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 ~35,000 lettuce 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 traits and studies of synteny with other plant species. This is part of the Compositae Genome Project (http://compgenomics.ucdavis.edu/) and will be located in the UC Davis Genome Center (http://genomecenter.ucdavis.edu ).

JOB DESCRIPTION:
The successful candidate will be responsible for developing custom tools to handle and analyze lettuce 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 have to be developed as well as for measurement of gene expression using the highly redundant probe sets provided by the chip. In most cases, custom scripts and programs to analyze data will have to be created de novo because of the 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.

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 http://genomecenter.ucdavis.edu/ or to rwmichelmore@ucdavis.edu. This will require a CV, cover letter and the contact information for three references.

UC Davis is an equal opportunity employer.