Jonathan Eisen

Jonathan A. Eisen is an American evolutionary biologist, currently working at University of California, Davis.^[4][5] His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the academic editor-in-chief of the open-access journal PLoS Biology.^[6][7]

In 2011 Eisen was awarded the Benjamin Franklin Award (Bioinformatics) for promoting open access in the life sciences.^[8]

Eisen together with Nick Barton, Derek E.G. Briggs, David B. Goldstein, and Nipam H. Patel is an author of the undergraduate textbook, Evolution, that integrates molecular biology, genomics, and human genetics with traditional evolutionary studies.^[1] According to Google Scholar^[9] his most cited peer-reviewed papers are on the genome sequence of Plasmodium falciparum,^[10] sequencing the Sargasso Sea ^[11] and a paper on the genome of Thermotoga maritima.^[12]

Prior to working at UC Davis he was an Investigator at The Institute for Genomic Research.

Eisen and his work is routinely discussed in the scientific and popular press. Examples include a New York Times article on the Genomic Encyclopedia of Bacteria and Archaea in 2009 ^[13] and extensive coverage of work on searching for a "fourth domain" of life ^{[14] [15]}. In addition, Eisen's blogging and microblogging work is frequently written about including for example ^{[16] [17] [18]}

Selected Publications

• Wu, D.; Hugenholtz, P.; Mavromatis, K.; Pukall, R. �D.; Dalin, E.; Ivanova, N. N.; Kunin, V.; Goodwin, L. et al. (2009). "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature 462 (7276): 1056–1060. Bibcode 2009Natur.462.1056W. doi:10.1038/nature08656. PMC 3073058. PMID 20033048. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3073058.  edit
• Eisen, J. A.; MacCallum, C. J. (2009). "Genomics of Emerging Infectious Disease: A PLoS Collection". PLoS Biology 7 (10): e1000224. doi:10.1371/journal.pbio.1000224. PMC 2757914. PMID 19855830. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2757914.  edit
• Eisen, J. A. (2007). "Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes". PLoS Biology 5 (3): e82. doi:10.1371/journal.pbio.0050082. PMC 1821061. PMID 17355177. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1821061.  edit
• Eisen, J. A.; Coyne, R. S.; Wu, M.; Wu, D.; Thiagarajan, M.; Wortman, J. R.; Badger, J. H.; Ren, Q. et al. (2006). "Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote". PLoS Biology 4 (9): e286. doi:10.1371/journal.pbio.0040286. PMC 1557398. PMID 16933976. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1557398.  edit
• Wu, D.; Daugherty, S. C.; Van Aken, S. E.; Pai, G. H.; Watkins, K. L.; Khouri, H.; Tallon, L. J.; Zaborsky, J. M. et al. (2006). "Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters". PLoS Biology 4 (6): e188. doi:10.1371/journal.pbio.0040188. PMC 1472245. PMID 16729848. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1472245.  edit
• Seshadri, R.; Adrian, L.; Fouts, D.; Eisen, J.; Phillippy, A.; Methe, B.; Ward, N.; Nelson, W. et al. (2005). "Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes". Science 307 (5706): 105–108. doi:10.1126/science.1102226. PMID 15637277.  edit
• Venter, J. C.; Remington, K.; Heidelberg, J.; Halpern, A.; Rusch, D.; Eisen, J.; Wu, D.; Paulsen, I. et al. (2004). "Environmental Genome Shotgun Sequencing of the Sargasso Sea". Science 304 (5667): 66–74. Bibcode 2004Sci...304...66V. doi:10.1126/science.1093857. PMID 15001713.  edit
• Ward, N.; Larsen, Ø.; Sakwa, J.; Bruseth, L.; Khouri, H.; Durkin, A. S.; Dimitrov, G.; Jiang, L. et al. (2004). "Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)". PLoS Biology 2 (10): e303. doi:10.1371/journal.pbio.0020303. PMC 517821. PMID 15383840. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=517821.  edit
• Wu, M.; Sun, L. V.; Vamathevan, J.; Riegler, M.; Deboy, R.; Brownlie, J. C.; McGraw, E. A.; Martin, W. et al. (2004). "Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements". PLoS Biology 2 (3): e69. doi:10.1371/journal.pbio.0020069. PMC 368164. PMID 15024419. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=368164.  edit
• Eisen, J.; Fraser, C. (2003). "Phylogenomics: intersection of evolution and genomics". Science 300 (5626): 1706–1707. Bibcode 2003Sci...300.1706E. doi:10.1126/science.1086292. PMID 12805538.  edit
• Read, T. D.; Peterson, S. N.; Tourasse, N.; Baillie, L. W.; Paulsen, I. T.; Nelson, K. E.; Tettelin, H.; Fouts, D. E. et al. (2003). "The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria". Nature 423 (6935): 81–86. doi:10.1038/nature01586. PMID 12721629.  edit
• Gardner, M. J.; Hall, N.; Fung, E.; White, O.; Berriman, M.; Hyman, R. W.; Carlton, J. M.; Pain, A. et al. (2002). "Genome sequence of the human malaria parasite Plasmodium falciparum". Nature 419 (6906): 498–511. doi:10.1038/nature01097. PMID 12368864.  edit
• Béjà, O.; Suzuki, M. T.; Heidelberg, J. F.; Nelson, W. C.; Preston, C. M.; Hamada, T.; Eisen, J. A.; Fraser, C. M. et al. (2002). "Unsuspected diversity among marine aerobic anoxygenic phototrophs". Nature 415 (6872): 630. doi:10.1038/415630a. PMID 11832943.  edit
• Ward, N.; Eisen, J.; Fraser, C.; Stackebrandt, E. (2001). "Sequenced strains must be saved from extinction". Nature 414 (6860): 148–148. doi:10.1038/35102737. PMID 11700527.  edit
• Eisen, J. A. (2001). "Microbiology: Gastrogenomics". Nature 409 (6819): 463–466. doi:10.1038/35054158. PMID 11206526.  edit
• Salzberg, S. L.; White, O.; Peterson, J.; Eisen, J. (2001). "Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?". Science 292 (5523): 1903–1906. doi:10.1126/science.1061036. PMID 11358996.  edit
• The Arabidopsis Genome Initiative, I. (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature 408 (6814): 796–815. doi:10.1038/35048692. PMID 11130711.  edit
• Fraser, C. M.; Heidelberg, J. F.; Eisen, J. A.; Nelson, W. C.; Clayton, R. A.; Gwinn, M. L.; Dodson, R. J.; Haft, D. H. et al. (2000). "DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae". Nature 406 (6795): 477–483. doi:10.1038/35020000. PMID 10952301.  edit
• Fraser, C. M.; Eisen, J. A.; Salzberg, S. L. (2000). "Microbial genome sequencing". Nature 406 (6797): 799–803. doi:10.1038/35021244. PMID 10963611.  edit
• Lin, X.; Kaul, S.; Rounsley, S.; Shea, T. P.; Benito, M. I.; Town, C. D.; Fujii, C. Y.; Mason, T. et al. (1999). "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana". Nature 402 (6763): 761–768. doi:10.1038/45471. PMID 10617197.  edit
• White, O.; Eisen, J.; Heidelberg, J.; Hickey, E.; Peterson, J.; Dodson, R.; Haft, D.; Gwinn, M. et al. (1999). "Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1". Science 286 (5444): 1571–1577. doi:10.1126/science.286.5444.1571. PMID 10567266.  edit
• Fraser, C. M.; Nelson, K. E.; Clayton, R. A.; Gill, S. R.; Gwinn, M. L.; Dodson, R. J.; Haft, D. H.; Hickey, E. K. et al. (1999). "Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima". Nature 399 (6734): 323–329. Bibcode 1999Natur.399..323N. doi:10.1038/20601. PMID 10360571.  edit

References

External links

• Jonathan Eisen on Twitter
• Jonathan Eisen's "Tree of Life" Blog
• Lab Web Page
• Jonathan Eisen's Mendeley Page