Eisen:Publications

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(Journals and Book Chapters)
(Evolution Textbook)
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*[http://www.amazon.com/gp/product/0879696842?ie=UTF8&tag=thtrofli-20&link_code=as3&camp=211189&creative=373489&creativeASIN=0879696842  Amazon Page]
*[http://www.amazon.com/gp/product/0879696842?ie=UTF8&tag=thtrofli-20&link_code=as3&camp=211189&creative=373489&creativeASIN=0879696842  Amazon Page]
*[http://evolution-textbook.org Book site at Cold Spring Harbor Press]
*[http://evolution-textbook.org Book site at Cold Spring Harbor Press]
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=2011=
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* Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Distributed globally, limited locally: drivers of beta-diversity depend on spatial scale. Proc. Natl. Acad. Sci. USA. 108: 7850-7854 PMID: 21518859.
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* 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.
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* Sharpton TJ, Risenfeld S, Kembel SW, Ladau J, O’Dwyer J, Green JL, Eisen JA, Pollard KS. 2011. PLoS Computational Biology. PhylOTU: A High-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology.  7(1):e1001061. PMID: 21283775.
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=2010=
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* Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. The genome sequence of Methanohalophilus mahii SLP reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline Environments. Archaea 2010: 690737. PMID: 21234345
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* 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.
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* Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting Report. The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Standards in Genomic Sciences, 3(3): 243-248. PMID: 21304727.
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* Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4): e10209. PMID: 20419134.
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* Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4): e10071. PMID: 20418944.
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* Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. 2010. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One, 5(3): e9605. PMID: 20333302.
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=2009=
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* 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.
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*Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. 2009. '''Human gut microbiome adopts an alternative state following small bowel transplantation. [http://www.pnas.org/content/106/40/17187.long Proc Natl Acad Sci U S A. 106(40):17187-92.]
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* 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). '''[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006085 PLoS One. 2009 Jul 1;4(7):e6085.]
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* Eisen JA. 2009. '''Genomic evolvability and the origin of novelty: Studying the past, interpreting the present, and predicting the future. In Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg'''. [http://homepage.mac.com/jonathan_eisen/PDFs/108.Eisen.NAS.2009.pdf PDF here]. See http://www.nap.edu/catalog/12586.html for full book.
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* Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. 2009. '''Assembling the marine metagenome, one cell at a time. '''[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005299 PLoS One. 4(4):e5299]
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* Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. 2009. '''Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola.''' [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000362 PLoS Genet. 2009 Feb;5(2):e1000362. Epub 2009 Feb 6.]
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* Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham J E.,. Bryant DA, Robb FT Colman AS,. Tallon L J,  BadgerJH, Madupu R,. Ward NL, Eisen JA. 2009. '''Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum.''' [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004207 PLoS ONE 4(1) e4207.]
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=2008=
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* Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. '''CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads.''' RECOMB 2008. Also available in ArXiV at http://eprintweb.org/S/authors/All/ei/Eisen/1
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* Wu D, Hartman A, Ward N, Eisen JA. 2008. '''An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP).''' [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002566 PLoS ONE 3(7): e2566. doi:10.1371/journal.pone.0002566]
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* Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R 2nd, Eisen JA, Holmes DS. 2008. '''''Acidithiobacillus ferrooxidans'' metabolism: from genome sequence to industrial applications.''' [http://www.biomedcentral.com/1471-2164/9/59 BMC Genomics. 2008 Dec 11;9:597 7]
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* Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methe BA. 2008. '''Refined annotation and assembly of the ''Tetrahymena thermophila'' genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.''' [http://www.biomedcentral.com/1471-2164/9/562 BMC Genomics. 9(1): 562. PMID: 19036158.]
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* 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''.'''  [http://genomebiology.com/2008/9/11/R158 Genome Biol. 9(11): R158. PMID: 19000309.]
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* Wu M, Eisen JA. 2008. '''A simple, fast, and accurate method of phylogenomic inference.''' [http://genomebiology.com/2008/9/10/R151 Genome Biology 2008, 9:R151. PMID: 18851752.]
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* Eisen JA. '''PLoS Biology 2.0.''' [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060048 PLoS Biol. 2008 Feb;6(2):e48.]
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=2007=
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*Hazen TH, Wu D, Eisen JA, Sobecky PA. 2007. '''Sequence characterization and comparative analysis of three plasmids isolated from environmental ''Vibrio'' spp. '''[http://aem.asm.org/cgi/content/full/73/23/7703?view=long&pmid=17921277 Appl Environ Microbiol. 2007 73(23):7703-10]. PMID: 17921277.
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*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? [http://ijs.sgmjournals.org/cgi/content/full/57/8/1677 Int J Syst Evol Microbiol 57: 1677-8]. PMID: 17684235.
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*Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. 2007. Identification of a new family of lycopene cyclases in photosynthetic bacteria. [http://www.pnas.org/cgi/content/full/104/28/11784 Proc Natl Acad Sci U S A 104: 11784-9].
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*Norais C, Hawkins M, Eisen JA, Hartman A, Myllkallio H, Allers T. 2007. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. [http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030077 PLoS Genetics 3(5) e77.]
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*Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 PLoS Biology 5(3): e82].
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*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.  [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016 PLoS Biology 5(3): e16].
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*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.  [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050077 PLoS Biology 5(3): e77].
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* Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, <B>Eisen JA</B>, Cavanaugh CM. ''The Calyptogena magnifica chemoautotrophic symbiont genome.'' Science. 2007 Feb 16;315(5814):998-1000. <span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17303757&query_hl=1&itool=pubmed_docsum PubMed]<font color="#aaa">[Newton-2007]</font></span>
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=2006=
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* Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, <B>Eisen JA</B>, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. ''Evolution of sensory complexity recorded in a myxobacterial genome.'' Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5. <span class="noprint">[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17015832&query_hl=1&itool=pubmed_docsum PubMed] [http://www.pnas.org/cgi/reprint/103/41/15200 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Goldman-2006]</font></span>
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* <B>Eisen JA</B>, 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 Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. ''Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.'' PLoS Biol. 2006 Sep;4(9):e286. <span class="noprint">[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16933976&query_hl=1&itool=pubmed_docsum PubMed][http://biology.plosjournals.org/archive/1545-7885/4/9/pdf/10.1371_journal.pbio.0040286-L.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Eisen-2006]</font></span>
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* Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, <B>Eisen JA</B>, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. ''Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).'' OMICS. 2006 Summer;10(2):231-7. <span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16901231&query_hl=1&itool=pubmed_docsum  PubMed]<font color="#aaa">[Leebens-Mack-2006]</font></span>
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* Hamilton EP, Dear PH, Rowland T, Saks K, <B>Eisen JA</B>, and Orias E. ''Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome.'' Genomics 2006 Jun 16. <span class="noprint">[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16782302 PubMed] [http://www.hubmed.org/display.cgi?uids=16782302 HubMed]<font color="#aaa">[Hamilton-2006]</font></span>
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* Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, <B>Eisen JA</B>, 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, and Tettelin H. ''Comparative genomics of emerging human ehrlichiosis agents.'' PLoS Genet 2006 Feb; 2(2) e21.<span class="noprint">[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16482227 PubMed] [http://www.hubmed.org/display.cgi?uids=16482227 HubMed][http://genetics.plosjournals.org/archive/1553-7404/2/2/pdf/10.1371_journal.pgen.0020021-L.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg] <font color="#aaa">[Dunning-2006]</font></span>
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* Wu D, Daugherty SC, Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, and <B>Eisen JA</B>. ''Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters.'' PLoS Biol 2006 Jun 6; 4(6) e188.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16729848 PubMed] [http://www.hubmed.org/display.cgi?uids=16729848 HubMed][http://biology.plosjournals.org/archive/1545-7885/4/6/pdf/10.1371_journal.pbio.0040188-L.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Wu-2006]</font></span>
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* Penn K, Wu D, <B>Eisen JA</B>, and Ward N. ''Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts.'' Appl Environ Microbiol 2006 Feb; 72(2) 1680-3.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16461727 PubMed] [http://www.hubmed.org/display.cgi?uids=16461727 HubMed][http://aem.asm.org/cgi/reprint/72/2/1680 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Penn-2006]</font></span>
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= 2005 =
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* Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, and <B>Eisen JA</B>. ''Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.'' PLoS Genet 2005 Nov; 1(5) e65.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16311624 PubMed] [http://www.hubmed.org/display.cgi?uids=16311624 HubMed][http://genetics.plosjournals.org/archive/1553-7404/1/5/pdf/10.1371_journal.pgen.0010065-L.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg] <font color="#aaa">[Wu-2005]</font></span>
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* Robb FT, Gonzalez JM, Sokolova T, Chernyh N, Lebedinski A, Tallon LJ, Jones K, Wu M, <B>Eisen JA</B>. 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. <span class="noprint"><font color="#aaa">[Robb-2005]</font></span>
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* Schmidt EW, Nelson JT, Rasko DA, Sudek S, <B>Eisen JA</B>, Haygood MG, and Ravel J. ''Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella.'' Proc Natl Acad Sci U S A 2005 May 17; 102(20) 7315-20.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15883371 PubMed] [http://www.hubmed.org/display.cgi?uids=15883371 HubMed][http://www.pnas.org/cgi/reprint/102/20/7315 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Schmidt-2005]</font></span>
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* Badger JH, <B>Eisen JA</B>, and Ward NL. ''Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales.'' Int J Syst Evol Microbiol 2005 May; 55(Pt 3) 1021-6.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15879228 PubMed] [http://www.hubmed.org/display.cgi?uids=15879228 HubMed]<font color="#aaa">[Badger-2005]</font></span>
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* Desjardins C, <B>Eisen JA</B>, and Nene V. ''New evolutionary frontiers from unusual virus genomes.'' Genome Biol 2005; 6(3) 212.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15774035 PubMed] [http://www.hubmed.org/display.cgi?uids=15774035 HubMed][http://genomebiology.com/content/pdf/gb-2005-6-3-212.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Desjardins-2005]</font></span>
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* Seshadri R, Adrian L, Fouts DE, <B>Eisen JA</B>, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, and Heidelberg JF. ''Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.'' Science 2005 Jan 7; 307(5706) 105-8.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15637277 PubMed] [http://www.hubmed.org/display.cgi?uids=15637277 HubMed]<font color="#aaa">[Seshadri-2005]</font></span>
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= 2004 =
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* Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, <B>Eisen JA</B>, 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, and Ward N. ''Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.'' Nature 2004 Dec 16; 432(7019) 910-3.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15602564 PubMed] [http://www.hubmed.org/display.cgi?uids=15602564 HubMed]<font color="#aaa">[Moran-2004]</font></span>
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* Tanaka M, Earl AM, Howell HA, Park MJ, <B>Eisen JA</B>, Peterson SN, and Battista JR. ''Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance.'' Genetics 2004 Sep; 168(1) 21-33.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15454524 PubMed] [http://www.hubmed.org/display.cgi?uids=15454524 HubMed][http://www.genetics.org/cgi/reprint/168/1/21 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Tanaka-2004]</font></span>
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* Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, and <B>Eisen JA</B>. ''Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).'' PLoS Biol 2004 Oct; 2(10) e303.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15383840 PubMed] [http://www.hubmed.org/display.cgi?uids=15383840 HubMed][http://biology.plosjournals.org/archive/1545-7885/2/10/pdf/10.1371_journal.pbio.0020303-L.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Ward-2004]</font></span>
 +
* Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, <B>Eisen JA</B>, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, and Smith HO. ''Environmental genome shotgun sequencing of the Sargasso Sea.'' Science 2004 Apr 2; 304(5667) 66-74.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15001713 PubMed] [http://www.hubmed.org/display.cgi?uids=15001713 HubMed]<font color="#aaa">[Venter-2004]</font></span>
 +
* Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, and <B>Eisen JA</B>. ''Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.'' PLoS Biol 2004 Mar; 2(3) E69.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15024419 PubMed] [http://www.hubmed.org/display.cgi?uids=15024419 HubMed][http://biology.plosjournals.org/archive/1545-7885/2/3/pdf/10.1371_journal.pbio.0020069-L.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Wu-2004]</font></span>
 +
* Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, <B>Eisen JA</B> Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg S, Adams MD, White O, Hall N, Stuart K, Fraser CM, and El-Sayed NM. ''Gene synteny and evolution of genome architecture in trypanosomatids.'' Mol Biochem Parasitol 2004 Apr; 134(2) 183-91.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15003838 PubMed] [http://www.hubmed.org/display.cgi?uids=15003838 HubMed]<font color="#aaa">[Ghedin-2004]</font></span>
 +
* Seshadri R, Myers GS, Tettelin H, <B>Eisen JA</B>, 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, and Paulsen IT. ''Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes.'' Proc Natl Acad Sci U S A 2004 Apr 13; 101(15) 5646-51.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15064399 PubMed] [http://www.hubmed.org/display.cgi?uids=15064399 HubMed][http://www.pnas.org/cgi/reprint/101/15/5646 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Seshadri-2004]</font></span>
 +
* Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, <B>Eisen JA</B>, 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, and Fraser CM. ''The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.'' Nat Biotechnol 2004 May; 22(5) 554-9.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15077118 PubMed] [http://www.hubmed.org/display.cgi?uids=15077118 HubMed]<font color="#aaa">[Heidelberg-2004]</font></span>
 +
 +
= 2003 =
 +
* Methe BA, Nelson KE, <B>Eisen JA</B>, 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, and Fraser CM. ''Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.'' Science 2003 Dec 12; 302(5652) 1967-9.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14671304 PubMed] [http://www.hubmed.org/display.cgi?uids=14671304 HubMed]<font color="#aaa">[Methe-2003]</font></span>
 +
* Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, <B>Eisen JA</B>, 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, and Fraser CM. ''Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.'' J Bacteriol 2003 Sep; 185(18) 5591-601.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12949112 PubMed] [http://www.hubmed.org/display.cgi?uids=12949112 HubMed][http://jb.asm.org/cgi/reprint/185/18/5591 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Nelson-2003]</font></span>
 +
* Miller ES, Heidelberg JF, <B>Eisen JA</B>, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, and Fraser CM. ''Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage.'' J Bacteriol 2003 Sep; 185(17) 5220-33.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12923095 PubMed] [http://www.hubmed.org/display.cgi?uids=12923095 HubMed][http://jb.asm.org/cgi/reprint/185/17/5220 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Miller-2003]</font></span>
 +
* Yang RZ, Huang Q, Xu A, McLenithan JC, <B>Eisen JA</B>, Shuldiner AR, Alkan S, and Gong DW. ''Comparative studies of resistin expression and phylogenomics in human and mouse.'' Biochem Biophys Res Commun 2003 Oct 24; 310(3) 927-35.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14550293 PubMed] [http://www.hubmed.org/display.cgi?uids=14550293 HubMed][Yang-2003]</font></span>
 +
* Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, <B>Eisen JA</B>, Fraser CM, and Fleischmann RD. ''Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.'' J Bacteriol 2003 Jun; 185(11) 3392-9.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12754238 PubMed] [http://www.hubmed.org/display.cgi?uids=12754238 HubMed][http://jb.asm.org/cgi/reprint/185/11/3392 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Alland-2003]</font></span>
 +
* Seshadri R, Paulsen IT, <B>Eisen JA</B>, 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, and Heidelberg JF. ''Complete genome sequence of the Q-fever pathogen Coxiella burnetii.'' Proc Natl Acad Sci U S A 2003 Apr 29; 100(9) 5455-60.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12704232 PubMed] [http://www.hubmed.org/display.cgi?uids=12704232 HubMed][http://www.pnas.org/cgi/reprint/100/9/5455 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Seshadri-2003]</font></span>
 +
* <B>Eisen JA</B> and Fraser CM. ''Phylogenomics: intersection of evolution and genomics.'' Science 2003 Jun 13; 300(5626) 1706-7.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12805538 PubMed] [http://www.hubmed.org/display.cgi?uids=12805538 HubMed]<font color="#aaa">[Eisen-and_Fraser-2003]</font></span>
 +
* Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, <B>Eisen JA</B>, 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, and Fraser CM. ''Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.'' Science 2003 Mar 28; 299(5615) 2071-4.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12663927 PubMed] [http://www.hubmed.org/display.cgi?uids=12663927 HubMed]<font color="#aaa">[Paulsen-2003]</font></span>
 +
* Ermolaeva MD, Wu M, <B>Eisen JA</B>, and Salzberg SL. ''The age of the Arabidopsis thaliana genome duplication.'' Plant Mol Biol 2003 Apr; 51(6) 859-66.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12777046 PubMed] [http://www.hubmed.org/display.cgi?uids=12777046 HubMed]<font color="#aaa">[Ermolaeva-2003]</font></span>
 +
* 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, <B>Eisen JA</B>. 2003. ''Deep submergence synergy: Alvin and ABE explore the Galápagos Rift at 86°W.'' EOS 84: 425, 432-433. <span class="noprint"><font color="#aaa">[Shank-2003]</font></span>
 +
 +
= 2002 =
 +
* DiRuggiero J, Nandakumar R, <B>Eisen JA</B>, Schwartz M, Thomas R, Davila J, Ofman L, Robb FT. 2002. ''Genomic and physiological studies on extremophiles: model systems for exobiology.'' In “Frontiers of Astrobiology. Proceedings of the Astrobiology Workshop”, St Petersburg, Russia. Pavlov A. (Ed. ). <span class="noprint"><font color="#aaa">[DiRuggiero-2002]</font></span>
 +
* Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, <B>Eisen JA</B>, 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, and Fraser CM. ''The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.'' Nature 2003 May 1; 423(6935) 81-6.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12721629 PubMed] [http://www.hubmed.org/display.cgi?uids=12721629 HubMed]<font color="#aaa">[Read-2002]</font></span>
 +
* 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, <B>Eisen JA</B>, Timmis KN, Dusterhoft A, Tummler B, and Fraser CM. ''Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.'' Environ Microbiol 2002 Dec; 4(12) 799-808.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12534463 PubMed] [http://www.hubmed.org/display.cgi?uids=12534463 HubMed][http://www.blackwell-synergy.com/doi/pdf/10.1046/j.1462-2920.2002.00366.x http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Nelson-2002]</font></span>
 +
* <B>Eisen JA</B>. ''Brouhaha over the other yeast.'' Nature 2002 Feb 21; 415(6874) 845-8.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11859347 PubMed] [http://www.hubmed.org/display.cgi?uids=11859347 HubMed]<font color="#aaa">[Eisen-2002]</font></span>
 +
* <B>Eisen JA</B>, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, and Fraser CM. ''The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.'' Proc Natl Acad Sci U S A 2002 Jul 9; 99(14) 9509-14.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12093901 PubMed] [http://www.hubmed.org/display.cgi?uids=12093901 HubMed][http://www.pnas.org/cgi/reprint/99/14/9509 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Eisen-2002]</font></span>
 +
* <B>Eisen JA</B> and Wu M. ''Phylogenetic analysis and gene functional predictions: phylogenomics in action.'' Theor Popul Biol 2002 Jun; 61(4) 481-7.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12167367 PubMed] [http://www.hubmed.org/display.cgi?uids=12167367 HubMed]<font color="#aaa">[Eisen-2002]</font></span>
 +
* Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, <B>Eisen JA</B>, 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, and Fraser CM. ''Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.'' Nat Biotechnol 2002 Nov; 20(11) 1118-23.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12368813 PubMed] [http://www.hubmed.org/display.cgi?uids=12368813 HubMed]<font color="#aaa">[Heidelberg-2002]</font></span>
 +
* Van Houten B, <B>Eisen JA</B>, and Hanawalt PC. ''A cut above: discovery of an alternative excision repair pathway in bacteria.'' Proc Natl Acad Sci U S A 2002 Mar 5; 99(5) 2581-3.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11880612 PubMed] [http://www.hubmed.org/display.cgi?uids=11880612 HubMed][http://www.pnas.org/cgi/reprint/99/5/2581 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[VanHouten-2002]</font></span>
 +
* Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, <B>Eisen JA</B>, 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, and Barrell B. ''Genome sequence of the human malaria parasite Plasmodium falciparum.'' Nature 2002 Oct 3; 419(6906) 498-511.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12368864 PubMed] [http://www.hubmed.org/display.cgi?uids=12368864 HubMed]<font color="#aaa">[Gardner-2002]</font></span>
 +
* Paulsen IT, Seshadri R, Nelson KE, <B>Eisen JA</B>, 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, and Fraser CM. ''The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.'' Proc Natl Acad Sci U S A 2002 Oct 1; 99(20) 13148-53.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12271122 PubMed] [http://www.hubmed.org/display.cgi?uids=12271122 HubMed][http://www.pnas.org/cgi/reprint/99/20/13148 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Paulsen-2002]</font></span>
 +
* Fraser CM, <B>Eisen JA</B>, Nelson KE, Paulsen IT, and Salzberg SL. ''The value of complete microbial genome sequencing (you get what you pay for).'' J Bacteriol 2002 Dec; 184(23) 6403-5; discusion 6405.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12426324 PubMed] [http://www.hubmed.org/display.cgi?uids=12426324 HubMed][http://jb.asm.org/cgi/reprint/184/23/6403 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Fraser-2002]</font></span>
 +
* Fleischmann RD, Alland D, <B>Eisen JA</B>, 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 Jr WR Jr, Venter JC, and Fraser CM. ''Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.'' J Bacteriol 2002 Oct; 184(19) 5479-90.<<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12218036 PubMed] [http://www.hubmed.org/display.cgi?uids=12218036 HubMed][http://jb.asm.org/cgi/reprint/184/19/5479 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Fleischmann-2002]</font></span>
 +
* Tettelin H, Masignani V, Cieslewicz MJ, <B>Eisen JA</B>, 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, and Fraser CM. ''Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae.'' Proc Natl Acad Sci U S A 2002 Sep 17; 99(19) 12391-6.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12200547 PubMed] [http://www.hubmed.org/display.cgi?uids=12200547 HubMed][http://www.pnas.org/cgi/reprint/99/19/12391 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Tettelin-2002]</font></span>
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* Beja O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, <B>Eisen JA</B>, Fraser CM, and DeLong EF. ''Unsuspected diversity among marine aerobic anoxygenic phototrophs.'' Nature 2002 Feb 7; 415(6872) 630-3.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11832943 PubMed] [http://www.hubmed.org/display.cgi?uids=11832943 HubMed]<font color="#aaa">[Beja-2002]</font></span>
 +
* Dassarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, <B>Eisen JA</B>, Johnson CH, and Hood L. ''Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon.'' Photosynth Res 2001; 70(1) 3-17.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16228359 PubMed] [http://www.hubmed.org/display.cgi?uids=16228359 HubMed]<font color="#aaa">[Dassarma-2002]</font></span>
 +
 +
= 2001 =
 +
* Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, <B>Eisen JA</B>, and Slatko B. ''Sequencing and analysis of a 63 kb bacterial artificial chromosome insert from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi.'' Int J Parasitol 2002 Feb; 32(2) 159-66.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11812492 PubMed] [http://www.hubmed.org/display.cgi?uids=11812492 HubMed]<font color="#aaa">[Ware-2001]</font></span>
 +
* Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF Jr, Woo L, Chen Y, Paulsen IT, <B>Eisen JA</B>, Karp PD, Bovee D Sr, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, 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 ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, and Nester EW. ''The genome of the natural genetic engineer Agrobacterium tumefaciens C58.'' Science 2001 Dec 14; 294(5550) 2317-23.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11743193 PubMed] [http://www.hubmed.org/display.cgi?uids=11743193 HubMed]<font color="#aaa">[Wood-2001]</font></span>
 +
* <B>Eisen JA</B>. ''Gastrogenomics.'' Nature 2001 Jan 25; 409(6819) 463, 465-6.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11206526 PubMed] [http://www.hubmed.org/display.cgi?uids=11206526 HubMed]<font color="#aaa">[Eisen-2001]</font></span>
 +
* <B>Eisen JA</B>. 2001. ''Response to Mackiewicz et al.'' Genome Biology, 2 (12): interactions1004. 1-1004. <span class="noprint"><font color="#aaa">[Eisen-2001]</font></span>
 +
* Tettelin H, Nelson KE, Paulsen IT, <B>Eisen JA</B>, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, 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, and Fraser CM. ''Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.'' Science 2001 Jul 20; 293(5529) 498-506.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11463916 PubMed] [http://www.hubmed.org/display.cgi?uids=11463916 HubMed]<font color="#aaa">[Tettelin-2001]</font></span>
 +
* Ward N, <B>Eisen JA</B>, Fraser C, and Stackebrandt E. ''Sequenced strains must be saved from extinction.'' Nature 2001 Nov 8; 414(6860) 148.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11700527 PubMed] [http://www.hubmed.org/display.cgi?uids=11700527 HubMed]<font color="#aaa">[Ward-2001]</font></span>
 +
* Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, <B>Eisen JA</B>, 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, and Fraser CM. ''Complete genome sequence of Caulobacter crescentus.'' Proc Natl Acad Sci U S A 2001 Mar 27; 98(7) 4136-41.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11259647 PubMed] [http://www.hubmed.org/display.cgi?uids=11259647 HubMed] [http://www.pnas.org/cgi/reprint/98/7/4136  http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Nierman-2001]</font></span>
 +
* Salzberg SL and <B>Eisen JA</B>. ''Lateral gene transfer or viral colonization?.'' Science 2001 Aug 10; 293(5532) 1048.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11503638 PubMed] [http://www.hubmed.org/display.cgi?uids=11503638 HubMed]<font color="#aaa">[Salzberg-2001b]</font></span>
 +
* Salzberg SL, White O, Peterson J, and <B>Eisen JA</B>. ''Microbial genes in the human genome: lateral transfer or gene loss?.'' Science 2001 Jun 8; 292(5523) 1903-6.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11358996 PubMed] [http://www.hubmed.org/display.cgi?uids=11358996 HubMed]<font color="#aaa">[Salzberg-2001a]</font></span>
 +
* Bevan M, Mayer K, White O, <B>Eisen JA</B>, Preuss D, Bureau T, Salzberg SL, and Mewes HW. ''Sequence and analysis of the Arabidopsis genome.'' Curr Opin Plant Biol 2001 Apr; 4(2) 105-10.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11228431 PubMed] [http://www.hubmed.org/display.cgi?uids=11228431 HubMed]<font color="#aaa">[Bevan-2001]</font></span>
 +
* Nelson KE, <B>Eisen JA</B>, and Fraser CM. ''Genome of Thermotoga maritima MSB8.'' Methods Enzymol 2001; 330 169-80.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11210497 PubMed] [http://www.hubmed.org/display.cgi?uids=11210497 HubMed]<font color="#aaa">[Nelson-2001]</font></span>
 +
* Haft DH, Loftus BJ, Richardson DL, Yang F, <B>Eisen JA</B>, Paulsen IT, and White O. ''TIGRFAMs: a protein family resource for the functional identification of proteins.'' Nucleic Acids Res 2001 Jan 1; 29(1) 41-3.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11125044 PubMed] [http://www.hubmed.org/display.cgi?uids=11125044 HubMed] [http://nar.oxfordjournals.org/cgi/reprint/29/1/41 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Haft-2001]</font></span>
 +
 +
= 2000 =
 +
 +
* <B>Eisen JA</B>. 2000. ''Microbial and plant genomics''. Journal of Biolaw and Business, Special Supplement. 21-24. <span class="noprint"><font color="#aaa">[Eisen-2000]</font></span>
 +
* 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, <B>Eisen JA</B> and Fraser CM. ''Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.'' Nucleic Acids Res 2000 Mar 15; 28(6) 1397-406.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10684935 PubMed] [http://www.hubmed.org/display.cgi?uids=10684935 HubMed][http://nar.oxfordjournals.org/cgi/content/full/28/6/1397 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Read-2000]</font></span>
 +
* Arabidopsis Genome Initiative. ''Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.'' Nature 2000 Dec 14; 408(6814) 796-815.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11130711 PubMed] [http://www.hubmed.org/display.cgi?uids=11130711 HubMed]<font color="#aaa">[AGI-2000]</font></span>
 +
* Nierman WC, <B>Eisen JA</B>, Fleischmann RD, and Fraser CM. ''Genome data: what do we learn?.'' Curr Opin Struct Biol 2000 Jun; 10(3) 343-8.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10851186 PubMed] [http://www.hubmed.org/display.cgi?uids=10851186 HubMed]<font color="#aaa">[Nierman-2000b]</font></span>
 +
* Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, <B>Eisen JA</B>, 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, and Venter JC. ''Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.'' Science 2000 Mar 10; 287(5459) 1809-15.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10710307 PubMed] [http://www.hubmed.org/display.cgi?uids=10710307 HubMed]<font color="#aaa">[Tettelin-2000]</font></span>
 +
* Coleman MA, <B>Eisen JA</B>, and Mohrenweiser HW. ''Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse.'' Genomics 2000 May 1; 65(3) 274-82.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10857751 PubMed] [http://www.hubmed.org/display.cgi?uids=10857751 HubMed]<font color="#aaa">[Coleman-2000]</font></span>
 +
* Heidelberg JF, <B>Eisen JA</B>, 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, and Fraser CM. ''DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.'' Nature 2000 Aug 3; 406(6795) 477-83.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10952301 PubMed] [http://www.hubmed.org/display.cgi?uids=10952301 HubMed]<font color="#aaa">[Heidelberg-2000]</font></span>
 +
* <B>Eisen JA</B>, Heidelberg JF, White O, and Salzberg SL. ''Evidence for symmetric chromosomal inversions around the replication origin in bacteria.'' Genome Biol 2000; 1(6) RESEARCH0011.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11178265 PubMed] [http://www.hubmed.org/display.cgi?uids=11178265 HubMed][http://genomebiology.com/content/pdf/gb-2000-1-6-research0011.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Eisen-etal-2000]</font></span>
 +
* Pollock DD, <B>Eisen JA</B>, Doggett NA, and Cummings MP. ''A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.'' Mol Biol Evol 2000 Dec; 17(12) 1776-88.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11110893 PubMed] [http://www.hubmed.org/display.cgi?uids=11110893 HubMed][http://mbe.oxfordjournals.org/cgi/reprint/17/12/1776 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Pollock-2000]</font></span>
 +
* <B>Eisen JA</B>. ''Horizontal gene transfer among microbial genomes: new insights from complete genome analysis.'' Curr Opin Genet Dev 2000 Dec; 10(6) 606-11.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11088009 PubMed] [http://www.hubmed.org/display.cgi?uids=11088009 HubMed]<font color="#aaa">[Eisen-2000b]</font></span>
 +
* <B>Eisen JA</B>. ''Assessing evolutionary relationships among microbes from whole-genome analysis.'' Curr Opin Microbiol 2000 Oct; 3(5) 475-80.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11050445 PubMed] [http://www.hubmed.org/display.cgi?uids=11050445 HubMed]<font color="#aaa">[Eisen-2000a]</font></span>
 +
* Fraser CM, <B>Eisen JA</B> Fleischmann RD, Ketchum KA, and Peterson S. ''Comparative genomics and understanding of microbial biology.'' Emerg Infect Dis 2000 Sep-Oct; 6(5) 505-12.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10998382 PubMed] [http://www.hubmed.org/display.cgi?uids=10998382 HubMed]<font color="#aaa">[Fraaser-2000b]</font></span>
 +
* Fraser CM, <B>Eisen JA</B>, and Salzberg SL. ''Microbial genome sequencing.'' Nature 2000 Aug 17; 406(6797) 799-803.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10963611 PubMed] [http://www.hubmed.org/display.cgi?uids=10963611 HubMed]<font color="#aaa">[Fraser-2000a]</font></span>
 +
* Nierman W, <B>Eisen JA</B>, and Fraser CM. ''Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis.'' Res Microbiol 2000 Mar; 151(2) 79-84.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10865951 PubMed] [http://www.hubmed.org/display.cgi?uids=10865951 HubMed]<font color="#aaa">[Nierman-2000]</font></span>
 +
 +
= Pre 2000 =
 +
 +
* Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, 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, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, <B>Eisen JA</B>, Salzberg SL, Fraser CM, and Venter JC. ''Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.'' Nature 1999 Dec 16; 402(6763) 761-8.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10617197 PubMed] [http://www.hubmed.org/display.cgi?uids=10617197 HubMed]<font color="#aaa">[Lin-1999]</font></span>
 +
* <B>Eisen JA</B> and Hanawalt PC. ''A phylogenomic study of DNA repair genes, proteins, and processes.'' Mutat Res 1999 Dec 7; 435(3) 171-213.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10606811 PubMed] [http://www.hubmed.org/display.cgi?uids=10606811 HubMed]<font color="#aaa">[Eisen-and-Hanawalt-1999]</font></span>
 +
* <B>Eisen JA</B>. ''Going to extremes. Archaea: bridging the gap between bacteria and eukarya (A Keystone Symposia), Taos, NM, USA, 9-14 January 1999.'' Trends Genet 1999 Jun; 15(6) 218-9.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10419407 PubMed] [http://www.hubmed.org/display.cgi?uids=10419407 HubMed]<font color="#aaa">[Eisen-1999b]</font></span>
 +
* <B>Eisen JA</B>. ''Mechanistic basis for microsatelite instability'' In David B. Goldstein and Christian Schlötterer. Microsatellites. Oxford; Oxford University Press, 1999" isbn=0198504071 <span class="noprint"><font color="#aaa">[Eisen-1999a-]</font></span>
 +
* White O, <B>Eisen JA</B>, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, JiangL, 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 S, Smith HO, Venter JC, and Fraser CM. ''Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.'' Science 1999 Nov 19; 286(5444) 1571-7.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10567266 PubMed] [http://www.hubmed.org/display.cgi?uids=10567266 HubMed]<font color="#aaa">[White-1999]</font></span>
 +
* 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, <B>Eisen JA</B>, White O, Salzberg SL, Smith HO, Venter JC, and Fraser CM. ''Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.'' Nature 1999 May 27; 399(6734) 323-9.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10360571 PubMed] [http://www.hubmed.org/display.cgi?uids=10360571 HubMed][http://www.nature.com/nature/journal/v399/n6734/pdf/399323a0.pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Nelson-1999]</font></span>
 +
* Wei MH, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, <B>Eisen JA</B>, and Lerman MI. ''In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules.'' Hum Genet 1998 Sep; 103(3) 355-64.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9799093 PubMed] [http://www.hubmed.org/display.cgi?uids=9799093 HubMed]<font color="#aaa">[Wei-1998]</font></span>
 +
* <B>Eisen JA</B>. ''Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.'' Genome Res 1998 Mar; 8(3) 163-7.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9521918 PubMed] [http://www.hubmed.org/display.cgi?uids=9521918 HubMed][http://www.genome.org/cgi/reprint/8/3/163 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Eisen-1998]</font></span>
 +
* <B>Eisen JA</B>. ''A phylogenomic study of the MutS family of proteins.'' Nucleic Acids Res 1998 Sep 15; 26(18) 4291-300.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9722651 PubMed] [http://www.hubmed.org/display.cgi?uids=9722651 HubMed][http://nar.oxfordjournals.org/cgi/content/full/26/18/4291 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Eisen-1998]</font></span>
 +
* Gruber TM, <B>Eisen JA</B>, Gish K, and Bryant DA. ''The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences.'' FEMS Microbiol Lett 1998 May 1; 162(1) 53-60.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9595663 PubMed] [http://www.hubmed.org/display.cgi?uids=9595663 HubMed]<font color="#aaa">[Gruber-1998]</font></span>
 +
* White RB, <B>Eisen JA</B>, Kasten TL, and Fernald RD. ''Second gene for gonadotropin-releasing hormone in humans.'' Proc Natl Acad Sci U S A 1998 Jan 6; 95(1) 305-9.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9419371 PubMed] [http://www.hubmed.org/display.cgi?uids=9419371 HubMed][http://www.pnas.org/cgi/reprint/95/1/305 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[White-1998]</font></span>
 +
* <B>Eisen JA</B>, Kaiser D, and Myers RM. ''Gastrogenomic delights: a movable feast.'' Nat Med 1997 Oct; 3(10) 1076-8.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9334711 PubMed] [http://www.hubmed.org/display.cgi?uids=9334711 HubMed]<font color="#aaa">[Eisen-etal-1997]</font></span>
 +
* <B>Eisen JA</B>. ''The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package.'' Methods Mol Biol 1997; 70 13-38.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9089600 PubMed] [http://www.hubmed.org/display.cgi?uids=9089600 HubMed]<font color="#aaa">[Eisen-1997]</font></span>
 +
* Shafer RW, <B>Eisen JA</B>, Merigan TC, and Katzenstein DA. ''Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe.'' J Virol 1997 Jul; 71(7) 5441-8.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9188616 PubMed] [http://www.hubmed.org/display.cgi?uids=9188616 HubMed][http://jvi.asm.org/cgi/reprint/71/7/5441?view=long&pmid=9188616 http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Shafer-1997]</font></span>
 +
* <B>Eisen JA</B>. ''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 1995 Dec; 41(6) 1105-23.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8587109 PubMed] [http://www.hubmed.org/display.cgi?uids=8587109 HubMed]<font color="#aaa">[Eisen-1995]</font></span>
 +
* <B>Eisen JA</B>, Sweder KS, and Hanawalt PC. ''Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions.'' Nucleic Acids Res 1995 Jul 25; 23(14) 2715-23.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7651832 PubMed] [http://www.hubmed.org/display.cgi?uids=7651832 HubMed][http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=307096&blobtype=pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Eisen-etal-1995]</font></span>
 +
* <B>Eisen JA</B>, Benito MI, and Walbot V. ''Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences.'' Nucleic Acids Res 1994 Jul 11; 22(13) 2634-6.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8041625 PubMed] [http://www.hubmed.org/display.cgi?uids=8041625 HubMed] [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=308220&blobtype=pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg] <font color="#aaa">[Eisen-1994]</font></span>
 +
* Liu SK, <B>Eisen JA</B>, Hanawalt PC, and Tessman I. ''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 1993 Oct; 175(20) 6518-29.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8407828 PubMed] [http://www.hubmed.org/display.cgi?uids=8407828 HubMed][http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=206762&blobtype=pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Liu-1993]</font></span>
 +
* <B>Eisen JA</B>, Smith SW, and Cavanaugh CM. ''Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis.'' J Bacteriol 1992 May; 174(10) 3416-21.<span class="noprint"> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1577710 PubMed] [http://www.hubmed.org/display.cgi?uids=1577710 HubMed][http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=206016&blobtype=pdf http://bobcat.genomecenter.ucdavis.edu/mediawiki/images/0/08/Pdf-logo.jpg]<font color="#aaa">[Eisen-1992]</font></span>
 +
 +
 +
<span class="noprint">All Medline abstracts: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17303757,17015832,16933976,16901231,16782302,16482227,16729848,16461727,16311624,15883371,15879228,15774035,15637277,15602564,15454524,15383840,15001713,15024419,15003838,15064399,15077118,14671304,12949112,12923095,14550293,12754238,12704232,12805538,12663927,12777046,12721629,12534463,11859347,12093901,12167367,12368813,11880612,12368864,12271122,12426324,12218036,12200547,11832943,16228359,11812492,11743193,11206526,11463916,11700527,11259647,11503638,11358996,11228431,11210497,11125044,10684935,11130711,10851186,10710307,10857751,10952301,11178265,11110893,11088009,11050445,10998382,10963611,10865951,10617197,10606811,10419407,10567266,10360571,9799093,9521918,9722651,9595663,9419371,9334711,9089600,9188616,8587109,7651832,8041625,8407828,1577710 PubMed] [http://www.hubmed.org/display.cgi?uids=17303757,17015832,16933976,16901231,16782302,16482227,16729848,16461727,16311624,15883371,15879228,15774035,15637277,15602564,15454524,15383840,15001713,15024419,15003838,15064399,15077118,14671304,12949112,12923095,14550293,12754238,12704232,12805538,12663927,12777046,12721629,12534463,11859347,12093901,12167367,12368813,11880612,12368864,12271122,12426324,12218036,12200547,11832943,16228359,11812492,11743193,11206526,11463916,11700527,11259647,11503638,11358996,11228431,11210497,11125044,10684935,11130711,10851186,10710307,10857751,10952301,11178265,11110893,11088009,11050445,10998382,10963611,10865951,10617197,10606811,10419407,10567266,10360571,9799093,9521918,9722651,9595663,9419371,9334711,9089600,9188616,8587109,7651832,8041625,8407828,1577710 HubMed]</span>
=Journals and Book Chapters=
=Journals and Book Chapters=

Revision as of 18:08, 15 July 2011


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Contents

Evolution Textbook


2011

  • Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Distributed globally, limited locally: drivers of beta-diversity depend on spatial scale. Proc. Natl. Acad. Sci. USA. 108: 7850-7854 PMID: 21518859.
  • 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.
  • Sharpton TJ, Risenfeld S, Kembel SW, Ladau J, O’Dwyer J, Green JL, Eisen JA, Pollard KS. 2011. PLoS Computational Biology. PhylOTU: A High-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology. 7(1):e1001061. PMID: 21283775.


2010

  • Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. The genome sequence of Methanohalophilus mahii SLP reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline Environments. Archaea 2010: 690737. PMID: 21234345
  • 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.
  • Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting Report. The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Standards in Genomic Sciences, 3(3): 243-248. PMID: 21304727.
  • Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4): e10209. PMID: 20419134.
  • Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4): e10071. PMID: 20418944.
  • Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. 2010. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One, 5(3): e9605. PMID: 20333302.


2009

  • 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.
  • 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. 2009 Jul 1;4(7):e6085.
  • Eisen JA. 2009. Genomic evolvability and the origin of novelty: Studying the past, interpreting the present, and predicting the future. In Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. PDF here. See http://www.nap.edu/catalog/12586.html for full book.
  • Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. 2009. Assembling the marine metagenome, one cell at a time. PLoS One. 4(4):e5299
  • Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. 2009. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet. 2009 Feb;5(2):e1000362. Epub 2009 Feb 6.
  • Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham J E.,. Bryant DA, Robb FT Colman AS,. Tallon L J, BadgerJH, Madupu R,. Ward NL, Eisen JA. 2009. Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum. PLoS ONE 4(1) e4207.

2008

  • Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R 2nd, Eisen JA, Holmes DS. 2008. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics. 2008 Dec 11;9:597 7
  • Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methe BA. 2008. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics. 9(1): 562. PMID: 19036158.
  • 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.

2007

  • 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.
  • 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.
  • Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. 2007. Identification of a new family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A 104: 11784-9.
  • 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.
  • Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3): e82.
  • 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.
  • 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.
  • Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. The Calyptogena magnifica chemoautotrophic symbiont genome. Science. 2007 Feb 16;315(5814):998-1000. PubMed[Newton-2007]

2006

  • Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5. PubMed Pdf-logo.jpg[Goldman-2006]
  • 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 Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol. 2006 Sep;4(9):e286. PubMedPdf-logo.jpg[Eisen-2006]
  • Leebens-Mack 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, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS. 2006 Summer;10(2):231-7. PubMed[Leebens-Mack-2006]
  • Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, and Orias E. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics 2006 Jun 16. PubMed HubMed[Hamilton-2006]
  • 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, and Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet 2006 Feb; 2(2) e21.PubMed HubMedPdf-logo.jpg [Dunning-2006]
  • Wu D, Daugherty SC, Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, and Eisen JA. Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters. PLoS Biol 2006 Jun 6; 4(6) e188. PubMed HubMedPdf-logo.jpg[Wu-2006]
  • Penn K, Wu D, Eisen JA, and Ward N. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Appl Environ Microbiol 2006 Feb; 72(2) 1680-3. PubMed HubMedPdf-logo.jpg[Penn-2006]

2005

  • Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, and Eisen JA. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet 2005 Nov; 1(5) e65. PubMed HubMedPdf-logo.jpg [Wu-2005]
  • 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. [Robb-2005]
  • Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, and Ravel J. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proc Natl Acad Sci U S A 2005 May 17; 102(20) 7315-20. PubMed HubMedPdf-logo.jpg[Schmidt-2005]
  • Badger JH, Eisen JA, and Ward NL. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. Int J Syst Evol Microbiol 2005 May; 55(Pt 3) 1021-6. PubMed HubMed[Badger-2005]
  • Desjardins C, Eisen JA, and Nene V. New evolutionary frontiers from unusual virus genomes. Genome Biol 2005; 6(3) 212. PubMed HubMedPdf-logo.jpg[Desjardins-2005]
  • Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, and Heidelberg JF. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 2005 Jan 7; 307(5706) 105-8. PubMed HubMed[Seshadri-2005]

2004

  • Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen 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, and Ward N. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 2004 Dec 16; 432(7019) 910-3. PubMed HubMed[Moran-2004]
  • Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, and Battista JR. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics 2004 Sep; 168(1) 21-33. PubMed HubMedPdf-logo.jpg[Tanaka-2004]
  • Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, and Eisen JA. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2004 Oct; 2(10) e303. PubMed HubMedPdf-logo.jpg[Ward-2004]
  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, and Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004 Apr 2; 304(5667) 66-74. PubMed HubMed[Venter-2004]
  • Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, and Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2004 Mar; 2(3) E69. PubMed HubMedPdf-logo.jpg[Wu-2004]
  • 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, and El-Sayed NM. Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol 2004 Apr; 134(2) 183-91. PubMed HubMed[Ghedin-2004]
  • 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, and Paulsen IT. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A 2004 Apr 13; 101(15) 5646-51. PubMed HubMedPdf-logo.jpg[Seshadri-2004]
  • 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, and Fraser CM. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol 2004 May; 22(5) 554-9. PubMed HubMed[Heidelberg-2004]

2003

  • Methe 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, and Fraser CM. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 2003 Dec 12; 302(5652) 1967-9. PubMed HubMed[Methe-2003]
  • 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, and Fraser CM. Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol 2003 Sep; 185(18) 5591-601. PubMed HubMedPdf-logo.jpg[Nelson-2003]
  • Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, and Fraser CM. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol 2003 Sep; 185(17) 5220-33. PubMed HubMedPdf-logo.jpg[Miller-2003]
  • Yang RZ, Huang Q, Xu A, McLenithan JC, Eisen JA, Shuldiner AR, Alkan S, and Gong DW. Comparative studies of resistin expression and phylogenomics in human and mouse. Biochem Biophys Res Commun 2003 Oct 24; 310(3) 927-35. PubMed HubMed[Yang-2003]</font>
  • Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, and Fleischmann RD. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J Bacteriol 2003 Jun; 185(11) 3392-9. PubMed HubMedPdf-logo.jpg[Alland-2003]
  • 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, and Heidelberg JF. Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proc Natl Acad Sci U S A 2003 Apr 29; 100(9) 5455-60. PubMed HubMedPdf-logo.jpg[Seshadri-2003]
  • Eisen JA and Fraser CM. Phylogenomics: intersection of evolution and genomics. Science 2003 Jun 13; 300(5626) 1706-7. PubMed HubMed[Eisen-and_Fraser-2003]
  • 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, and Fraser CM. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 2003 Mar 28; 299(5615) 2071-4. PubMed HubMed[Paulsen-2003]
  • Ermolaeva MD, Wu M, Eisen JA, and Salzberg SL. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 2003 Apr; 51(6) 859-66. PubMed HubMed[Ermolaeva-2003]
  • 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. [Shank-2003]

2002

  • DiRuggiero J, Nandakumar R, Eisen JA, Schwartz M, Thomas R, Davila J, Ofman L, Robb FT. 2002. Genomic and physiological studies on extremophiles: model systems for exobiology. In “Frontiers of Astrobiology. Proceedings of the Astrobiology Workshop”, St Petersburg, Russia. Pavlov A. (Ed. ). [DiRuggiero-2002]
  • 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, and Fraser CM. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003 May 1; 423(6935) 81-6. PubMed HubMed[Read-2002]
  • 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, and Fraser CM. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 2002 Dec; 4(12) 799-808. PubMed HubMedPdf-logo.jpg[Nelson-2002]
  • Eisen JA. Brouhaha over the other yeast. Nature 2002 Feb 21; 415(6874) 845-8. PubMed HubMed[Eisen-2002]
  • 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, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, and Fraser CM. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A 2002 Jul 9; 99(14) 9509-14. PubMed HubMedPdf-logo.jpg[Eisen-2002]
  • Eisen JA and Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol 2002 Jun; 61(4) 481-7. PubMed HubMed[Eisen-2002]
  • 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, and Fraser CM. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol 2002 Nov; 20(11) 1118-23. PubMed HubMed[Heidelberg-2002]
  • Van Houten B, Eisen JA, and Hanawalt PC. A cut above: discovery of an alternative excision repair pathway in bacteria. Proc Natl Acad Sci U S A 2002 Mar 5; 99(5) 2581-3. PubMed HubMedPdf-logo.jpg[VanHouten-2002]
  • 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, and Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002 Oct 3; 419(6906) 498-511. PubMed HubMed[Gardner-2002]
  • 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, and Fraser CM. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A 2002 Oct 1; 99(20) 13148-53. PubMed HubMedPdf-logo.jpg[Paulsen-2002]
  • Fraser CM, Eisen JA, Nelson KE, Paulsen IT, and Salzberg SL. The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol 2002 Dec; 184(23) 6403-5; discusion 6405. PubMed HubMedPdf-logo.jpg[Fraser-2002]
  • 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 Jr WR Jr, Venter JC, and Fraser CM. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 2002 Oct; 184(19) 5479-90.< PubMed HubMedPdf-logo.jpg[Fleischmann-2002]
  • 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, and Fraser CM. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A 2002 Sep 17; 99(19) 12391-6. PubMed HubMedPdf-logo.jpg[Tettelin-2002]
  • Beja O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, and DeLong EF. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 2002 Feb 7; 415(6872) 630-3. PubMed HubMed[Beja-2002]
  • Dassarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, and Hood L. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth Res 2001; 70(1) 3-17. PubMed HubMed[Dassarma-2002]

2001

  • Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, Eisen JA, and Slatko B. Sequencing and analysis of a 63 kb bacterial artificial chromosome insert from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi. Int J Parasitol 2002 Feb; 32(2) 159-66. PubMed HubMed[Ware-2001]
  • Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF Jr, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D Sr, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, 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 ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, and Nester EW. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 2001 Dec 14; 294(5550) 2317-23. PubMed HubMed[Wood-2001]
  • Eisen JA. Gastrogenomics. Nature 2001 Jan 25; 409(6819) 463, 465-6. PubMed HubMed[Eisen-2001]
  • Eisen JA. 2001. Response to Mackiewicz et al. Genome Biology, 2 (12): interactions1004. 1-1004. [Eisen-2001]
  • Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, 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, and Fraser CM. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 2001 Jul 20; 293(5529) 498-506. PubMed HubMed[Tettelin-2001]
  • Ward N, Eisen JA, Fraser C, and Stackebrandt E. Sequenced strains must be saved from extinction. Nature 2001 Nov 8; 414(6860) 148. PubMed HubMed[Ward-2001]
  • 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, and Fraser CM. Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A 2001 Mar 27; 98(7) 4136-41. PubMed HubMed Pdf-logo.jpg[Nierman-2001]
  • Salzberg SL and Eisen JA. Lateral gene transfer or viral colonization?. Science 2001 Aug 10; 293(5532) 1048. PubMed HubMed[Salzberg-2001b]
  • Salzberg SL, White O, Peterson J, and Eisen JA. Microbial genes in the human genome: lateral transfer or gene loss?. Science 2001 Jun 8; 292(5523) 1903-6. PubMed HubMed[Salzberg-2001a]
  • Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, and Mewes HW. Sequence and analysis of the Arabidopsis genome. Curr Opin Plant Biol 2001 Apr; 4(2) 105-10. PubMed HubMed[Bevan-2001]
  • Nelson KE, Eisen JA, and Fraser CM. Genome of Thermotoga maritima MSB8. Methods Enzymol 2001; 330 169-80. PubMed HubMed[Nelson-2001]
  • Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, and White O. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res 2001 Jan 1; 29(1) 41-3. PubMed HubMed Pdf-logo.jpg[Haft-2001]

2000

  • Eisen JA. 2000. Microbial and plant genomics. Journal of Biolaw and Business, Special Supplement. 21-24. [Eisen-2000]
  • 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 and Fraser CM. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res 2000 Mar 15; 28(6) 1397-406. PubMed HubMedPdf-logo.jpg[Read-2000]
  • Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000 Dec 14; 408(6814) 796-815. PubMed HubMed[AGI-2000]
  • Nierman WC, Eisen JA, Fleischmann RD, and Fraser CM. Genome data: what do we learn?. Curr Opin Struct Biol 2000 Jun; 10(3) 343-8. PubMed HubMed[Nierman-2000b]
  • 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, and Venter JC. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 2000 Mar 10; 287(5459) 1809-15. PubMed HubMed[Tettelin-2000]
  • Coleman MA, Eisen JA, and Mohrenweiser HW. Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse. Genomics 2000 May 1; 65(3) 274-82. PubMed HubMed[Coleman-2000]
  • 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, and Fraser CM. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 2000 Aug 3; 406(6795) 477-83. PubMed HubMed[Heidelberg-2000]
  • Eisen JA, Heidelberg JF, White O, and Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol 2000; 1(6) RESEARCH0011. PubMed HubMedPdf-logo.jpg[Eisen-etal-2000]
  • Pollock DD, Eisen JA, Doggett NA, and Cummings MP. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol 2000 Dec; 17(12) 1776-88. PubMed HubMedPdf-logo.jpg[Pollock-2000]
  • Eisen JA. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev 2000 Dec; 10(6) 606-11. PubMed HubMed[Eisen-2000b]
  • Eisen JA. Assessing evolutionary relationships among microbes from whole-genome analysis. Curr Opin Microbiol 2000 Oct; 3(5) 475-80. PubMed HubMed[Eisen-2000a]
  • Fraser CM, Eisen JA Fleischmann RD, Ketchum KA, and Peterson S. Comparative genomics and understanding of microbial biology. Emerg Infect Dis 2000 Sep-Oct; 6(5) 505-12. PubMed HubMed[Fraaser-2000b]
  • Fraser CM, Eisen JA, and Salzberg SL. Microbial genome sequencing. Nature 2000 Aug 17; 406(6797) 799-803. PubMed HubMed[Fraser-2000a]
  • Nierman W, Eisen JA, and Fraser CM. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis. Res Microbiol 2000 Mar; 151(2) 79-84. PubMed HubMed[Nierman-2000]

Pre 2000

  • Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, 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, Van Aken S, 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, and Venter JC. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 1999 Dec 16; 402(6763) 761-8. PubMed HubMed[Lin-1999]
  • Eisen JA and Hanawalt PC. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res 1999 Dec 7; 435(3) 171-213. PubMed HubMed[Eisen-and-Hanawalt-1999]
  • Eisen JA. Going to extremes. Archaea: bridging the gap between bacteria and eukarya (A Keystone Symposia), Taos, NM, USA, 9-14 January 1999. Trends Genet 1999 Jun; 15(6) 218-9. PubMed HubMed[Eisen-1999b]
  • Eisen JA. Mechanistic basis for microsatelite instability In David B. Goldstein and Christian Schlötterer. Microsatellites. Oxford; Oxford University Press, 1999" isbn=0198504071 [Eisen-1999a-]
  • White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, JiangL, 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 S, Smith HO, Venter JC, and Fraser CM. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 1999 Nov 19; 286(5444) 1571-7. PubMed HubMed[White-1999]
  • 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, and Fraser CM. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999 May 27; 399(6734) 323-9. PubMed HubMedPdf-logo.jpg[Nelson-1999]
  • Wei MH, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA, and Lerman MI. In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. Hum Genet 1998 Sep; 103(3) 355-64. PubMed HubMed[Wei-1998]
  • Eisen JA. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 1998 Mar; 8(3) 163-7. PubMed HubMedPdf-logo.jpg[Eisen-1998]
  • Eisen JA. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res 1998 Sep 15; 26(18) 4291-300. PubMed HubMedPdf-logo.jpg[Eisen-1998]
  • Gruber TM, Eisen JA, Gish K, and Bryant DA. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS Microbiol Lett 1998 May 1; 162(1) 53-60. PubMed HubMed[Gruber-1998]
  • White RB, Eisen JA, Kasten TL, and Fernald RD. Second gene for gonadotropin-releasing hormone in humans. Proc Natl Acad Sci U S A 1998 Jan 6; 95(1) 305-9. PubMed HubMedPdf-logo.jpg[White-1998]
  • Eisen JA, Kaiser D, and Myers RM. Gastrogenomic delights: a movable feast. Nat Med 1997 Oct; 3(10) 1076-8. PubMed HubMed[Eisen-etal-1997]
  • Eisen JA. The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package. Methods Mol Biol 1997; 70 13-38. PubMed HubMed[Eisen-1997]
  • Shafer RW, Eisen JA, Merigan TC, and Katzenstein DA. Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe. J Virol 1997 Jul; 71(7) 5441-8. PubMed HubMedPdf-logo.jpg[Shafer-1997]
  • Eisen JA. 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 1995 Dec; 41(6) 1105-23. PubMed HubMed[Eisen-1995]
  • Eisen JA, Sweder KS, and Hanawalt PC. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res 1995 Jul 25; 23(14) 2715-23. PubMed HubMedPdf-logo.jpg[Eisen-etal-1995]
  • Eisen JA, Benito MI, and Walbot V. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Res 1994 Jul 11; 22(13) 2634-6. PubMed HubMed Pdf-logo.jpg [Eisen-1994]
  • Liu SK, Eisen JA, Hanawalt PC, and Tessman I. 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 1993 Oct; 175(20) 6518-29. PubMed HubMedPdf-logo.jpg[Liu-1993]
  • Eisen JA, Smith SW, and Cavanaugh CM. Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. J Bacteriol 1992 May; 174(10) 3416-21. PubMed HubMedPdf-logo.jpg[Eisen-1992]


All Medline abstracts: PubMed HubMed

Journals and Book Chapters

  1. Hartman AL, Riddle S, McPhillips T, Ludäscher B, and Eisen JA. . pmid:20540779. PubMed HubMed [WATERS-2010]
  2. Morgan JL, Darling AE, and Eisen JA. . pmid:20419134. PubMed HubMed [Metasim-2010]
  3. Langille MG and Eisen JA. . pmid:20418944. PubMed HubMed [Biotorrents-2010]
  4. 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, and Eisen JA. . pmid:20333302. PubMed HubMed [Haloferax-2010]
  5. 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, and Eisen JA. . pmid:20033048. PubMed HubMed [GEBA-2009]
  6. Eisen JA and MacCallum CJ. . pmid:19855830. PubMed HubMed [PLOS-2009]
  7. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, and Eisen JA. . pmid:19805153. PubMed HubMed [Hartman-2009]
  8. 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, and Distel DL. . pmid:19568419. PubMed HubMed [Wang-2009]
  9. 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, and Stepanauskas R. . pmid:19390573. PubMed HubMed [Woyke-2009]
  10. Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, and Cary SC. . pmid:19197347. PubMed HubMed [Campbell-2009]
  11. Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, and Eisen JA. . pmid:19148287. PubMed HubMed [Wu-2009]
  12. Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R 2nd, Eisen JA, and Holmes DS. . pmid:19077236. PubMed HubMed [Valdes-2008]
  13. 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, and Methé BA. . pmid:19036158. PubMed HubMed [Coyne-2008]
  14. 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 Jr, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, and Stetter KO. . pmid:19000309. PubMed HubMed [Podar-2008]
  15. Wu M and Eisen JA. . pmid:18851752. PubMed HubMed [WuEisen-2008]
  16. Wu D, Hartman A, Ward N, and Eisen JA. . pmid:18596968. PubMed HubMed [Wu-2008]
  17. Chatterji S, Yamazaki I, Bai Z, Eisen JA. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. RECOMB 2008. [Chatterji-2008]
  18. Eisen JA. . pmid:18303952. PubMed HubMed [Eisen-2008]
    My first editorial as the new Academic Editor in Chief of PLoS Biology

  19. Hazen TH, Wu D, Eisen JA, and Sobecky PA. . pmid:17921277. PubMed HubMed [Hazen-2007]
    A paper on sequencing and analysis of plasmids isolated from marine sediments. This was a collaboration with Patty Sobecky's lab at Georgia Tech.

  20. Pfarr K, Foster J, Slatko B, Hoerauf A, and Eisen JA. . pmid:17684235. PubMed HubMed [Pfarr-2007]
    A letter discussing the nomenclature for strains of Wolbachia.

  21. Maresca JA, Graham JE, Wu M, Eisen JA, and Bryant DA. . pmid:17606904. PubMed HubMed [Maresca-2007]
    A paper in which we used phylogenetic profiling to help identify a new type of gene involved in photosynthesis. This was a collaboration with Don Bryant's lab at Penn St.

  22. Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, and Allers T. . pmid:17511521. PubMed HubMed [Norais-2007]
    A collaboration with Thorsten Allers' lab on identifying replication origins.

  23. Eisen JA. . pmid:17355177. PubMed HubMed [Eisen-2007]
    A review I wrote on methods for characterizing uncultured microbes, focusing on the lead in to metagenomics.

  24. 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, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, and Venter JC. . pmid:17355176. PubMed HubMed [Rusch-2007]
    One of the papers from Craig Venter's group on the "Global Ocean Survey." This one focused on microbial diversity.

  25. 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, and Venter JC. . pmid:17355171. PubMed HubMed [Yooseph-2007]
    Another of the papers from Craig Venter's group on the "Global Ocean Survey." This one focused on protein families.

  26. Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, and Cavanaugh CM. . pmid:17303757. PubMed HubMed [Newton-2007]
    A collaboration with Colleen Cavanaugh's lab (she was my undergraduate advisor) and JGI on sequencing and analysis of the first genome of a chemosynthetic symbiont.

  27. Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, and Kaplan HB. . pmid:17015832. PubMed HubMed [Goldman-2006]
  28. 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 Jr, 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, and Orias E. . pmid:16933976. PubMed HubMed [Eisen-2006]
  29. Leebens-Mack 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, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, and Zmasek C. . pmid:16901231. PubMed HubMed [Leebens-Mack-2006]
  30. Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, and Orias E. . pmid:16782302. PubMed HubMed [Hamilton-2006]
  31. 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, and Tettelin H. . pmid:16482227. PubMed HubMed [Dunning-2006]
  32. Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, and Eisen JA. . pmid:16729848. PubMed HubMed [Wu-2006]
  33. Penn K, Wu D, Eisen JA, and Ward N. . pmid:16461727. PubMed HubMed [Penn-2006]
  34. Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, and Eisen JA. . pmid:16311624. PubMed HubMed [Wu-2005]
  35. 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. [Robb-2005]
  36. Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, and Ravel J. . pmid:15883371. PubMed HubMed [Schmidt-2005]
  37. Badger JH, Eisen JA, and Ward NL. . pmid:15879228. PubMed HubMed [Badger-2005]
  38. Desjardins C, Eisen JA, and Nene V. . pmid:15774035. PubMed HubMed [Desjardins-2005]
  39. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, and Heidelberg JF. . pmid:15637277. PubMed HubMed [Seshadri-2005]
  40. Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen 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, and Ward N. . pmid:15602564. PubMed HubMed [Moran-2004]
  41. Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, and Battista JR. . pmid:15454524. PubMed HubMed [Tanaka-2004]
  42. Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, and Eisen JA. . pmid:15383840. PubMed HubMed [Ward-2004]
  43. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, and Smith HO. . pmid:15001713. PubMed HubMed [Venter-2004]
  44. Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, and Eisen JA. . pmid:15024419. PubMed HubMed [Wu-2004]
  45. Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen J, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg S, Adams MD, White O, Hall N, Stuart K, Fraser CM, and El-Sayed NM. . pmid:15003838. PubMed HubMed [Ghedin-2004]
  46. 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, and Paulsen IT. . pmid:15064399. PubMed HubMed [Seshadri-2004]
  47. 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, and Fraser CM. . pmid:15077118. PubMed HubMed [Heidelberg-2004]
  48. 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, and Fraser CM. . pmid:14671304. PubMed HubMed [Methe-2003]
  49. 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, and Fraser CM. . pmid:12949112. PubMed HubMed [Nelson-2003]
  50. Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, and Fraser CM. . pmid:12923095. PubMed HubMed [Miller-2003]
  51. Yang RZ, Huang Q, Xu A, McLenithan JC, Eisen JA, Shuldiner AR, Alkan S, and Gong DW. . pmid:14550293. PubMed HubMed [Yang-2003]
  52. Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, and Fleischmann RD. . pmid:12754238. PubMed HubMed [Alland-2003]
  53. 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, and Heidelberg JF. . pmid:12704232. PubMed HubMed [Seshadri-2003]
  54. Eisen JA and Fraser CM. . pmid:12805538. PubMed HubMed [Eisen-and_Fraser-2003]
  55. 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, and Fraser CM. . pmid:12663927. PubMed HubMed [Paulsen-2003]
  56. Ermolaeva MD, Wu M, Eisen JA, and Salzberg SL. . pmid:12777046. PubMed HubMed [Ermolaeva-2003]
  57. 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. [Shank-2003]
  58. DiRuggiero J, Nandakumar R, Eisen JA, Schwartz M, Thomas R, Davila J, Ofman L, Robb FT. 2002. Genomic and physiological studies on extremophiles: model systems for exobiology. In “Frontiers of Astrobiology. Proceedings of the Astrobiology Workshop”, St Petersburg, Russia. Pavlov A. (Ed. ). [DiRuggiero-2002]
  59. 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, Kolstø AB, and Fraser CM. . pmid:12721629. PubMed HubMed [Read-2002]
  60. 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, Düsterhöft A, Tümmler B, and Fraser CM. . pmid:12534463. PubMed HubMed [Nelson-2002]
  61. Eisen JA. . pmid:11859347. PubMed HubMed [Eisen-2002]
  62. 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, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, and Fraser CM. . pmid:12093901. PubMed HubMed [Eisen-2002]
  63. Eisen JA and Wu M. . pmid:12167367. PubMed HubMed [Eisen-2002]
  64. 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, and Fraser CM. . pmid:12368813. PubMed HubMed [Heidelberg-2002]
  65. Van Houten B, Eisen JA, and Hanawalt PC. . pmid:11880612. PubMed HubMed [VanHouten-2002]
  66. 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, and Barrell B. . pmid:12368864. PubMed HubMed [Gardner-2002]
  67. 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, and Fraser CM. . pmid:12271122. PubMed HubMed [Paulsen-2002]
  68. Fraser CM, Eisen JA, Nelson KE, Paulsen IT, and Salzberg SL. . pmid:12426324. PubMed HubMed [Fraser-2002]
  69. 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 Jr WR Jr, Venter JC, and Fraser CM. . pmid:12218036. PubMed HubMed [Fleischmann-2002]
  70. 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, and Fraser CM. . pmid:12200547. PubMed HubMed [Tettelin-2002]
  71. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, and DeLong EF. . pmid:11832943. PubMed HubMed [Beja-2002]
  72. Dassarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, and Hood L. . pmid:16228359. PubMed HubMed [Dassarma-2002]
  73. Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, Eisen J, and Slatko B. . pmid:11812492. PubMed HubMed [Ware-2001]
  74. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF Jr, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D Sr, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, 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 ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, and Nester EW. . pmid:11743193. PubMed HubMed [Wood-2001]
  75. Eisen JA. . pmid:11206526. PubMed HubMed [Eisen-2001]
  76. Eisen JA. 2001. Response to Mackiewicz et al. Genome Biology, 2 (12): interactions1004. 1-1004. [Eisen-2001]
  77. Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, 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, and Fraser CM. . pmid:11463916. PubMed HubMed [Tettelin-2001]
  78. Ward N, Eisen J, Fraser C, and Stackebrandt E. . pmid:11700527. PubMed HubMed [Ward-2001]
  79. 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, and Fraser CM. . pmid:11259647. PubMed HubMed [Nierman-2001]
  80. Salzberg SL and Eisen JA. . pmid:11503638. PubMed HubMed [Salzberg-2001b]
  81. Salzberg SL, White O, Peterson J, and Eisen JA. . pmid:11358996. PubMed HubMed [Salzberg-2001a]
  82. Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, and Mewes HW. . pmid:11228431. PubMed HubMed [Bevan-2001]
  83. Nelson KE, Eisen JA, and Fraser CM. . pmid:11210497. PubMed HubMed [Nelson-2001]
  84. Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, and White O. . pmid:11125044. PubMed HubMed [Haft-2000]
  85. Eisen JA. 2000. Microbial and plant genomics. Journal of Biolaw and Business, Special Supplement. 21-24. [Eisen-2000]
  86. 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 J, and Fraser CM. . pmid:10684935. PubMed HubMed [Read-2000]
  87. Arabidopsis Genome Initiative. . pmid:11130711. PubMed HubMed [AGI-2000]
  88. Nierman WC, Eisen JA, Fleischmann RD, and Fraser CM. . pmid:10851186. PubMed HubMed [Nierman-2000b]
  89. 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, and Venter JC. . pmid:10710307. PubMed HubMed [Tettelin-2000]
  90. Coleman MA, Eisen JA, and Mohrenweiser HW. . pmid:10857751. PubMed HubMed [Coleman-2000]
  91. 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, and Fraser CM. . pmid:10952301. PubMed HubMed [Heidelberg-2000]
  92. Eisen JA, Heidelberg JF, White O, and Salzberg SL. . pmid:11178265. PubMed HubMed [Eisen-etal-2000]
  93. Pollock DD, Eisen JA, Doggett NA, and Cummings MP. . pmid:11110893. PubMed HubMed [Pollock-2000]
  94. Eisen JA. . pmid:11088009. PubMed HubMed [Eisen-2000b]
  95. Eisen JA. . pmid:11050445. PubMed HubMed [Eisen-2000a]
  96. Fraser CM, Eisen J, Fleischmann RD, Ketchum KA, and Peterson S. . pmid:10998382. PubMed HubMed [Fraaser-2000b]
  97. Fraser CM, Eisen JA, and Salzberg SL. . pmid:10963611. PubMed HubMed [Fraser-2000a]
  98. Nierman W, Eisen JA, and Fraser CM. . pmid:10865951. PubMed HubMed [Nierman-2000]
  99. Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, 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, Van Aken S, 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, and Venter JC. . pmid:10617197. PubMed HubMed [Lin-1999]
  100. Eisen JA and Hanawalt PC. . pmid:10606811. PubMed HubMed [Eisen-and-Hanawalt-1999]
  101. Eisen JA. . pmid:10419407. PubMed HubMed [Eisen-1999b]
  102. "Mechanistic basis for microsatelite instability in David B. Goldstein and Christian Schlötterer. Microsatellites. Oxford; Oxford University Press, 1999" isbn=0198504071 [Eisen-1999a-]
  103. 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 S, Smith HO, Venter JC, and Fraser CM. . pmid:10567266. PubMed HubMed [White-1999]
  104. 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, and Fraser CM. . pmid:10360571. PubMed HubMed [Nelson-1999]
  105. Wei MH, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA, and Lerman MI. . pmid:9799093. PubMed HubMed [Wei-1998]
  106. Eisen JA. . pmid:9521918. PubMed HubMed [Eisen-1998]
  107. Eisen JA. . pmid:9722651. PubMed HubMed [Eisen-1998]
  108. Gruber TM, Eisen JA, Gish K, and Bryant DA. . pmid:9595663. PubMed HubMed [Gruber-1998]
  109. White RB, Eisen JA, Kasten TL, and Fernald RD. . pmid:9419371. PubMed HubMed [White-1998]
  110. Eisen JA, Kaiser D, and Myers RM. . pmid:9334711. PubMed HubMed [Eisen-etal-1997]
  111. Eisen JA. . pmid:9089600. PubMed HubMed [Eisen-1997]
  112. Shafer RW, Eisen JA, Merigan TC, and Katzenstein DA. . pmid:9188616. PubMed HubMed [Shafer-1997]
  113. Eisen JA. . pmid:8587109. PubMed HubMed [Eisen-1995]
  114. Eisen JA, Sweder KS, and Hanawalt PC. . pmid:7651832. PubMed HubMed [Eisen-etal-1995]
  115. Eisen JA, Benito MI, and Walbot V. . pmid:8041625. PubMed HubMed [Eisen-1994]
  116. Liu SK, Eisen JA, Hanawalt PC, and Tessman I. . pmid:8407828. PubMed HubMed [Liu-1993]
  117. Eisen JA, Smith SW, and Cavanaugh CM. . pmid:1577710. PubMed HubMed [Eisen-1992]
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