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

Love these QTL experiment where microbe relative abundance is the quantitative trait being studied

Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group.  I really really love this new approach of doing QTL experiments where the quantitative trait being measured is the relative abundance of various microbes.  The first paper of this kind I know of that did such a QTL analysis was Benson et al. 2010 in PNAS in mouse.  There have been a few others using this approach (e.g., Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits) and I am sure we will see many many more.  Basically this approach allows one to identify genes / polymorphisms / regions of the genome in a host that influence the relative abundance of specific microbes.  And such information will be critical in understanding the interactions of microbial communities with hosts.

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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.

——–

Assistant Professor Position in #Microbiology at UC Berkeley

Just got this ad — for a faculty position in the Department of Plant and Microbial Biology at UC Berkeley. Looks interesting. Though of course if you are really good in microbiology you should really consider applying for the open position at UC Davis in the same area.

See https://recruit.ucdavis.edu/apply/JPF00129/

And a PDF of the UC Davis ad:
http://microbiology.ucdavis.edu/wp-content/uploads/2013/05/ad-for-assistant-professor.pdf

Davis has some seriously amazing stuff going on in microbiology these days across diverse Departments and programs including

* a great Microbiology graduate group
https://myhs.ucdmc.ucdavis.edu/web/microbiology-graduate-group/home

* critical mass of people enough to have an annual retreat in host-microbe interactions with >100 participants
http://www.ucdmc.ucdavis.edu/medmicro/microbial%20affiliation/host_microbe_retreat_mr.html

* researchers focusing on microbial questions across many schools including the Medical School (e.g., the Med. Micro. and Immunology department http://www.ucdmc.ucdavis.edu/medmicro/ which I am part of) which just hosted a nice workshop on mucosal health
http://www.cevs.ucdavis.edu/confreg/?confid=651 and the Vet. School (e.g., http://www.vetmed.ucdavis.edu/pmi/) and the College of Biological Sciences (http://microbiology.ucdavis.edu)

I could go on and on … Microbiology is going bonkers at UC Davis …
BerkeleyPMBMicroAd.pdf

Bioinformatics Facility Director Position at UC Riverside

POSITION ANNOUNCEMENT

The Institute for Integrative Genome Biology (IIGB) at the University of California, Riverside is seeking a Ph.D. level bioinformatician to coordinate its bioinformatics research activities, data analysis workshop program and computing facility.

TITLE/RANK
Bioinformatics Facility Director. Salary will be competitive and commensurate with accomplishments.

LOCATION
IIGB at the University of California, Riverside.

BACKGROUND
Successful candidates will join an innovative and multidisciplinary Institute for Integrative Genome Biology (IIGB) that connects theoretical and experimental researchers from different departments in Life, Physical and Mathematical Sciences, Medicine, Engineering and various campus based Centers. The IIGB is organized around a 10,000 sq.ft. suite of Instrumentation Facilities that serve as a centralized, shared-use resource for faculty, staff and students, offering advanced tools in bioinformatics, microscopy, proteomics and genomics. Its bioinformatic component is equipped with a modern high-performance compute (HPC) infrastructure.

QUALIFICATIONS
Applicants must have a Ph.D. from a recognized university in bioinformatics; or combined degrees in computer science and a biological science; or a degree in either computer science combined with relevant experience in biological science; or a degree in a biological science combined with relevant experience in computer science. The successful candidate will have at least two years professional hands-on experience with next generation sequence data analysis, and basic knowledge of high-performance computing and cloud computing technologies. Another requirement is several years of professional experience with common programming languages/environments used in scientific data analysis, such as Python, R or C++. Experience with web development frameworks and relational database design will also be a plus.

RESPONSIBILITIES
The Bioinformatics Facility Director leads IIGB’s bioinformatics facility staff and manages its computational infrastructure. The incumbent will engage in collaborative research activities, contribute to scientific publications, and participate in the preparation of joint grant applications. The teaching expectations include the development of a state-of-the-art workshop program on scientific data analysis.

TO APPLY
Review of applications will begin October 11, 2013 and continue until the position is filled. Interested individuals should: (1) submit a curriculum vitae, (2) provide a statement of research interests, and (3) arrange to have three letters of reference sent on their behalf. All information should be addressed to:

Thomas Girke
Institute for Integrative Genome Biology
University of California
Riverside, CA 92521
thomas.girke@ucr.edu

WEBSITE
http://facility.bioinformatics.ucr.edu/position-opening

POLICY
The University of California is an Equal Opportunity/Affirmative Action Employer. In accordance with Federal law, we are making available our Campus Security Report to all prospective employees.

Who are the microbes in your neighborhood? Quite a few are from Melainabacteria – a new phylum sister to Cyanobacteria

I just love this paper … The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | eLife from the labs of Ruth Ley and Jill Banfield (1st author is the co-first authors are Sara C. Di Rienzi and Itai Sharon).  It represents a landmark study in something that has intrigued many microbial diversity / human microbiome researchers for many years.  Early in the history of sequencing rRNA genes from human microbiome samples, researchers discovered something a bit weird – quite a few sequences were coming from what appeared to be close relatives of Cyanobacteria.  This was weird because all known Cyanobacteria were thought to be photosynthetic and – well – there is not too much light in the human gut.

Now – one possible explanation for this was that these sequences were coming from photosynthetic bacteria but these bacteria were not residents of the human gut but came via consumable items (i.e., food and drink).  Perhaps they were actually from chloroplasts of something in the diet (after all – chloroplasts are derived versions of cyanobacteria). This idea was discussed at many meetings I attended.  But there was no evidence for this.  Another possibility was that there was in fact some light in the human gut – leaking through from the outside or being produced from the inside. And perhaps this was enough to do a little photosynthesis.  Sound crazy?  Well, not so crazy after reports of photosynthesis in the deep sea.  A third possibility was that these sequences were coming from residents of the human gut that were related to (or even within) cyanobacteria but were not photosynthetic.  More detail on possible explanations are in this new paper and in some of the material cited therein.

Anyway – Ruth Ley has been discussing these unusual sequences for years and now in this paper her group and the group of Jill Banfield at Berkeley (along with some others) has used metagenomics and detailed assembly and phylogenetic analysis to reveal many new insights into these sequences.  I could write much more about this.  But, I think the paper really speaks for itself.  And it is open access so anyone and everyone can check it out.  And you should.  It is wonderful.

Fig 2 from Di Rienzi et al.

UPDATED 10/9/2013 to correct that there were co-first 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.

——–

Faculty positions in Bioinformatics/Computational Biology at the new Francis Crick Institute in London

Faculty positions for Bioinformatics and Computational Biology Francis Crick Institute group leaders at the CRUK London Research Institute

An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis.

The Francis Crick Institute http://www.crick.ac.uk
The Francis Crick Institute will open at St Pancras in central London in 2015. Its research will use interdisciplinary approaches to investigate the biology of human health and disease, supported by core funding from CRUK, the MRC, and the Wellcome Trust, and by grants from UK and international funding agencies.

The Crick is expanding Computational Biology research as a key component of its scientific strategy. The institute will offer an outstanding environment for computational research, with excellent opportunities for wet/dry collaborations across the range of biomedical and clinical research disciplines, supported by a strategic alliance with the Wellcome Trust Sanger Institute. The new Crick laboratories will feature excellent computational facilities including a state-of-the-art data centre.

The London Research Institute http://www.london-research-institute.org.uk The London Research Institute (LRI) is the largest Cancer Research UK research institute, with 40 research groups focusing on fundamental cancer biology. The Institute is based in well-equipped laboratories at Lincoln’s Inn Fields in central London, and at Clare Hall in Hertfordshire.

Computational Biology in Cancer http://tinyurl.com/ohgnxw8
An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. The LRI recruitment process for 2013 will carried out jointly with the Crick Institute. We shall appoint outstanding scientists seeking to establish independent and innovative research programmes focussed on:

Newly appointed group leaders will receive core funding for research personnel, travel and consumables, and access to the Institute’s comprehensive computational core facilities, backed by competitive employment terms. The new group leaders will move to the Crick laboratories in 2015.

Website: http://tinyurl.com/ohgnxw8
Application deadline: 22 November 2013
Informal enquiries may be made by e-mail to nicholas.luscombe@cancer.org.uk

Crick-CompBio-Faculty-2013.pdf

The government shutdown of science – a screenshot gallery

https://static.googleusercontent.com/external_content/picasaweb.googleusercontent.com/slideshow.swf

See full screen slideshow via Picasa here. Individual pics below:

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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.

——–

Bioinformatician / graduate student/ post-doc openings at Ohio State in microbial community genomics

Kelly Wrighton, a new faculty member at Ohio State is looking to hire a bioinformatician and also looking for graduate students and a post doc to work on various aspects of microbial community genomics.

The job ad:

Title: Research Associate 2-B/H
Department: Microbiology Admin
Posting Number: 378550

Performs analysis and interpretation of high throughput genomic data; develops experimental procedures and analyzes data; translates biological questions into computational goals using existing methods or developing new algorithms and tools when existing methods are inadequate; designs, develops, modifies, tests, evaluates and maintains customized scripting programs for analyzing, preparing, converting biological data (Illumina and other NGS platforms) for import and export; trains and assists research group members in UNIX/Linux methodologies; performs system administration work including interfacing with collocation facility; orders supplies; configures new computers; maintains quality assurance documentation.

If you are interested in this position, you can apply on our employment site at: www.jobsatosu.com

 

If you don’t know Dr. Wrighton, well, you should.  She is brilliant and has done some phenomenal work on microbial diversity.  See her Google Scholar page here and her faculty page here. And check out the paper I co-authored with her (and many others):  Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. 

Interesting faculty job at UCLA focusing on those w/ commitment to underrepresented/ underserved mentorship

Life Sciences Open Rank Tenure Track Faculty Position Job Announcement
University of California Los Angeles

The Division of Life Sciences in the UCLA College of Letters and Sciences announces the continuance of its special initiative to recruit excellent research scientists with a history and commitment to the mentorship of students from underrepresented and underserved populations. Candidates should have outstanding records of scholarly publications, research support, and teaching and be eligible for Academic Senate appointment in one of the following departments of Life Sciences

See flyer: MentorProfessor-ad-2013rev2

A message from UC President Napolitano

Figured this was worth posting:

 

Figured this was worth posting:

———- Forwarded message ———-
From: Office of the President – Strategic Communications <communications@ucop.edu>
Date: Mon, Sep 30, 2013 at 10:40 AM
Subject: A message from UC President Napolitano
To: “UC Davis Faculty, Staff and Students”

September 30, 2013

UC COMMUNITY OF LEARNING

Dear Friends:

It is a privilege and an honor to write to you today, my first day as the twentieth President of the University of California. I am both excited and humbled by the challenges and opportunities that lie ahead. I look forward to working with you.

I bring many things with me to California, beginning with an unshakeable belief in the transformative power of education. I also bring a deep appreciation for the greatness of this university, and for what that has meant, and will mean, for the past, present, and future of the state, the nation, and the world.

It is my intent, beginning today, to serve as the strongest advocate possible for the University of California, ready to stand up at every opportunity on its behalf, in any venue that will have me. Together, let us strive not only to maintain UC’s position as the world’s premier public university, but also to push the University forward to ever new heights. The University of California, and California itself, expect and deserve nothing less from all of us.

Very truly yours,

Janet Napolitano
President

Time for a Nobel Prize for the human microbiome? I think so … what do you think?

Well, previously I have written about how I thought that there should have been a Nobel Prize awarded  to Carl Woese and Norm Pace for pioneering work on microbial diversity.  See for example “Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize“.  Alas Carl Woese passed away recently and is no longer eligible.  However, in a way this opens up things to a perhaps more medical driven Nobel prize in Medicine for the microbiome.  I believe that the human microbiome has been shown to be important enough in medicine to be deserving of a Nobel Prize in medicine.

And if that is true, then we can ask “Are there any people who would deserve a prize in this area?”  And the answer is pretty clearly yes.  I would suggest that there are two people who deserve such a recognition: Norm Pace and Jeff Gordon.  Norm Pace for his pioneering work on characterizing microbes indirectly via sequencing their RNA and DNA, especially their ribosomal RNA genes.  And Jeffrey Gordon for his pioneering work on animal and the human micro biome and in showing that the microbiome plays fundamental roles in animals and human health and phenotypes.

I will write more about this later but just wanted to get this thought out there … and see what people think.

UPDATE September 2015 I note. I have been and continue to be concerned with the spread of “microbiomania” which is the term I use to refer to “Overselling the Microbiome“. Even though this still is a problem, I also believe the microbiome has now been clearly shown to be critically important to human health in diverse ways and I do think it is appropriate to award a Nobel Prize in this area.

Also note Reuters is reporting that Jeffrey Gordon is on their candidate list this year (based on ISI predictions).

——–
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.

——–