Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). 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

Yes, Virginia, Cell Phones Have Bacteria on Them … And this means????

A new report is out with a discussion of microbes on cell phones: Study: Cellphones can be more germ-infested than toilet handle | News – Home. Not sure what was done in the study but regardless it seems to be focused on culture based work. And as is usually, the finding of some microbes related to ones known to cause disease leads to the inevitable conclusion that we must kill everything on the phones.
It seems to me that we need a bit more detail on what microbes are found on cell phones before bringing out the cleaners and the irradiation and such.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Playing w/ Google Scholar’s "Citations" system – some nice features but in need of a little fine tuning

Been playing around with Google Scholar‘s Citations system that allows anyone to create a mini page with their publications.  Here is a link to mine: Jonathan Eisen.  I recommend that everyone out there who has any publications create a Scholar Citations page for themselves. Instructions can be found here.

I quite like the simplicity yet informativeness of the Scholar Citations front page:

Yet there are many other things I wish were there.  For example, I really wish the “Institution” part was an active link and led to other people at UC Davis.  Alas, not so.  So I had to use the search function to pull out other people from UC Davis (searching for UC Davis in the search for Authors in the box in the upper right from my home page).

The list comes out in order of numbers of citations, which is good and bad.  Here are some of the top people from the list:

I also like the “Co-authors” function:
And the page where I can see lovely pictures of some of my co-authors all together
But this function still leaves a bit to be desired.  For example, finding other Co-Authors with Scholar pages is very hard for me since, well, I have hundreds and hundreds of Co-authors.  And though there is a function where Google Scholar makes suggestions for who to search for

It would be nice if it had a way to display the whole list not just their top suggestions.  But there is no way to see the next page and the only way to see other suggestions is to delete some of them.  I know – not everyone will have this issue but at least some other genomics focused folks probably will/do.
Anyway – it is worth playing around with – a good addition to the relatively simplistic Google Scholar search tools.
UPDATE 7 PM 3/4/2012
I figured out a way to find co-authors of papers of mine on Google Scholar Citations.  If I search for the paper title and restrict the search to the site I can find them.  For example searching for:
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. site:scholar.google.com/citations
This pulls out all the people in Scholar Citations who are authors on the paper … 
Then alas I have to retype their name into the Author Search box and I get to add them as coauthors …
Also… searching for Eisen JA in the site: scholar.google.com/citations finds some co-authors 
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Genome Center Network Focus Group – Reminder

The Genome Center

Network Focus

Group Presents

Dana Pe`er

Assistant Professor, Department of Biology

Columbia University

"On the road to personalized therapy, a systems approach“

Abstract: Systematic characterization of cancer genomes has revealed a staggering complexity of aberrations among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remains poorly defined. A major challenge involves the development of analysis methods to integrate the flood of genome-wide data on tumors towards patient-specific tumor network models. We will elaborate on two computational approaches: (1) Integration of genetic and genomic data to identify genetic determinants of cancer and model how these alter the regulatory network, as well as drug response. (2) Single cell models of cancer signaling based on mass cytometry, a novel technology that can accurately measure more than forty signaling molecules simultaneously single cells. We will demonstrate the utility of these applications of these approaches across a broad range of different cancers.

Monday, March 5, 2012

10:00 a.m., 1005 GBSF Auditorium

Dana Peer.pdf

And now Spam from Elsevier – thanks – but no thanks

Just got an email from Elsevier for something called “Reviewers’ Update” which starts off:

Dear Dr Eisen,

As a valued contributor to Elsevier’s journals we thought you may be interested in receiving the Reviewers’ Update – our free quarterly e-update for reviewers – which contains advice for reviewers, updates on how Elsevier supports the peer review process as well as information which we hope proves useful to you when reviewing manuscripts.

Click on the headings below for access to a selection of articles in Issues 8 and 9, or browse through the full archive on the Reviewers’ Update homepage.

Would you like to receive the next issue of Reviewers’ Update as well as future reviewer updates?

If so, please register here.

Kind regards,

Andrea Hoogenkamp-O’Brien, PhD
Communications Manager, Elsevier

That leads me to wonder – just what did I do to become a valued contributor?  I cannot for the life of me remember the last time I reviewed for any Elsevier journal.   And the last time I was an author on a paper in an Elsevier journal was 2006 and that was only because I did not really realize that is where collaborators were submitting a paper.  Thanks Elsevier, but I will skip registering for this service.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Misha Angrist Seminars Speaker-March 7,8

From Angus Chandler:

Next week’s Evolution and Ecology seminar speaker is Dr. Misha Angrist from Duke University. Misha is invited as part of the "Big Read: Open Access Science" partnership. In addition to his academic talk during the usual EVE seminar spot (Thursday, March 8th at 4:10 in 2 Wellman), he will also be speaking at the Davis public library on Wednesday March 7th at 7:30 pm. More information can be found here: http://sciencenovels.wordpress.com/

Misha’s EVE talk is entitled:

"To Put Away Childish Things: The Burgeoning Rebellion of Human Research Participants”

We continue to argue about who should have access to our biological samples and data and the degree to which openness with them will lead to all sorts of bad things. I would like to re-frame the discussion and ask a different set of questions: What are the opportunity costs to research participants, the research enterprise, and society of an insistence upon biological anonymity and business as usual? What do we lose by holding fast to genomic exceptionalism in an age of cheap sequencing and social media? What can we learn from the experiences of those who have opted to eat from the tree of knowledge?

Some answers to "Wanted-good simple guide to the statistics of sampling design for field ecology studies"

I asked a question on twitter “Wanted – good simple guide to the statistics of sampling design for field ecology studies” and got some useful answers, which I have “storified” below. Any additional suggestions welcome. http://storify.com/phylogenomics/suggestions-for-simple-guides-to-statistics-of-sam.js[<a href=”http://storify.com/phylogenomics/suggestions-for-simple-guides-to-statistics-of-sam” target=”_blank”>View the story “Suggestions for simple guides to statistics of sampling design” on Storify</a>]

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Full list of 2012 American Academy of Microbiology Fellows Announced

Just got this email and well, I thought I would share.  I would share even if I was not on the list since, well, I love microbes and microbiology.  Note the list is also available on the AAM Web site here.


The American Academy of Microbiology is honored to welcome these new Fellows, elected in recognition of their records of scientific achievement and original contributions that have advanced microbiology:
  • James B. Anderson, Ph.D., University of Toronto, Mississauga, ON, Canada
  • Dan I. Andersson, Ph.D., Uppsala University, Sweden
  • Raul Andino, Ph.D., University of California, San Francisco
  • Brenda J. Andrews, Ph.D., University of Toronto, BC, Canada
  • Charles Barlowe, Ph.D., Dartmouth Medical School, Hanover, NH
  • Joel B. Baseman, Ph.D., University of Texas Health Science Center, San Antonio
  • Ruth L. Berkelman, M.D., Emory University, Atlanta, GA
  • Robert E. Blankenship, Ph.D., Washington University, St. Louis
  • James B. Bliska, Ph.D., Stony Brook University, NY
  • Kerry S. Bloom, Ph.D., University of North Carolina, Chapel Hill
  • Jef D. Boeke, Ph.D., D. Sc., Johns Hopkins School of Medicine, Baltimore, MD
  • Charles M. Boone, Ph.D., University of Toronto, BC, Canada
  • Stephen Buratowski, Ph.D., Harvard Medical School, Boston, MA
  • George Church, Ph.D., Harvard Medical School, Boston, MA
  • Daniel G. Colley, Ph.D., University of Georgia, Athens
  • Patricia A. Conrad, Ph.D., D.V.M., University of California, Davis
  • Ross E. Dalbey, Ph.D., Ohio State University, Columbus
  • Roger J. Davis, Ph.D., Howard Hughes Medical Institute and University of Massachusetts Medical School, Worester
  • Piet A.J. de Boer, Ph.D., Case Western Reserve University School of Medicine, Cleveland, OH
  • Mark R. Denison, M.D., Vanderbilt University Medical Center, Nashville, TN
  • Shou-Wei Ding, Ph.D., University of California, Riverside
  • Jonathan Eisen, Ph.D., University of California, Davis
  • Luis Enjuanes, Ph.D., National Center of Biotechnology-Spanish National Research Council (CNB-CSIC), Campus Universidad Autonoma, Madrid, Spain
  • Tom Fenchel, Ph.D., D. Sc., University of Copenhagen, Denmark
  • Robert L. Garcea, M.D., University of Colorado, Boulder
  • Reid Gilmore, Ph.D., University of Massachusetts Medical School, Worcester
  • Douglas T. Golenbock, M.D., University of Massachusetts Medical School, Worcester
  • Robert M. Goodman, Ph.D., School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
  • Daniel E. Gottschling, Ph.D., Fred Hutchinson Cancer Research Center, Seattle, WA
  • Glenda Gray, M.B. B.Ch., F.C. Paeds., Perinatal HIV Research Unit, Baragwanath Academic Hospital, Soweto and University of the Witwatersrand, Johannesburg, South Africa
  • F. Ulrich Hartl, M.D., Dr. Med., Dr. Med. Habil, Max Planck Institute of Biochemistry, Martinsried, Germany
  • Regine Hengge, Ph.D., Freie Universität Berlin, Germany
  • John E. Heuser, M.D., Washington University, St. Louis and Kyoto University, Japan
  • Wolf-Dietrich Heyer, Ph.D., University of California, Davis
  • Edward A. Hoover, D.V.M., Ph.D., Colorado State University, Fort Collins
  • Barbara J. Howlett, Ph.D., The University of Melbourne, Australia
  • Philip Hugenholtz, Ph.D., University of Queensland, St. Lucia, Australia
  • James M. Hughes, M.D., Emory University School of Medicine, Atlanta, GA
  • Eric Hunter, Ph.D., Emory University, Atlanta, GA
  • Regine Kahmann, Ph.D., Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
  • Albert Z. Kapikian, M.D., NIAID, NIH, Bethesda, MD
  • Patrick Keeling, Ph.D., University of British Columbia, Vancouver, Canada
  • Karla Kirkegaard, Ph.D., Stanford University, CA
  • Eugene V. Koonin, Ph.D., NCBI, NLM, NIH, Bethesda, MD
  • Thomas M. Kristie, Ph.D., National Institutes of Health, Bethesda, MD
  • Nirbhay Kumar, Ph.D., Tulane University, New Orleans, LA
  • Ching Kung, Ph.D., University of Wisconsin, Madison
  • Jean-Paul Latge, Ph.D., Institut Pasteur, Paris, France
  • Jeffrey G. Lawrence, Ph.D., University of Pittsburgh, PA
  • Jared R. Leadbetter, Ph.D., California Institute of Technology, Pasadena, CA
  • Maxine L. Linial, Ph.D., Fred Hutchinson Cancer Research Center, Seattle, WA
  • Alison McBride, Ph.D., NIH, Bethesda, MD
  • Xiang-Jin Meng, M.D., Ph.D, Virginia Polytechnic Institute and State University, Blacksburg, VA
  • Hiroaki Mitsuya, M.D., Ph.D., National Cancer Institute, NIH, Bethesda, MD
  • Edward Mocarski, Jr., Ph.D., Stanford University School of Medicine, CA
  • Jens Nielsen, Ph.D., Dr. Technology, Chalmers University of Technology, Gothenburg, Sweden
  • Victor Nizet, M.D., University of California, San Diego
  • Paul A. Offit, M.D., Children’s Hospital of Philadelphia, PA
  • Joseph S. Pagano, M.D., University of North Carolina, Chapel Hill
  • Julian Parkhill, Ph.D., The Sanger Institute, Cambridge, United Kingdom
  • Robin Patel, M.D., Mayo Clinic, Rochester, MN
  • John T. Patton, Ph.D., NIAID, NIH, Bethesda, MD
  • Martin Polz, Ph.D., Massachusetts Institute of Technology, Cambridge
  • Markus Ribbe, Ph.D., University of California, Irvine
  • Naomi Rosenberg, Ph.D., Tufts University, Boston, MA
  • Eric J. Rubin, M.D., Ph.D., Harvard School of Public Health, Boston, MA
  • Peter Sarnow, Ph.D., Stanford University School of Medicine, CA
  • Christa M. Schleper, Ph.D., University of Vienna, Austria
  • Olaf Schneewind, M.D., Ph.D., University of Chicago, IL
  • David M. Serwadda, M.B.ChB., M. Med., M.P.H., Makerere University School of Public Health, Kampala, Uganda
  • Eric J. Snijder, Ph.D., Leiden University Medical Center, Netherlands
  • Roger E. Summons, Ph.D., Massachusetts Institute of Technology, Cambridge
  • Michele S. Swanson, Ph.D., University of Michigan Medical School, Ann Arbor, MI
  • Rudolf K. Thauer, Dr. rer. nat., Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
  • Kenneth L. Tyler, M.D., University of Colorado School of Medicine, Denver
  • Rytas Vilgalys, Ph.D., Duke University, Durham, NC
  • Peter R. Williamson, M.D., Ph.D., NIAID, NIH, Bethesda, MD
  • Thomas A. Wynn, Ph.D., NIAID, Bethesda, MD
  • X. Sunney Xie, Ph.D., Harvard University, Cambridge, MA
  • Arturo Zychlinsky, Ph.D., Max Planck Institute for Infection Biology, Berlin, Germany
We hope that you will join us in welcoming the new Fellows at the Fellows Luncheon and Meeting at the General Meeting in San Francisco on June 19th. 
Sincerely yours,
Bonnie L. Bassler, Ph.D. 
Chair, Board of Governors 
American Academy of Microbiology
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

My obsession with a Field Guide for Microbes

Recently I gave a talk at the AAAS Meeting in Vancouver on my dream of having “A Field Guide to the Microbes”.  The talk was part of a session on the “Earth Microbiome Project” organized by Jack Gilbert and others.

You can see a slideshow with audio of my talk below:

It seems that my talk has sparked a lot of interest as I have been interviewed by various people and publications about this concept.

For example, Holly Menninger recently interviewed me for a blog post for the “Your Wild Life” blog:
Is a Field Guide for Microbes in Our Future? Q & A with Microbiologist Jonathan Eisen.

And today a wonderfully illustrated piece came out at Wired.Com by Daniela Hernandez titled “Book of Germs: A Quest for a Field Guide to Microbes.”

If you are interested in some more background on what I have been thinking about a Field Guide to the Microbes here are some previous things I have written or said or commented on relating to this topic:

And if you want to check out some “Field Guide” like books on the topic of microbes I am posting some recommendations on an Amazon Page. My favorite is “A Field Guide to Bacteria” by Betsey Dyer.  
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Task force investigating #UCDavis Pepper Spray Incident report to be released 3/6

Just got an email from UC Communications

“Former California Supreme Court Associate Justice Cruz Reynoso, chair of the task force investigating the pepper-spray incident on November 18, 2011, said today the task force is working toward public release of findings and recommendations on Tuesday, March 6, at a time and location on the UC Davis campus to be determined. 


Additional information will be provided as soon as it is available.”

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Last call for applications (due March 4): Phylotastic! hackathon at NESCent (June 4 to 8)

Email I just got from Ariln Stoltzfus

Dear Colleague,

Hello. I’m writing to make sure you are aware of the opportunity provided by the Phylotastic! hackathon planned at NESCent in June, a week-long event that will bring together scientist-programmers to develop an open system that will democratize research access to the Tree of Life.

Below is the open call for participation– anyone can apply, and funding is available.

I would appreciate if you could forward this to anyone who might be interested in applying. We especially encourage women and members of traditionally under-represented minorities to apply. The online application takes about 15 minutes (deadline: March 4 at midnight EST).

Thanks for your time. With regards,

Arlin Stoltzfus