BioinformaticsOnline

Three postdoctoral fellowships in machine learning and computational biology are available in the lab of William Stafford Noble in the Department of Genome Sciences at the University of Washington, Seattle, WA, USA.

Our research group develops and applies computational techniques for modeling and understanding biological processes at the molecular level. Our research emphasizes the application of statistical and machine learning techniques, such as dynamic Bayesian networks and support vector machines. We apply these techniques to various types of biological data, including DNA and protein sequence data, shotgun proteomics mass spectrometry data, and a variety of high-throughput genomic data types. More information is available at http://noble.gs.washington.edu.

The three positions are as follows:

• Interpreting shotgun proteomics mass spectrometry data. In collaboration with Michael MacCoss (UW Genome Sciences), Jeff Bilmes (UW EE) and Jason Weston (NEC Research), we are developing new methods for identifying and quantifying proteins in complex biological samples on the basis of shotgun proteomics mass spectrometry data. Currently, this project involves a variety of techniques, including dynamic Bayesian networks, supervised and semi-supervised classification algorithms, and statistical confidence estimation procedures. The postdoc working on this project will develop new methods that either improve on existing methods by incorporating more prior knowledge or new types of data, or solve new problems that are of interest to the MacCoss lab and other mass spectrometrists.
• Predicting properties of proteins and protein complexes. The Yeast Resource Center (http://depts.washington.edu/yeastrc) is a multi-PI center housed at the UW which focuses on the characterization of proteins and protein complexes using a combination of wet lab and computational methods. In addition to William Noble, PIs in the center include Trisha Davis (fluoresence microsopy), Michael MacCoss (mass spectrometry), David Baker (protein structure prediction), Stanley Fields (yeast two-hybrid) and John Yates (mass spectrometry). In collaboration with other members of the YRC, this postdoc will develop methods for predicting properties of proteins, including function, secondary and tertiary structure, and interactions with DNA and other proteins.
• Identifying and characterizing functional elements in the human genome. The aim of the NIH-funded ENCODE consortium is to identify and catalog all functional elements in the human genome. The second phase of the ENCODE project, which is just beginning, involves scaling existing technologies from 1% of the human genome (phase I) to the entire genome (phase II). The person holding this position will be a member of the ENCODE Data Analysis Center, which is led by Ewan Birney (EBI, UK) and involves investigators at the UW, UC Berkeley, UC Santa Cruz, Penn State, Yale, and UMass. The postdoc will develop and apply tools for the analysis of the high-throughput data being generated by the ENCODE consortium.

The start dates for these positions are flexible.

An ideal candidate would have training both in machine learning and computational biology. However, talented individuals who lack significant background in one of these two areas will also be considered.

The Department of Genome Sciences was founded in September 2001 as the fusion of the Departments of Genetics and Molecular Biotechnology. Research in the department addresses leading edge questions in biology and medicine by developing and applying genetic, genomic and computational approaches that take advantage of genomic information now available for humans, model organisms and a host of other species. Nine faculty are members of the National Academy of Sciences, including 2001 Nobel Prize winner Dr. Lee Hartwell. Five training faculty are Howard Hughes Medical Institute Investigators. The department moved into the new William H. Foege Building in 2006.

The University of Washington is consistently ranked as one of the top research universities in the country and has more than 25,000 undergraduates and 9,000 others enrolled in its professional and graduate programs. Seattle is considered one of the nation's most beautiful and livable cities, boasting an array of cultural activities, parks, sports teams and restaurants, and serving as the gateway to National Parks and Forests, as well as boating, skiing and hiking areas.

The University of Washington is a culturally diverse community, and we strongly encourage applications from women and minority candidates. The University of Washington is an Affirmative Action/Equal Opportunity Employer.

Applications will be accepted until the positions are filled. Please submit a letter of interest, CV, research statement and names of at least three references to .