Home Postdoctoral Positions in Metagenomic Informatics
Microbes play fundamental roles in all biology-associated processes on the planet. A powerful new tool in such studies is metagenomics wherein one uses high throughput DNA sequencing methods on DNA isolated directly from environmental samples. Metagenomics has the potential to revolutionize our understanding of the normally hidden yet incredibly important world of microorganisms. However this great potential comes with enormous challenges in the analysis of the sequence data, including (i) the fragmentary nature of sequence data, (ii) the sparse sampling of genomes, populations and communities, and (iii) the unknown phylogenetic diversity and ecological structure of the communities being sampled.
We are seeking five post-doctoral scientists and a bioinformatics engineer to work on methodology for analysis of metagenomic data as part of a new collaborative project: Integrating Statistical Evolutionary, and Ecological Approaches to Metagenomics (iSEEM). The iSEEM Project, funded by the Gordon and Betty Moore Foundation, takes an integrated, interdisciplinary approach to metagenomic analysis. We will be working with the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) to make any methods we develop available to the broader community. The project spans three labs, each with different areas of focus and two institutions (UC Davis and U Oregon). Each position will be associated with one of the PIs at their home institution.
More information available at:http://iseem.org
Qualifications
We are looking for people with a demonstrated interest in working at the interface between the quantitative and biological sciences. We will offer a generous salary and benefits commensurate with experience.
Postdocs: Applicants should have a PhD in a biological, computational, mathematical, or statistical field. Programming skills are highly desirable.
Bioinformatics Engineer: Applicants should have substantial experience with database programming (e.g. SQL), scripting (e.g. Perl or Python), and bioinformatics tools.
Term
Appointments will last 2 years beginning in Summer 2008.
To Apply
Please apply using our online application system. You will be asked for:
(1) a brief cover letter explaining your background, career interests, and preferred geographical location for work (if any),
(2) CV (including publications),
(3) names and contact information for three references.
Online Application System:
Bioinformatics Engineer in Metagenomics
Postdoc in Metagenomics
All applications will be evaluated by all PIs. The locations of hires will be determined mutually by the applicants and the PIs. We will evaluate applications as they arrive, until the positions are filled.
The Labs
Jonathan A. Eisen (UC Davis)
U. C. Davis Genome Center
Center for Population Biology
Section of Evolution and Ecology
Department of Medical Microbiology and Immunology
Website
Jessica L. Green (U Oregon)
Center for Ecology and Evolutionary Biology
Department of Biology
Website
Katherine S. Pollard (UC Davis)
U. C. Davis Genome Center
Center for Population Biology
Department of Statistics
Website
Dr. Katherine Pollard
postdoc@wald.ucdavis.edu
A postdoctoral position is available in the research group of Dr. Katherine Pollard at the UC Davis Genome Center. We recently developed a computational approach to detect rapidly evolving genomic regions and applied it to identify the elements of the human genome that have diverged most since our common ancestor with chimps. The successful candidate will take a lead role in extending these comparative genomic methods to study lineage-specific evolution in vertebrates, flies, and possibly other phylogenies.
The applicant must have a PhD in (bio)statistics, applied math, computer science, bioinformatics, molecular biology or a related field, with experience analyzing genomic data. Ability to program (e.g. in R/Splus, C, or Perl) is essential. Candidates interested in doing some experimental work are invited to apply – opportunities may be available in the labs of collaborators.
Please apply by email to postdoc@wald.ucdavis.edu and include:
More info at http://docpollard.com
and http://genomics.ucdavis.edu.
Dr. Yong Duan
duan@ucdavis.edu
Postdoctoral fellows: computational molecular biophysics and biochemistry.
Multiple post-doc positions are available in the lab to work on the development and application of molecular modeling techniques to understand the structure, function and dynamics of proteins. One postdoc will work on the development of methods for accurate protein structure prediction, one will work on the understanding of the sequence determinants of protein structure and dynamics, and the third person will work on GPCR modeling. Applicants are required to have experience in at least one of these areas. To apply, send your CV in an email describing your scientific interests and career goals.
BIOINFORMATICS POSTDOCTORAL RESEARCHER FOR MARKER DISCOVERY AND MASSIVELY PARALLEL GENOTYPING
PROJECT DESCRIPTION:
We are developing a custom 6.6 million feature Affymetrix GeneChip for robust, massively-parallel genotyping based on Single Feature Polymorphisms (SFPs) as well as for gene expression analysis. Approximately 175 probes per DNA sequence will be tiled in 2 bp increments for ~30,000 pepper unigenes. These chips will be used to assess genetic variation, develop ultra-high density genetic maps, and for expression analysis. The resultant data will be used for dissection of agriculturally important disease, agronomic and fruit quality traits. This project will be located in the UC Davis Seed Biotechnology Center http://sbc.ucdavis.edu in collaboration with the UC Davis Genome Center http://genomecenter.ucdavis.edu.
JOB DESCRIPTION:
The successful candidate will be responsible for developing and applying custom tools to design and analyze pepper Affymetrix GeneChip data. Scripts are required to curate and process raw GeneChip hybridization data into relational a mySQL database for further analysis. It is anticipated that the project will generate over 1 Tb of data. Therefore efficient algorithms will be required for manipulating and querying the data. Methods for identification and validation SFPs will need to be developed as well as for measurement of gene expression using the highly redundant probe sets provided by the chip. Many of these algorithms can be adapted from a similar project in lettuce with the same unique chip design. Re-usage and modifications of existing modules such as BioConductor would be highly desirable. Results will be entered into a mySQL database and visualized on web pages using PHP scripts. The candidate will also be responsible to supervise a high level technician to process samples and generate the data.
QUALIFICATIONS:
Ph.D. in biology- or bioinformatics-related discipline. Candidate must have demonstrated experience in computational approaches to manipulate and analyze large genetic and molecular datasets. Experience with at least one scripting language such as Perl, PHP, Python, R or equivalent is required. Basic knowledge of relational mySQL database is desirable. Previous experience with Affymetrix GeneChip data is an advantage.
Please apply at avandeynze@ucdavis.edu. This will require a CV, cover letter and the contact information for three references.
UC Davis is an equal opportunity employer.
Unsolicited Applications
The genome center welcomes applications at any time. Unsolicited applications will be reviewed as positions become available, and will be held for 6 months.
Apply Online