My CV

JONATHAN A. EISEN



Full Professor

Phone: 530-752-3498

University of California, Davis

Email: jaeisen@ucdavis.edu

Dept. of Evolution and Ecology

Lab: phylogenomics.me

Dept. of Medical Microbiology and Immunology

Blog: phylogenomics.blogspot.com

UC Davis Genome Center

Other links: linktr.ee/jonathaneisen

EDUCATION

1991-1998

Stanford University, Ph.D., Biological Sciences, 1998 

1986-1990

Harvard College, A.B., Biology, Cum Laude, 1990

PROFESSIONAL EMPLOYMENT

2006-

Full Professor, University of California, Davis. Genome Center, Dept. of Medical Microbiology & Immunology, Dept. of Evolution and Ecology

2006-2019

Adjunct Scientist, LBNL, Department of Energy-Joint Genome Institute

2018-2021

Director, UC Davis Microbiome Special Research Program

2000-2008

Adjunct Faculty, Johns Hopkins University, Department of Biology

2002-2006

Full Investigator, The Institute for Genomic Research (TIGR)

1998-2002

Assistant Investigator, The Institute for Genomic Research (TIGR)

1991-1998

PhD Student, Stanford University in the lab of Prof. Philip C. Hanawalt

1994-1998

Bioinformatics Consultant, Molecular Applications Group, Palo Alto, CA

1991

Summer Field Assistant, RMBL with Prof. Ward Watt

1989-1991

Research Assistant, Harvard University. Lab of Prof. Colleen A. Cavanaugh 

1988-1989

Research Assistant, Harvard University. Lab of Prof. Fakhri A. Bazzaz 

1988

Summer Field Assistant, RMBL with Prof. William A. Calder III

HONORS, AWARDS and RECOGNITION

2020

Elected Fellow - American Association for the Advancement of Science (AAAS)

2020

Time Magazine, 16 People and Groups Fighting for a More Equal America

2019

UC Davis Aggie Hero Award

2019

UC Davis ADVANCE Scholar Award

2017-2020

AAAS Council, elected representative of the Section on Biological Sciences

2014,2015

ASUCD (Associated Students, UC Davis) Teaching Award Finalist 

2012

Talk on “Meet your microbes” featured on TED.

2012

Elected Fellow, American Academy of Microbiology

2011

Benjamin Franklin Award for Open Access in the Life Sciences

2010-2014

Member, Institute of Medicine Forum on Microbial Threats

2010

Chair, Division R, American Society for Microbiology

2008

Blog post in "Open Laboratory 2008" collection of best science blog posts.

2004

Selected Member, Defense Science Studies Group (DSSG)

2002

Selected one of Esquire Magazine’s “Best and Brightest Innovators

1999

Martin Rodbell Fellowship, The Institute for Genomic Research

1997

Walter J. Gores Award for Excellence in Teaching, Stanford University

1993,1997

Stanford University Centennial Teaching Assistant Award

1991-1994

National Science Foundation Predoctoral Fellowship

OTHER PROFESSIONAL EXPERIENCE

Journals and Publishing

2013-

Advisory Board, bioRxiv (founding member)

2013-

Editorial Board, PeerJ (founding member)

2004-

Editorial Board, PLOS Computational Biology

2003-

Editorial Board, PLOS Biology (founding member)

2016-2022

Senior Editor, mSystems (founding member)

2015-2016

Advisory Board, RIO Journal

2014-2018

NIH Pubmed Central National Advisory Committee

2012-2014

Chair of the Advisory Board, PLOS Biology 

2012-2016

Board of Reviewers, PLOS Currents Tree of Life

2010-2012

Steering Committee, PLOS Hub in Biodiversity

2006-2007

Editorial Board, Biology Direct

2008-2012

Academic Editor in Chief, PLOS Biology

2004-2006

Editorial Board, Journal of Molecular Evolution

2003-2007

Editorial Board, Molecular Biology and Evolution

2002-2009

Member, Faculty of 1000

2001-2003

Editorial Board, Microbiology

1999-2007

Editorial Board, Genome Research

Advisory Boards and Committees

2021-

Advisory Board, HDTV Building Performance Series

2018-

Scientific Advisory Board, Zymo Corporation

2016-

Scientific Advisory Board, AnimalBiome

2016-

Member, UC Davis Strategic Communications Advisory Group

2013-

Member, Chancellor's Colloquium Speaker Selection Committee

2014-2023

Member, The Provost’s Forums on the Public University and the Social Good

2018-2021

DOE Joint Genome Institute Diversity and Inclusion Advisory Committee

2018-2020

Advisory Board, UC Davis "A pathway to inclusion for STEM researchers"

2018-2020

Advisory Board, IndoorChem Project

2016-2018

Editorial advisor for HHMI's/Tangled Bank production of "I contain Multitudes"

2016-2018

Planning Committee, National Microbiome Data Center

2015-2016

Sigma Xi Committee on Lectureships

2015-2017

Governance Board, Institute for Food & Agricultural Literacy

2015-2022

Scientific Advisory Board, Phylagen

2014-2020

Scientific Advisory Board, Symbiota and Indigo Agriculture

2015-2017

Advisory Board, Critical Assessment of Metagenomic Interpretation (CAMI)

2012-2014

Scientific Advisory Board, ICBG Indonesia Biodiversity Project

2011-2015

Scientific Advisory Board, The Earth Microbiome Project

2010-2012

Member, Communications Committee, American Society for Microbiology

2009-2016

Advisory Committee, JGI Microbial Genome & Metagenome Programs

2008-2009

Committee on Life Sciences, National Academy of Sciences

2007-2012

Science & Technology Advisory Board on Biosecurity, LLNL

2004-2009

Scientific Advisory Board, National Evolutionary Synthesis Center

2003-2008

Scientific Advisory Board, Saccharomyces Genome Database

2001-2003

Advisory Board, Carver Center for Comparative Genomics, University of Iowa

2000-2003

Scientific Advisory Board, Geneformatics

Research Cruises

2002

Atlantis/Alvin Research Cruise. Galápagos Rift Hydrothermal Vents Expedition 6: May 24-June 4, 2002. See Cruise Web Site.

1992

Atlantis/Alvin Research Cruise. Cruise 125, Leg43, Dives 2541, 2542.

TEACHING AND CURRICULAR DEVELOPMENT

2008-current

Co-Instructor, BIS2C: Biodiversity and the Tree of Life, UC Davis.

2008-current

Instructor, EVE161: Microbial Phylogenomics, UC Davis.

2006-current

Membership in UC Davis Graduate Groups in Population Biology, Ecology, Microbiology, Computer Science, Integrative Genetics & Genomics, Biophysics.

2020-2021

Designer and Instructor, “Covid Mass Testing” Course at UC Davis.

2000-2022

Guest lectures on “Genomics” or “Phylogenomics” in a diversity of courses at UC Davis, UMD, and JHU.

2019

Instructor: PBG 298 / ECL 290: Marine Microbial Ecology Discussion Group 

2015-2018

UC Davis Quantitative Biology (qBio) Curriculum Committee.

2007-2014

Guest Lecturer, Workshop in Applied Phylogenetics, Bodega Marine Lab.

2010-2016

Advisor, UC Davis Collaborative Learning at the Interface of Mathematics and Biology (CLIMB) program.

2003

Visiting Fellow, Comparative Genomics IGERT, University of Arizona.

2002-2004

Lecturer and Co-Designer, Genome Sequencing & Analysis Course, MBL.

1999-2003

Guest Lecturer, Short Course on Molecular Evolution, MBL.

1999-2001

Guest Lecturer, Cold Spring Harbor Laboratory Genomics Course

1999-2003

Guest Lecturer, Jackson Lab Genome Sequence Analysis Course.

1996-1998

Head Teaching Assistant and Co-Course Designer, Stanford University “SME Core: The Heart” with Profs. David Botstein, Rick Myers, David Cox, et al.

1995-1998

Stanford Science Design Committee. Responsible for redesigning the Science, Math and Engineering requirements for non-science majors at Stanford.

1991-1998

TA at Stanford for Evolution & Ecology (Carol Boggs), Genetics & Molecular Biology (Robert Simoni), and DNA Replication (Philip C. Hanawalt).

1988-1990

Biology Undergraduate Group Committee, Harvard College.

1989

Prepared invited proposal for the creation of Environmental Science and Public Policy Major at Harvard.

1989-1990

TA, Organismal & Evolutionary Biology, Harvard (taught by Karel Liem).

TRAINEES

  • Post Docs Supervised or Co-Supervised: 18 as of 2023

  • PhD’s Supervised and Awarded: 12 as of 2023

  • Masters Supervised and Awarded: 3 as of 2023

  • Undergraduate researchers: 92 as of 2023

PUBLICATIONS

60 Highlighted Journal Publications. People in the Eisen lab when work was done are in bold.

  • 2022. Wilbanks EG, Doré H, Ashby MH, Heiner C, Roberts RJ, Eisen JA. Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. ISME J. 16:1921-1931.

  • Rojas CA, Holekamp KE, Viladomat MJ, Souza V, Eisen JA, Theis KR. 2022. Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study. mSystems 19: e0096522.

  • 2021. Osvatic JT, Wilkins LGE, Leibrecht L, Leray M, Zauner S, Polzin J, Camacho Y, Gros O, van Gils JA, Eisen JA, Petersen JM, Yuen B. Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. PNAS USA 118: e2104378118.

  • 2021. Leray M, Wilkins LGE, Apprill A, Bik HM, Clever F, Connolly SR, De León ME, Duffy JE, many others, Eisen JA. Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution. PLOS Biology 19: e3001322.

  • 2021. Ettinger CL, Vann LE, Eisen JA. Global diversity and biogeography of the Zostera marina mycobiome. Appl. & Env. Microbiol. 87 (12): e02795-20. 

  • 2020. Dietz L, Horve PF, Coil DA, Fretz M, Eisen JA, Van Den Wymelenberg K. 2019 novel coronavirus (COVID-19) pandemic: built environment considerations to reduce transmission. mSystems 5: e00245-20.

  • 2019. Wilkins LGE, Leray M, Yuen B, Peixoto R, Pereira TJ, Bik HM, Coil DA, Duffy JE, many others, Wilbanks EG, Eisen JA. Host-associated microbiomes and their roles in marine ecosystem functions. PLOS Biology 17(11): e3000533.

  • 2019. Rosado PM, Leite DCA, Duarte GAS, Chaloub RM, Jospin G, Nunes da Rocha U, P Saraiva J, Dini-Andreote F, Eisen JA, Bourne DG, Peixoto RS. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J. 13: 921-936.

  • 2019. Yamaguchi MS, Ganz HH, Cho AW, Zaw TH, Jospin G, McCartney MM, Davis CE, Eisen JA, Coil DA. Bacteria isolated from Bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds potentially associated with animal signaling. PLOS One 14: e0216846.

  • 2018. Van Deynze A, Zamora P, Delaux PM, Heitmann C, many others, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology 16: e2006352.

  • 2017. Fahimipour AK, Kardish MR, Lang JM, Green JL, Eisen JA, Stachowicz JJ. Global-scale structure of the eelgrass microbiome. AEM 83: e03391-16.

  • 2017. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. A microbial survey of the International Space Station (ISS). PeerJ 5: e4029.

  • 2015. Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLOS Computational Biology 11(11): e1004573.

  • 2015. Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. Swabs to genomes: a comprehensive workflow. PeerJ 3: e960.

  • 2015. Edwards J, Johnson C, Santos-Medellin C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V. Structure, variation, and assembly of the root associated microbiomes of rice. PNAS USA 12: E911-20

  • Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. 2014. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2: e415.

  • 2014. Lang JM, Eisen JA, Zivcovik A. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of model meals. Peer J 2: e659.

  • 2014. Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2: e243.

  • 2013. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.

  • 2013. Wu D, Jospin G, Eisen JA. Systematic identification of gene families for use as “Markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLOS ONE 8: e77033.

  • 2013. Lang JM, Darling AE, Eisen JA. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLOS ONE 8: e62510.

  • 2012. Traag B, Pugliese A, Eisen JA, Losick R. Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis. J. Bacteriology 195: 253-260.

  • 2012. Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLOS Comp. Biol. 8: e1002743. 

  • 2012. Wu M, Chatterji S, Eisen JA. Accounting for alignment uncertainty in phylogenomics. PLOS ONE 7: e30288.

  • 2011. Darling A, Tritt A, Eisen JA, Facciotti M. Mauve assembly metrics. Bioinformatics 27: 2756-2757. 

  • 2011. Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system. PLOS Genetics 7: e1002272.

  • 2011. Kembel S, Eisen JA, Pollard KS, Green JL. The phylogenetic diversity of metagenomes. PLOS ONE 6: e23214.

  • 2011. Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. Drivers of bacterial β-diversity depend on spatial scale. PNAS USA 108: 7850-7854.

  • 2010. Morgan JL, Darling A, Eisen JA. Metagenomic sequencing of an in vitro-simulated microbial community. PLOS ONE 5: e10209.

  • 2009. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, many others, Klenk HP, Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.

  • 2009. Eisen JA, MacCallum CJ. Genomics of emerging infectious disease: A PLoS collection. PLOS Biology 7: e1000224.

  • 2009. Hartman A, Lough D, Fiehn O, Barupal D, Fishbein T, Zasloff M, Eisen JA. Human gut microbiome adopts an alternative state following small bowel transplantation. PNAS USA 106: 17187-17192.

  • 2008. Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9: R151.

  • 2008. Chatterji S, Yamazaki I, Bai Z, Eisen JA. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. RECOMB 2008.

  • 2007. Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998-1000.

  • 2007. Eisen JA. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLOS Biology 5: e82.

  • 2007. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, et al. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLOS Biology 5: e16. 

  • 2006. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLOS Biology 4: e286.

  • 2006. Wu D, Daugherty SC, van Aken S, Pai G, Watkins K, Khouri H, Tallon L, Zaborsky J, Dunbar H, Tran P, Moran NA, Eisen JA. Metabolic complementarity and genomics of the dual symbiosis of sharpshooters. PLOS Biology 4: e188.

  • 2005. Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLOS Genetics 1: e65. 

  • 2004. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, et al. Environmental whole genome shotgun sequencing: the Sargasso Sea. Science 304: 66-74.

  • 2004. Wu M, Sun L, Vamathevan J, Riegler M, Deboy R, Brownlie J, McGraw E, many others, O’Neill S, Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome massively infected with mobile genetic elements. PLOS Biology 2: 327-341.

  • 2003. Eisen JA, Fraser CM. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707.

  • 2003. Shank T, Fornari D, Yoerger S, Humphries S, Bradley A, Hammond S, Lupton J, Schierer D, Collier R, Reysenbach A-L, Ding K, Seyfried W, Butterfield D, Olson E, Lilley M, Ward N, Eisen JA. Deep submergence synergy: Alvin and ABE explore the Galápagos Rift at 86°W. EOS 84: 425, 432-433.

  • 2002. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, et al.  Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511. 

  • 2002. Eisen JA, Wu M. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theoretical & Population Biology 61: 481-487.

  • 2002. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM, DeLong EF. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633.

  • 2002. Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, et al.. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. PNAS USA 99: 9509-9514.

  • 2001. Salzberg SL, White O, Peterson J, Eisen JA. Microbial genes in the human genome: lateral transfer or gene loss?  Science 292: 1903-1906.

  • 2000. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.

  • 2000. Eisen JA, Heidelberg JF, White O, Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1: research 0011.1-0011.9.

  • 2000. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, et al. The genome sequence of Vibrio cholerae, the etiologic agent of cholera. Nature 406: 477-483.

  • 2000. Eisen JA. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Current Opinion in Genetics & Dvlp. 10: 606-611.

  • 1999. Eisen JA, Hanawalt PC. A phylogenomic study of DNA repair genes, proteins, and processes.  Mutation Research 435: 171-213.

  • 1999. White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, et al. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286: 1571-1577.

  • 1998. Eisen JA. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.  Genome Research 8: 163-167.

  • 1998. Eisen JA. A phylogenomic study of the MutS family of proteins. Nucl. Acids Res. 26: 4291-4300.

  • 1995. Eisen JA. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41: 1105-1123.

  • 1995. Eisen JA, Sweder KS, Hanawalt PC. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Research 23: 2715-2723.

  • 1992. Eisen JA, Smith SW, Cavanaugh CM. 1992. Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum Say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. J. Bacteriology 174: 3416-3421.

Selected Other Publications

  • 2021. Eisen JA. Legionella is scary disease that grows in contaminated water. Sacramento Bee. 

  • 2009. A New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. (2009). National Research Council (US) Committee on a New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution. Washington (DC): National Academies Press (US). (Report from NAS Committee to which I contributed).

  • 2007. Barton NH, Briggs DEG, Eisen JA, Goldstein DB, Patel NH. Evolution (Textbook). Cold Spring Harbor Press.

  • 2007. Schlom DG, Gall KA, Eisen JA, Joseph AD, Murphy CJ. 2007. Passive and semi-passive nanomaterial-based sensors for multi-year remote detection. Defense Science Study Group 2004-2005 Papers.

  • 2007. Brodley C, Eisen JA. 2007. Tampering with DNA: National Security Needs for Detection and Design. Defense Science Study Group 2004-2005 Papers.

  • 2007. Eisen JA. 2007. Toward a global field guide for microorganisms. Defense Science Study Group 2004-2005 Papers.

Scholarly Communications through Blogging, Microblogging and Social Media and similar sites

  • Tree of Life Blog. I have a personal blog called “The Tree of Life” where I have been blogging since 2005. In total I have more than 2000 posts there and over the years my posts have been quite widely read and reasonably impactful. I have received some awards for my writing there (e.g., one of my posts was included in a compendium of the best science writing online) and have 1000s of subscribers and followers. I have a few series in particular there that have had a lot of impact. For example I have a running thread on “Overselling the Microbiome” on my blog on this general topic area and I have made a major impact on the communications relating to microbiome science via these posts. My writings on this are regularly referenced in social media, traditional media, and even in scientific publications. Also I have a series on Diversity in STEM focusing  on issues such as gender diversity at conferences, sexual harassment, and other topics relating to diversity in academia. My writings on this topic are also regularly referenced in social media, traditional media, and occasionally in scientific publications. Although my frequency of posting has dropped over the last few years with the rise of microblogging platforms like Twitter, I am returning to posting more there. Overall, this blog has had over 10,000,000 views, has been referenced in dozens of news stories and scientific publications, and has been linked to thousands of times on various social media platforms. 

  • The microbiology of the Built Environment network blog and web resource. For ~10 years (2010-2020), my lab ran the microBEnet project, funded by the Sloan Foundation. One product from this project was the creation of the microBEnet web site and associated resources including blog posts, resources about the field, and more. In total I authored dozens of web pages and more than 850 blog posts. Many of these were simple information sharing of links or stories but a significant number were more detailed discussions of the field. Many of these have been referenced externally including in scholarly publications. See http://microbe.net. Some of these posts were crossposted to The Winnower” in order to get DOIs. See for example, What does the term microbiome mean? And where did it come from? A bit of a surprise and 11+ things everyone needs to know about microbes and Methylisothiazolinone in household items - a growing (or well, killing) problem #germophobia 

  • Social Media sites. I have used social media (e.g., Twitter, LinkedIn, Facebook and now Mastodon and Threads) extensively as a means of communicating about science, diversity, academia and related topics. I make significant efforts to use this platform to promote both the general discussion of science, some of the fields I work in, and also activities at UC Davis and nearby. My posts are frequently quoted in the press and in related sites.

  • iNaturalist. I have been using iNaturalist as a means of sharing and cataloging nature observations and also as a means of engaging a broad community in thinking about and observing biodiversity. I have given multiple talks about iNaturalist, shared observations through various social media platforms and in my teaching, participated in and promoted multiple “BioBlitzes”, and overall believe I have made a significant impact in engaging the public about biodiversity in my area and more broadly. In addition, because I post all my photographs with an open CC license, many have been used in scientific publications, web sites, news stories, and in field guides. I believe that systems like iNaturalist are excellent tools for engaging students and the public in science and plan to make more use of these tools in teaching and outreach in the future. See https://www.inaturalist.org/people/phylogenomics

  • Slideshare. I have posted slides from >100 presentations to Slideshare and these have been viewed, referenced, and used extensively. Some of these have had audio included. See http://www.slideshare.net/phylogenomics

  • Figshare. In addition to using Figshare to post data and code from papers I have used Figshare to share other information about papers and scientific work. See https://figshare.com/authors/jonathan-eisen/97599

  • Youtube channel. I have posted videos of many scientific presentations and related activities to Youtube. See for example My Talks.


SELECTED TALKS AND PRESENTATIONS

  • Mar. 2022. #STEMDiversity. Don’t Just Wait For Others. Do Something. NUHS Women in Science & Healthcare (WISH) International Women’s Day Conference. Via web. Youtube.

  • Feb. 2022. Knowledge is Power: COVID and Vaccines discussion for youth!. Invited Talk for First Place for Youth Forum. Via web.

  • Feb. 2022. A field guide to Sars COV2. Yolo County Community of Practice. Via web.

  • Dec. 2021. Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically under-appreciated). Keynote talk. Microbial Virtual International Forum. Via web. Youtube. Slideshare. Panel.

  • Jul. 2021. Phylogenomic Case Studies: The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies.Keynote talk. Bioinformatics - From Algorithms to Applications (BIATA) 2021. Via web. Slideshare. Youtube.

  • Apr. 2021. A renewed need for a genomic field guide to microbes. Keynote talk. Bay Area Ecology and Evolution of Infectious Diseases (BAEEID). Youtube. Slideshare.

  • Oct. 2020. The Microbiome: from decoding nature to biotech breakthroughs. Invited talk. Synbio Beta. Panel plus live discussion. Agenda. More.

  • Dec. 2019. Searching for a Unicorn in Host-Microbiome Systems. Invited talk. Marine Microbiomes Symposium. Panama City, Panama. Slideshare.

  • Nov. 2019. Marine Host Microbiome Interactions: Challenges and Opportunities. Invited talk, Scripps Institute for Oceanography Seminar Series. Slideshare. Youtube.

  • Nov. 2019. Four Eras of DNA Sequencing Microbes and Microbiomes. Invited talk via web to University of the Philippines.

  • Oct. 2019. ######## #STEMDiversity #YAMMM #Manels #ClosedAccess. The power and peril of social media in improving the culture and practice of science. UC Davis Advance Award Annual Meeting. Slideshare.

  • Sep. 2019. A field guide to the microbes. Invited talk. 10th Anniversary Waterkeeper Symposium. Sandpoint, Idaho.

  • Jun. 2019. Co-Chaired Session on “Community microbiology: moving beyond crowdsourcing to active, participatory science by the public. ASM Microbe 2019, San Francisco, CA. Report.

  • Apr. 2019. The Twisted Tree of Life Awards. Invited Talk for NELLI (Symposium on New Lineages of Life). San Francisco, CA. Slideshare. Youtube.

  • Feb. 2019. Panel on “Breaking the Glass Ceiling: How do we solve the gender imbalance in STEM? CIMM - Center for Microbiome Innovation Meeting, San Diego, CA.

  • Oct. 2018. A field guide to the microbes. Invited talk. Synbio Beta. San Francisco, CA.

  • Jun. 2018. A field guide to the microbes. SciFoo Camp, Google X, Mountain View, CA.

  • Jun. 2018. The microbes among us: the human microbiome. Keynote talk for Annual Meeting of APIC - the Association for Professionals in Infection Control and Epidemiology. Minneapolis, MN. .

  • Oct. 2017. microBEnet: Perspectives on trying to nurture a growing MoBE field. Invited talk. Natl. Academy of Sciences “Microbiomes of the Built Environment.” Washington, DC. Slides. Youtube.

  • Aug. 2017. Microbial Forensics. SciFoo meeting, Mountain View, CA..

  • May. 2017. Evolution of DNA Repair. Invited talk. DNA Repair Meeting, Asilomar, CA.

  • May. 2017. microBEnet - the microbiology of the built environment network. Invited Talk. BioBE Center, U. Oregon. Eugene, OR.

  • Jan. 2017. Evolution and functional prediction. Invited talk. Pacific Symposium in Biocomputing 17. Waimea, HI. Slideshare.

  • Sep. 2016. Session leader on “Role of male advocates & allies” and panelist on “Overcoming Implicit Bias to Foster Better Research and Healthcare. “Gender Bias Under the Microscope” 1st Annual Meeting at Rosalind Franklin University. Chicago, IL. Wakelet.

  • Jun. 2016. Spotlight Health session on “The Microbiome”. Invited talk. Aspen Institute. Aspen, CO. Meeting site. Recording.

  • Apr. 2016. Phylogenomic Approaches to the Study of Microbes and Microbiomes. Invited talk. Bayer Crop Sciences. West Sacramento, CA.

  • Dec. 2015. Searching for Novel Forms of Life. Invited talk. Search for New Life Workshop. Pacifica, CA.

  • Oct. 2015. Do Something. Invited talk and panelist. “Digital Science Spotlight – Bridging the Gender Gap #WiSTEMspotlight.” Via Web. Digital Science. Slideshare.

  • Sep. 2015. Approaches to the Study of Microbes and Microbiomes. Invited talk. Stanford University, Stanford, CA.

  • Sep. 2015. Phylogeny driven approaches to the study of microbial diversity. Keynote talk. Queenstown Computational Genomics Conference (via Skype). Slideshare.

  • Jun. 2015. Diversity Diversity Diversity Diversity Diversity Diversity. Invited talk. Society for the Study of Evolution Annual Meeting. Snowbird, UT. Slideshare.

  • Apr. 2015. The Rise of the Microbiome: Challenges and Opportunities. Invited talk. Association of Health Care Journalists Annual Meeting. Santa Clara, CA. News.

  • Apr. 2015. Genetically Engineered Crops and the Microbiome. Invited talk. National Academy of Sciences Committee on “A Science Based Look at Genetically Engineered Crops.” Via Web. Vimeo. More Details.

  • Mar. 2015. The Era of the Microbiome. South by Southwest discussion w/ Carl Zimmer. Austin, TX.

  • Mar. 2015. Evolution of DNA Sequencing. Invited talk. Workshop in Applied Phylogenetics at the Bodega Bay Marine Lab. Bodega Bay, CA. Slideshare. Youtube.

  • Mar. 2015. Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology. Invited talk. Future of Genomic Medicine. San Diego, CA. Slideshare. Youtube.

  • Feb. 2015. Phylogeny-driven approaches to studies of microbial and microbiome diversity. Invited talk. UCSB EEMB Graduate Student Symposium. Santa Barbara, CA. Slideshare. Youtube.

  • Jul. 2014. All microbes all the time. Invited talk. Defense Science Research Council. Chantilly, VA.

  • Jun. 2014. The Quest for a Field Guide to the Microbes. Invited talk. Gordon and Betty Moore Foundation. Palo Alto, CA.

  • May. 2014. microBEnet: microbiology of the Built Environment network. Invited talk. Sequencing the City Meeting. San Jose, CA. Youtube.

  • Apr. 2014. The Bleeting Edge: Blog & Tweet or Perish. Invited talk. Publication Mismatches Workshop. UC Davis. Youtube. Slideshare.

  • Mar. 2014. microBEnet: the microbiology of the Built Environment network. Invited talk. AAAS Microbiology of the Built Environment meeting. Washington, DC. Slideshare. Storify. Video.

  • Jan. 2014. The quest for a field guide to the microbes. Invited talk. “Science in the River City” teacher’s education series. Sacramento, CA. Slideshare. Audio Slideshow.

  • Nov. 2013. Phylogeny-driven approaches to genomics and metagenomics. Invited talk. IHU Méditerranée Infection. Marseilles, France. Video.

  • Oct. 2013. Facilitating the Spread of Scientific Knowledge via Open Science. Invited talk. Infectious Disease Week Meeting. San Francisco, CA.

  • Aug. 2013. Bayesian Taxonomic Assignment for the Next-Generation Metagenomics. Invited talk. Department of Homeland Security Workshop on Microbial Forensics.

  • Jul. 2013. Phylogenetic and Phylogenomic Approaches to Studying the Dark Matter of Biology. Invited talk. UC Berkeley Evolution Institute. Berkeley, CA.

  • May. 2013. microBEnet – the microbiology of the Built Environment network. Invited talk. Annual Meeting of the Sloan Foundation Program in Microbiology of the Built Environment. Boulder, CO. Audio Slideshow. Slideshare.

  • May. 2013. Phylogeny-Driven Approaches to Genomics and Metagenomics. Invited talk. Fresno State University. Fresno, CA.

  • Mar. 2013. Microbiomes and DNA based Studies of Microbial Diversity. Invited talk. Singularity University. Palo Alto, CA. Slideshare.

  • Mar. 2013. The Human Microbiome 101. Invited talk. Future of Genomic Medicine 13. San Diego, CA. Slideshare.

  • Sep. 2012. Phylogenomic approaches to the study of microbial diversity. Keynote Talk at Lake Arrowhead Microbial Genomes Meeting, Lake Arrowhead, CA. Slideshare. Audio Slideshow.

  • Sep. 2012. Phylogenomic approaches to the study of microbial diversity. Invited talk. Bay Area Illumina Users Meeting. Slideshare. Audio Slideshow.

  • Jul. 2012. Phylogenomic approaches to functional prediction. Invited talk. AFP “Automated functional prediction” submeeting during ISMB 2012, Long Beach, CA. Slideshow. Slideshare.

  • Jul. 2012. Networks in genomics & bioinformatics: from phylogeny to Twitter. Invited talk. International Society for Computational Biology 2012 (ISCB2012) submeeting at ISMB2012, Long Beach, CA. Slideshow. Slideshare.

  • Jul. 2012. Science Wants to Be Open, If Only We Could Get Out of the Way. Invited talk. Bioinformatics Open Source Conference 2012 (BOSC2012) submeeting during Intelligent Systems for Molecular Biology 2012 (ISMB2012). Slideshow. Slideshare.

  • Jun. 2012. Phylogeny driven approaches to genomics & metagenomics. Invited talk. Canadian Society for Microbiology Meeting. Vancouver, Canada. Slideshow. Slideshare.

  • Jun. 2012. The microbiology of the built environment network. Invited talk. American Society for Microbiology 2012 Annual Meeting. Youtube.

  • Jun. 2012. The microbiology of the built environment network. Invited talk. Microbiology of the Built Environment, Sloan Foundation program meeting. Boulder, CO. Audio Slideshow.

  • Apr. 2012. DNA sequencing and the hidden world of microbes. Invited talk. Institute for Systems Biology. Symposium on Systems Biology & the Microbiome. Seattle, WA. Vimeo. Audio Slideshow.

  • Apr. 2012. Meet Your Microbes. Invited talk. TEDMED 2012 at the Kennedy Center, Washington DC. TED. Tedmed. Interview.

  • Mar. 2012. Phylogenetic approaches to analysis of genomes and metagenomes. Invited talk. National Academy of SciencesInstitute of Medicine Meeting on Social Biology of Microbes. Washington, DC. Slideshow. Slideshare.

  • Feb. 2012. Open Science and Scientific Data. Invited talk. “Hacking Life” meeting. TTI Vanguard. San Jose, CA.

  • Feb. 2012. Towards a Field Guide to the Microbes. Invited talk. AAAS 2012 Meeting, Vancouver, Canada. Slideshow. Slideshare.

RESEARCH SUPPORT

MEETINGS, WORKSHOPS and SESSIONS ORGANIZED

  • Sep 2022. Lake Arrowhead Microbial Genomics Meeting. Lake Arrowhead, CA. Co-organizer. PLOS Biology paper.

  • Dec 2019. Marine Microbiome Workshop. Bocas del Toro, Panama. Co-organizer.

  • Jun 2019. ASM Microbe Community microbiology: moving beyond crowdsourcing to active, participatory science by the public. San Francisco, CA. Session organizer and co-chair. Twitter thread.

  • Apr 2019. New Lineages of Life. San Francisco, CA. Co-organizer.

  • Dec 2018. BASF-UC Davis Microbiome Workshop. Davis, CA. Organizer.

  • Dec 2018. Marine Microbiome Workshop. Bocas del Toro, Panama. Co-organizer. PLOS Biology meeting synthesis.

  • Sep 2018. Lake Arrowhead Microbial Genomics 2018. Lake Arrowhead, CA. Co-organizer. Blog post.

  • Oct 2017. UC Davis Genome Center microBOOme Symposium. Davis, CA. Organizer. Notes.

  • May 2017. An Open Digital Global South. Davis, CA. Co-organizer.

  • Nov 2016. Keystone Symposium: Phytobiomes and the Future of Food, Health, Energy, and the Environment. Santa Fe, NM. Co-organizer. Web Site.

  • Sep 2016. Marine Algal and Plant Microbiomes Workshop. Asilomar, CA. Organizer.

  • Sep 2016. Lake Arrowhead Microbial Genomics 2016. Lake Arrowhead, CA. Co-organizer. Meeting reports here, here, here and here. MoBE Session.

  • Feb 2016. Gaming Metrics: Innovation and Surveillance in Academic Misconduct. Davis, CA. Co-organizer. .

  • Oct 2015. University and Industry Consortium, Annual Meeting. Two sessions on microbiomes. Davis, CA. Organized session.

  • May 2015. American Institute of Architects (AIA) Annual Meeting sessions on “Microbiology of the Built Environment.”. Atlanta, GA. Co-organized sessions.

  • Apr 2015. Association of Health Care Journalists, Annual Meeting Session on “The Microbiome.”. Santa Clara, CA. Assisted in organizing session. Program. Report.

  • Mar 2015. South by Southwest session on “The Era of the Microbiome.”. Austin, TX. Assisted in planning and promotion of a session. Summary.

  • Jan 2015. Pacific Symposium on Biocomputing. Session on “Inviting the Public.”. Hawaii. Assisted in organizing session.

  • Oct, 2014. Animals in the Built Environment Workshop. Davis, CA. Co-organizer. Report.

  • Sep 2014. 20th Annual International Meeting on Microbial Genomics. Lake Arrowhead, CA. Co-organizer.

  • Jun 2014. SBSE “Society of Building Science Educators” Session on “Microbiology and Design.”. Biosphere 2. Co-organized session. Info.

  • Mar 2014. AAAS Symposium on Microbiomes of the Built Environment. Washington, DC. Assisted with planning and promotion of the meeting. Web. Pre-Meet Notes.

  • Feb 2014. Publish or Perish – the Future of Scholarly Publishing and Careers. Davis, CA. Co-organizer. Storify Day2. Storify Day 1.

  • Jul 2013. Society for Molecular Biology and Evolution (SMBE) Annual Meeting. Session on “Diversity and Evolution of Microbes and their Genomes.”. Chicago, IL. Organized. Wakelet.

  • May 2013. American Society for Microbiology Annual Meeting. Session on Citizen Microbiology. Denver, CO. Co-organized Session. Storify of Tweets. Wakelet. Nature.

  • Sep 2012. 19th Annual International Meeting on Microbial Genomics. Lake Arrowhead, CA. Co-organizer. Talks.

  • Jun  2012. The Science and Applications of Microbial Genomics. National Academy of Sciences Keck Center. Co-organizer.

  • Jun 2012. American Society for Microbiology (ASM) Annual Meeting. Session on indoor microbial ecology. San Francisco, CA. Co-organized session. Bhatnagar Summary. Wilbanks Summary. Eisen Notes. Storify.

  • Feb 2012. AAAS 2012.  Session on the Earth Microbiome Project. Vancouver, BC. Co-organized session. Meeting Report.

  • Jan 2012. Citizen Microbiology Workshop. Davis, CA. Co-organized. Report.

  • Jun 2011. Indoor Air Meeting. Sessions on “Microbiology of the Built Environment.”. Austin, TX. Co-organized sessions. Slides.

  • Dec 2005. The Tapestry of Life: Lateral transfers of heritable elements. Beckman Center of the National Academies, Irvine, CA. Co-organizer. Web site.

  • Dec 2001. Protist Genomics Workshop. Rockville, MD. Co-organizer.

SELECTED MEDIA AND PRESS COVERAGE

CONTRIBUTIONS TO DIVERSITY

I have played an active role in many areas related to academia generally and STEM fields in particular.  Some examples of this work and recognition of it are below.


Advisory Boards and other Service related to STEM Diversity.

  • 2019. Search Committee for CBS “Contributions to Diversity” based faculty search.

  • 2018-2022. Advisory Board, UC Davis NSF IGE "A pathway to inclusion for STEM researchers."

  • 2018-2022. DOE JGI Diversity and Inclusion Advisory Committee.

  • 2016-2017. COACHE Survey Advisory Committee.

  • 2013-2014. Member, UC Davis Advance Project, Policies & Practices Committee.


Invited speaker and panelist on the topic of STEM Diversity.

  • 2019 - Feb. Panel member for International Microbiome Meeting on “Breaking the Glass Ceiling: How do we solve the gender imbalance in STEM?

  • 2016 - Sep. Session leader and panelist for “Gender Bias Under the Microscope” 1st Annual Meeting at Rosalind Franklin University

  • 2016 - Jan. Speaker. Women in Science Summit at California Academy of Sciences

  • 2015 - Oct. Speaker and panelist for “Bridging the Gender Gap #WiSTEMspotlight”

  • 2015 - Jun. “Diversity Diversity Diversity Diversity Diversity Diversity” talk for Society for the Study of Evolution Annual Meeting

  • 2014 - Oct. Opening Up to Diversity. UC Davis Pre-Health Student Alliance Meeting


Extensive writing and commentary to press on the topic of STEM Diversity. See for example The Tree of Life: STEM Diversity. Example press coverage below:



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