JONATHAN A. EISEN
EDUCATION
PROFESSIONAL EMPLOYMENT
HONORS, AWARDS and RECOGNITION
OTHER PROFESSIONAL EXPERIENCE
Journals and Publishing
Advisory Boards and Committees
Research Cruises
TEACHING AND CURRICULAR DEVELOPMENT
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
Google Scholar Page here.
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
2020-10 to 2024-09. Collaborative Research MTM 1: Microbial Genomic, Transcriptomic, and Survival Response to Common Built Environment Lighting. NSF #2025661. $173,893. Kevin Van Den Wymelenberg (PI), Eisen (CoPI)
2020-05 to 2024-10. Develop And Share Methods For Manipulating The Microbiome Of Zostera marina. Gordon and Betty Moore Foundation. $300,000. Eisen (PI))
2020-05 to 2021-03. Citris: Validating the Use of Propidium Monoazide (PMA) Qrt-Pcr to Detect Viability of Sars-Cov-2 without the Need For Bsl3 Tissue Culture. UC Regents. $25,000. Eisen (PI)
2020-04 to 2021-01. Developing Environmental Monitoring of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the Built Environment at UC Davis. UC Regents. $25,000. Eisen (PI)
2019-12 to 2020-12. Spacecraft Associated Genome Analysis (SAGAn) Workshop. NASA-JPL. $23,660. Elinne Becket (PI), Eisen (CoPI)
2018-10 to 2023-09. Genome Encyclopedia of Spacecraft Associated Microbes (GESAM). NASA. $75,000. Vaishampayan (PI), Eisen (CoPI)
2018-05 to 2020-04. Evolution of Oxygenic Photosynthesis as Preserved in Melainabacterial Genomes from Lake Vanda, Antarctica. NSF #1745341. $323,861. Dawn Sumner (PI), Eisen (CoPI)
2018-01 to 2020-01. Utilizing Microbiome and Bioinformatic Tools to Reduce Energy Use and Food Waste in Poultry. Innovation Institute for Food and Health. $41,000. Jessica Metcalf (PI), Eisen (CoPI)
2017-07 to 2020-06. Developing Information Infrastructure for Managing Antibiotics and Endocrine Disrupting Substances In Pampanga River Basin and its Coastal Environs: Maps, Transport Models and Bioindicators of Ecological and Public Health Risks. Philippine-California Advanced Research Institutes. $240,396. Eisen (PI)
2017-03 to 2020-04. Evolution of Microbiomes in Shallow Marine Water Organisms Split by the Isthmus of Panama in the Western Atlantic vs. Eastern Pacific Oceans. Gordon and Betty Moore Foundation. $528,500. Will Wcislo (PI), Eisen (CoPI)
2015-09 to 2018-08. NRT-IGE: Data Science for the Built Environment. NSF #1545193. $499,466. Deb Niemeier (PI), Eisen (CoPI)
2015-07 to 2017-12. Microbenet: A Network For Microbiology of the Built Environment. Alfred P. Sloan Foundation. $995,000. Eisen (PI)
2015-04 to 2015-12. Integration of PressForward Plugin into the MircoBEnet Website. Alfred P. Sloan Foundation. $15,217. Eisen (PI)
2014-10 to 2018-09. Collaborative research: Untangling the Deep Genealogy of Microbial Dark Matter. NSF #1441717. $400,000. Ramunas Stepanauskas (PI), Eisen (CoPI)
2014-09 to 2017-08. Genomics of Host-Microbiome Interactions in Rice. NSF #1444974. $1,304,644. Sundaresan (PI), Eisen (CoPI)
2014-01 to 2017-06. Evolution, Ecology, and Function of Microbial Communities Associated with Seagrass. Gordon and Betty Moore Foundation. $770,000. Eisen (PI)
2013-09 to 2019-08. Collaborative Research: RCN EukHiTS: Eukaryotic Biodiversity Research using High-Throughput Sequencing. NSF #1262480. $262,480. Eisen (PI) transferred from Holly Bik
2013-07 to 2018-06. Assessing Benthic Meiofaunal Community Structure in the Alaskan Arctic: A high-Throughput DNA Sequencing Approach. North Pacific Research Board. $8,854. Eisen (PI)
2013-07 to 2016-06. Innovating the Communication of Scholarship. IFHA Program at UC Davis. $750,000. Mario Biagioli (PI), Eisen (CoPI)
2013-06 to 2015-07. Identification of Genomic Determinants of Virulence by Whole-Genome Sequencing of Human Septicemic E. coli and High-Throughput Electronic Patient Phenotyping. UC Davis CTSC. $25,000. Eisen (PI)
2013-05 to 2015-04. Protecting the Fragile Intestine: Integrating Microbiota and Mucosal Health. RISE - UC Davis. $860,000. Satya Dandekar (PI), Eisen (Asst. Researcher)
2012-12 to 2015-11. Development And Use Of Metagenomic Approaches To Address Challenging Soil Borne Disease Problems In Horticultural Crops. USDA. $128,532. Eisen (PI)
2012-08 to 2015-09. Innate Immunity and Alteration of the Oral Microbiome in SIV Infected Rhesus Macaques. NIH. $484,280. Michael George (PI). Eisen (CoPI)
2012-06 to 2015-05. The Environmental Niche Atlas: Global Mapping of Microbial Functions. Gordon and Betty Moore Foundation. $1,513,352. Katherine Pollard (PI), Eisen (CoPI)
2011-08 to 2012-08. Bayesian Taxonomic Assignment for the Next Generation Metagenomics. Department of Homeland Security. $252,362. Eisen (PI)
2010-12 to 2013-12. Canine Oral Microbiome Project. MARS Corporation. $1,200,000. Eisen (PI)
2010-07 to 2014-06. Microbenet: A Network For Microbiology Of The Built Environment. Alfred P. Sloan Foundation. $1,250,000. Eisen (PI)
2010-07 to 2013-06. Corn Associated Microbes. MARS Corporation. $500,000. Eisen (PI)
2010-07 to 2012-10. The Genomic Encyclopedia of Bacteria and Archaea. DOE. $450,000. Eisen (PI)
2009-10 to 2012-09. Microbial Genome Sequencing: High-Resolution Phylogenomics of Halophilic Archaea. NSF #0949453. $724,678. Marc Facotti (PI), Eisen (coPI), Darling (coPI)
2009-08 to 2012-07. The Effects Of The Microbiome On The Rice Transcriptome. NSF #0923806. $1,900,000. Bais (PI), Eisen (CoPI)
2009-08 to 2013-07. MRI: Acquisition of a Roche Genome Sequence Titanium System for Studies of Microbial Communities. NSF #0923556. $610,620. Eisen (PI)
2008-02 to 2010-01. The Phylofacts: Phylogenomic Encyclopedia Of Microbial Protein Families. NSF #0732065. $1,900,000. Kimmen Sjolander (PI), Eisen (CoPI)
2007-12 to 2011-10. Iseem: Integrating Statistical, Evolutionary, Ecological Approaches To Metagenomics. Gordon and Betty Moore Foundation. $1,790,000. Eisen (PI)
2007-12 to 2011-03. Microstates to Microdynamics: A New Mathematics of Biology. DARPA. $135,000. Simon Levin (PI) Eisen (Co-PI)
2007-09 to 2008-12. Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA). Gordon and Betty Moore Foundation. $325,253. Larry Smarr (PI), Eisen (PI of subcontract)
2006-11 to 2007-10. Microbial Diversity in Ileal Transplants. Broad Medical Research Foundation.$ 35,000. Michael Zasloff (PI), Eisen (CoPI)
2006-06 to 2007-05. Detecting Natural Versus Unnatural DNA. DARPA. $74,833. Carla Brodley (PI), Eisen (CoPI)
2006-05 to 2007-05. Microbial Genome Sequencing: The Complete Genome Sequence Of Teredinibacter Turnerae T7902t (Gamma-Proteobacterium), The Cultivable Intracellular Endosymbiont Of Wood-Boring Marine Mollusk Lyrodus Pedicellatus. NSF #0523862. $149,431. Dan Distel (PI), Eisen (CoPI)
2005-12 to 2008-11. Microbial Genome Sequencing: EST Survey of Charophycean green Algae. NSF #0523719. $270,645. Charles Delwiche (PI), Eisen (CoPI)
2005-01 to 2006-04. CAREER: Integrating Bacterial Diversity into Environmental Change Research and Education. NSF #0347324. $86,338. Jen Hughes (PI), Eisen (CoPI)
2004-09 to 2009-03. Comparative Genomics of Chemosynthetic Symbionts. NSF #0412205. $748,718. Colleen Cavanaugh (PI), Eisen (CoPI)
2004-06 to 2006-06. Biodefense Resource Centers for Biodefense of Emerging/Re-emerging Infectious Diseases. NIH-HHSSN266200400038C. $21,110,385. Owen White (PI), Eisen (Asst. Researcher)
2004-02 to 2009-02. NIH Biodefense Pathogen Genome Resource (BPGR). NIH. $19,931,966. Owen White (PI), Eisen (Asst. Researcher)
2004-01 to 2007-01. Microbial Genome Sequencing: Genome Sequence of Prochloron didemni: An Obligate Cyanobacterial Symbiont. NSF #0412226. $705,417. Jacques Ravel (PI), Eisen (CoPI)
2004-01 to 2005-12. Microbial Genome Sequencing: Genomic Sequencing of two Globally Ubiquitous Members of the Epsilon Proteobacteria. NSF #0333203. $121,500. Craig Cary (PI), Eisen (CoPI)
2003-09 to 2005-08. A high speed network connection for Genomic Research. NSF ANI-0333537. $164,732. Steven Salzberg (PI), Eisen (CoPI)
2003-09 to 2006-08. Interactive Studies of Wolbachia–Eukaryotic Interactions: Genomes to Communities and Back. NSF #0328363. $211,645. Jack Warren (PI), Eisen (Asst. Researcher)
2003-08 to 2007-01. Microbial Genome Sequencing: Complete Genome Sequencing of the Extremely Halophilic Archaea Haloferax volcanii. NSF #0243492. $247,185. Eisen (PI)
2003-05 to 2007-04. Microbial Observatories: Collaborative Research: Kamchatka, a Geothermal Microbial Observatory. NSF#0238407. $201,748. Juergen Weigel (PI), Eisen (CoPI)
2003-04 to 2009-03. Tetrahymena Genome Sequencing Project. NIH-NIGMS #R01 GM067012. $3,873,442. Eisen (PI)
2003-03 to 2007-06. Microbial Genome Sequencing: Shotgun Sequencing of Tetrahymena thermophila. NSF #024036. $2,567,000. Eisen (PI)
2002-10 to 2007-09. ATOL: Phylogenomics: A Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life. NSF#022865. $2,480,000. Eisen (PI)
2002-10 to 2004-09. Effects of Host Environment on Bacterial Genome Evolution. U. Arizona. $216,458. Nancy Moran (PI), Eisen (PI of subcontract)
2002-01 to 2004-12. Pathogen Functional Genomics Resource Center- Anthracis Supplement. NIH #N01-AI-15447. $7,381,926. Tim Read (PI), Eisen (Asst. Researcher)
2001-09 to 2004-08. Continuation of the Comprehensive Microbial Resource. DOE #DE-FG02-01ER6320. $2,047,000. Owen White (PI), Eisen (CoPI)
2001-07 to 2004-07. Identifying The Proteins That Mediate The Ionizing Of Gene Expression In The Radiation Resistant Organism D. Radiodurans Strain D1. DOE. $503,300. John Battista (PI), Eisen (Asst. Researcher)
2000-12 to 2002-11. The Whole Genome Sequence of Actinomyces naeslundi. NIH. $615,483. Tim Read (PI), Eisen (CoPI)
2000-10 to 2003-09. Environmental Genomics And Microbial Observatories: Analysis Of Genetic Variability, Gene Content, And Genomic Potential In Uncultivated Marine Picoplankton. NSF #0084211. 1,043,031. John Heidelberg (PI), Eisen (CoPI)
2000-04 to 2002-04. Complete Genome Sequence of M. capsulatus. DOE/University of Bergen. $658,000. Eisen (PI)
2000-04 to 2001-03. Comparative Genomics of Wolbachia. NIH – NIAID #U01 AI46517-01. $280,383. Scott O’ Neill (PI), Eisen (CoPI)
1999-09 to 2002-08. Intelligent Computational Genomic Analysis. NSF #9980088. $156,692. Simon Kasif (PI), Eisen (Asst. Researchers)
1999-07 to 2001-09. Shotgun Sequencing of Plasmids from Marine Sediment Bacteria Genetic Exploration. ONR #N000149910860. $114,592. Eisen (PI)
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
Aug 2022. CapRadio. By Janelle Salanga. New variants, wastewater data, long COVID: What Sacramento region experts are watching.
Mar 2022. In Style. By Claire Sibonney. The Experts Are Begging You: Stop Buying Vaginal Probiotics.
Feb 2022. California Aggie. By Monica Manmadkar. UC Davis researchers become the first to link insulin sensitivity in Black and white women to differences in the gut microbiome.
Feb 2022. Washington Post. By Tyler Pager. Top White House scientist keeps his job after review finds he demeaned staff.
Jan 2022. Newsweek. By Ned Potter & Fred Guterl. The Forever Virus: What Science Says About the Future of COVID.
Dec 2021. SacTown Magazine. By Charles McDermid. UC Davis microbiome expert weighs in on the Omicron variant and shares his evolving thoughts on eating out, indoor events and long Covid.
Nov 2021. Ars Technica. By Diana Gitig. Autism affects the microbiome, not the other way around.
Nov 2021. Wall Street Journal Podcast. By Amy Marcus. The Biotech Startup that Became an FBI Target.
Jun 2021. Popular Science. By Claire Maldarelli. You might be overusing hand sanitizer.
Jun 2021. MIT Tech Review. By Antonio Regalado. They called it a conspiracy theory. But Alina Chan tweeted life into the idea that the virus came from a lab.
May 2021. Newsweek. By Fred Guterl. The Wuhan Lab and the Virus: The Dr. Fauci, Rand Paul Debate Fact-Checked and Explained.
Mar 2021. ZME Science. By Mihai Andrei. Our phones have their own microbial communities, just like us.
Mar 2021. Digital Journal. By Tim Sandle. Approaching the opening of public spaces: COVID-19 safety.
Dec 2020. UC Davis. By Sarah Colwell. Research for the Public Good.
Nov 2020. CBS 13 TV. By Ryan Hill. COVID-19 Crash Course: UC Davis Students Sign Up For Course Credit At Testing Kiosk.
Sep 2020. Boston Magazine. By Rowan Jacobsen. Could COVID-19 Have Escaped from a Lab?
Jun 2020. Time. By Alice Park. Pressure on Good Science During a Pandemic Is Leading to Confusing, and Conflicting Advice on COVID-19.
May 2020. Undark Magazine. By Sophie Strosberg. Opinion: Society Is Becoming Germaphobic. Let’s Not Stay That Way.
Apr 2020. Newsweek. By Fred Guterl, Naveed Jamali, Tom O’Connor. The controversial experiments and Wuhan lab suspected of starting the coronavirus pandemic.
Apr 2020. CNBC. By Cristina Farr. These high-risk Americans expect to shelter in place for a year or longer to avoid Covid-19.
Apr 2020. NPR. By Hannah Hagemann. Coronavirus Fears Prompt Suspensions Of Bans On Single-Use Plastic Bags.
Apr 2020. Washington Post. By Helen Carefoot. Even with coronavirus spreading, your phone probably won’t make you sick (but you should clean it).
Feb 2020. UC Davis Dateline. Jonathan Eisen: From Aggie Hero to Time.
Feb 2020. Time. These 16 People and Groups Are Fighting for a More Equal America.
Feb 2020. Nature. By Jeffrey Perkel. Just say “no” to manels.
Jan 2020. Symmetry Magazine. By Catherine N. Steffel. When Kids Interview Scientists.
Dec 2019. Massive Science. By Lauren McKee. Cats communicate w/ help of bacteria living in their butts.
Nov 2019. UC Davis News. By Thomas O'Donnel. 2019 Advance Scholar Award.
Oct 2019. UC Davis News. By Tanya Perez. UC Davis Aggie Hero award.
Oct 2019. NY Times. By Christina Caron. Why Do Parents Keep Hearing About the Microbiome?
Sep 2019. Nature. By Holly Else. How to banish manels and manferences from scientific meetings.
Jun 2019. Time. By Alice Park. NIH Director Francis Collins Has a Plan to Help Eliminate "Manels".
May 2019. LiveScience. By Grant Currin. Cats 'Farm' Bacteria in Their Butts. Here's Why.
Feb 2019. New Scientist. By Richard Gray. Your phone & shoes are home to completely unknown life forms.
Jan 2019. NPR - WHYY. The Inner Working of Hospitals.
Aug 2018. The Scientist. By Diana Kwon. To Highlight Gender Gaps, Scientists Decline Opportunities.
Aug 2018. Stat. By Leah Shaffer. As microbiome testing firms proliferate, so do questions about their claims.
Jun 2018. Buzzfeed. By Luia Reinstein. RateMyProfessors. com Is Dropping The "Hotness" Rating After Professors Called It Sexist.
May 2018. Popular Science. By Jessica Boddy. How to handle a koala-chlamydia epidemic. Sex, drugs, and baby koalas.
May 2018. Wired. By Adam Rogers. Scientists are subverting formal publishing.
May 2018. STAT. By Sharon Begley. As Twitter explodes, Eric Lander apologizes for toasting James Watson.
May 2018. NY Times. By Isabella Kwai. Everything You (and John Oliver) Need to Know About Koala Chlamydia.
Jan 2018. Outside Magazine. By David Ferry. Does Your Gut Hold the Secret to Performance?
Dec 2017. Popular Science. By Claire Maldarelli. Is hand sanitizer bad for my microbiome?
Dec 2017. Washington Post. By Sarah Kaplan. The International Space Station is Super Germy.
Aug 2017. Wired. By Sara Scoles. The plan to end science's sexist Manel problem.
Jul 2017. Science Magazine. By Meredith Wadman. Salk Institute under fire for ‘smear’ on women suing it for discrimination.
Jun 2017. Washington Post. By Marissa Payne. Move over, blood doping; cyclists might be 'poop doping' soon.
Mar 2017. Nature. By Amber Dance. Antisocial Media.
Mar 2017. arsTechnica. By Jonathan Gitlin. My cats poop for science.
Mar 2017. Miami Herald. By Sammy Caiola. Are your kids too clean? Microbiome research reveals dangers of killing germs.
Mar 2017. FastCompany. By Christina Farr. Why We Need Scientists On Social Media, Now More Than Ever.
Jan 2017. Nova Next. By Carrie Arnold. The Never-Ending Quest to Rewrite the Tree of Life.
Sep 2016. Stat. By Meghana Keshavan. Overwhelmingly white male lineup at a medical conference sparks ‘public shaming’.
Sep 2016. Moore Foundation. By Aditi Risbud. Beyond the Lab: Jonathan Eisen.
Aug 2016. NPR All Things Considered. By Michaeleen Doucleff. Your Gut’s Gone Viral, And That Might Be Good For Your Health.
Aug 2016. NPR Fresh Air. Eating Yogurt Is Not Enough: Rebalancing The Ecosystem Of 'The Microbes Within Us.
May 2016. FiveThirtyEight. By Christie Aschwanden. How Your Gut Affects Your Mood.
May 2016. New Scientist. By Sally Adee. Microbiomania: The truth behind the hype about our bodily bugs.
May 2016. NY Times. By Gardiner Harris. Federal Microbiome Project Aims to Solve Tiny Riddles of Science.
Apr 2016. STAT. By Rob Waters. This microbiologist loves bugs, hates hype & wants you to send him your cat’s poop.
Apr 2016. The Scientist. By Ashley Taylor. Branching Out.
Apr 2016. The Atlantic. By Ed Yong. Most of the Tree of Life is a Complete Mystery.
Apr 2016. Stat. By Eric Boodman. Killer snails & assassin bugs: secrets of the world’s deadliest creatures.
Mar 2016. KQED. By Lisa Marie Potter and Jon Brooks. Yes, Even CRISPR Pioneer Jennifer Doudna Experiences Gender Bias.
Feb 2016. Health News Review. MIT’s misleading PR headline on autism.
Feb 2016. Wired. By Matt Simon. Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud.
Jan 2016. Wired UK. By Emma Bryce. Do probiotics cure asthma? Don't believe the hype.
Dec 2015. Biotechniques. By Jeffrey Perkel. The Bacteria Among Us.
Dec 2015. Gender Avenger. Jonathan Eisen: A Champion GenderAvenger in the Sciences.
Nov 2015. The Atlantic. By Nocholette Zeliadt. Autism's Microbiome.
Aug 2015. Wired. By Sarah Zhang. Airplane Poop Could Help Track Global Disease Outbreaks.
Jul 2015. Science. By Carrie Arnold. Countering gender bias at conferences.
Jul 2015. Popular Science. By Rinku Patel. Bugged.
Jun 2015. New York. By Alan Levinovitz. The Problem With David Perlmutter, the Grain Brain Doctor.
Jun 2015. Washington Post. By Rachel Feltman. Does treating koala chlamydia hurt their gut microbes?
Jun 2015. Scientific American. By Katherine Courage. Treating Koala STDs May also Quash Their Essential Gut Microbes.
Apr 2015. Chronicle for Higher Education. By Jennifer Howard. To Be a Featured Speaker at a Scholarly Meeting, It Helps to Be Male.
Mar 2015. American Microbiome Institute Microbiome Podcast. All things microbiome w/ Dr. Jonathan Eisen.
Mar 2015. Mother Jones’ Inquiring Minds Podcast. By Indre Viskontas and Kishore Hari. Jonathan Eisen - the Tiny World of Microbes Inside You.
Mar 2015. Motherboard. By AV Flox. Enter the Vaginome: Meet the Microbes that Live in Our Vaginas.
Feb 2015. Wired. By Maryn McKenna. Resistance: The Movie That Will Make You Care About Antibiotic Misuse.
Feb 2015. Wall Street Journal. By Robert Lee Hotz. Big Data and Bacteria: Mapping the New York Subway’s DNA.
Jan 2015. WHYY. By Maiken Scott. Should Scrubs Be Worn Only Inside Hospitals to Limit Spread of Germs?
Dec 2014. Motherboard. By Maddie Stone. Here’s How Many Microbes You Eat in a Single Day.
Dec 2014. Daily Cal. By Megan Messerly. Citations for sale.
Nov 2014. Genetic Literacy Project. By Meredith Knight. Separating Gut Bacteria Hype From Science.
Nov 2014. The Scientist. By Jef Akst. The End of Science Sexism?
Nov 2014. Io9. By Robbie Gonzalez. The Ideal Microbiome is a Myth.
Oct 2014. Mother Jones. By Gabrielle Canon. Can Poop Save Us From the Next Global Epidemic?
Oct 2014. Nature SciTable: Women in Science. By Laura Hoopes. Eisen Says Find a Woman!
Oct 2014. Columbia Spectator. By Laura Booth. Where are the women speakers in the sciences?
Oct 2014. Science Careers Blog. By Beryl Lieff Benderly. To Tweet or Not To Tweet.
Sep 2014. Sacramento News and Review. By Janelle Bitker. The Science of Equality.
Aug 2014. Nature. By William Hanage. Microbiome science needs a healthy dose of scepticism.
Jul 2014. Davis Enterprise. By Elizabeth Case. UCD professor turns down lectureship to protest gender inequality.
Jul 2014. Env. Health Perspectives. By Carrie Arnold. Rethinking Sterile: The Hospital Microbiome.
Jun 2014. Time. By Alexandra Sifferin. Exercise Helps Your Gut Bacteria: Amazing, Overblown, or Plain Incorrect?
May 2014. Popular Science. By Kate Gammon. I Got It From My Momma: 4 Surprising Things To Thank Mom For.
May 2014. Vox. By Brad Plumer. No, mosquitoes aren't deadlier than humans.
Apr 2014. Nova. By Carrie Arnold. The Man Who Rewrote the Tree of Life.
Apr 2014. Nova Next. By Brooke Borel. Manipulating the Unseen Microbial Ecosystem—The Future of Hospitals?
Mar 2014. Sac Bee. By Edward Ortiz. UC Davis teams w/ cheerleaders to launch microbes into space.
Mar 2014. Philadelphia Inquirer. By Sam Wood. A tale of cheerleaders, microbes, and orbit.
Feb 2014. TechEmergence. By Daniel Faggella. Jonathan Eisen & the Wild West of the Human Microbiome.
Jan 2014. The New Yorker. By Betsy Morais. A Killer Phone.
Dec 2013. Sacramento Bee. By Edward Ortiz. Bioterrorism concerns keep genetic code for new strain of botulism under wraps.
Nov 2013. Forbes. By Matt Herper. Why Is The New York Times Breathlessly Promoting A Science Book It Panned?
Sep 2013. All Things Considered. By Rob Stein. Microbe Transplants Treat Some Diseases That Drugs Can’t Fix.
Jul 2013. NPR Morning Edition. By Rob Stein. Staying Healthy May Mean Learning To Love Our Microbiomes.
Jun 2013. The Scientist. By Ed Yong. Bacterial DNA in Human Genomes.
May 2013. Wired. By Maryn McKenna. Fecal Transplants: The FDA Steps In.
May 2013. Smithsonian. By Richard Coniff. Microbes: The Trillions of Creatures Governing Your Health .
Mar 2013. NY Times. By Rebecca Skloot. The Immortal Life of Henrietta Lacks, the Sequel.
Dec 2012. NY Times. By Laura Geggel. These Were a Few of Their Favorite Things.
Oct 2012. Discover. By Bruce Barcott. Earth’s Last Unexplored Wilderness: Your Very Own Home.
Aug 2012. Wall St. Journal. By Robert Hotz. Here’s an Omical Tale: Scientists Discover Spreading Suffix.
Jul 2012. Nature. By Virginia Gewin. Microbes en masse: The sequencing machine.
Jul 2012. The Atlantic. By Rebecca Rosen. The Case (Study) of Arsenic Life: How the Internet Can Make Science Better.
Jun 2012. Microbe World Podcast. MWV Episode 72 - Jonathan Eisen - Evolvability, the Built Environment and Open Science.
Jun 2012. Forbes. By Matt Herper. A Master Of The Microbiome & His Quest To Re-Publish His Father's Papers.
Mar 2012. Nature. By Ed Yong. Microbiome sequencing offers hope for diagnostics.
Mar 2012. Wired. By Daniella Hernandez. Birds, Poop and Roadkill: A Field Guide to Field Guides.
Mar 2012. Wired. By Daniella Hernandez. Book of Germs: The Quest for a Field Guide to Microbes.
Feb 2012. MSNBC. By Alan Boyle. What’s Living on Your Smartphone?
Oct 2011. PLOS Blogs. By Stacy Konkiel. How deep social network “roots” help scientists communicate their research.
Oct 2011. Australian Radio Future Tense. By Antony Funnell. Indoor Ecology.
Aug 2011. Wired. By David Dobbs. Academic Publishers: Making Murdoch Look Good.
Aug 2011. Boston Globe. By Courtney Humphries. Ecosystem sweet ecosystem.
Aug 2011. NY Times. By Carl Zimmer. How Many Species on Earth? It’s Tricky.
Aug 2011. The Scientist. By Edyta Zielinska. Arsenic-Based Life, Open to Critique.
Aug 2011. Nature. By Gwyneth Dickey Zakaib. The challenge of microbial diversity: Out on a limb.
May 2011. Wired. By David Dobbs. Free Science, One Paper at a Time.
Mar 2011. The Economist. A new domain of life: plenty more bugs in the sea.
Mar 2011. BioIT World. UC Davis’ Jonathan Eisen Wins 2011 Benjamin Franklin Award.
Jan 2011. Nature. By Apoorva Mandavilli. Peer review: Trial by Twitter.
Dec 2010. Wired. By David Dobbs. Wired: Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?
Oct 2009. Cell. By Laura Bonetta. Should You Be Tweeting?
Oct 2010. By Bob Grant. You Aren’t Blogging Yet?!?
Oct 2010. SPARC. Science in the genes.
July 2010. Dr. Kiki’s Science Hour 55. Pieces of The Evolutionary Puzzle.
Apr 2010. ARS Technica. By John Timmer. BitTorrenting biology, getting the big picture in search.
Apr 2010. Science News. By Chelsea Ward. Scientists Embrace Openness.
Apr 2010. The Loom. By Carl Zimmer. Yet-Another-Genome-Syndrome.
Dec 2009. NY Times. By Carl Zimmer. Scientists Start a Genomic Catalog of Earth’s Abundant Microbes.
Dec 2009. Ars Technica. By John Timmer. Presenting a genomic encyclopedia of bacteria (and archaea).
Nov 2009. Nature. By Elie Dolgin. Biologists rally to sequence ‘neglected’ microbes.
Oct 2009. Genome Technology. Meredith Salisbury. Is peer review broken?
Sep 2009. UPI. Ileostomy patients: Different gut bacteria.
Sep 2009. Microbe Magazine. By Jeffrey Fox. Genomic Analyses Could Lead to “Field Guide to Microbes”.
Jul 2009. Bioscience. By Elia Ben-Ari. Twitter - What's All the Chirping About.
May 2009. Nature Magazine. BY Apoorva Mandavilli. Straight from the gut.
Apr 2009. New Yorker. My Margaret Talbot. Brain gain: The underground world of “neuroenhancing” drugs.
Jun 2008. Science. By Elizabeth Pennisi. Building the Tree of Life, Genome by Genome.
Sep 2007. Nature. By Ewen Calloway. Genomes within genomes.
Mar 2007. Nature. By John Whitfield. We Are Family. Linnaeus at 300.
Mar 2007. Nature. By Heidi Ledford. Microbes reveal extent of biodiversity.
Feb 2007. Science Magazine. By Robert Koenig. Saving Species With Potential.
Dec 2006. Sacramento News and Review. By Ralph Brave. Life Itself.
Jun 2006. Science. Dinner for Three.
Nov 2004. LA Times. Editorial. Priceless Information.
Sep 2004. East Bay Express. By Will Harper. Publisher for the People.
Apr 2004. The Scientist. By Dave Secko. A sleek genome, except for all the junk.
Mar 2004. Japan Times. By Rowan Hooper. Male-killers on the loose.
Feb 2003. Nature. By Carina Dennis. Draft guidelines ease restrictions on use of genome sequence data.
Dec 2002. Esquire Magazine. Best and Brightest.
Nov 2002. New Scientist. By Jeff Hecht. From bugs to birds to giant reptiles, we're finally growing a tree of life.
Jul 2002. US News and World Report. By Thomas Hayden. A Theory Evolves.
Dec 2001. US News & World Report. By Thomas Hayden. The Big Brains are Searching for Solutions. But there are no easy fixes.
Nov 2001. US News and World Report. By Thomas Hayden. Bugs Bared
May 2001. BioWorld. David Leff. Was It Promiscuous Lateral Swap Or Lost Genes That Put Bacterial DNA Into Humans?
May 1999. Science. By Mark Sincell. Hot trail of stolen genes.
Jun 1997. Stanford News. Six scholars win Gores Awards for teaching excellence.
Apr 1997. Stanford News. The Science Core experiment: Snapshots of the first year.
Apr 1995. Stanford News. Faculty from 15 departments talk over new science core course.
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:
2022 - Feb. The Scientist. Eric Lander Allegedly Bullied, Disrespected Staff.
2020 - Feb. Nature. Just say “no” to manels.
2020 - Feb. Time. These 16 People and Groups Are Fighting for a More Equal America.
2019 - Oct. UC Davis News. UC Davis Aggie Hero award.
2019 - Oct. UC Davis News. UC Davis ADVANCE Scholar Award Recipients.
2019 - Sep. Nature. How to banish manels and manferences from scientific meetings.
2019 - Jun. Time. NIH Director Francis Collins Has a Plan to Help Eliminate "Manels"
2018 - Aug. The Scientist. To Highlight Gender Gaps, Scientists Decline Opportunities.
2018 - May. STAT. As Twitter explodes, Eric Lander apologizes for toasting James Watson.
2017 - Aug. Wired. The plan to end science's sexist Manel problem.
2017 - Jun. Science. Salk under fire for ‘smear’ on women suing it for discrimination.
2016 - Jul. Science. Countering Gender Bias at Conferences.
2014 - Jul. Davis Enterprise. UCD professor turns down lectureship to protest gender inequality.