Born: Brookline, MA
Grew up: Bethesda, MD
College: Harvard College
Graduate School: Stanford University, laboratory of Philip C. Hanawalt
First Faculty Job: The Institute for Genomic Research
Current Position: Professor, U. C. Davis Genome Center, Section of Evolution and Ecology and the Deparmtent of Medical Microbiology and Immunology
Scientific Interests: evolution, genomics, DNA repair, extremophiles, phylogenomics, uncultured microbes, symbioses.

Contact details: jaeisen@ucdavis.edu

http://phylogenomics.blogspot.com

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. Meyer F, Paarmann D, …, Wilkening J, Edwards RA BMC Bioinformatics 2008 Sep 19 9(1):386 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A. Eisen Evaluated 29 Sep 2008 Microbial ecology of four coral atolls in the Northern Line Islands. Dinsdale EA, Pantos O, …, Knowlton N, Rohwer F PLoS ONE 2008 3(2):e1584 [abstract on PubMed] [related articles] [FREE full text] Selected by | Niyaz Ahmed / Jonathan A. Eisen Evaluated 29 Sep 2008 Automated protein subfamily identification and classification. Brown DP, Krishnamurthy N, Sjölander K PLoS Comput Biol 2007 Aug 17 3:1526-1538 [abstract on PubMed] [related articles] [FREE full text] Selected by | Christine Orengo / Jonathan A. Eisen Evaluated 16 Nov 2007 Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. Begun DJ, Holloway AK, …, Myers E, Langley CH PLoS Biol 2007 Nov 6 5(11):e310 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A. Eisen Evaluated 16 Nov 2007 UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. Lozupone C, Hamady M, Knight R BMC Bioinformatics 2006 7:371 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 3 Oct 2006 High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae. Bayliss CD, Callaghan MJ, Moxon ER Nucleic Acids Res 2006 34(14):4046-59 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 28 Sep 2006 The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1. Crowley DJ, Boubriak I, …, DasSarma S, McCready S Saline Systems 2006 2:11 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 28 Sep 2006 Symbiosis insights through metagenomic analysis of a microbial consortium. Woyke T, Teeling H, …, Rubin EM, Dubilier N Nature 2006 Oct 26 443(7114):950-5 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Jonathan A Eisen Evaluated 27 Sep 2006 Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Lin Z, Kong H, Nei M, Ma H Proc Natl Acad Sci U S A 2006 Jul 5 103(27):10328-33 [abstract on PubMed] [related articles] [FREE full text] Selected by | Guenter Theissen Dissenters | Jonathan A Eisen Author Response | Masatoshi Nei Evaluated 25 Aug 2006 Metagenomic DNA fragments that affect Escherichia coli mutational pathways. Yang H, To KH, Aguila SJ, Miller JH Mol Microbiol 2006 Aug 61(4):960-77 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Jonathan A Eisen Evaluated 15 Aug 2006 A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Goldberg SM, Johnson J, …, Frazier M, Venter JC Proc Natl Acad Sci U S A 2006 Jul 25 103(30):11240-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 9 Aug 2006 Microbial diversity in the deep sea and the underexplored "rare biosphere". Sogin ML, Morrison HG, …, Arrieta JM, Herndl GJ Proc Natl Acad Sci U S A 2006 Aug 8 103(32):12115-20 [abstract on PubMed] [related articles] [FREE full text] Selected by | Anna-Louise Reysenbach / Jonathan A Eisen / Carlos Pedrós-Alió / Ian M Head Evaluated 9 Aug 2006 Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. Sullivan MB, Lindell D, …, Bielawski JP, Chisholm SW PLoS Biol 2006 Jul 4(8):e234 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 6 Jul 2006 Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Flaus A, Martin DM, Barton GJ, Owen-Hughes T Nucleic Acids Res 2006 34(10):2887-905 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 13 Jun 2006 Biochemical and molecular characterisation of Tetrahymena thermophila extracellular cysteine proteases. Herrmann L, Erkelenz M, …, Tiedtke A, Hartmann MW BMC Microbiol 2006 6:19 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 15 Mar 2006 Distribution, expression, and motif variability of ankyrin domain genes in Wolbachia pipientis. Iturbe-Ormaetxe I, Burke GR, Riegler M, O'Neill SL J Bacteriol 2005 Aug 187(15):5136-45 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 19 Sep 2005 Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Filée J, Tétart F, Suttle CA, Krisch HM Proc Natl Acad Sci U S A 2005 Aug 30 102(35):12471-6 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 19 Sep 2005 Evolutionary origins of genomic repertoires in bacteria. Lerat E, Daubin V, Ochman H, Moran NA PLoS Biol 2005 May 3(5):e130 [abstract on PubMed] [related articles] [FREE full text] Selected by | Mark D Adams / Arcady Mushegian / Jonathan A Eisen Evaluated 16 May 2005 The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. Foster J, Ganatra M, …, Koonin E, Slatko B PLoS Biol 2005 Apr 3(4):e121 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 29 Apr 2005 Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers. Chen J, Call GB, …, Milchanowski A, Banerjee U PLoS Biol 2005 Feb 3(2):e59 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 29 Mar 2005 Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. Fraser JA, Diezmann S, …, Dietrich FS, Heitman J PLoS Biol 2004 Dec 2(12):e384 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 14 Dec 2004 Textpresso: an ontology-based information retrieval and extraction system for biological literature. Müller HM, Kenny EE, Sternberg PW PLoS Biol 2004 Nov 2:e309 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 14 Dec 2004 The 1.2-megabase genome sequence of Mimivirus. Raoult D, Audic S, …, Suzan M, Claverie JM Science 2004 Nov 19 306(5700):1344-50 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen / Michael Wagner / Fiona Brinkman Evaluated 25 Oct 2004 Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Hebert PD, Penton EH, …, Janzen DH, Hallwachs W Proc Natl Acad Sci U S A 2004 Oct 12 101(41):14812-7 [abstract on PubMed] [related articles] [FREE full text] Selected by | Eaton E. Lattman Dissenters | Jonathan A Eisen Author Response | Paul Hebert Evaluated 21 Oct 2004 Preserving genome integrity: the DdrA protein of Deinococcus radiodurans R1. Harris DR, Tanaka M, …, Cox MM, Battista JR PLoS Biol 2004 Oct 2(10):e304 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen / Joe Heitman Evaluated 21 Sep 2004 An RNA ligase from Deinococcus radiodurans. Martins A, Shuman S J Biol Chem 2004 Dec 3 279(49):50654-61 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 3 Sep 2004 The bacterial catalase from filarial DNA preparations derives from common pseudomonad contaminants and not from Wolbachia endosymbionts. Foster J, Baldo L, …, Slatko B, Bandi C Parasitol Res 2004 Sep 94(2):141-6 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Jonathan A Eisen Evaluated 3 Sep 2004 Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. Frigaard NU, Maresca JA, …, Jones AD, Bryant DA J Bacteriol 2004 Aug 186(16):5210-20 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 13 Aug 2004 Trends between gene content and genome size in prokaryotic species with larger genomes. Konstantinidis KT, Tiedje JM Proc Natl Acad Sci U S A 2004 Mar 2 101(9):3160-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Peter Williams / Jonathan A Eisen / Christos Ouzounis Evaluated 22 Mar 2004 Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes. Frigaard NU, Li H, Milks KJ, Bryant DA J Bacteriol 2004 Feb 186(3):646-53 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 9 Feb 2004 Enhanced repair of cyclobutane pyrimidine dimers and improved UV resistance in photolyase transgenic mice. Schul W, Jans J, …, Hoeijmakers JH, van der Horst GT EMBO J 2002 Sep 2 21(17):4719-29 [abstract on PubMed] [related articles] [order article] Selected by | Jonathan A Eisen Evaluated 1 Oct 2002 Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Brinkman FS, Blanchard JL, …, Jones SJ, Greberg H Genome Res 2002 Aug 12(8):1159-67 [abstract on PubMed] [related articles] [FREE full text] Selected by | William Martin / Jonathan A Eisen Evaluated 26 Sep 2002 Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Akman L, Yamashita A, …, Hattori M, Aksoy S Nat Genet 2002 Nov 32(3):402-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Jonathan A Eisen / Paul J. Brindley Evaluated 24 Sep 2002 Meiotic arrest and aneuploidy in MLH3-deficient mice. Lipkin SM, Moens PB, …, Collins FS, Cohen PE Nat Genet 2002 Aug 31(4):385-90 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Martin Marinus / Jonathan A Eisen Evaluated 23 Sep 2002 Identification of a DNA nonhomologous end-joining complex in bacteria. Weller GR, Kysela B, …, Jackson SP, Doherty AJ Science 2002 Sep 6 297(5587):1686-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Martin Marinus / Jonathan A Eisen / Lucio Comai Evaluated 20 Sep 2002 Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Martin W, Rujan T, …, Hasegawa M, Penny D Proc Natl Acad Sci U S A 2002 Sep 17 99(19):12246-51 [abstract on PubMed] [related articles] [FREE full text] Selected by | Michael Purugganan / Jonathan A Eisen / Deborah Charlesworth / Renate Schmidt / Debashish Bhattacharya Evaluated 20 Sep 2002 The methionine salvage pathway in Bacillus subtilis. Sekowska A, Danchin A BMC Microbiol 2002 Apr 25 2:8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 18 Jun 2002 Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Stackebrandt E, Frederiksen W, …, Ward AC, Whitman WB Int J Syst Evol Microbiol 2002 May 52(Pt 3):1043-7 [abstract on PubMed] [related articles] [order article] Selected by | Jonathan A Eisen Evaluated 18 Jun 2002 The role of endosymbiotic Wolbachia bacteria in the pathogenesis of river blindness. Saint André A, Blackwell NM, …, Diaconu E, Pearlman E Science 2002 Mar 8 295(5561):1892-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Ken Wilson / Thomas Nutman / Jonathan A Eisen / Peter Openshaw Evaluated 1 May 2002 Convergent evolution of MutS and topoisomerase II for clamping DNA crossovers and stacked Holliday junctions. Timsit Y J Biomol Struct Dyn 2001 Oct 19(2):215-8 [abstract on PubMed] [related articles] [order article] Selected by | Jonathan A Eisen Evaluated 21 Dec 2001 A phylogenomic approach to microbial evolution. Sicheritz-Pontén T, Andersson SG Nucleic Acids Res 2001 Jan 15 29(2):545-52 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen / Bruno Sobral Evaluated 21 Dec 2001 A simple algorithm to infer gene duplication and speciation events on a gene tree. Zmasek CM, Eddy SR Bioinformatics 2001 Sep 17(9):821-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Nick Grishin / Jonathan A Eisen Evaluated 27 Nov 2001 Effects of size and temperature on metabolic rate. Gillooly JF, Brown JH, …, Savage VM, Charnov EL Science 2001 Sep 21 293(5538):2248-51 [abstract on PubMed] [related articles] [FREE full text] Selected by | Jonathan A Eisen Evaluated 22 Nov 2001 Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Ogata H, Audic S, …, Claverie JM, Raoult D Science 2001 Sep 14 293(5537):2093-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Greg Gibson / Jonathan A Eisen / Christoph Dehio / Siv Andersson Evaluated 23 Oct 2001

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