Michael Eisen

Last updated
Michael Eisen
Plos eisen.jpg
Born
Michael Bruce Eisen

(1967-04-13) April 13, 1967 (age 56)
Boston, Massachusetts, United States
NationalityAmerican
Alma mater Harvard University (AB, PhD)
Known for Public Library of Science (PLOS)
Awards Benjamin Franklin Award (Bioinformatics) (2002)
Scientific career
Fields
Institutions University of California, Berkeley
Thesis Structural Studies of Influenza A Virus Proteins  (1996)
Doctoral advisor Don Craig Wiley [ citation needed ]
Website michaeleisen.org

Michael Bruce Eisen (born April 13, 1967) is an American computational biologist and the former [2] editor-in-chief of the journal eLife. [3] He is a professor of genetics, genomics and development at University of California, Berkeley. [4] [5] [6] [7] [8] 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. [9]

Contents

Early life and education

Born in Boston, Eisen and his brother Jonathan were raised in a family of scientists. Their grandfather was an x-ray crystallographer, their father, Howard Eisen a physician, and mother, Laura [10] a biochemist. They moved to Bethesda, Maryland when Eisen was four or five years old. The brothers spent summers in Long Island with their grandparents. Eisen states that he loved frogs and salamanders '"Even more than I have a frog fetish, I have a swamp fetish. I really like being in swamps."' He was also very interested in math and was captain of the high school math team. Eisen graduated from Walt Whitman High School in 1985. Intending to major in mathematics at Harvard University, he realized that there [he may encounter] other more brilliant math students, it was a Good Will Hunting moment and he decided that he did not want to major in mathematics, '"You don't want to be Salieri to Mozart."' During his years at Harvard, Eisen worked on "unlocking the three-dimensional structures of proteins." He was shown a DNA microarray which taught him a '"new way of doing biology"'. [11]

Eisen completed his PhD at Harvard University in biophysics and a B.S. (also from Harvard) in Math. [12] He was under the supervision of Don Craig Wiley [13] while studying Influenza A virus Proteins. [14]

There are things that are really really difficult, those are the kinds of problems you do want to work on. It's not that easy to tell the difference between impossible problems and a problem that is really really difficult. But learning to do so is critically important. - Things I learned from working with Pat Brown (Patrick O. Brown) - 2015 [13]

After earning his doctorate, Eisen was a Postdoctoral Fellow at Stanford University in the lab of David Botstein, where he most notably developed a method for interpreting gene expression data from microarrays. The seminal research publication that Eisen authored about this project has been cited over 16,000 times. [15]

Baseball and biology

When Eisen lived in Tennessee he worked as a play-by-play announcer for a minor league baseball team, [12] the Columbia Mules. He is a self-proclaimed Red Sox fanatic. [11] He and computational biologist James Fraser recorded a video for iBiology about the role baseball statistics influenced their research. Their argument is that sequencing DNA is similar to scoring a baseball game, and that many computational biologists learned to think about science computations from an obsessive interest in baseball stats. The exercise of comparing a specific player's stats to a database of other similar players allows a baseball fan to predict future performance. This same system works with proteins and predicting functions. As tools are developed that break down and track all stats concerning baseball players, so will technology improve with genetics. With both baseball and genetics, tools are being developed that refine the models. [16] In a lecture in 2015, Eisen stated that he received a computer from his grandfather for his twelfth birthday and spent the next five years teaching himself how to program so that he could keep track of baseball stats. [13]

Research

His academic research focuses on the evolution of gene regulation. [17] [18] [19] [20] Despite this focus, Eisen's work has historically spanned very diverse disciplines. For example, his 5 most cited papers cover a broad range of topics including methods for hierarchical clustering, [17] applications to human breast cancers (with David Botstein and Charles Perou), [6] and discovery of tumor subtypes in diffuse large B cell lymphoma (with Ash Alizadeh and Louis Staudt). [18] His more recent research work has been on fruit flies and Drosophila [21] and how they "develop from a tiny single-celled egg to a mature adult. He says they hold insights into what goes wrong in people as they age." [12] He receives funding from the Howard Hughes Medical Institute for his research. [21]

2018 U.S. Senate race

Eisen announced through Twitter on January 25 his intent to run for U.S. Senate from California in 2018 for Democratic Senator Dianne Feinstein's seat, registering the Twitter handle SenatorPhD. [22] His campaign slogan was "Liberty, Equality, Reality". Eisen's reasons for running for Congress included his perception that the Trump administration was unresponsive to climate change and other science-related issues. Another reason Eisen decided to run was his experience watching Cabinet appointees being interviewed by the Senate about climate change. He thought '“It would be really nice to have scientists ask the questions of the Cabinet appointees, because the senators don’t seem to understand the issue and aren’t asking the right questions.”' [12] He feels that if science is to be on the forefront of policy making, '"scientists need to run for office."' He felt that 2018's California jungle primaries afforded him a better chance at making the final two for the general election, but he did not make the final two (which were Dianne Feinstein and Kevin de León). [12]

For a really long time, scientists have watched political processes erode — and have watched politicians openly deride science, dismissing the role that science plays in our everyday life. Scientists have been sitting here hoping that someone would come along and defend those principals. Politics, in my mind, should function similar to science. We should try to figure out what’s going on in the world and then debate the best way to do it, to make the world better. The best tools we have to characterize reality are the observational tools that science uses all the time. Too much of politics has rejected that basic principle that scientists live and breathe all the time. [12]

Eisen dropped out of the race when he failed to qualify for the June 2018 primary ballot. [23]

eLife editorship and firing

In 2019, Eisen was named the second editor-in-chief of the open-access scientific journal eLife. Under his leadership, the journal moved away from the traditional "review, then publish" model, instead requiring authors to submit preprints and then publishing journal editors' reviews alongside manuscripts, meaning that the journal neither accepted nor rejected submissions. [24] Eisen said that the move was intended to reduce the prominence of the publisher, and instead focus attention on authors and their work.

Eisen was fired from eLife on October 23, 2023 after tweeting a story by The Onion with the headline: "Dying Gazans Criticized For Not Using Last Words To Condemn Hamas." Eisen said "The Onion speaks with more courage, insight and moral clarity than the leaders of every academic institution put together. I wish there were a @TheOnion university". [25] At least five of eLife 's editors resigned and other scientists said they would stop participating in eLife events in solidarity with Eisen. A petition letter was organised to protest against Eisen’s firing. The petition, which was signed by over 2,000 scientists, academics and researchers, said eLife 's action is having a "chilling effect" on freedom of expression in academia. [26]

Open access advocacy

Throughout his career he has been an advocate for "open science", which is the free release of the material and intellectual product of scientific research. He is a leading advocate of open access scientific publishing [27] [28] [29] and is co-founder of Public Library of Science (PLOS) and serves on the PLOS board, the Academic Steering & Advocacy Committee of Open Library of Humanities, [30] and is an adviser to Science Commons.

In 2012 Eisen began protesting against the Research Works Act as part of his appeal to promote open access to information. [31]

Awards and honors

In 2002, Eisen was awarded the inaugural Benjamin Franklin Award in bioinformatics, for his work on PLOS and the open-access availability of his microarray cluster analysis software. [32]

Related Research Articles

<span class="mw-page-title-main">PLOS</span> Nonprofit open-access publisher

PLOS is a nonprofit publisher of open-access journals in science, technology, and medicine and other scientific literature, under an open-content license. It was founded in 2000 and launched its first journal, PLOS Biology, in October 2003.

<span class="mw-page-title-main">DNA microarray</span> Collection of microscopic DNA spots attached to a solid surface

A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown. An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression.

<span class="mw-page-title-main">Eric Lander</span> American mathematician (born 1957)

Eric Steven Lander is an American mathematician and geneticist who is a professor of biology at the Massachusetts Institute of Technology (MIT), and a professor of systems biology at Harvard Medical School. Eric Lander is founding director emeritus of the Broad Institute of MIT and Harvard.

<span class="mw-page-title-main">Harold E. Varmus</span> American scientist (born 1939)

Harold Eliot Varmus is an American Nobel Prize-winning scientist. He is currently the Lewis Thomas University Professor of Medicine at Weill Cornell Medicine and a senior associate at the New York Genome Center.

<span class="mw-page-title-main">Don Craig Wiley</span> American biologist (1944–2001)

Don Craig Wiley was an American structural biologist.

<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.

<span class="mw-page-title-main">Heat map</span> Data visualization technique

A heat map is a 2-dimensional data visualization technique that represents the magnitude of individual values within a dataset as a color. The variation in color may be by hue or intensity.

<span class="mw-page-title-main">Joseph DeRisi</span> American biochemist

Joseph Lyman DeRisi is an American biochemist, specializing in molecular biology, parasitology, genomics, virology, and computational biology.

<span class="mw-page-title-main">Patrick O. Brown</span> American scientist and businessman

Patrick O'Reilly Brown is an American scientist and businessman who is the founder of Impossible Foods Inc. and professor emeritus in the department of biochemistry at Stanford University. Brown is co-founder of the Public Library of Science, inventor of the DNA microarray, and a former investigator at Howard Hughes Medical Institute.

<span class="mw-page-title-main">David Botstein</span> American biologist

David Botstein is an American biologist who is the chief scientific officer of Calico. He was the director of the Lewis-Sigler Institute for Integrative Genomics at Princeton University from 2003 to 2013, where he remains an Anthony B. Evnin Professor of Genomics.

<i>PLOS One</i> Peer-reviewed open-access scientific journal

PLOS One is a peer-reviewed open access mega journal published by the Public Library of Science (PLOS) since 2006. The journal covers primary research from any discipline within science and medicine. The Public Library of Science began in 2000 with an online petition initiative by Nobel Prize winner Harold Varmus, formerly director of the National Institutes of Health and at that time director of Memorial Sloan–Kettering Cancer Center; Patrick O. Brown, a biochemist at Stanford University; and Michael Eisen, a computational biologist at the University of California, Berkeley, and the Lawrence Berkeley National Laboratory.

Peter Anthony Lawrence is a British developmental biologist at the Laboratory of Molecular Biology and the Zoology Department of the University of Cambridge. He was a staff scientist of the Medical Research Council from 1969 to 2006.

<span class="mw-page-title-main">ChIP-on-chip</span> Molecular biology method

ChIP-on-chip is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray ("chip"). Like regular ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA in vivo. Specifically, it allows the identification of the cistrome, the sum of binding sites, for DNA-binding proteins on a genome-wide basis. Whole-genome analysis can be performed to determine the locations of binding sites for almost any protein of interest. As the name of the technique suggests, such proteins are generally those operating in the context of chromatin. The most prominent representatives of this class are transcription factors, replication-related proteins, like origin recognition complex protein (ORC), histones, their variants, and histone modifications.

<span class="mw-page-title-main">Terry Speed</span> Australian statistician at the Walter and Eliza Hall Institute of Medical Research

Terence Paul "Terry" Speed, FAA FRS is an Australian statistician. A senior principal research scientist at the Walter and Eliza Hall Institute of Medical Research, he is known for his contributions to the analysis of variance and bioinformatics, and in particular to the analysis of microarray data.

Gerald Mayer Rubin is an American biologist, notable for pioneering the use of transposable P elements in genetics, and for leading the public project to sequence the Drosophila melanogaster genome. Related to his genomics work, Rubin's lab is notable for development of genetic and genomics tools and studies of signal transduction and gene regulation. Rubin also serves as a vice president of the Howard Hughes Medical Institute and executive director of the Janelia Research Campus.

<span class="mw-page-title-main">SALL2</span> Protein-coding gene in the species Homo sapiens

Sal-like protein 2 is a protein that in humans is encoded by the SALL2 gene.

<span class="mw-page-title-main">Jonathan Eisen</span> American evolutionary biologist

Jonathan Andrew Eisen is an American evolutionary biologist, currently working at University of California, Davis. 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.

<span class="mw-page-title-main">Olga Troyanskaya</span> American academic

Olga G. Troyanskaya is a Professor in the Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics at Princeton University and the Deputy Director for Genomics at the Flatiron Institute's Center for Computational Biology in NYC. She studies protein function and interactions in biological pathways by analyzing genomic data using computational tools.

<span class="mw-page-title-main">Chris Sander (scientist)</span> Bioinformatician

Chris Sander is a computational biologist based at the Dana-Farber Cancer Center and Harvard Medical School. Previously he was chair of the Computational Biology Programme at the Memorial Sloan–Kettering Cancer Center in New York City. In 2015, he moved his lab to the Dana–Farber Cancer Institute and the Cell Biology Department at Harvard Medical School.

<span class="mw-page-title-main">Alex Bateman</span> British bioinformatician

Alexander George Bateman is a computational biologist and Head of Protein Sequence Resources at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Cambridge, UK. He has led the development of the Pfam biological database and introduced the Rfam database of RNA families. He has also been involved in the use of Wikipedia for community-based annotation of biological databases.

References

  1. ↑ Michael Eisen publications indexed by Google Scholar
  2. ↑ Science News Staff (24 October 2023). "Prominent journal editor fired for endorsing satirical article about Israel-Hamas conflict". Science. Archived from the original on 24 October 2023. Retrieved 24 October 2023.
  3. ↑ "eLife welcomes Michael Eisen as Editor-in-Chief". eLife. 2019-03-05. Retrieved 2019-03-05.
  4. ↑ "Michael B. Eisen, PhD". Howard Hughes Medical Institute. Retrieved 23 September 2013.
  5. ↑ Michael Eisen's publications indexed by the Scopus bibliographic database. (subscription required)
  6. 1 2 Perou, C. M.; Sørlie, T; Eisen, M. B.; Van De Rijn, M; Jeffrey, S. S.; Rees, C. A.; Pollack, J. R.; Ross, D. T.; Johnsen, H; Akslen, L. A.; Fluge, O; Pergamenschikov, A; Williams, C; Zhu, S. X.; Lønning, P. E.; Børresen-Dale, A. L.; Brown, P. O.; Botstein, D (2000). "Molecular portraits of human breast tumours". Nature. 406 (6797): 747–52. Bibcode:2000Natur.406..747P. doi:10.1038/35021093. PMID   10963602. S2CID   1280204.
  7. ↑ Iyer, V. R. (1999). "The Transcriptional Program in the Response of Human Fibroblasts to Serum". Science. 283 (5398): 83–7. Bibcode:1999Sci...283...83I. doi:10.1126/science.283.5398.83. PMID   9872747.
  8. ↑ Ross, D. T.; Scherf, U; Eisen, M. B.; Perou, C. M.; Rees, C; Spellman, P; Iyer, V; Jeffrey, S. S.; Van De Rijn, M; Waltham, M; Pergamenschikov, A; Lee, J. C.; Lashkari, D; Shalon, D; Myers, T. G.; Weinstein, J. N.; Botstein, D; Brown, P. O. (2000). "Systematic variation in gene expression patterns in human cancer cell lines". Nature Genetics. 24 (3): 227–35. doi:10.1038/73432. PMID   10700174. S2CID   1135137.
  9. ↑ Cohen, Jon (2017-01-27). "Q&A: Michael Eisen bids to be first fly biologist in the U.S. Senate". Science | AAAS. Retrieved 2020-04-13.
  10. ↑ Okie, Susan. "NIH SCIENTIST A SUICIDE AMID PROBE OF PAPER". Washington Post. Retrieved 7 February 2017.
  11. 1 2 Mechanic, Michael. "Steal This Research Paper! (You Already Paid for It.)". Mother Jones. Retrieved 7 February 2017.
  12. 1 2 3 4 5 6 Krieger, Lisa (2017-02-04). "Bay Area molecular biologist Michael Eisen announces bid for U.S. Senate". San Jose Mercury News. Retrieved 7 February 2017.
  13. 1 2 3 "Michael Eisen: Baseball, mathematics and biology". India Bio Science. Archived from the original on 2021-12-21. Retrieved 7 February 2017.
  14. ↑ Eisen, Michael Bruce (1996). Structural Studies of Influenza A Virus Proteins (PhD thesis). Harvard University. OCLC   48938206.
  15. ↑ Eisen, MB; Spellman, PT; Brown, PO; Botstein, D (8 December 1998). "Cluster analysis and display of genome-wide expression patterns". Proc Natl Acad Sci U S A. 95 (25): 14863–8. Bibcode:1998PNAS...9514863E. doi: 10.1073/pnas.95.25.14863 . PMC   24541 . PMID   9843981.
  16. ↑ "James Fraser & Michael Eisen: Baseball Meets Biology". Education. iBiology. Retrieved 7 February 2017.
  17. 1 2 Eisen, M.; Spellman, P.; Brown, P.; Botstein, D. (1998). "Cluster analysis and display of genome-wide expression patterns". Proceedings of the National Academy of Sciences of the United States of America. 95 (25): 14863–14868. Bibcode:1998PNAS...9514863E. doi: 10.1073/pnas.95.25.14863 . PMC   24541 . PMID   9843981.
  18. 1 2 Alizadeh, A. A.; Eisen, M. B.; Davis, R. E.; Ma, C.; Lossos, I. S.; Rosenwald, A.; Boldrick, J. C.; Sabet, H.; Tran, T.; Yu, X.; Powell, J. I.; Yang, L.; Marti, G. E.; Moore, T.; Hudson Jr, J.; Lu, L.; Lewis, D. B.; Tibshirani, R.; Sherlock, G.; Chan, W. C.; Greiner, T. C.; Weisenburger, D. D.; Armitage, J. O.; Warnke, R.; Levy, R.; Wilson, W.; Grever, M. R.; Byrd, J. C.; Botstein, D.; Brown, P. O. (2000). "Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling". Nature. 403 (6769): 503–511. Bibcode:2000Natur.403..503A. doi:10.1038/35000501. PMID   10676951. S2CID   4382833.
  19. ↑ Clark, A. G.; et al. (2007). "Evolution of genes and genomes on the Drosophila phylogeny". Nature. 450 (7167): 203–18. Bibcode:2007Natur.450..203C. doi: 10.1038/nature06341 . PMID   17994087.
  20. ↑ Spellman, P. T.; Sherlock, G.; Zhang, M. Q.; Iyer, V. R.; Anders, K.; Eisen, M. B.; Brown, P. O.; Botstein, D.; Futcher, B. (1998). "Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization". Molecular Biology of the Cell. 9 (12): 3273–97. doi:10.1091/mbc.9.12.3273. PMC   25624 . PMID   9843569.
  21. 1 2 Harmon, Amy; Henry Fountain (2017-02-06). "In Age of Trump, Scientists Show Signs of a Political Pulse". The New York Times. Retrieved 7 February 2017.
  22. ↑ Reardon, Sara (2017). "Geneticist launches bid for US Senate". Nature. doi: 10.1038/nature.2017.21381 . S2CID   78431422 . Retrieved 7 February 2017.
  23. ↑ "Michael Eisen". Ballotpedia. Retrieved 2020-04-13.
  24. ↑ Brainard, Jeffrey (20 October 2022). "Journal seeks to upend scientific publishing by only reviewing—not accepting—manuscripts". Science News. Retrieved 24 October 2023.
  25. ↑ "Prominent journal editor fired for endorsing satirical article about Israel-Hamas conflict". Science. 2023-10-24. Retrieved 2023-10-24.
  26. ↑ "Firing of science journal editor after Gaza post sparks free speech rift". NBC News. 2023-10-26. Retrieved 2023-11-01.
  27. ↑ Eisen, Michael (8 October 2003). "Publish and be praised". Guardian. Retrieved 23 September 2013.
  28. ↑ Brown, P. O.; Eisen, M. B.; Varmus, H. E. (2003). "Why PLoS Became a Publisher". PLOS Biology. 1 (1): E36. doi: 10.1371/journal.pbio.0000036 . PMC   212706 . PMID   14551926.
  29. ↑ WIRED Staff. "The 2004 Wired Rave Awards". Wired. ISSN   1059-1028 . Retrieved 2023-08-11.
  30. ↑ Howard, Jennifer (29 January 2013). "Project Aims to Bring PLoS-Style Openness to the Humanities". The Chronicle of Higher Education. Retrieved 19 November 2013.
  31. ↑ Dobbs, David (6 January 2012). "Congress Considers Paywalling Science You Already Paid For". wired.com. Retrieved 12 February 2012.
  32. ↑ "Benjamin Franklin Award - Bioinformatics.org". www.bioinformatics.org. Retrieved 7 February 2017.
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