Epernicus: Jonathan A. Eisen, Ph.D.

Jonathan A. Eisen, Ph.D.

Positions:
Professor

Evolution and Ecology

Genome Center

University of California, Davis (Davis, CA)

Adjunct Scientist

The Joint Genome Institute

Lawrence Berkeley National Laboratory (Berkeley, CA)

Academic Editor in Chief

PLoS Biology
Degrees:

Ph.D., Biological Sciences, Stanford University (Stanford, CA)

A.B., Biology, Harvard College (Cambridge, MA)
Past Advisors:

Philip C. Hanawalt (as Graduate Student - Ph.D.)

Colleen M. Cavanaugh (as Undergraduate Student)
Research:
My lab studies the genomic basis for the origin of novelty in microorganisms.
Other Experience:
2007-present Science and Technology Advisory Board on Biosecurity, LLNL

2004-2007 Scientific Advisory Board, National Evolutionary Synthesis Center, North Carolina

2003-2007 Scientific Advisory Board, Saccharomyces Genome Database, Stanford University

1998-2006 Investigator, The Institute for Genomic Research (TIGR)

2000-2002 Scientific Advisory Board, Geneformatics Inc.
Honors:
2004-2006 Member, Defense Science Studies Group

2002 Esquire Magazine, Best and Brightest Innovators

1999 Martin Rodbell Fellowship, T.I.G.R.

1997 Walter J. Gores Award for excellence in teaching, Stanford University

1997 Centennial Teaching Assistant, Stanford University

1993 Centennial Teaching Assistant, Stanford University

1991-1994 National Science Foundation Predoctoral Fellowship

Communities:

Jonathan Eisen's Genealogy

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Jonathan Eisen's Publications (235)

Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges.
Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ

Environmental microbiology. 2012 Jan;14(1):162-76
Accounting for alignment uncertainty in phylogenomics.
Wu M, Chatterji S, Eisen JA

PloS one. 2012;7(1):e30288
Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila.
Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K

G3 (Bethesda, Md.). 2011 Nov;1(6):515-22
Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).
Woyke T, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Mwirichia R, Sikorski J, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC

Standards in genomic sciences. 2011 Oct 15;5(1):21-9
Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).
Liolios K, Sikorski J, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Kotsyurbenko O, Rohde M, Tindall BJ, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC

Standards in genomic sciences. 2011 Oct 15;5(1):30-40
Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Raine
Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Mavromatis K, Daum C, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Jeffries CD, Detter JC, Rohde M, Abt B, Pukall R, Göker M, Bristow J, Markowitz V, Hugenholtz P, Eisen JA

Standards in genomic sciences. 2011 Oct 15;5(1):121-34
Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10).
Lapidus A, Chertkov O, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Abt B, Spring S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T

Standards in genomic sciences. 2011 Oct 15;5(1):86-96
Mauve assembly metrics.
Darling AE, Tritt A, Eisen JA, Facciotti MT

Bioinformatics (Oxford, England). 2011 Oct 1;27(19):2756-7
Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).
Chang YJ, Land M, Hauser L, Chertkov O, Del Rio TG, Nolan M, Copeland A, Tice H, Cheng JF, Lucas S, Han C, Goodwin L, Pitluck S, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Mavromatis K, Liolios K, Brettin T, Fiebig A, Rohde M, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A

Standards in genomic sciences. 2011 Oct 15;5(1):97-111
Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).
Pati A, Gronow S, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Mikhailova N, Huntemann M, Chen A, Palaniappan K, Land M, Hauser L, Detter JC, Brambilla EM, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N

Standards in genomic sciences. 2011 Oct 15;5(1):41-9
Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system.
Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A

PLoS genetics. 2011 Sep;7(9):e1002272
Complete genome sequence of Haliscomenobacter hydrossis type strain (O).
Daligault H, Lapidus A, Zeytun A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T

Standards in genomic sciences. 2011 Jul 1;4(3):352-60
Complete genome sequence of Mahella australiensis type strain (50-1 BON).
Sikorski J, Teshima H, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Ngatchou-Djao OD, Rohde M, Pukall R, Spring S, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP, Lapidus A

Standards in genomic sciences. 2011 Jul 1;4(3):331-41
Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).
Anderson I, Sikorski J, Zeytun A, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Ngatchou-Djao OD, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC

Standards in genomic sciences. 2011 Jul 1;4(3):322-30
Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).
Han C, Mwirichia R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC

Standards in genomic sciences. 2011 Jul 1;4(3):371-80
Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).
Göker M, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP

Standards in genomic sciences. 2011 Jul 1;4(3):393-401
Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL).
Ivanova N, Sikorski J, Chertkov O, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Kannan KP, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A

Standards in genomic sciences. 2011 Jul 1;4(3):312-21
Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A).
Anderson I, Göker M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Huber H, Yasawong M, Rohde M, Spring S, Abt B, Sikorski J, Wirth R, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A

Standards in genomic sciences. 2011 Jul 1;4(3):381-92
Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)).
Huntemann M, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K

Standards in genomic sciences. 2011 Jul 1;4(3):303-11
Complete genome sequence of Treponema succinifaciens type strain (6091).
Han C, Gronow S, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Zeytun A, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC

Standards in genomic sciences. 2011 Jul 1;4(3):361-70
Complete genome sequence of Tsukamurella paurometabola type strain (no. 33).
Munk AC, Lapidus A, Lucas S, Nolan M, Tice H, Cheng JF, Del Rio TG, Goodwin L, Pitluck S, Liolios K, Huntemann M, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Tapia R, Han C, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Yasawong M, Brambilla EM, Rohde M, Sikorski J, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP

Standards in genomic sciences. 2011 Jul 1;4(3):342-51
Drivers of bacterial beta-diversity depend on spatial scale.
Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC

Proceedings of the National Academy of Sciences of the United States of America. 2011 May 10;108(19):7850-4
Complete genome sequence of Bacteroides salanitronis type strain (BL78).
Gronow S, Held B, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA

Standards in genomic sciences. 2011 Apr 29;4(2):191-9
Complete genome sequence of Cellulophaga lytica type strain (LIM-21).
Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Kannan KP, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N

Standards in genomic sciences. 2011 Apr 29;4(2):221-32
Complete genome sequence of Deinococcus maricopensis type strain (LB-34).
Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP

Standards in genomic sciences. 2011 Apr 29;4(2):163-72

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One Figure

Predicted Metabolic Pathways in Baumannia and the Predicted Amino Acid Biosynthesis Pathways Encoded by the Partial Genome Sequence of Sulcia

Genes that are present are in red and the corresponding catalytic pathways are illustrated in solid black line

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Jonathan A. Eisen, Ph.D.

Professor

Adjunct Scientist

Academic Editor in Chief

My lab studies the genomic basis for the origin of novelty in microorganisms.

Jonathan Eisen's Genealogy

Jonathan Eisen's Publications (235)

One Figure

Websites