Jonathan Eisen

Last updated

Jonathan Eisen
Jonathan Eisen - PLOS Biology Tenth Anniversary (cropped).png
Eisen in 2013
Born
Jonathan Andrew Eisen

(1968-08-31) August 31, 1968 (age 55)
Nationality American
Alma mater
Known for
Awards
Scientific career
Fields
Institutions
Thesis The evolution of DNA repair genes, proteins, and processes  (1998)
Doctoral advisor Philip Hanawalt
Website www.genomecenter.ucdavis.edu/people/jaeisen

Jonathan Andrew Eisen (born August 31, 1968) [5] is an American evolutionary biologist, currently working at University of California, Davis. [4] [6] 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 . [7] [8] [9] [10] [11]

Contents

Education

Eisen completed his undergraduate studies at Harvard College in 1990, earning an AB degree in biology. [12] He graduated as a Doctor of Philosophy from Stanford University in 1998 with a thesis on the evolution of DNA repair genes, proteins, and processes in 1998, supervised by Philip Hanawalt. [13]

Research

Eisen featured in a comic strip by Jorge Cham on the occasion of Open Access Week 2012.

Eisen's research [4] [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 using phylogenomic analysis.

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 [4] his most cited peer-reviewed papers are on the genome sequence of Plasmodium falciparum , [16] sequencing the Sargasso Sea [17] and a paper on the genome of Thermotoga maritima . [18]

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 [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 brother Michael Eisen is also a biologist.

Awards and honors

Eisen was awarded the Benjamin Franklin Award (Bioinformatics) in 2011 and the Esquire Magazine's Best and Brightest in 2002. [25] He was awarded the Walter J. Gores Award, Faculty Achievement Awards for Excellence in Teaching. [2] He was elected a Fellow of the American Society for Microbiology (FAAM). [3] 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.

Related Research Articles

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Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

<span class="mw-page-title-main">Comparative genomics</span> Field of biological research

Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparison of whole genome sequences provides a highly detailed view of how organisms are related to each other at the gene level. By comparing whole genome sequences, researchers gain insights into genetic relationships between organisms and study evolutionary changes. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, Comparative genomics provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give unique characteristics of each organism. Moreover, these studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms.

<span class="mw-page-title-main">J. Craig Venter Institute</span> Non-profit genomics research institute

The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research (TIGR), the Institute for Biological Energy Alternatives, and the J. Craig Venter Science Foundation Joint Technology Center. It has facilities in Rockville, Maryland and San Diego, California.

<span class="mw-page-title-main">Michael Ashburner</span> English biologist (1942–2023)

Michael Ashburner was an English biologist and Professor in the Department of Genetics at University of Cambridge. He was also the former joint-head and co-founder of the European Bioinformatics Institute (EBI) of the European Molecular Biology Laboratory (EMBL) and a Fellow of Churchill College, Cambridge.

Nicholas Hamilton Barton is a British evolutionary biologist.

<span class="mw-page-title-main">Michael Eisen</span> American computational biologist and journal editor

Michael Bruce Eisen is an American computational biologist and the former editor-in-chief of the journal eLife. He is a professor of genetics, genomics and development at University of California, Berkeley. He is a leading advocate of open access scientific publishing and is co-founder of Public Library of Science (PLOS). In 2018, Eisen announced his candidacy U.S. Senate from California as an Independent, though he failed to qualify for the ballot.

Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics:

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Mark Bender Gerstein is an American scientist working in bioinformatics and Data Science. As of 2009, he is co-director of the Yale Computational Biology and Bioinformatics program.

Population genomics is the large-scale comparison of DNA sequences of populations. Population genomics is a neologism that is associated with population genetics. Population genomics studies genome-wide effects to improve our understanding of microevolution so that we may learn the phylogenetic history and demography of a population.

<span class="mw-page-title-main">Horizontal gene transfer in evolution</span> Evolutionary consequences of transfer of genetic material between organisms of different taxa

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Martin Edward Kreitman is an American geneticist at the University of Chicago, most well known for the McDonald–Kreitman test that is used to infer the amount of adaptive evolution in population genetic studies.

Biological dark matter is an informal term for unclassified or poorly understood genetic material. This genetic material may refer to genetic material produced by unclassified microorganisms. By extension, biological dark matter may also refer to the un-isolated microorganism whose existence can only be inferred from the genetic material that they produce. Some of the genetic material may not fall under the three existing domains of life: Bacteria, Archaea and Eukaryota; thus, it has been suggested that a possible fourth domain of life may yet be discovered, although other explanations are also probable. Alternatively, the genetic material may refer to non-coding DNA and non-coding RNA produced by known organisms.

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<span class="mw-page-title-main">Peter Keightley</span>

Peter D. Keightley FRS is Professor of Evolutionary Genetics at the Institute of Evolutionary Biology in School of Biological Sciences at the University of Edinburgh.

Microbial dark matter (MDM) comprises the vast majority of microbial organisms that microbiologists are unable to culture in the laboratory, due to lack of knowledge or ability to supply the required growth conditions. Microbial dark matter is analogous to the dark matter of physics and cosmology due to its elusiveness in research and importance to our understanding of biological diversity. Microbial dark matter can be found ubiquitously and abundantly across multiple ecosystems, but remains difficult to study due to difficulties in detecting and culturing these species, posing challenges to research efforts. It is difficult to estimate its relative magnitude, but the accepted gross estimate is that as little as one percent of microbial species in a given ecological niche are culturable. In recent years, more effort has been directed towards deciphering microbial dark matter by means of recovering genome DNA sequences from environmental samples via culture independent methods such as single cell genomics and metagenomics. These studies have enabled insights into the evolutionary history and the metabolism of the sequenced genomes, providing valuable knowledge required for the cultivation of microbial dark matter lineages. However, microbial dark matter research remains comparatively undeveloped and is hypothesized to provide insight into processes radically different from known biology, new understandings of microbial communities, and increasing understanding of how life survives in extreme environments.

References

  1. 1 2 Nipam H. Patel; Barton, Nicholas John; Derek E. G. Briggs; Eisen, Jonathan; Goldstein, David I. (2007). Evolution. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN   978-0-87969-684-9.
  2. 1 2 "Office of the University Registrar – Walter J. Gores Awards | Student Affairs". Archived from the original on July 25, 2011. Retrieved March 23, 2011.
  3. 1 2 http://www.ucdmc.ucdavis.edu/publish/news/leadership/6291 Archived May 14, 2016, at the Wayback Machine UC DAVIS PROFESSOR NAMED AMERICAN ACADEMY OF MICROBIOLOGY FELLOW
  4. 1 2 3 4 Jonathan A. Eisen publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  5. ↑ 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. Retrieved February 25, 2017. Jonathan Eisen: 44, evolutionary biologist, University of California, Davis, and academic editor in chief of PLoS Biology
  6. ↑ McDermid, Charles (December 30, 2021). "UC Davis microbiome expert weighs in on the Omicron variant and shares his evolving thoughts on eating out, indoor events and long Covid". Sactown Magazine. Archived from the original on April 16, 2023. Retrieved April 28, 2023.
  7. ↑ Eisen, J. A. (2008). "PLoS Biology 2.0". PLOS Biology. 6 (2): e48. doi: 10.1371/journal.pbio.0060048 . PMC   2253640 . PMID   18303952.
  8. ↑ "A new domain of life: Plenty more bugs in the sea, The Economist". March 24, 2011. Archived from the original on June 10, 2011. Retrieved June 9, 2011. article about Jonathan Eisen in The Economist
  9. ↑ Eisen, Jonathan A.'s publications indexed by the Scopus bibliographic database. (subscription required)
  10. ↑ The Arabidopsis Genome Initiative, I. (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature. 408 (6814): 796–815. Bibcode:2000Natur.408..796T. doi: 10.1038/35048692 . PMID   11130711.
  11. ↑ "Jonathan Eisen: Meet your microbes (TEDMED 2012)". Archived from the original on January 18, 2015. Retrieved January 26, 2015.
  12. ↑ "Jonathan Eisen » Faculty". UC Davis Genome Center. Archived from the original on September 25, 2015. Retrieved January 25, 2015.
  13. ↑ Eisen, Jonathan Andrew (1998). The evolution of DNA repair genes, proteins, and processes (PhD thesis). Stanford University.
  14. ↑ Jonathan Eisen publications indexed by Microsoft Academic
  15. ↑ Jonathan A. Eisen at DBLP Bibliography Server OOjs UI icon edit-ltr-progressive.svg
  16. ↑ 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. PMC   3836256 . PMID   12368864.
  17. ↑ 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. CiteSeerX   10.1.1.124.1840 . doi:10.1126/science.1093857. PMID   15001713. S2CID   1454587.
  18. ↑ 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. PMID   10360571. S2CID   4420157.
  19. ↑ Zimmer, Carl (December 29, 2009). "Scientists Start a Genomic Catalog of Earth's Abundant Microbes". The New York Times. Archived from the original on October 12, 2017. Retrieved February 25, 2017.
  20. ↑ "Plenty more bugs in the sea". The Economist. March 24, 2011. Archived from the original on June 10, 2011. Retrieved June 9, 2011.
  21. ↑ Dickey Zakaib, G. (2011). "The challenge of microbial diversity: Out on a limb". Nature. 476 (7358): 20–21. doi: 10.1038/476020a . PMID   21814255.
  22. ↑ Mandavilli, A. (2011). "Peer review: Trial by Twitter". Nature. 469 (7330): 286–287. Bibcode:2011Natur.469..286M. doi: 10.1038/469286a . PMID   21248816.
  23. ↑ "The Scientist Magazine® - Magazines". Archived from the original on April 12, 2011. Retrieved August 7, 2011.
  24. ↑ Brumfiel, G. (2009). "Science journalism: Breaking the convention?". Nature. 459 (7250): 1050–1051. doi: 10.1038/4591050a . PMID   19553969.
  25. ↑ The Maverick – Esquire Archived October 13, 2012, at the Wayback Machine
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