Author: Jonathan Eisen

I am 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. 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).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.

Microbial Ecosystem Ecologist at Colorado State University

By Jonathan Eisen   Posted in Job postings
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Position Announcement Colorado State University Department of Ecosystem Science and Sustainability POSITION: Assistant Professor, Microbial Ecosystem Ecology DESCRIPTION: Tenure track, 9-month academic faculty position The Department of Ecosystem Science and Sustainability at Colorado State University (CSU) invites applications for a tenure track faculty position in Microbial Ecosystem Ecology at the rank of assistant professor. We …

Post doc opportunity: urban methane dynamics

By Jonathan Eisen   Posted in Built Environment Topics Job postings
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Of possible interest: Dear Colleagues- Please forward this to lists within your institution and to individuals who may be interested: We seek an outstanding individual to contribute to a collaboration between Google, the Environmental Defense Fund and Colorado State University that is having direct impact on the amount of methane being emitted from cities. In …

Announcement of VERVE Net on protocols.io — a forum for discussing methods in virus ecology

By Jonathan Eisen   Posted in Methods and Tools Scholarly Communication
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Posting this which I received by email: Colleagues, We are thrilled to announce the launch of VERVE Net (https://www.protocols.io/g/verve-net), an on-line platform that equips the virus ecology community with a means to easily run, modify, publish and discuss laboratory, field and bioinformatic protocols. The forum also provides new ways to navigate the literature (a publication …

Storify wrap up of #PSB16 Session on Computational Microbiology #microbiomes

By Jonathan Eisen   Posted in .Featured Bioinformatics Meetings and Talks Methods and Tools Sequencing
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I made a Storify summary of the Tweets from a workshop at the Pacific Symposium on Biocomputing that I attended on Tuesday on Computational Microbiology (with a big focus on microbiomes). [<a href="//storify.com/phylogenomics/psb16-session-on-microbiomes” target=”_blank”>View the story “#PSB16 session on computational microbiome #microbiomes ” on Storify]

Nice microbiology of the built environment paper: Sources of indoor air bacteria in residences

By Jonathan Eisen   Posted in .Featured Buildings Scholarly Literature (Journals, Books, Reports) Sequencing
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Source: Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences | Microbiome | Full Text Another very useful paper from the Microbiome journal.  This one from Marzia Miletto and Steven Lindow.  Here is the Abstract: Abstract Background The study of the microbial communities in the built …

A must read on indoor microbiology: Sources of airborne microorganisms in the built environment 

By Jonathan Eisen   Posted in .Featured Animals and the Built Environment Buildings Microbiology of the Built Environment Scholarly Literature (Journals, Books, Reports) Sequencing
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2013-5-19MBPF Source: Sources of airborne microorganisms in the built environment | Microbiome | Full Text Really nice new review paper by Aaron Prissin and Linsey Marr. It covers research on sources of airborne microbes including Humans Pets Plants Plumbing HVACs Water damage Dust Outdoor air Really thorough with tons of references and discussion of the …

Near perfect balance in a microbiome paper – hopeful yet no hype: The microbiome of the built environment and mental health

By Jonathan Eisen   Posted in .Featured Animals and the Built Environment Buildings Built Environment Topics Research Scholarly Literature (Journals, Books, Reports) Sequencing Sloan MoBE Program
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Source: The microbiome of the built environment and mental health | Microbiome | Full Text Andrew J. Hoisington, Lisa A. Brenner, Kerry A. Kinney, Teodor T. Postolache and Christopher A. Lowry When I saw the title of this I cringed a bit, worried that this paper would be overselling what we know about the microbiome and …

Fascinating look at the design of a science infographic (on life in dust)

By Jonathan Eisen   Posted in .Featured Art and Science Buildings Research Sequencing
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Designers Martin Krzywinski and Barbara Jeannie Hunnicutt provide a peek behind the scenes, and explain how they developed a data visualization based on bacterial genome information derived from dust. Source: The Evolution of a Scientific American Infographic: Secret Life in Household Dust – Scientific American Blog Network This is an absolutely fascinating look behind the …