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

New Course=> PHA 250 Functional Genomics: from Bench to Bedside

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PHA250: Functional Genomics: from Bench to Bedside
CRN: 84839
Spring 2012
Tuesdays/Thursdays 9:00-10:30am
Location: Tupper 2133

Instructor of Record (IOR): David Segal

COURSE GOALS AND ORGANIZATION: The purpose of the course is to familiarize
students with topics in Functional Genomics, with an emphasis on clinical
relevance and applications (e.g., genetic variation and disease, cancer
therapeutics, and biomarker discovery). Specific topics that will be covered
include detection of altered gene sequences, and measurements of the changes
in chromatin and RNA that occur in human diseases. Technologies that will be
covered include DNA and RNA microarrays and next generation sequencing
methods. Other topics will include data visualization and interpretation.
The overall goal of the class is to provide an overview of the cutting edge
technologies currently being developed in basic science laboratories, and
illustrate how these technologies can be used to improve public health.
Students will actively participate in group presentations. There will be
four guest lecturers who will add breadth to the program.

PREREQUISITE: Permission of Instructor
UNITS: 3 U (letter grade)

PHA250_2012_flyer.doc

Wanted – opinions/details on online systems for annotation of genomes and metagenomes

Doing a little survey/snooping around.  Trying to compile a list of available online tools for annotating microbial genomes and metagenomes.  And I am also trying to get comments on what people think of the various tools.  There are some obvious candidates to think about

But given that there are certainly many many more out there I decided to post a request to Twitter and Google plus and got some responses.

And from Google Plus where I asked “Researching blog post on free/online microbial genome/metagenome annotation services – looking for examples beyond IMG & RAST “:

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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.

——–

Worst new omics word award: circomics – running circles around my head

Wow – this is really not a good “omics” word.  Check out this paper title and it’s abstract Circular DNA genomics (circomics) exemplified for g… [Virology. 2012] – PubMed – NCBI

Circomics was coined to describe the combination of rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) and pyro-sequencing to investigate the genome structures of small circular DNAs. A batch procedure is described using 61 plant samples from Asia, South America and Central America which revealed 83 contig sequences of geminiviral DNA components and 4 contig sequences of DNA satellites. The usefulness of this approach is validated for the Brazilian begomoviruses, and the sequence fidelity is determined by comparing the results with those of conventional cloning and sequencing of Bolivian begomoviruses reported recently. Therefore, circomics has been proven to be a major step forward to economize costs and labor and to characterize reliably geminiviral genomes in their population structure of the quasi species.

This definitely fits the category of a “bad omics” word which I have history of complaining about but had been ignoring for a bit.  But I am back.  I am giving “Circomics” a “Worst New Omics Word Award” here because, well, it seems completely unnecessary and distracting.

Hat tip to AJ Cann for pointing this one out on Google Plus.

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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.

——–

Who is hiring research fellows and/or instructors in microbiology?

A colleague emailed me the following question

 “A good friend of mine is looking for a position as a research fellow or instructor in microbiology with an emphasis on teaching. While she’s exploring options herself I figured it couldn’t hurt asking; I usually know who is hiring in [my area of expertise] but this is way outside my usual networks, and from what I’ve been learning positions with an emphasis on teaching are surprisingly rare. Any pointers to departments or groups that might be hiring would be highly appreciated (as are tips on how to find such a position).” 

And alas I did not have a good answer. So, with this person’s permission I am reaching out to the blogosphere to see if anyone has suggestions for good places/sources of information about job openings in teaching and/or research fellow positions in 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.

——–

Social Biology of Microbes 2012 #SocialMicrobes12 wrapup via Storify

Meeting details: 

Welcoming remarks: 

  • David Relman (presentation) (audio)
  • James Hughes (audio)
  • Lonnie King (audio)
  • KEYNOTE: 

Sociomicrobiology: 

  • Quorum sensing, biofilms, and territoriality (presentation) (audio) E. Peter Greenberg, University of Washington
  • Moderator: David Relman DISCUSSION (audio)
SESSION I: Formation and Function of Microbial Communities

  • Moderator: Jacque Fletcher
  • Symbiont community complexity 
    • The fungal gardens of leafcutter ants
      • (presentation) (audio)
      • Cameron R. Currie, University of Wisconsin – Madison
    • The role of oxygen in shaping the structure and function of microbial communities
      • (presentation) (audio)
      • Thomas M. Schmidt, Michigan State University
  • Source-sink dynamics: 
    • Marine invertebrate-associated and free-living chemosynthetic symbionts
    • Colleen Cavanaugh, Harvard University DISCUSSION (audio)
SESSION II: Factors Contributing to Community Stability 

  • Moderator: David Relman
    • Social evolutionary theory, cooperation, and the expression of virulence in microbial communities
    • (presentation) (audio)
  • Sam Brown, University of Edinburgh
    • Ecological factors and processes during evolutionary transitions in Darwinian individuality
    • (presentation) (audio)
  • Paul Rainey, New Zealand Institute for Advanced Study & Max Planck Institute for Evolutionary Biology
    • Evolution of cooperation and control of cheating in the social amoeba:
  • Dictyostelium discoideum
    • (presentation: part 1 part 2) (audio)
    • Joan E. Strassmann, Washington University\
  • Swarming bacteria as freight haulage systems (presentation) (audio)
    • Colin J. Ingham, Wageningen University
    • Emergence and robustness of multicellular behavior in bacteria (presentation) (audio)
  • Joao Xavier, Memorial Sloan-Kettering Cancer Center
    • Mathematical and computational challenges in the study of complex adaptive systems
    • (presentation) (audio)
  • Simon A. Levin, Princeton University
    • DISCUSSION (audio) page2image12752 page2image12912 page2image13072 page2image13232 page2image13392 page2image13552 page2image13712 page2image13872 page2image14032 page2image14192 page2image14352 page2image14512 page2image14672 page2image14832
DAY 2: WEDNESDAY, MARCH 7, 2012
]
SESSION III: 

  • Summary of Day One: David Relman (presentation) (audio)
  • Edith Widder, Ocean Research & Conservation Association
    • KEYNOTE: Glowing corpses & radiant excrement: The role of bioluminescence in microbial communities
    • (presentation) (audio)
    • Moderator: Lonnie King DISCUSSION (audio)page3image6024 page3image6184 page3image6344 page3image6504
  • Jo Handelsman, Yale University
    • Interspecies interactions among rhizosphere and soil bacteria (presentation) (audio
    • Moderator: David Rizzo
  • David Low, University of California – Santa Barbara
    • Contact dependent mechanisms of communication in bacteria (presentation) (audio)
  • Vanessa Sperandio, The University of Texas Southwestern Medical Center 
    • Interactions between symbiotic microbes, their mammalian host, and invading pathogens
    • (presentation) (audio)
    • Moderator: Carole Heilman
  • Jonathan Eisen, University of California – Davis
    • Phylogenetic and phylogenomic approaches to studies of microbial communities
    • (presentation) (audio)
SESSION IV: What More Do We Need to Know about Microbial Community Dynamics?

page3image14888 page3image15048 page3image15208 page3image15368 page3image15528 page3image15688

  • DISCUSSION (audio) 
  • Jared R. Leadbetter, California Institute of Technology
    • Discovery and applications of the metabolic diversity of microbial communities
    • (presentation) (audio)
    • Statistical tools for integrating community networks, spatial and clinical data (presentation) (audio)
  • Jill Banfield, University of California – Berkeley
    • Microbial community assembly and dynamics: From acidophilic biofilms to the premature infant gut
    • (presentation) (audio)
  • David A. Relman, Stanford University
    • Human-microbe mutualism in health and disease (presentation) (audio)
  • DISCUSSION (audio) 
  • Concluding Remarks (audio) 

Just got back from a meeting on the “Social Biology of Microbes”. Here are some notes from my trip and from the talks at the meeting, done via Storify. Here it is as a slideshow: http://storify.com/phylogenomics/social-biology-of-microbes-socialmicrobes2012.js?template=slideshow[&amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;a href=”http://storify.com/phylogenomics/social-biology-of-microbes-socialmicrobes2012&#8243; target=”_blank”&amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;View the story “Social Biology of Microbes #SocialMicrobes2012” on Storify&amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;]

And here it is a a full scrollable presentation


http://storify.com/phylogenomics/social-biology-of-microbes-socialmicrobes2012.js[View the story “Social Biology of Microbes #SocialMicrobes2012” on Storify]

——–
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.

——–

Interesting upcoming conference Exploring Human Host-Microbiome Interactions in Health and Disease

Interesting upcoming conference:

Exploring Human Host-Microbiome Interactions in Health and Disease.

8-10 May 2012 Wellcome Trust Conference Centre
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK

See WT Scientific conferences for more detail.

——–
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.

——–

A day of field guides at #UCDavis and @Wired

Well, how perfect is this.  Today Wired ran a follow up “Birds, Poop and Roadkill: A field guide to Field Guides” to an article that came out last week about my drive for a full field guide to the microbes.  Last weeks article was “Book of Germs: The Quest for a Field Guide to Microbes.”  It is by Daniela Hernandez and was a follow up on my talk at AAAS on “A Field Guide to the Microbes” which you can see on YouTube here.  I wrote a blog post with more detail on my obsession with field guides and microbes here.

While Daniela was writing the article I told her about how I collected field guides.  And I sent her a link to a private album I had made of me and my field guides which I am now making public:

https://picasaweb.google.com/s/c/bin/slideshow.swf

For the follow up Daniela and a photographer from Wired Jon Snyder came to my office and lab and took some pictures of me and my field guides (with assistance from Russell Neches in my lab to help set up some of the “scenes).

Here are some pics from their visit.

And now today, the Wired article came out and and amazing coincidence happened.  I was taking a walk around campus with Misha Angrist who is giving a talk at UC Davis today.  And on the walk first we saw a collection of turkeys wandering around campus:

So my birding sense was turned up.  And then we walked across to the UC Davis Arboretum along Putah Creek and bumped into a “birding tour” of the Arboretum.  In six years here I have never seen one of these.  There were some teachers and kids carrying around field guides looking for particular species of birds.

And I note – one even had a field guide I do not have – the “Birds of Northern California” which I will be getting very very soon.  I think today will only serve to boost my obsession with field guides, but that is OK by me.

I note – I love the Wired photo spread of my field guides and my lab.  I particularly am happy that they includes some of the funnier field guides out there like “Flattened Fauna.” And I am glad they got in Betsy Dyer’s Field Guide to Bacteria because it is one of my favorite field guides of all time.  Thanks to Russell Neches for helping out with it and Daniela Hernandez and Jon Snyder for their work.

——–
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.

——–

Social Biology of Microbial Communities

Off to DC for a meeting on the “Social Biology of Microbial Communities” and I thought people out there might like to see the schedule.  Going to try to live blog/tweet so stay tuned …

——–
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.

——–

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.

——–

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 
——–
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.

——–