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Jonathan Eisen
Works at University Of California, Davis
Attended Harvard College
Lives in Davis, CA
19,233 followers|17,044,044 views
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Jonathan Eisen

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Getting a bit more angry about this misleading Press Release, Title and Commentary on Alzheimers and the Gut Microbiome from U. Chicago today ...
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Disappointing misleading stuff from U. Chicago on Alzheimer's and the microbiome
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Just a quick post here.  There is a new paper of interest: Teaching indoor environmental quality – Nazaroff – 2016 – Indoor Air – Wiley Online Library It leads off with How is a new generation of professionals to be educated about indoor environmental…
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Just a quick post here.  Multiple stories out about the Laying Hen Housing Research Project by the Coalition for Sustainable Egg Supply that maybe of interest. From: Hen housing trade offs: Food safety, workers and consumers | Food Safety News As it turns…
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Rob Dunn is one of the true pioneers of Citizen Science and in Citizen Science projects involving microbes.  And here is another fascinating project from Dunn and colleagues. The Wild Life of Showerheads Photo by Lea Shell- Rob Dunn Lab When Anton Von…
Rob Dunn is one of the true pioneers of Citizen Science and in Citizen Science projects involving microbes. And here is another fascinating project from Dunn and colleagues. The Wild Life of Showe…
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Jonathan Eisen

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Just a quick post about the fact that researchers from the Jet Propulsion Laboratory (JPL) are sending radiation resistant (even radiation-loving) fungi for some experiments on the International Space Station (ISS).  They are looking for changes that…
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So both Hal Levin and I have posted and/or commented on the topic of plants “cleaning” the air in buildings.  Most of what’s out there is either anecdotal or based on an old NASA study that would require hundreds of plants in a home to make any…
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This reminds me of how scientists trying to figure out what was going on with air and phlogiston and fire didn't believe their results until they used plants that weren't pretty-smelling. I suspect there's a lot of wishful and aesthetic thinking getting mixed in when it comes to the benefits of indoor plants. 
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As of last week, the QIIME 2 alpha release is now live and ready for testing! The best way to see where we are with QIIME 2 is to watch my SciPy 2016 presentation on QIIME 2 (the slides are available here). In this talk I give a bottom-up description of…
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Microbes in the clinic Glove Contamination during Endodontic Treatment Is One of the Sources of Nosocomial Endodontic Propionibacterium acnes Infections – Sadia Ambreen Niazi – Journal of Endodontics ($35.95) The opportunistic Propionibacterium acnes…
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19,233 people
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Work
Occupation
Professor at UC Davis
Employment
  • University Of California, Davis
    Professor, 2006 - present
  • DOE Joint Genome Institute
    Adjunct Scientist, 2006 - 2011
  • The Institute For Genomic Research,
    Investigator, 1998 - 2006
  • The Johns Hopkins University
    Adjunct Professor, 2000 - 2010
  • The Public Defender Service of the District of Columbia
    Intern, 1987 - 1987
  • The Rocky Mountain Biological Lab
    Field Assistant, 1988 - 1988
Places
Map of the places this user has livedMap of the places this user has livedMap of the places this user has lived
Currently
Davis, CA
Previously
Bethesda, MD - Gaithersburg, MD - Boston, MA - Cambridge, MA - Stanford, CA - Gothic, CO - Brookline, MA - Medford, MA
Story
Tagline
All microbes, all the time.
Introduction
I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. In addition I hold an Adjunct appointment at the Department of Energy Joint Genome Institute in Walnut Creek, CA. 

My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  I am an author on more than 200 scientific publications as well as an Evolution textbook and a variety of other things.  

In addition to research, I am heavily involved in the Open Access publishing movement and am Academic Editor in Chief of PLoS Biology

Prior to moving to UC Davis I was on the faculty at The Institute for Genomic Research (TIGR) with an Adjunct Appointment in the Biology Department at the Johns Hopkins University. I did my PhD at Stanford studying the evolution of DNA repair processes in the lab of Phil Hanawalt and my undergraduate studies at Harvard College.

See my blog or tweets or Google+ Feed for the latest on what is going on in my lab and life and for conference reports, opinions on papers, and related information.

Finally, if you have made it this far and want to know more, here are some of my favorite stories written by others about me or my work
Education
  • Harvard College
    AB, Biological Sciences, 1986 - 1990
  • Stanford University
    PhD, Biology, 1991 - 1998
  • Walt Whitman High School, Bethesda, MD
    1983 - 1986
Basic Information
Gender
Male
Relationship
Married
Other names
Jon
Jonathan Eisen's +1's are the things they like, agree with, or want to recommend.
Overselling the Microbiome Award for @nytimes on thumb sucking, nail bit...
phylogenomics.blogspot.com

I am continually torn about handing out "overselling the microbiome" awards to many "stories" that are coming out recently on new scientific

Total RNA Sequencing reveals microbial communities in human blood and di...
biorxiv.org

An increasing body of evidence suggests an important role of the human microbiome in health and disease. We propose a 'lost and found' pipel

Reference-free comparison of microbial communities via de Bruijn graphs
biorxiv.org

Microbial communities inhabiting the human body exhibit significant variability across different individuals and tissues, and are suggested

How to get some extra eyes on your publication – email everyone cited in it
phylogenomics.wordpress.com

Interesting way of getting people to look at a paper. I am sure other places do this but I have not seen it too often (though this was in SP

Faculty Positions at #UCDavis in Disease Biology (1 in Entomology, 1 in ...
phylogenomics.wordpress.com

UC DAVIS FACULTY POSITION ANNOUNCEMENTS UC Davis is recruiting two faculty, one each in Entomology and Plant Pathology, to work on organisms

On pastrami and the business of PLOS
www.michaeleisen.org

Last week my friend Andy Kern (a population geneticist at Rutgers) went on a bit of a bender on Twitter prompted by his discovery of PLOS's

At #UCDavis 3/9: “Authorship and the Promises of Digital Dissemination,”
phylogenomics.wordpress.com

A cross-disciplinary panel discussion on authorship in the digital age, with a focus on the specific goals and needs of academic authors.Aut

The Villain of CRISPR
www.michaeleisen.org

There is something mesmerizing about an evil genius at the height of their craft, and Eric Lander is an evil genius at the height of his cra

1/15 at #UCDavis: Tandy Warnow: New methods for species tree estimation ...
phylogenomics.wordpress.com

Special Seminar: Tandy Warnow The University of Illinois at Urbana-Champaign New methods for species tree estimation in the presence of gene

Removing my name from the author list of #closedaccess "Unified Microbio...
phylogenomics.blogspot.com

[View the story "Removing my name from the author list of #closedaccess "Unified Microbiome Initiative" paper in Science" on Storify]

Genome Engineering #GESB16 in Gent - for Men Only #YAMMM
phylogenomics.blogspot.com

So I just got an invite to this meeting: Looks interesting. Not that I work in the field. But I decided to check it out. So I went to the we

‘Antibiotic addict’ India losing fight against lethal bacteria - The Tim...
timesofindia.indiatimes.com

India is the world’s antibiotic popping capital, recording the highest number of such pills consumed annually — 13 billion pills as against

Microbiomania
phylogenomics.blogspot.com

I love microbiome research. I have been doing it for 10+ years. However many people oversell it. Here are some posts on this. Posts tageed "

Innovative Genomic Initiative Post Doc Fellowship at #UCDavis and some o...
phylogenomics.wordpress.com

Got this in email: The IGI is pleased to announce its first Postdoctoral Fellowship Award. This Award will provide 2 years of financial supp

Waiting for our room right now. Woman at the front desk - Erin - is being very rude
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