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.

Opinions / facts / comments wanted: are indoor plant microbiomes beneficial to human health

By Jonathan Eisen   Posted in Scholarly Literature (Journals, Books, Reports)
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New paper out of possible interest to those studying the microbiology of the built environment: Frontiers | Beneficial effects of plant-associated microbes on indoor microbiomes and human health? | Frontiers in Plant-Microbe Interaction.  The paper makes some arguments regarding possible connections between indoor plant microbiomes and human health.  I am posting this here without commentary in …

Art and microbiology meet again but not in the way you might have expected

By Jonathan Eisen   Posted in Scholarly Literature (Journals, Books, Reports)
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Well, I have always told people that we need more mixing of art and science.  In recent years we have seen lots of attempts to do some sort of art inspired by – or even incorporating – microbes.  But this is perhaps the other side of the coin.  Art is significantly influenced by microbes in …

New publications on ribosomal RNA tools (databases, software, etc)

By Jonathan Eisen   Posted in Scholarly Literature (Journals, Books, Reports)
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For those doing microbial diversity studies, analysis of rRNA genes via PCR is still a fundamental tool.  And thankfully many people keep maintaining various databases and tools for people to use to carry out analysis of rRNA data.  Here are some new papers of relevance: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. …

New paper of interest on combining qPCR & sequencing to quantify fungi in aerosols

By Jonathan Eisen   Posted in Scholarly Literature (Journals, Books, Reports)
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Nice new paper from Karen Dannemiller et al. (the senior author is Jordan Peccia from Yale): Citation: Dannemiller, K. C., Lang-Yona, N., Yamamoto, N., Rudich, Y., & Peccia, J. (2013). Combining Real-Time PCR and Next-Generation DNA Sequencing to Provide Quantitative Comparisons of Fungal Aerosol Populations. Atmospheric Environment in Press. The abstract is copied below.  Basically, they …

I never meta data I didn’t like – especially re: standards for the built environment #IndoorMicro

By Jonathan Eisen   Posted in Scholarly Literature (Journals, Books, Reports)
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New paper out from the microbiology of the built environment community: MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. The joint first authors are Elizabeth Glass and Yekaterina Dribinsky.  And the senior author is Lynn Schriml.  The paper is simple but I think very important – it describes …