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

Three talks, 1.5 days at #ISMB … phylogeny, phylogenomics, open science and more

Gave three talks in 1.5 days here in Long Beach as part of the satellite meetings associated with the “Intelligent Systems for Molecular Biology” (ISMB) 2012 Conference. I will write more about the meeting and the craziness of giving three very different talks in 1.5 days. But for now I wanted to at least get my talks posted here since I posted the slides to slideshare and recorded the audio in synch with the slides and posted these “slideshows” to YouTube. Here are the talks below:

Talk 1 for the “Bioinformatics Open Source Conference” BOSC2012.  Was asked to talk about Open Science … so … I did …

Slides: Jonathan Eisen talk on “Open Science” at #BOSC2012 #ISMB

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Slideshow with audio:
 

Talk 2 for the Student Council Symposium SCS2012. Sort of supposed to be a career guidance discussion so I geared my talk on the lines of “lessons learned” …


Slides:Jonathan Eisen talk for #SCS2012 at #ISMB “Networks in genomics and bioinformatics: from phylogeny to Twitter”

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Slideshow with audio:

Talk 3 for the “Automated function prediction” AFP2012 satellite meeting.  I decided to talk about phylogenetic and phylogenomics approaches to functional prediction …

Slides:Jonathan Eisen talk “Phylogneomic approaches to functional prediction”a #AFP2012 #ISMB

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Slideshow with audio:

http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings.js[<a href=”http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings” target=”_blank”>View the story “Jonathan Eisen @phylogenomics talks at #ISMB Satellite Meetings” 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.

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My new paper in #Gigascience: #Badomics words and the power and peril of the ome-meme

I have a new paper in the new Open Access journal Gigascience:  GigaScience | Full text | Badomics words and the power and peril of the ome-meme.  It is basically a text version of my obsession with #badomics words.

It was inspired by a paper also in this first issue of Gigascience The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome by Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J Caporaso.

For more on my obsession with badomics words see some of these earlier posts:

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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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Posted to Twitter, FB, etc but had to post to blog too: best genomics Venn Diagram ever

Words do not do this justice.  This is just stunning.
From here.
Ref: “The banana (Musa acuminata) genome and the evolution of monocotyledonous plants” Nature 2012 doi:10.1038/nature11241
Also see this Storify.
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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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Lake Arrowhead Microbial Genomes 2012 #Genomes #Microbes #Mountains #Lake #Fun #Wine #MustGo

Helping the organizers plan the Lake Arrowhead Microbial Genomes meeting this year (see Microbial Genomics – ARROWHEAD 2012).  In particular I organized a session on Microbiology of the Built Environment relating to the http://microbe.net project.

This session should be good

  • Session Chair: Jonathan Eisen – University of California, Davis, CA “Alfred P. Sloan Foundation Workshop”
  • Anne M. Womack – University of Oregon, Eugene, OR “Microbial Ecology of the Built Environment”
  • Jason E. Stajich – University of California, Riverside, CA “Fungi in the Built Environment”
  • Laura Sauder – University of Waterloo, Waterloo, Ontario “Archaea in the Built Environment”
  • Scott Kelley – San Diego State University, San Diego, CA “The Indoor Microbiome: Bacterial and Metagenomic Approaches for Studying the Built Environment”
  • Susanna Remold – University of Louisville, Louisville, KY “Pseudomonas as a Model for Studies of Microbes in the Home”

And the other sessions that the meeting also look good (see program here).  But whatever you think of the speaker list, the best part of the Lake Arrowhead meetings is the venue and the interactions among people.  I have been going to this meeting for many years and here are some posts of mine about previous meetings

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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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Can food safety be fun? Not sure, but this video is OK. #microbes

Continuing with my running theme of microbe-related music videos here is another one. It has good and bad parts. But then again, don’t we all …

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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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#UCDavis Fall2012 Intro to Bio: Principles in Ecol & Evol (BIS2B) Temp Lecturer Position

Google/ Blogger "Dynamic Views" – Fancy but limited

So – I keep switching back and forth between the current view on my blog and Google’s “Dynamic Views” system.  Right now I am annoyed with the Dynamic Views so switched it off.

To see Dynamic Views check out

Each has its benefits but the whole Dynamic Views system is incompatible with many things I would like to do with my blog – examples include embedding Storify stories (the embeds don’t work in dynamic views); jump breaks (to show only the beginning of a story with a species transition point); and much more. 
So – anyway – apologies for switching back and forth.  Still playing with what to have as a default …
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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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Visit to Capitol Public Radio HQ & appearance on "Insight" w/ @CapRadioRuyak

Just got back from a brief visit to Sacramento (which is 15 minutes or so my where I live in Davis, CA). I had a mini 10 minute or so appearance on “Insight” a radio show on Capitol Public Radio.

My visit all started maybe a few weeks ago when I bumped into Lin Weaver in Davis.  Lin was showing some friends of hers around Davis and we chatted for a while on the sidewalk.  One of the topics was my recent fun giving a Tedmed talk.

Anyway – we chatted for 15-20 minutes or so and then I headed home.  And a few days later I got an email from Lin inviting me to be a guest on Insight.  Cool.  I love the show – and listen to it whenever I can.  So I said I had to check some details and then got back to her later and said “yes.”

Lin and the folks at Capitol Public Radio then sent me some additional details and asked for some links to use for their website.

And this AM I headed on in to town.  I was asked to get to their studio at 9:45 AM.  Their studio is on the campus of Sacramento State and I headed on in early and got their at about 9:30.  Of course – I took some pics and posted some stuff to twitter …

Got a parking permit at the desk and then was led into the back of the building to
“The Green Room” and got a look at the studio:

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And of course posted to twitter 

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I then relaxed in the Green room.  A few minutes before ten the host of insight Beth Ruyak came by.  She instantly made me relax about the interview (was not stressed per se, but somehow felt even more relaxed after the minute with her).  She told me I would be up second and then she left to get ready for the show. 
I took some more pictures and posted a few more tweets

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I continued to hang out in the Green Room and got to listen to the interview with the previous guest – Marcos Breton – a reporter for the Sacramento Bee who’s stuff I actually know a little bit of since he covers baseball.

While listening to them chatting away on the air, I decided to add some microbes to the Insight guest book:

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And then the assistant producer came out and told me it was almost time to go into the studio.  And then I was in.  Sat down and talked for 10 or so minutes with Ruyak.  We talked about diabetes, microbes, me, twitter, and more. And then it was over.

I took a few pics of the office on the way out:

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And that was it.

And it seems it is already on the web.

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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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Extra fruit in your trees? Don’t let it rot – donate it #DavisCA #VillageHarvest

Today, one of our neighbor came over and told us that the “Village Harvest” group was at their house to collect fruit from their trees and she wanted to know if they could come into our yard as part of the collection.  I said “please … and tell them they can collect from our tree too.”  You see, we have a pluot tree that produces more fruit than I can keep up with (and I note – we get a lot of the pluots from our neighbors tree too since it leans over our yard).  I have made 40+ jars of jam, 40+ fruit rolls, froze a bunch of pulp for later projects and still there was more fruit.  So I invited people over to collect some of the pluots and still there was more fruit.  So I was very happy to see the Village Harvest folks next door.  

Village Harvest is a ” a nonprofit volunteer organization in the greater San Francisco Bay Area which harvests fruit from backyards and small orchards, then passes it along to local food agencies to feed the hungry.”

And they have a Davis chapter: http://www.villageharvest.org/davis/

And so they came over and started collecting some of the pluots and I took some pictures and video of the event …

 

Definitely going to sign up for this for all cases when we can’t use all of our fruit …

Img_4275 Img_4270 Img_4274 Img_4272 Img_4276 Img_4271 Img_4278 Img_4277

See the full gallery on Posterous

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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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Possibly new (not sure) connection between colic and Helicobacter pylori infections

Interesting article: JAMA Network | Archives of Pediatrics & Adolescent Medicine | Helicobacter pylori and Infantile Colic.  The study basically suggests that infants with colic have a much higher incidence of Helicobacter pylori infections than do a control group of infants.  No causal relationship was established – just a correlation.

The article has been picked up by a few bloggers/news sources such as:

I was surprised that this was suggested to be a completely new connection – between HP and colic.  Given the amount of work on HP this just seemed odd.  So of course I decided to snoop around the web.  And I found a few things that were related especially:
So it seems that others have noticed a possible connection between HP and colic previously.  But in the end there is not a lot of literature out there on the topic.   If anyone out there knows anything else on this topic, please post …
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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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