Eisen's research[3][14][15] focuses on the origin of novelty, how new processes and functions originate in living things. To study this, he focuses on sequencing and analyzing genomes of organisms, especially microbes and usingphylogenomic analysis.
Eisen together withNick 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.[4] According toGoogle Scholar[3] his most cited peer-reviewed papers are on the genome sequence ofPlasmodium falciparum,[16] sequencing theSargasso Sea[17] and a paper on the genome ofThermotoga maritima.[18]
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[19] and extensive coverage of work on searching for a "fourth domain" of life.[20][21] In addition, Eisen's blogging and microblogging work is frequently written about including for example.[22][23][24] His brotherMichael Eisen is also a biologist.
Eisen was awarded theBenjamin Franklin Award (Bioinformatics) in 2011 and theEsquire Magazine's Best and Brightest in 2002.[25] He was awarded the Walter J. Gores Award, Faculty Achievement Awards for Excellence in Teaching.[1] He was elected a Fellow of theAmerican Society for Microbiology (FAAM).[2] He was awarded the UC Davis ADVANCE Scholar Award in 2019, for his work to improve gender equity in STEM through teaching, research, and service.
^abNipam H. Patel; Barton, Nicholas John; Derek E. G. Briggs; Eisen, Jonathan; Goldstein, David I. (2007).Evolution. Plainview, N.Y: Cold Spring Harbor Laboratory Press.ISBN978-0-87969-684-9.
^Gegger, Laura (December 24, 2012)."These Were a Few of Their Favorite Things".The New York Times.Archived from the original on September 6, 2019. RetrievedFebruary 25, 2017.Jonathan Eisen: 44, evolutionary biologist, University of California, Davis, and academic editor in chief of PLoS Biology
^Gardner, M. J.; Hall, N.; Fung, E.; White, O.; Berriman, M.; Hyman, R. W.; Carlton, J. M.; Pain, A.; Nelson, K. E.; Bowman, S.; Paulsen, I. T.; James, K.; Eisen, J. A.; Rutherford, K.; Salzberg, S. L.; Craig, A.; Kyes, S.; Chan, M. S.; Nene, V.; Shallom, S. J.; Suh, B.; Peterson, J.; Angiuoli, S.; Pertea, M.; Allen, J.; Selengut, J.; Haft, D.; Mather, M. W.; Vaidya, A. B.; Martin, D. M. A. (2002)."Genome sequence of the human malaria parasite Plasmodium falciparum".Nature.419 (6906):498–511.Bibcode:2002Natur.419..498G.doi:10.1038/nature01097.PMC3836256.PMID12368864.
^Venter, J. C.; Remington, K.; Heidelberg, J.; Halpern, A.; Rusch, D.; Eisen, J.; Wu, D.; Paulsen, I.; Nelson, K.; Nelson, W.; Fouts, D. E.; Levy, S.; Knap, A. H.; Lomas, M. W.; Nealson, K.; White, O.; Peterson, J.; Hoffman, J.; Parsons, R.; Baden-Tillson, H.; Pfannkoch, C.; Rogers, Y. H.; Smith, H. O. (2004). "Environmental Genome Shotgun Sequencing of the Sargasso Sea".Science.304 (5667):66–74.Bibcode:2004Sci...304...66V.CiteSeerX10.1.1.124.1840.doi:10.1126/science.1093857.PMID15001713.S2CID1454587.
^Fraser, C. M.; Clayton, K. E.; Gill, R. A.; Gwinn, S. R.; Dodson, M. L.; Haft, R. J.; Hickey, D. H.; Peterson, E. K.; Nelson, J. D.; Ketchum, W. C.; McDonald, K. A.; Utterback, L.; Malek, T. R.; Linher, J. A.; Garrett, K. D.; Stewart, M. M.; Cotton, A. M.; Pratt, M. D.; Phillips, M. S.; Richardson, C. A.; Heidelberg, D.; Sutton, J.; Fleischmann, G. G.; Eisen, R. D.; White, J. A.; Salzberg, O.; Smith, S. L.; Venter, H. O.; Fraser, J. C. (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.PMID10360571.S2CID4420157.
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