, Benjamin Franklin Award for Open Science
2010                Chair, Division R, American Society for Microbiology
2009                Finalist for the Benjamin Franklin Award for Open Science
2009                Selected by Scientific American as one of six scientists to follow on Twitter
2008                Blog posting selected for "The Open Laboratory 2008" a collection of the best science blog postings of the year
2004-2006       Member, Defense Science Studies Group
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

2010-current   ASM Communications Committee
2009-current   Joint Genome Institute's Program Advisory Committee for the Microbial Genome & Metagenome Programs
2008-2009       National Academy of Sciences, Committee on Life Sciences, 2008-2009. The report from the Committee was published in September 2009.
2007-current   UC Davis Genome Center Nucleic Acids Core Facility Advisory Group
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.
Ongoing           Panelist for multiple DOE, NSF and Genome Canada grant programs
Ongoing           Ad Hoc Reviewer for NSF, NASA, DOE, NIH, and other grants

EDITORIAL BOARDS
2008-present  Academic Editor in Chief, PLoS Biology
2006-present  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 EXPERIENCE
2008-2010       UC Davis, Fall Quarter, Biological Sciences 2C: Biodiversity and the Tree of Life, Co-taught with other faculty including James Doyle, Brad Shaffer, and Susan Keen, 600 students
2007-2010       UC Davis, Spring Quarter, Workshop in Applied Phylogenetics, Guest Lecture
2008, 2010      UC Davis, Microbial Phylogenomics, Taught full course
2007                UC Davis, Spring Quarter, CLIMB (Collaborative Learning in Mathematics and Biology), Guest module lectures
2002-2004       MBL Genome Sequencing and Analysis Course, Co-design and guest lectures
2003                IGERT Visiting Fellow in Comparative Genomics, U. Arizona, 1 week
1999-2003       MBL, Short Course on Molecular Evolution, Guest Lecturer
1999-2001       CSHL Genomics Course, Guest Lecturer
1999-2003       Jackson Lab Genome Sequence Analysis Course, Guest Lecturer
1996-1998       Stanford University “SME Core: The Heart”. Head Teaching Assistant and Co-Course Designer with Profs. David Botstein, Rick Myers, David Cox, et al.
Ongoing           Guest lectures on “Genomics” or “Phylogenomics” in dozens of courses at UC Davis, UMD, and JHU over the last 14 years.

C.    Peer-reviewed publications (in reverse chronological order, PMIDs and hotlinks included when available)

1.     Mindell DP, Fisher BL, Roopnarine P, Eisen JA, Mace GM, Page RDM, Pyle RL. Submitted. Aggregating, tagging and integrating biodiversity research.
2.     Sharpton TJ, Risenfeld S, Kembel SW, Ladau J, O’Dwyer J, Green JL, Eisen JA, Pollard KS. Submitted. PhylOTU: A High-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.
3.     Kembel S, Eisen JA, Pollard KS, Green JL. Submitted. The phylogenetic ecology of metagenomes: insights into microbial diversity and community assembly.
4.     Wu D, Wu M, Halpern A, Rusch D, Yooseph S, Frazier M, Venter JC, Eisen JA. Submitted. Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic trees.
5.     Wu M, Chatterji S, Eisen JA. Submitted. Accounting for alignment uncertainly in phylogenomics.
6.     Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. Submitted. Distributed globally, limited locally: drivers of beta-diversity depend on spatial scale.
7.     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.
8.     Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial communityPLoS ONE 5(4): e10209. PMID: 20419134.
9.     Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific dataPLoS ONE 5(4): e10071. PMID: 20418944.
10.  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 archaeonPLoS One, 5(3): e9605. PMID: 20333302.
11.  Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaNature, 462(7276): 1056-60. PMID: 20033048.
12.  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 transplantationProc. Natl. Acad. Sci. USA, 106(40): 17187-92. PMID: 19805153.
13.  Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collectionPLoS Biol, 7(10): e1000224. PMID: 19855830.
14.  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(7): e6085. 2009.
15.  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 profundicolaPLoS Genet, 5(2): e1000362.
16.  Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. 2009. Assembling the marine metagenome, one cell at a timePLoS ONE, 4(4): e5299.
17.  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(1) e4207.
18.  Valdes J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. 2008. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applicationsBMC Genomics 9:597
19.  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 closureBMC Genomics. 9(1): 562. PMID: 19036158.
20.  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 Biol. 9(11): R158. PMID: 19000309.
21.  Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inferenceGenome Biology 2008, 9:R151. PMID: 18851752.
22.  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(7): e2566. PMID: 18596968.
23.  Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. RECOMB 2008.
24.  Hazen TH, Wu D, Eisen JA, Sobecky PA. 2007. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Appl Environ Microbiol 2007 73(23):7703-10. PMID: 17921277.
25.  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? Int J Syst Evol Microbiol 57: 1677-8. PMID: 17684235.
26.  Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. 2007. Identification of a new family of lycopene cyclases in photosynthetic bacteriaProc Natl Acad Sci U S A 104: 11784-9. PMID: 1760690.
27.  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(5) e77. PMID: 17511521.
28.  Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbesPLoS Biology 5(3): e82.    PMID: 17355177.
29.  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.
30.  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.
31.  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.
32.  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 genomeProc Natl Acad Sci U S A 103:15200-5. PMID: 17015832.
33.  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.
34.  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.
35.  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.
36.  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(2): 231-238.
37.  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(4): 443-451.
38.  Penn K, Wu D, Eisen JA, Ward N. 2006. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Appl Environ Microbiol 72: 1680-1683. PMID: 16461727.
39.  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.
40.  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 “Geothermal biology and geochemistry in Yellowstone National Park.”Inskeep WP and McDermott TR, pp 163-170. Montana State University Thermal Biology Institute.
41.  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). Proc Natl Acad Sci USA 102: 7315-7320. PMID: 15883371.
42.  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. Int J System Evol Microbiol 55: 1021-1026.PMID: 15879228.
43.  Desjardins C, Eisen JA, Nene V. 2005. New evolutionary frontiers from unusual virus genomesGenome Biology 6: 212-213. PMID: 15774035.
44.  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.
45.  Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RB, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N. 2004. Genome sequence of Silicibacter pomeroyi reveals unique adaptations to the marine environmentNature 432: 910-913. PMID: 15602564.
46.  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.
47.  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.
48.  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.
49.  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.
50.  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 S, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NM. 2004. Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol 134: 183-191. PMID: 15003838.
51.  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. Proc Natl Acad Sci USA 101: 5646-5651. PMID: 15064399.
52.  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 Biotechnol 22: 554-559. PMID: 15077118.
53.  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.
54.  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. J Bacteriol 185: 5591-5601. PMID: 12949112.
55.  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 bacteriophageJ Bacteriol 185: 5220-5233. PMID: 12923095.
56.  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. Bioch Biophys Res Commun 310: 927–935. PMID: 14550293.
57.  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. J Bacteriol 185: 3392-3399. PMID: 12754238.
58.  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. Proc Natl Acad Sci USA 100: 5455-5460. PMID: 12704232.
59.  Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. PMID: 12805538.
60.  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 faecalisScience 299: 2071-2074. PMID: 12663927.
61.  Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. 2003. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 51: 859-866. PMID: 12777046.
62.  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.
63.  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.
64.  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. Environ Microbiol 4: 799-808. PMID: 12534463.
65.  Eisen JA, Wu M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Pop Biol 61: 481-487. PMID: 12167367
66.  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 Biotechnol 20: 1118-1123. PMID: 12368813.
67.  Van Houten B, Eisen JA, Hanawalt PC. 2002. A cut above: discovery of an alternative excision repair pathway in bacteriaProc Natl Acad Sci USA 99: 2581-2583. PMID: 11880612.
68.  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.
69.  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 symbiontsProc Natl Acad Sci USA 99: 13148-13153. PMID: 12271122.
70.  Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. 2002. The value of complete microbial genome sequencing (You get what you pay for). J Bacteriol 184: 6403-6405. PMID: 12426324.
71.  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. J Bacteriol 184: 5479-5490. PMID: 12218036.
72.  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 agalactiaeProc Natl Acad Sci USA 99: 12391-12396. PMID: 12200547.
73.  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.
74.  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.Proc Natl Acad Sci USA 99: 9509-9514. PMID: 12093901.
75.  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.Photosyn Res 70: 3-17. PMID: 16228359. DOI: 10.1023/A:1013879706863.
76.  Eisen JA. 2002. Brouhaha over the other yeast. Nature 415: 845-848. PMID: 11859347.
77.  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. Int J Parasitol 32: 159-166. PMID: 11812492.
78.  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.
79.  Eisen JA. 2001. Response to Mackiewicz et alGenome Biology 2: interactions1004.1-1004.4.
80.  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: 498-506PMID: 11463916.
81.  Ward N, Eisen JA, Fraser CM, Stackebrandt E. 2001. Sequenced strains must be saved from extinction. Nature 414: 148. PMID: 11700527.
82.  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. Proc Natl Acad Sci USA 98: 4136-4141.PMID: 11259647.
83.  Salzberg SL, Eisen JA. 2001. Lateral gene transfer or viral colonization? Science 293:1048. PMID: 11503638.
84.  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.
85.  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. Curr Opin Plant Biol 4: 105-110. PMID: 11228431.
86.  Nelson KE, Eisen JA, Fraser CM. 2001. The genome of Thermotoga maritima MSB8. Meth Enzymol 330: 169-180. PMID: 11210497.
87.  Eisen JA. 2001. GastrogenomicsNature 409: 463-465. PMID: 11206526.
88.  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. Nucl Acids Res 29: 41-43. PMID: 11125044.
89.  Eisen JA. 2000. Microbial and plant genomicsJ Biolaw and Business, Spec Supp 21-24.
90.  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. Nucl Acids Res 28: 1397-1406. PMID: 10684935.
91.  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.
92.  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.
93.  Nierman W, Eisen JA, Fleischmann RD, Fraser CM. 2000. Genome data: what do we learn? Curr Opin Struct Biol 10: 343-348. PMID: 10851186.
94.  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.
95.  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.
96.  Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM. 2000. The genome sequence of Vibrio cholerae, the etiologic agent of choleraNature 406:477-483. PMID: 10952301.
97.  Eisen JA, Heidelberg JF, White O, Salzberg SL. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol 1: research 0011.1-0011.9. PMID: 11178265.
98.  Pollock DD, Eisen JA, Doggett NA, Cummings MP. 2000. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol 7: 1776-1788PMID: 11110893.
99.  Eisen JA. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genetics Dev 10: 606-611. PMID: 11088009.
100.     Eisen JA. 2000. Assessing evolutionary relationships among microbes from whole genome analysis. Curr Opin Microbiol 3: 475-480PMID: 11050445.
101.     Fraser CM, Eisen JA, Fleischmann RD, Ketchum KA, Peterson S. 2000. Comparative genomics and understanding of microbial biology. Emerg Infect Dis 6: 505-512PMID: 10998382.
102.     Fraser CM, Eisen JA, Salzberg SL. 2000. Microbial genome sequencingNature 406: 799-803. PMID: 10963611.
103.     Nierman W, Eisen JA, Fraser CM. 2000. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis. Res Microbiol 151: 79-84.. PMID: 10865951.
104.     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.
105.     Eisen JA, Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mut Res 435: 171-213. PMID: 10606811.
106.     Eisen JA. 1999. Going to extremesTrends Genet 15: 218-219PMID: 10419407.
107.     Eisen JA. 1999. Mechanistic basis of microsatellite instability. In Microsatellites: Evolution and Applications (DB Goldstein and C Schlotterer, eds). Oxford University Press, Oxford.
108.     White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg SL, Smith HO, Venter JC, Fraser CM. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1Science 286: 1571-1577. PMID: 10567266.
109.     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.
110.     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. Hum Genet 103: 355-364.PMID: 9799093.
111.     Eisen JA. 1998. A phylogenomic study of the MutS family of proteins. Nucl Acids Res 26: 4291-4300. PMID: 9722651.
112.     Gruber TM, Eisen JA, Gish K, Bryant DA. 1998. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS Microbiol Lett 162: 53-60. PMID: 9595663.
113.     Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysisGenome Res 8: 163-167. PMID: 9521918.
114.     White RB, Eisen JA, Kasten TW, Fernald RD. 1998. Second gene for gonadotropin-releasing hormone in humansProc Natl Acad Sci USA 95: 305-309. PMID: 941937.
115.     Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feastNature Medicine 3: 1076-1078. PMID: 9334711.
116.     Eisen JA. 1997. The genetic data environment: a user modifiable and expandable multiple sequence analysis package, In Meth Mol Biol, vol 70: Sequence Data Analysis Guidebook (SR Swindell, ed), Humana, Totowa, NJ, pp. 13-38. PMID: 90896.
117.     Shafer RW, Eisen JA, Merigan TC, Katzenstein DA. 1997. Sequence and drug susceptibility of subtype C reverse transcriptase from HIV-1-seroconverters in ZimbabweJ Virol 71: 5441-5448. PMID: 9188616.
118.     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. J Mol Evol 41: 1105-1123. PMID: 8587109.
119.     Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucl Acids Res 23: 2715-2723. PMID: 7651832.
120.     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. Nucl Acids Res 22: 2634-2636. PMID: 8041625.
121.     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. J Bacteriol 175: 6518-6529. PMID: 8407828.
122.     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 analysisJ Bacteriol 174: 3416-3421. PMID: 1577710.

D.       Genome report publications. We have now begun publishing simple “report” papers for each genome we are sequencing. I am listing them separately because of the large number of reports.

123.     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 and Klenk H-P. 2010. Complete genome sequence of Cellulomonas flavigena type strain (134T)Standards in Genomic Sciences 3: 15-25.
124.     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 and Klenk H-P. 2010. Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)Standards in Genomic Sciences 3: 1-14.
125.     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 and Klenk H-P. 2010. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T)Standards in Genomic Sciences 2: 280-289.
126.     Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavromatis K, Lucas S, Glavina Del Rio T, Nolan M, Chen F, Tice H, Pitluck S, Cheng J-F, 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 Y-J, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P and Lapidus A. 2010. Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)Standards in Genomic Sciences 2: 228-228.
127.     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 and Lapidus A. 2010. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)Standards in Genomic Sciences 2: 1-8.
128.     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 and Lucas S. 2010. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T)Standards in Genomic Sciences 2: 87-95.
129.     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 and Lucas S. 2010. Complete genome sequence of Veillonella parvula type strain (Te3T)Standards in Genomic Sciences 2: 57-65.
130.     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 and Chen F. 2010. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T)Standards in Genomic Sciences 2: 220-227.
131.     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 and Kyrpides NC. 2010. Complete genome sequence of Gordonia bronchialis type strain (3410T)Standards in Genomic Sciences 2: 19-28.
132.     Ivanova N, Sikorski J, Jando M, Munk C, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S and Others. 2010. Complete genome sequence of Geodermatophilus obscurus type strain (G-20T)Standards in Genomic Sciences 2: 158.
133.     Johannes Sikorski AL, Chertkov O, Lucas S, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng J-F, 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 Y-J, Jeffries C-D, Rohde M, Göker M, Spring S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz PC, Kyrpides NC, Klenk H-P. 2010. Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T)Standards in Genomic Sciences 3: 57-65.
134.     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 and Klenk H-P. 2010. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)Standards in Genomic Sciences 2: 270-279.
135.     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 and Lapidus A. 2010. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290T)Standards in Genomic Sciences 3: 47-56.
136.     Labutti K. SJ, Schneider S., Nolan M., Lucas S., Glavina Del Rio T., Tice H., Cheng J., Goodwin L., Pitluck S., Liolios K., Ivanova N., Mavromatis K., Mikhailova N., Pati A., Chen A., Palaniappan K., Land M., Hauser L., Chang Y., Jeffries C., Tindall B., Rohde M., Goker M., Woyke T., Bristow J., Eisen J., Markowitz V., Hugenholtz P., Kyrpides N., Klenk H., Lapidus A. 2010. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290T)Standards in Genomic Sciences 3: 47-56.
137.     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 and Chen F. 2010. Complete genome sequence of Spirosoma linguale type strain (1T)Standards in Genomic Sciences 2: 176-184.
138.     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 and Kyrpides NC. 2010. Complete genome sequence of Thermobispora bispora type strain (R51T)Standards in Genomic Sciences 2: 318-326.
139.     Lucas S, Lapidus A, Glavina Del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Kyrpides N, Mavromatis K, Mikhailova N, Teshima H, Brettin T, Detter JC, Tapia R, Han C, Larimer F, Land M, Hauser L, Markowitz V, Cheng J-F, Hugenholtz P, Woyke T, Wu D, Pukall R, Gehrich-Schroeter G, Schneider S, Klenk H-P, Eisen JA 2010. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)Standards in genomic sciences
140.     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 and Kyrpides NC. 2010. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)Standards in Genomic Sciences 2: 290-299.
141.     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 and Kyrpides NC. 2010. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)Standards in Genomic Sciences 2: 9-18.
142.     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 and Klenk H-P. 2010. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)Standards in Genomic Sciences 2: 29-37.
143.     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 and Kyrpides NC. 2010. Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)Standards in Genomic Sciences 2: 300-308.
144.     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 and Lapidus A. 2010. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T)Standards in Genomic Sciences 2: 49-56.
145.     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 and Klenk H-P. 2010. Complete genome sequence of Brachyspira murdochii type strain (56-150T)Standards in Genomic Sciences 2: 260-269.
146.     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 and Brettin T. 2010. Complete genome sequence of Kribbella flavida type strain (IFO 14399T)Standards in Genomic Sciences 2: 185-192.
147.     Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D and Others. 2010. Complete genome sequence of Conexibacter woesei type strain (ID131577T)Standards in Genomic Sciences 2.
148.     Sam Pitluck MY, Christine Munk, Matt Nolan, Alla Lapidus, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Lynne Goodwin, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk. 2010. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT)Standards in Genomic Sciences 3: 108-116.
149.     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 and Kyrpides NC. 2010. Complete genome sequence of Haloterrigena turkmenica type strain (4kT)Standards in Genomic Sciences 2: 107-116.
150.     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 and Klenk H-P. 2010. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)Standards in Genomic Sciences 2: 149-157.
151.     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 and Klenk H-P. 2010. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T).Standards in Genomic Sciences 2: 203-211.
152.     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 and Lapidus A. 2010. Complete genome sequence of Meiothermus silvanus type strain (VI-R2T)Standards in Genomic Sciences 3: 37-46.
153.     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 and Klenk H-P. 2010. Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)Standards in Genomic Sciences 2: 38-48.
154.     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 and Klenk H-P. 2010. Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)Standards in Genomic Sciences 2: 245-259.
155.     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 and Chen F. 2010. Complete genome sequence of Nakamurella multipartita type strain (Y-104T)Standards in Genomic Sciences 2: 168-175.
156.     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 and Lapidus A. 2010. Complete genome sequence of Meiothermus ruber type strain (21T)Standards in Genomic Sciences 3: 26-36.
157.     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 and Klenk H-P. 2010. Complete genome sequence of Thermocrinis albus type strain (HI 11/12T)Standards in Genomic Sciences 2: 194-202.
158.     Anderson IJ, Tindall BJ, Pomrenke H, Göker M, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Chen F, Tice H and Others. 2009. Complete genome sequence of Halorhabdus utahensis type strain (AX-2T)Standards in Genomic Sciences 1: 218.
159.     Chovatia M, Sikorski J, Schröder M, Lapidus A, Nolan M, Tice H, Glavina Del Rio T, Copeland A, Cheng JF, Lucas S and Others. 2009. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T)Standards in Genomic Sciences 1: 254.
160.     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 and Detter JC. 2009. Complete genome sequence of Atopobium parvulum type strain (IPP 1246T)Standards in Genomic Sciences 1: 166. Note erratum in Standards in Genomic Sciences 2: 361-362.
161.     Copeland A LA, 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.
162.     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 and Detter JC. 2009. Complete genome sequence of Kangiella koreensis type strain (SW-125T)Standards in Genomic Sciences 1: 226-233.
163.     Han C, Sikorski J, Lapidus A, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A and Others. 2009. Complete genome sequence of Kangiella koreensis type strain (SW-125T)Standards in Genomic Sciences 1: 226.
164.     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.
165.     Labutti K, Pukall R, Steenblock K, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M and Others. 2009. Complete genome sequence of Anaerococcus prevotii type strain (PC1T)Standards in Genomic Sciences 1: 159.
166.     Land M, Pukall R, Abt B, Göker M, Rohde M, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S and Others. 2009. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T)Standards in Genomic Sciences 1: 21.
167.     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.
168.     Lang E, Lapidus A, Chertkov O, Brettin T, Detter JC, Han C, Copeland A, Glavina Del Rio T, Nolan M, Chen F and Others. 2009. Complete genome sequence of Dyadobacter fermentans type strain (NS114T)Standards in Genomic Sciences 1: 133.
169.     Malfatti S, Tindall BJ, Schneider S, F\\ahnrich R, Lapidus A, LaButti K, Copeland A, Glavina Del Rio T, Nolan M, Chen F and Others. 2009. Complete genome sequence of Halogeometricum borinquense type strain (PR3T)Standards in Genomic Sciences 1: 150.
170.     Munk C, Lapidus A, Copeland A, Jando M, Mayilraj S, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H and Others. 2009. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T)Standards in Genomic Sciences 1: 292.
171.     Nolan M, Gronow S, Lapidus A, Ivanova N, Copeland A, Lucas S, Glavina Del Rio T, Chen F, Tice H, Pitluck S and Others. 2009. Complete genome sequence of Streptobacillus moniliformis type strain (9901T)Standards in Genomic Sciences 1: 300.
172.     Nolan M, Tindall BJ, Pomrenke H, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF and Others. 2009. Complete genome sequence of Rhodothermus marinus type strain (R-10T)Standards in Genomic Sciences 1: 283.
173.     Pukall R, Gehrich-Schröter G, Lapidus A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF and Others. 2009. Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T)Standards in Genomic Sciences 1: 262.
174.     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 and Hugenholtz P. 2009. Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1T)Standards in Genomic Sciences 1: 234-241.
175.     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 and Han C. 2009. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T)Standards in Genomic Sciences 1: 174-182.
176.     Spring S, Lapidus A, Schröder M, Gleim D, Sims D, Meincke L, Glavina Del Rio T, Tice H, Copeland A, Cheng JF and Others. 2009. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T)Standards in Genomic Sciences 1: 242.
177.     Tindall BJ, Schneider S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF and Others. 2009. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T)Standards in Genomic Sciences 1: 270.

E.       Other publications
1.     Barton N, Briggs D, Eisen JA, Goldstein DB, Patel N: Evolution, 833 p, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2.     Eisen JA. 2009. Genomic Evolvability and the Origin of Novelty: Studying the Past, Interpreting the Present, and Predicting the Future, David A. Relman, Margaret A. Hamburg, Eileen R. Choffnes, and Alison Mack, (ed), Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg, THE NATIONAL ACADEMIES PRESS, Washington, DC.
3.     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, Inskeep WP, McDermott TR, (ed), Geothermal biology and geochemistry in Yellowstone National Park, Montana State University Thermal Biology Institute, Bozeman, MT. 163-170.
4.     Eisen JA. 2005. Coordinating efforts to understand microbes in the environment. Letter to the Editor. Microbe, 71(4): 157.
5.     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.
6.     Brodley C, Eisen JA. 2007. Tampering with DNA: National Security Needs for Detection and Design. Defense Science Study Group 2004-2005 Papers.
7.     Eisen JA. 2007. Toward a global field guide for microorganisms. Defense Science Study Group 2004-2005 Papers.

F.       Research Support

Ongoing
·       Sloan Foundation, Eisen (PI); 7/1/2010-6/30/2012; microBEnet: a network for microbiology of the built environment. The goal of this project is to coordinate and create resources for communication and networking for the emerging field of microbiology of the built environment.
·       DARPA via subcontract from Princeton, Levin (PI); 04/01/2007-03/31/2011Microstates to Microdynamics: A New Mathematics of Biology; This goal of this project is to search for fundamental laws of biology; Role: Co-PI
·       Gordon and Betty Moore Foundation, Eisen (PI)   ; 12/01/2007-10/01/2011Integrating evolutionary, ecological and statistical approaches to metagenomics; This project focuses on the development and use of integrative computational tools for studying microbial diversity from metagenomic data; Role: PI
·       NSF DBI-0923556  MRI, Eisen (PI); 8/15/09-7/31/12; Acquisition of a Roche Genome Sequence Titanium System for Studies of Microbial Communities; The goal of this project is to provide sequencing capabilities to the UC Davis community. Role: PI
·       NSF 0949453  Facciotti (PI); 10/1/09-9/30/11; Microbial Genome Sequencing: High-Resolution Phylogenomics of Halophilic Archaea; The goal of this project is to sequence and analyze the genomes of 48 species of halophilic archaea. Role: CoPI
·       NSF DBI-0923806 (Bais, PI); 8/1/09-7/31/12   ; GEPR: The effects of the microbiome on the rice transcriptome; The goal of this project is to characterize the response of rice plants to communities of microbes applied to their roots.; Role: CoPI

Completed grants

·       11/15/1994 - 02/14/2001 Grant #DEFC0295ER61962, $5,949,330.00, Assistant Researcher, An Integrated Program in Microbial Genome Sequencing and Analysis, Claire M. Fraser (Principal Investigator), DOE, Percentage Effort=40%
·       07/01/1999 - 09/30/2001 Grant #N000149910860, $114,592, Principal Investigator, Shotgun Sequencing of Plasmids from Marine Sediment Bacteria – Genetic Exploration, ONR, Percentage Effort=10%
·       09/01/1999 - 08/30/2002 Grant #KDI-9980088, $156,692, Assistant Researcher, Intelligent Computational Genomic Analysis, Simon Kasif (Principal Investigator), NSF, Percentage Effort=10%
·       04/01/2000 - 03/31/2001 Grant #U01 AI46517-01, $280,383, Co-Investigator, Comparative Genomics of Wolbachia, Scott O (Principal Investigator), NIH-NIAID, Percentage Effort=25%
·       04/17/2000 - 04/16/2002 $658,000, Principal Investigator, Complete Genome Sequence of M. capsulatus, University of Bergen
·       10/01/2000 - 09/30/2003 Grant #MCB-0084211, $962,208, Co-Investigator, Environmental Genomics and Microbial Observatories: Analysis of genetic variability, gene content, and genomic potential in uncultivated marine picoplankton, John F. Heidelberg (Principal Investigator), NSF, Percentage Effort=10%
·       12/01/2005 - 11/30/2008 $270,645, Co-Investigator, Microbial Genome Sequencing “ EST Survey of Charophycean green Algae", Charles Delwiche (Principal Investigator), NSF
·       12/01/2000 - 11/30/2002 $615,483, Principal Investigator, The Whole Genome Sequence of Actinomyces naeslundi., Tim Read (Principal Investigator), NIH
·       07/15/2001 - 07/14/2004 $503,300, Assistant Researcher, Identifying the Proteins that Mediate the Ionizing of Gene expression in the radiation resistant organism D. radiodurans strain D1, John Battista (Principal Investigator), DOE
·       10/01/2002 - 09/30/2004 $216,458, Assistant Researcher, Effects of Host Environment on Bacterial Genome Evolution, Nancy Moran (Principal Investigator), NSF
·       09/15/2004 - 03/31/2009 $538,193, Co-Investigator, Comparative Genomics of Chemosynthetic Symbionts, Colleen Cavanaugh (Principal Investigator), NSF
·       01/01/2002 - 12/31/2004 Grant #N01-AI-15447, $7,381,926, Assistant Researcher, Pathogen Functional Genomics Resource Center- Anthracis Supplement, Tim Read (Principal Investigator), NIH
·       09/15/2003 - 08/31/2005 Grant #NSF-ANI-0333537, $164,732, Assistant Researcher, A high speed network connection for Genomic Research, NSF
·       09/01/2003 - 08/31/2006 $211,645, Assistant Researcher, Interactive Studies of Wolbachia –Eukaryotic Interactions: Genomes to Communities and Back, Jack Warren (Principal Investigator), NSF, Percentage Effort=5%
·       02/02/2004 - 02/01/2009 $19,931,966, Assistant Researcher, Biodefense Pathogen Genome Resource (BPGR) at TIGR, Owen White (Principal Investigator), NIH, Percentage Effort=0%
·       06/30/2004 - 06/29/2006 Grant #NIH-HHSSN266200400038C, $$21,110,385, Assistant Researcher, Biodefense Resource Centers for Biodense of Emerging/Re-emerging Infectious Diseases, Owen White (Principal Investigator), NIH, Percentage Effort=0%
·       05/01/2004 - 04/30/2006 Grant #MCB-0347324, $86, 338, Assistant Researcher, CAREER: Integrating Bacterial Diversity into Environmental Change Research and Education, Jen Hughes (Principal Investigator), NSF, Percentage Effort=0%
·       01/01/2004 - 12/31/2005 $121, 500, Co-Investigator, Project/Proposal Title: Genome Sequencing: Genomic Sequencing of two Globally Ubiquitous Members of the Epsilon Proteobacteria, Craig Cary (Principal Investigator), NSF, Percentage Effort=10%
·       09/01/2001 - 08/31/2004 Grant #DE-FG02-01ER6320, $$2,047,000, Co-Investigator, Continuation of the Comprehensive Microbial Resource, Owen White (Principal Investigator), DOE
·       09/15/2006 - 12/14/2008 $$325,253, Assistant Researcher, Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA), Larry Smarr (Principal Investigator), Gordon and Betty Moore Foundation
·       05/01/2003 - 04/31/2007 $201,748, Assistant Researcher, Biogeochemistry of Kamchatka thermophiles, Juergen Weigel (Principal Investigator), NSF
·       08/01/2003 - 01/30/2007 Grant #NSF-EF-0243492, $247,185, Principal Investigator, Microbial Genome Sequencing: Complete Genome Sequencing of the Extremely Halophilic Archaea Haloferax volcanii, NSF
·       05/30/2006 - 05/29/2007 $149,431, Assistant Researcher, Project/Proposal Title: The Complete Genome Sequence of Teredinibacter turnerae T7902T (g-proteobacterium), the cultivable Intracellular endosymbiont of wood-boring marine mollusk Lyrodus pedicellatus, Dan Distel (Principal Investigator), NSF
·       01/01/2004 - 01/01/2007 Grant #EF0412226, $705,417, Co-Investigator, Genome Sequence of Prochloron didemni: an obligate cyanobacterial symbiont of the ascidian Lissoclinum patella, Jacques Ravel (Principal Investigator), NSF
·       03/15/2003 - 06/30/2007 Grant #NSF-EF-024036, $2,567,000, Principal Investigator, Microbial Genome Sequencing: Shotgun Sequencing of Tetrahymena thermophila, NSF
·       10/01/2002 - 09/30/2007 Grant #DEB-022865, $2,480,000, Principal Investigator, Phylogenomics: A Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life, NSF
·       06/01/2006 - 05/31/2007 $$74,833, Co-Investigator, Detecting Natural versus Unnatural DNA, Carla Brodley (Principal Investigator), DARPA
·       04/01/2003 - 03/31/2009 Grant #R01 GM067012, $3,873, 442, Principal Investigator, Tetrahymena Genome Sequencing Project, NIH-NIGMS
·       11/01/2006 - 10/31/2007 $$35,000, Co-Investigator, Microbial diversity in ileal transplants, Michael Zasloff (Principal Investigator), Broad Medical Research Foundation

Sample of Recent Press Coverage and Outreach
·       November 2010: Microbiology goes digital. Microbe Magazine.
·       October 2010: You Aren’t Blogging Yet. The Scientist.
·       February 2010: Beyond Darwin’s Wildest Dreams. Genome Technology article.
·       December 2009: Scientists Start a Genomic Catalog of Earth’s Abundant Microbes. New York Times.
·       November 2009: Is peer review broken?. Genome Technology article.
·       November 2009: Biologists rally to sequence 'neglected' microbes, November 17, 2009, Nature Magazine article.
·       November 2009: MTS38 - An Embarrassment of Genomes, Podcast interview from Microbe World
·       July 2009: Twitter: What's All the Chirping About? Bioscience
·       June 2009: Science journalism: breaking the convention. Nature Magazine article.
·       June 2009: The Human Terrain. Energy Times article on human associated microbes.
·       May 2009: Microbiology: Straight from the gut. Article featuring work in the Eisen lab on intestinal transplants. Nature Magazine.
·       May 2009: Genes That Fit Podcast & Radio Show. From SETI radio. Interview w/ J. Eisen and others.
·       April 2009: Brain gain: The underground world of “neuroenhancing” drugs. New Yorker article
·       January 2009: Computing evolution. ScienceNews.