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Eisen Lab Research

Symbioses and Host Microbe Interactions

Organelle evolution

• Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000 Dec 14; 408(6814) 796-815.
• 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.

Mutualistic endosymbioses: chemosynthetic, nutritional, etc

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

Plant and animal microbiomes

• 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. Proc Natl Acad Sci U S A. 106(40):17187-92.
• 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.
• 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.

Non mutualistic endosymbioses

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

Eukaryotic pathogen genomics

• 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.
• 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.

Bacterial pathogen genomes

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

Phylogenetic and phylogenomic diversity of microbes

Phylogenetic diversity

• 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
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

Viral diversity

• Desjardins C, Eisen JA, and Nene V. New evolutionary frontiers from unusual virus genomes. Genome Biol 2005; 6(3) 212.
• 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.
• 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.

Review papers

• Eisen JA and Fraser CM. Phylogenomics: intersection of evolution and genomics. Science 2003 Jun 13; 300(5626) 1706-7.
• Eisen JA. Brouhaha over the other yeast. Nature 2002 Feb 21; 415(6874) 845-8.
• Ward N, Eisen JA, Fraser C, and Stackebrandt E. Sequenced strains must be saved from extinction. Nature 2001 Nov 8; 414(6860) 148.
• Eisen JA. 2000. Microbial and plant genomics. Journal of Biolaw and Business, Special Supplement. 21-24.
• 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.
• Eisen JA. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev 2000 Dec; 10(6) 606-11.
• Eisen JA. Assessing evolutionary relationships among microbes from whole-genome analysis. Curr Opin Microbiol 2000 Oct; 3(5) 475-80.
• 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.
• Fraser CM, Eisen JA, and Salzberg SL. Microbial genome sequencing. Nature 2000 Aug 17; 406(6797) 799-803.
• 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.

Population Biology: metagenomics, epidemiology, biogeopgraphy, forensics

Uncultured microbes with metagenomic methods

• 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
• 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.
• 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.
• 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.
• 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.
• 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.

Software and Methods

• 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.
• 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.
• Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4): e10209. PMID: 20419134.
• 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
• Wu D, Hartman A, Ward N, Eisen JA. 2008. An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP). PLoS ONE 3(7): e2566. doi:10.1371/journal.pone.0002566
• Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 2008, 9:R151. PMID: 18851752.

Biogeography

• 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
• 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.
• 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.

Genomics and evolution of C1 fixation and photobiology

Calvin cycle

• Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000 Dec 14; 408(6814) 796-815.
• 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.
• 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.

Methane

• 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.

CO

• 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.
• 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.
• 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.

Reverse TCA cycle

• 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.
• 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.

Photosynthesis

• 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.
• Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000 Dec 14; 408(6814) 796-815.
• 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.
• 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.
• 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.

Marine microbiology

• 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.

Mechanisms of evolvability

• 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.
• Eisen JA and Hanawalt PC. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res 1999 Dec 7; 435(3) 171-213.

Repair, Recombination, Replication, Duplication, Transposition

• 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.
• 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.
• 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.
• Eisen JA. 2001. Response to Mackiewicz et al. Genome Biology, 2 (12): interactions1004. 1-1004.
• 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.
• 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.
• 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.

• Eisen JA. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res 1998 Sep 15; 26(18) 4291-300.
• Eisen JA. Mechanistic basis for microsatelite instability In David B. Goldstein and Christian Schlötterer. Microsatellites. Oxford; Oxford University Press, 1999" isbn=0198504071
• Eisen JA, Kaiser D, and Myers RM. Gastrogenomic delights: a movable feast. Nat Med 1997 Oct; 3(10) 1076-8.
• 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.
• 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.
• 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.

LGT

• Eisen JA. Gastrogenomics. Nature 2001 Jan 25; 409(6819) 463, 465-6.
• Salzberg SL and Eisen JA. Lateral gene transfer or viral colonization?. Science 2001 Aug 10; 293(5532) 1048.
• 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.
• Nelson KE, Eisen JA, and Fraser CM. Genome of Thermotoga maritima MSB8. Methods Enzymol 2001; 330 169-80.

Extremophiles

• 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, 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.
• 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.
• 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
• 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.
• 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.
• 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.
• 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.
• 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. ).
• 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.
• Nelson KE, Eisen JA, and Fraser CM. Genome of Thermotoga maritima MSB8. Methods Enzymol 2001; 330 169-80.
• 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.
• 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.
• 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.

Functional prediction and gene family evolution

• 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.
• Eisen JA and Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol 2002 Jun; 61(4) 481-7.
• 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.
• 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.
• 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.
• Eisen JA. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 1998 Mar; 8(3) 163-7.
• Eisen JA. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res 1998 Sep 15; 26(18) 4291-300.
• 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.
• Eisen JA, Kaiser D, and Myers RM. Gastrogenomic delights: a movable feast. Nat Med 1997 Oct; 3(10) 1076-8.

Model organisms

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

Misc. genomes

• 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.
• 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.
• 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.
• 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.
• * 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.

Open science

• Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4): e10071. PMID: 20418944.
• Eisen JA. PLoS Biology 2.0. PLoS Biol. 2008 Feb;6(2):e48.
• Eisen JA. The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package. Methods Mol Biol 1997; 70 13-38.