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Three postdoctoral positions available, 2008
Postdoctoral fellowships in machine learning and computational biology
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:
o 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.
o 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.
o 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.
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 atleast three references to noble@gs.washington.edu.
Two postdoctoral positions available, 2007
Keywords: Bioinformatics, genomics, computational biology, phylogenetics, systems biology, algorithms, statistics, machine learning, cancer, aging, neurodegenerative diseases, dementia, Alzheimer's disease, biomarkers, microarray
I am seeking applications for up to two postdoctoral positions in my lab. The appointments will be two years, with potential extensions based on review and funding availability. Candidates may cover one or more of the following areas: algorithms, phylogenetics, systems biology, genomics, and statistical machine learning. Current projects include:
1. Bioinformatics and genomics for cancer, aging, and neurodegenerative diseases;
2. Statistical analysis of microarray experiments and disease biomarkers;
3. Developing novel algorithms for computational problems motivated by genomics and biomedical research.
Applicants should submit CV, two representative publications in PDF format, and a list of at least two potential recommendations with contact information by email to lswang@mail.med.upenn.edu. Additional inquiries should be directed (preferably by email) to:
Li-San Wang
Department of Pathology and Laboratory Medicine
Institute on Aging
Penn Center for Bioinformatics
University of Pennsylvania
Philadelphia, PA 19104
lswang (at) mail.med.upenn.edu
The University of Pennsylvania is an equal opportunity employer and does not discriminate on the basis of race, sex, sexual orientation, gender identity, religion, color, national or ethnic origin, age, disability, or status as a Vietnam Era veteran or disabled veteran.
Dear colleague,
I have NSF funding for one or 2 postdoctoral positions available for work on a project concerning RNA. Requirements include the following:
a) interest and knowledge in computational biology and structural biology, especially RNA secondary structure. Background in physical chemistry is a plus.
b) strong programming ability in C/C++ and in some scripting language, preferably Python.
NOTE: Algorithm development and programming skills are essential. For a strong computational student from computer science, math, physics, or chemistry, it learn the requisite computational biology on the job. This is an opportunity for a person desiring to move into the area of computational biology and bioinformatics.
Please encourage any strong recent PhDs to apply. As described below, by spending time in Boston, a postdoctoral associate has many research and cultural opportunities not often available.
APPLICATION WEB FORM:
http://clavius.bc.edu/~clote/Postdoc/
For citizens of a country other than the US, on a J1-visa scientific visa, during the first 2 years of stay in the US, a postdoctoral associate does not pay US tax (this depends on international tax treaties between the US and the country of citizenship, but to the best of my knowledge generally holds for members of the European Union).
Background Facts about life in Boston and at Boston College
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Boston College, unlike what is suggested by its name, is a university with strong research departments especially in biology, chemistry and physics. Conveniently located at the terminus of the B-line of the MBTA subway, Boston College has a scenic campus and very pleasant working conditions. The biology/physics building, recently renovated for $80 million, combines state-of-the-art laboratory facilities with an impressive architectural style, flooded with light.
It has been claimed that Boston is the number 1 city, with San Diego as the number 2 city with respect to the biotech industry in the United States. In addition to 9 major universities, which include Harvard, MIT, Boston College, Boston University, etc. there are numerous biotech/pharmaceutical companies (Novartis, Pfizer, Millenium, Genzyme, etc.) and research/teaching hospitals. This provides an unparalleled network of research collaboration opportunities.
Boston is a cultural center and a very musical city, with Berklee School of Jazz, New England Conservatory, etc. If you like jazz, look at: www.sharp11th.com
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Peter Clote, Ph.D.
Professor, Biology Department
Courtesy appt. Computer Science Department
Boston College
Higgins Hall 577 140 Commonwealth Avenue
617 552 1332 (office) Chestnut Hill, MA 02467
617 552 2011 (fax)
http://clavius.bc.edu/~clote/
http://bioinformatics.bc.edu/clotelab/
clote@bc.edu
Co-organizer of MIT Bioinformatics Seminar
http://www-math.mit.edu/compbiosem/
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last updated: January 30, 2007
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