Bioinformatics Jobs in Berkeley

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Digest from the bioinformatics mailing list:
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Date: Tue, 06 Nov 2007 15:45:44 -0800
From: Iddo Friedberg 
Subject: BioinfoList: Bioinformatics Programmer Position at UC
 Berkeley
To: bioinformatics@sdsc.edu
Message-ID: <4730fca8.7000009@burnham.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

University of California Berkeley
USA-California-Berkeley
Bioinformatics Programmer
Programming, database support and web programming for the PhyloFacts
resource (http://phylogenomics.berkeley.edu/phylofacts).

The aim of PhyloFacts is to integrate experimental data from across the
Tree of Life, to organize genes and their associated annotations into
hyperdimensional networks with connectivity based on homology, pathway
participation, evidence of protein-protein interaction, genomic locus,
etc. This will provide a framework for biologists to make specific and
powerful inferences of function and structure, with wiki-based
technology to support virtual collaborations.

This endeavor requires the development of new machine learning methods,
the integration of diverse experimental data, intuitive user interfaces,
information visualization and a robust computational infrastructure.

To achieve these goals we have gathered a diverse group of
investigators. Our members include PhDs and students in computer
science, math and different areas of biology. We collaborate with
experimental biologists, statisticians and other computational
biologists both at Berkeley and at other institutions. Our international
collaborations include investigators in Brazil, Mexico, Sweden, France
and the UK.

The programmer to be hired will participate in the development and
testing of new computational methods for protein structure prediction,
active site detection, evolutionary analysis and pathway prediction. We
are looking for someone who is excited about science, and enjoys working
in an interdisciplinary environment.

Required: Experience in managing large complex MySql databases. Strong
programming skills are essential (at least one of C, C++, Java or
equivalent) and experience in scripting languages (e.g., Perl, php or
Python). Previous participation in large programming projects a plus.
Communication skills are important.

Valuable but not required: Experience in bioinformatics methods such as
multiple sequence alignment, HMM construction, phylogenetic tree
construction and protein structure prediction. Training in statistics,
algorithms, data structures or machine learning is a big plus.

Contact Information
University of California Berkeley
Bioengineering
Kimmen Sjolander
phylo@phylogenomics.berkeley.edu
http://phylogenomics.berkeley.edu/phylofacts/index.php

How To Apply: Please send your resume, including a detailed description
of your programming background and database administration expertise,
and contact information (including email addresses) for three references
to phylo@phylogenomics.berkeley.edu.


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Date: Tue, 06 Nov 2007 15:50:17 -0800
From: Iddo 
Subject: BioinfoList: Postdoc position at UC Berkeley
To: bioinformatics@sdsc.edu
Message-ID: <4730fdb9.2040806@ucsd.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

University of California Berkeley
USA-California-Berkeley
Postdoc in microbial phylogenomics
We are seeking a postdoctoral scholar with a strong background in
microbiology (particularly prokaryotic) to participate in the
development of a microbial phylogenomic encyclopedia, funded by a grant
from the USDA-NSF Microbial Genome Sequencing Program. This is an
extension of the PhyloFacts resource funded by the NIH to model protein
families in animal genomes. Our funding is for three years.

The aim of PhyloFacts is to integrate experimental data from across the
Tree of Life, to organize genes and their associated annotations into
hyperdimensional networks with connectivity based on homology, pathway
participation, evidence of protein-protein interaction, genomic locus,
etc. This will provide a framework for biologists to make specific and
powerful inferences of function and structure, with wiki-based
technology to support virtual collaborations.

This endeavor requires the development of new machine learning methods,
the integration of diverse experimental data, intuitive user interfaces,
information visualization and a robust computational infrastructure.

To achieve these goals we have gathered a diverse group of
investigators. Our members include PhDs and students in computer
science, math and different areas of biology. We collaborate with
experimental biologists, statisticians and other computational
biologists both at Berkeley and at other institutions. Our international
collaborations include investigators in Brazil, Mexico, Sweden, France
and the UK.


This postdoctoral scholar will participate in the development and
validation of new computational methods for protein structure
prediction, evolutionary tree construction, pathway inference and more;
write papers describing the evolution of specific gene families; assist
in the supervision of graduate student project; and contribute lectures
to an undergraduate bioinformatics class.

The PhyloFacts resource is online at
http://phylogenomics.berkeley.edu/phylofacts/

Required: A PhD in microbiology or related field, with experience in
comparative genomics and bioinformatics methods. Strong writing and oral
presentation skills are necessary.

Helpful but not required: Experience in programming and/or scripting
languages.


Contact Information
University of California Berkeley
Bioengineering
Kimmen Sjolander
phylo@phylogenomics.berkeley.edu
http://bpg.berkeley.edu/postdoc.html
How To Apply: Your cover letter or CV should present your:
* training in molecular and cell biology
* specific knowledge of prokaryotic biology and evolution
* skilled use of bioinformatics and genomics methodologies and technologies
* publication record (highlighting any papers you have written
personally or to which you have made major contributions)
* oral presentations at meetings
* programming skills
* ability to work well in a collaborative environment with people from
different scientific and cultural backgrounds

Email your CV and contact information for three references to
phylo@phylogenomics.berkeley.edu.