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

Bad Ome-like word of the week: symbiome

Well I got pointed to this paper: Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome

And as many might guess – the word “symbiome” did not sit well with me.  Alas, they don’t define it in the paper.  So I can’t really quibble with their definition.  But I did find some other stuff out there that, well, at least helps see how other people are using the word:

I can’t really tell from most of these if “symbiome” can be a useful term or not sometimes.  Certainly the iPhylo example above has potential.  But in general, the word seems awkward at best.  Now – as far as I can tell, nobody is using it in the context of “genomics” so this does not fit in with my “badomics” obsession.  But it still does not make me feel warm and fuzzy so I am going to give it a pseudo-award – the Bad Ome-like word award.

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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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Outreach & Communication for K-12 Students Workshop for Grad Students & Postdocs

Next phyloseminar: Ed Delong on Carl Woese 5/13

Next talk on http://phyloseminar.org

"How Carl Woese transformed the field of microbial ecology"
Ed DeLong (MIT)

The challenges of dissecting naturally occurring microbial
assemblages, with respect to their community composition, interspecies
interactions, functional attributes, and activities, are numerous and
daunting. For many years, these challenges impeded our understanding
of the properties and dynamics of microbial communities, and thus
hindered development of the field of microbial ecology. Enter Carl
Woese: the theory and application of molecular phylogenetics and
genomics in studies of microbial evolution and ecology can be traced
directly to Woese and one of his primary collaborators, Norman Pace.
This lecture will trace the logic and roots of the application of
molecular phylogenetics and genomics to the study of microbial
ecology, through a historical review and examination of its past and
current applications.

West Coast USA: 10:00 (10:00 AM) on Monday, May 13
East Coast USA: 13:00 (01:00 PM) on Monday, May 13
UK: 18:00 (06:00 PM) on Monday, May 13
France: 19:00 (07:00 PM) on Monday, May 13
Japan: 02:00 (02:00 AM) on Tuesday, May 14
New Zealand: 05:00 (05:00 AM) on Tuesday, May 14

Seminar at #UCDavis 5/7 – David Botstein

Special Seminar

Department of Microbiology and Molecular Genetics

*Note the special time and day

Dr. David Botstein
(Anthony B. Evnin Professor of Genomics)

"Coordination of Growth Rate, Stress Response and Metabolic Activity in Yeast"

Tuesday, May 7, 2013

10:00 am

1022 Life Sciences

Botstein 5-7-13.doc

Storified tweets from the #UCDavisADVANCE Symposium on Increasing Diversity of STEM Faculty

I live tweeted a symposium at UC Davis yesterday that was part of the UC Davis ADVANCE project to increase diversity of STEM Faculty. Here are the notes.

  //storify.com/phylogenomics/ucdavisadvance-symposium.js[View the story “#UCDavisADVANCE symposium” on Storify]

For more on the project see

——–
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.

——–

So cool – NSF has a program to provide supplemental funds when CAREER PIs go on family leave

Just got pointed to this by Siobhan Brady from UC Davis:

US NSF – Dear Colleague Letter: FY 2013 Career-Life Balance (CLB)-Faculty Early Career Development Program (CAREER) Supplemental Funding Requests (nsf13075)

It is an NSF program to

“The purpose of this DCL is to announce the continuation of the supplemental funding opportunity initiated in FY 2012 for PIs supported in the CAREER program. CAREER Principal Investigators (PIs) are invited to submit supplemental funding requests to support additional personnel (e.g., research technicians or equivalent) to sustain research when the PI is on family leave. These requests may include funding for up to 3 months of salary support, for a maximum of $12,000 in salary compensation. The fringe benefits and associated indirect costs may be in addition to the salary payment and therefore, the total supplemental funding request may exceed $12,000.”

This is part of a larger program on Career-Life Balance:

Instituted in 2012, NSF’s Career-Life Balance (CLB) Initiative is an ambitious, ten-year initiative that will build on the best of family-friendly practices among individual NSF programs to expand them to activities NSF-wide.  This agency-level approach will help attract, retain, and advance graduate students, postdoctoral students, and early-career researchers in STEM fields.  This effort will help reduce the rate at which women depart from the STEM workforce.  By the end of this ten-year initiative (2021), it is expected that women will represent 41 percent of newly tenured doctoral S&E faculty—the same percentage as the available pool of women S&E doctorate recipients in 2009; and that women of color will comprise 17 percent of newly tenured faculty, the same percentage of their PhD production rate in 2009.  Further information on the CLB initiative may be found on the Foundation’s website.  

The primary emphasis of NSF’s CLB initiative in FY 2012 was focused on opportunities such as dependent-care issues (child birth/adoption and elder care).  These issues initially were addressed through NSF’s Faculty Early Career Development (CAREER) program, where career-life balance opportunities can help retain a significant fraction of early career STEM talent.  In FY 2013, the Foundation intends to further integrate CLB opportunities through other programs such as the Graduate Research Fellowship and postdoctoral fellowship programs, as well as expand opportunities such as dual career-hiring through the Increasing the Participation and Advancement of Women in Academic Science and Engineering Careers (ADVANCE) program.  Each of these opportunities will be described and implemented separately.

I am involved in the UC Davis ADVANCE program (minor advisory role) and am always on the lookout for ways that institutions and fundings agencies try to increase representation of women and minorities in STEM fields so if you know of other examples – please post details.

——–
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.

——–

If you are into microbial diversity and use R this may be worth checking out: phyloseq

Just got pointed (by the lead author) to this new paper: PLOS ONE: phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Abstract:

Background
The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.
Results
Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.
Conclusions
The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

Seems similar in some ways to the WATERs Kepler Workflow that we released a few years ago.   Anyway – if you use R and are into microbial diversity studies this may be worth checking out.  As a bonus – it has a strong emphasis on reproducibility – which is a good thing.

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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.

——–

Quick post: interesting article in Smithsonian on the human microbiome by Richard Conniff

Just q quick post here.  There is an interesting article about the human microbiome worth checking out: Microbes: The Trillions of Creatures Governing Your Health.  By Richard Conniff in Smithsonian Magazine. It also comes with some related videos and pictures. See for example http://player.ooyala.com/player.js?height=288&deepLinkEmbedCode=4zdTgwYjrLemfva768KtaJ1Lk_La8Ql1&width=512&embedCode=4zdTgwYjrLemfva768KtaJ1Lk_La8Ql1&video_pcode=VmM2U6ccX_RqI0rIzEgAxHoRsgRL and http://player.ooyala.com/player.js?height=288&deepLinkEmbedCode=41dTgwYjrKdXobNOQAlckTqHsXUsOKFk&width=512&embedCode=41dTgwYjrKdXobNOQAlckTqHsXUsOKFk&video_pcode=VmM2U6ccX_RqI0rIzEgAxHoRsgRL And it references my “Overselling the microbiome” award …

When a scientific team recently suggested that changes in gut bacteria could protect against stroke, Jonathan Eisen of the University of California at Davis lambasted them for “absurd, dangerous, self-serving claims that completely confuse the issue of correlation versus causation.” Eisen, a specialist in microbial genomics, now regularly presents “overselling the microbiome” awards on his blog. He says he doesn’t doubt the ultimate importance of the microbiome: “I believe the community of microbes that live in and on us is going to be shown to have major influences.” But believing that “is different from actually showing it, and showing it doesn’t mean that we have any idea what to do to treat it. There is danger here.”

And it even discusses a fecal transplant-like treatment called RePOOPulate. What could be better? Anyway – definitely worth checking out.

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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.

——–

Goodbye EL Konigsburg

ElKonigsbergElKonigsberg2ElKonigsberg4ElKonigsberg3Sad to hear that EL Konigsburg died a few days ago.  She was one of my favorite authors when I was a kid.  Here is a note I kept from her that she wrote (when I was very young) after I had written her a letter about loving her books …ElKonigsburg

Announcement: Intntl. BioInformatics Workshop on Virus Evolution & Molecular Epidemiology

This looks pretty good:

18th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
University of Florida, Emerging Pathogens Institute
Gainesville, Florida, USA.
August 25th – August 30th, 2013

Bioinformatics Methods Applied to Virology and Epidemiology

We are announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainsville and sponsored by several local partners.
We plan to organize a ‘Phylogenetic Inference’ module that offers the theoretical background and hands-on experience in phylogenetic analysis for those who have little or no prior expertise in sequence analysis. An ‘Evolutionary Hypothesis Testing’ is targeted to participants who are well familiar with alignments and phylogenetic trees, and would like to extend their expertise to likelihood and Bayesian inference in phylogenetics, coalescent and phylogeographic analyses (‘phylodynamics’) and molecular adaptation. A ‘Large Dataset Analysis’ module will cover the more complex analysis of full genomes, huge datasets of pathogens including Next Generation Sequencing data, and combined analyses of pathogen and host. Practical sessions in these modules will involve software like, PHYLIP, PAUP*, PHYML, MEGA, PAML or HYPHY, TREE-PUZZLE, SplitsTree, BEAST, MrBayes Simplot and RDP3.
We recommend participants to buy The Phylogenetic Handbook as a guide during the workshop, and to bring their own data set.
For further information and applications we refer to a dedicated website that will be announced here soon.
Abstract and application deadline is April 30th.
Selections will be made by end of May 2013.
The registration fee of 1000 USD covers attendance, lunches and coffee breaks.
Participation is limited to 25 scientists in each module and is dependent on a selection procedure based on the submitted abstract and statement of motivation. A limited number of grants are available for scientists who experience difficulties to attend because of financial reasons.
For further information and applications we refer this website: http://conferences.dce.ufl.edu/vemei/http://conferences.dce.ufl.edu/veme/ 
——–
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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