phylogenomics

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Jonathan Eisen
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AIM:jonathan.eisen@gmail.com |

Status:
Professor

Location:
U. C. Davis

Research Interests:
Phylogenomics, microbiology, evolution, DNA repair, metagenomics, extremophiles, symbioses,

Affiliations:
Academic

Homepage:
http://phylogenomics.blogspot.com

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Publications in PubMed

1. Eisen JA. PLoS Biology 2.0. PLoS biology 2008 6(2). DOI:10.1371/journal.pbio.0060048.
2. Hazen TH, Wu D, Eisen JA, Sobecky PA. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Applied and environmental microbiology 2007 73(23). DOI:10.1128/AEM.01577-07.
3. Pfarr K, Foster J, Slatko B, Hoerauf A, Eisen JA. On the taxonomic status of the intracellular bacterium Wolbachia pipientis: should this species name include the intracellular bacteria of filarial nematodes? International journal of systematic and evolutionary microbiology 2007 57. DOI:10.1099/ijs.0.65248-0.
4. Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proceedings of the National Academy of Sciences of the United States of America 2007 104(28). DOI:10.1073/pnas.0702984104.
5. Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, Allers T. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS genetics 2007 3(5). DOI:10.1371/journal.pgen.0030077.
6. Eisen JA. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS biology 2007 5(3). DOI:10.1371/journal.pbio.0050082.
7. 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, Venter JC. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS biology 2007 5(3). DOI:10.1371/journal.pbio.0050077.
8. 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. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS biology 2007 5(3). DOI:10.1371/journal.pbio.0050016.
9. 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 (New York, N.Y.) 2007 315(5814). DOI:10.1126/science.1138438.
10. Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Eisen J, 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. Proceedings of the National Academy of Sciences of the United States of America 2006 103(41). DOI:10.1073/pnas.0607335103.
11. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS biology 2006 4(9). DOI:10.1371/journal.pbio.0040286.
12. 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, Zmasek C. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). Omics : a journal of integrative biology 2006 10(2). DOI:10.1089/omi.2006.10.231.
13. Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics 2006 88(4). DOI:10.1016/j.ygeno.2006.05.002.
14. Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS genetics 2006 2(2). DOI:10.1371/journal.pgen.0020021.
15. Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS biology 2006 4(6). DOI:10.1371/journal.pbio.0040188.
16. Penn K, Wu D, Eisen JA, Ward N. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and environmental microbiology 2006 72(2). DOI:10.1128/AEM.72.2.1680-1683.2006.
17. 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, Eisen JA. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS genetics 2005 1(5). DOI:10.1371/journal.pgen.0010065.
18. Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, Ravel J. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proceedings of the National Academy of Sciences of the United States of America 2005 102(20). DOI:10.1073/pnas.0501424102.
19. Badger JH, Eisen JA, Ward NL. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. International journal of systematic and evolutionary microbiology 2005 55. DOI:10.1099/ijs.0.63510-0.
20. Desjardins C, Eisen JA, Nene V. New evolutionary frontiers from unusual virus genomes. Genome biology 2005 6(3). DOI:10.1186/gb-2005-6-3-212.
21. 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, Heidelberg JF. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science (New York, N.Y.) 2005 307(5706). DOI:10.1126/science.1102226.
22. 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, Ward N. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 2004 432(7019). DOI:10.1038/nature03170.
23. Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics 2004 168(1). DOI:10.1534/genetics.104.029249.
24. 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, Eisen JA. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS biology 2004 2(10). DOI:10.1371/journal.pbio.0020303.
25. 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, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science (New York, N.Y.) 2004 304(5667). DOI:10.1126/science.1093857.
26. 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, Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS biology 2004 2(3). DOI:10.1371/journal.pbio.0020069.
27. 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, El-Sayed NM. Gene synteny and evolution of genome architecture in trypanosomatids. Molecular and biochemical parasitology 2004 134(2). DOI:10.1016/j.molbiopara.2003.11.012.
28. Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proceedings of the National Academy of Sciences of the United States of America 2004 101(15). DOI:10.1073/pnas.0307639101.
29. Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature biotechnology 2004 22(5). DOI:10.1038/nbt959.
30. Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science (New York, N.Y.) 2003 302(5652). DOI:10.1126/science.1088727.
31. Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM. Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. Journal of bacteriology 2003 185(18). DOI:10.1126/science.1088727.
32. Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, Fraser CM. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. Journal of bacteriology 2003 185(17). DOI:10.1126/science.1088727.
33. Yang RZ, Huang Q, Xu A, McLenithan JC, Eisen JA, Shuldiner AR, Alkan S, Gong DW, Eison JA. Comparative studies of resistin expression and phylogenomics in human and mouse. Biochemical and biophysical research communications 2003 310(3). DOI:10.1126/science.1088727.
34. Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. Journal of bacteriology 2003 185(11). DOI:10.1126/science.1088727.
35. Seshadri R, Paulsen IT, Eisen JA, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM, Beanan MJ, Deboy RT, Daugherty SC, Brinkac LM, Madupu R, Dodson RJ, Khouri HM, Lee KH, Carty HA, Scanlan D, Heinzen RA, Thompson HA, Samuel JE, Fraser CM, Heidelberg JF. Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proceedings of the National Academy of Sciences of the United States of America 2003 100(9). DOI:10.1073/pnas.0931379100.
36. Eisen JA, Fraser CM. Phylogenomics: intersection of evolution and genomics. Science (New York, N.Y.) 2003 300(5626). DOI:10.1126/science.1086292.
37. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science (New York, N.Y.) 2003 299(5615). DOI:10.1126/science.1080613.
38. Ermolaeva MD, Wu M, Eisen JA, Salzberg SL. The age of the Arabidopsis thaliana genome duplication. Plant molecular biology 2003 51(6). DOI:10.1126/science.1080613.
39. 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, Fraser CM. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003 423(6935). DOI:10.1038/nature01586.
40. 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, Fraser CM. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental microbiology 2002 4(12). DOI:10.1038/nature01586.
41. Eisen JA, Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theoretical population biology 2002 61(4). DOI:10.1038/nature01586.
42. Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nature biotechnology 2002 20(11). DOI:10.1038/nbt749.
43. Van Houten B, Eisen JA, Hanawalt PC. A cut above: discovery of an alternative excision repair pathway in bacteria. Proceedings of the National Academy of Sciences of the United States of America 2002 99(5). DOI:10.1073/pnas.062062599.
44. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002 419(6906). DOI:10.1038/nature01097.
45. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proceedings of the National Academy of Sciences of the United States of America 2002 99(20). DOI:10.1073/pnas.192319099.
46. Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. The value of complete microbial genome sequencing (you get what you pay for). Journal of bacteriology 2002 184(23). DOI:10.1073/pnas.192319099.
47. 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, Venter JC, Fraser CM. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. Journal of bacteriology 2002 184(19). DOI:10.1073/pnas.192319099.
48. Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proceedings of the National Academy of Sciences of the United States of America 2002 99(19). DOI:10.1073/pnas.182380799.
49. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 2002 415(6872). DOI:10.1038/415630a.
50. 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, Fraser CM. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proceedings of the National Academy of Sciences of the United States of America 2002 99(14). DOI:10.1073/pnas.132181499.
51. Dassarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynthesis research 2001 70(1). DOI:10.1023/A:1013879706863.
52. Eisen JA. Brouhaha over the other yeast. Nature 2002 415(6874). DOI:10.1038/nature725.
53. Ware J, Moran L, Foster J, Posfai J, Vincze T, Guiliano D, Blaxter M, Eisen J, Slatko B. Sequencing and analysis of a 63 kb bacterial artificial chromosome insert from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi. International journal for parasitology 2002 32(2). DOI:10.1038/nature725.
54. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D, 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, Nester EW. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science (New York, N.Y.) 2001 294(5550). DOI:10.1126/science.1066804.
55. 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, Fraser CM. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science (New York, N.Y.) 2001 293(5529). DOI:10.1126/science.1061217.
56. Ward N, Eisen J, Fraser C, Stackebrandt E. Sequenced strains must be saved from extinction. Nature 2001 414(6860). DOI:10.1038/35102737.
57. Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM, Eisen J. Complete genome sequence of Caulobacter crescentus. Proceedings of the National Academy of Sciences of the United States of America 2001 98(7). DOI:10.1073/pnas.061029298.
58. Salzberg SL, Eisen JA. Lateral gene transfer or viral colonization? Science (New York, N.Y.) 2001 293(5532). DOI:10.1073/pnas.061029298.
59. Salzberg SL, White O, Peterson J, Eisen JA. Microbial genes in the human genome: lateral transfer or gene loss? Science (New York, N.Y.) 2001 292(5523). DOI:10.1126/science.1061036.
60. Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes HW. Sequence and analysis of the Arabidopsis genome. Current opinion in plant biology 2001 4(2). DOI:10.1126/science.1061036.
61. Nelson KE, Eisen JA, Fraser CM. Genome of Thermotoga maritima MSB8. Methods in enzymology 2001 330. DOI:10.1126/science.1061036.
62. Eisen JA. Gastrogenomics. Nature 2001 409(6819). DOI:10.1038/35054158.
63. Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic acids research 2001 29(1). DOI:10.1038/35054158.
64. 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, Fraser CM. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic acids research 2000 28(6). DOI:10.1038/35054158.
65. . Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000 408(6814). DOI:10.1038/35048692.
66. Nierman WC, Eisen JA, Fleischmann RD, Fraser CM. Genome data: what do we learn? Current opinion in structural biology 2000 10(3). DOI:10.1038/35048692.
67. Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science (New York, N.Y.) 2000 287(5459). DOI:10.1038/35048692.
68. Coleman MA, Eisen JA, Mohrenweiser HW. Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse. Genomics 2000 65(3). DOI:10.1006/geno.2000.6174.
69. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 2000 406(6795). DOI:10.1038/35020000.
70. Eisen JA, Heidelberg JF, White O, Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome biology 2000 1(6). DOI:10.1038/35020000.
71. Pollock DD, Eisen JA, Doggett NA, Cummings MP. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Molecular biology and evolution 2000 17(12). DOI:10.1038/35020000.
72. Eisen JA. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Current opinion in genetics&development 2000 10(6). DOI:10.1038/35020000.
73. Eisen JA. Assessing evolutionary relationships among microbes from whole-genome analysis. Current opinion in microbiology 2000 3(5). DOI:10.1038/35020000.
74. Fraser CM, Eisen J, Fleischmann RD, Ketchum KA, Peterson S. Comparative genomics and understanding of microbial biology. Emerging infectious diseases 6(5). DOI:10.1038/35020000.
75. Fraser CM, Eisen JA, Salzberg SL. Microbial genome sequencing. Nature 2000 406(6797). DOI:10.1038/35021244.
76. Nierman W, Eisen JA, Fraser CM. Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis. Research in microbiology 2000 151(2). DOI:10.1038/35021244.
77. 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, Venter JC. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 1999 402(6763). DOI:10.1038/45471.
78. Eisen JA, Hanawalt PC. A phylogenomic study of DNA repair genes, proteins, and processes. Mutation research 1999 435(3). DOI:10.1038/45471.
79. Eisen JA. Going to extremes. Archaea: bridging the gap between bacteria and eukarya (A Keystone Symposia), Taos, NM, USA, 9-14 January 1999. Trends in genetics : TIG 1999 15(6). DOI:10.1038/45471.
80. 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, Fraser CM. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science (New York, N.Y.) 1999 286(5444). DOI:10.1038/45471.
81. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999 399(6734). DOI:10.1038/20601.
82. Wei MH, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA, Lerman MI. In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. Human genetics 1998 103(3). DOI:10.1038/20601.
83. Eisen JA. A phylogenomic study of the MutS family of proteins. Nucleic acids research 1998 26(18). DOI:10.1038/20601.
84. Gruber TM, Eisen JA, Gish K, Bryant DA. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS microbiology letters 1998 162(1). DOI:10.1038/20601.
85. Eisen JA. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome research 1998 8(3). DOI:10.1038/20601.
86. White RB, Eisen JA, Kasten TL, Fernald RD. Second gene for gonadotropin-releasing hormone in humans. Proceedings of the National Academy of Sciences of the United States of America 1998 95(1). DOI:10.1038/20601.
87. Eisen JA, Kaiser D, Myers RM. Gastrogenomic delights: a movable feast. Nature medicine 1997 3(10). DOI:10.1038/20601.
88. Eisen JA. The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package. Methods in molecular biology (Clifton, N.J.) 1997 70. DOI:10.1038/20601.
89. Shafer RW, Eisen JA, Merigan TC, Katzenstein DA. Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe. Journal of virology 1997 71(7). DOI:10.1038/20601.
90. 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. Journal of molecular evolution 1995 41(6). DOI:10.1038/20601.
91. Eisen JA, Sweder KS, Hanawalt PC. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic acids research 1995 23(14). DOI:10.1038/20601.
92. Eisen JA, Benito MI, Walbot V. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic acids research 1994 22(13). DOI:10.1038/20601.
93. Liu SK, Eisen JA, Hanawalt PC, 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. Journal of bacteriology 1993 175(20). DOI:10.1038/20601.
94. Eisen JA, Smith SW, Cavanaugh CM. Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. Journal of bacteriology 1992 174(10). DOI:10.1038/20601.

 

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