Interdisciplinary Collaborations

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Collaborations with Biological Sciences Departments

1. Larry Ruzzo and Martin Tompa are Adjunct Professors of the Department of Genome Sciences. They and their graduate students are frequent speakers in that department's Computational Biology seminar series. Joe Felsenstein, Phil Green, Bill Noble, and Maynard Olson of Genome Sciences are Adjunct Professors in our department.
2. Larry Ruzzo and Martin Tompa are participating faculty on the university's NIH Genome Training Grant, Larry Ruzzo is on its steering committee, emeritus graduate student Emily Rocke was a predoctoral and postdoctoral fellow on that grant, emeritus graduate student Zasha Weinberg was a predoctoral fellow on that grant, and Jonathan Carlson is currently a predoctoral fellow on that grant.
3. Larry Ruzzo and Martin Tompa are participating faculty in the university's Interdisciplinary Computational Molecular Biology Program Committee, and graduate students Jonathan Carlson, Imran Rashid, Huei-Hun Tseng, and Rosalia Tungaraza are members of that program. Emeritus graduate student Zasha Weinberg was the very first Ph.D. to graduate from that program, and Amol Prakash a more recent graduate.
4. We have active research collaborations with David Baker (Biochemistry) on protein structure prediction and enzyme design; with David Sherman (Pathobiology) on transcriptional regulation of M. tuberculosis; with Christopher Wilson (Immunology) on regulatory elements in the interferon gamma locus; with Ray Monnat (Pathology) on engineering new homing endonucleases; with Eugene Nester (Microbiology) on the regulation of virulence genes in A. tumefaciens; with Karol Bomsztyk (Nephrology) on the role of K protein in regulation; with David Haynor (Radiology) on clustering gene expression data; with Steve Schwartz and Eileen Mulvihill (Pathology) on microarray analysis; and with Heather McCune, M.K. Raghuraman, Walt Fangman and Bonnie Brewer (Genome Sciences) who are using our simulator to analyze their yeast chromosome replication experiments.

Collaborations with Industry and Research Laboratories

1. Martin Tompa consulted for Rosetta Inpharmatics on the discovery of transcription factor binding sites, and emeritus graduate student Ka Yee Yeung collaborated with Rosetta scientists on gene regulatory networks.
2. Martin Tompa spent his 2000-2001 sabbatical year as a Visiting Scientist at ZymoGenetics, collaborating with bioinformaticists and molecular biologists, emeritus graduate student Zasha Weinberg was a summer intern there, as were graduate students Adrienne Wang and Huei-Hun Tseng.
3. We have a multifaceted collaboration with the Institute for Systems Biology. Its founder Lee Hood is an Affiliate Professor in our department, as is their former faculty member Benno Schwikowski (now at the Pasteur Institut in Paris). Graduate students Mathieu Blanchette, Jeremy Buhler, Amol Prakash, Saurabh Sinha, Brian Tjaden, and Tammy VanDeGrift were actively involved in collaborative projects at ISB. Larry Ruzzo spent his 2002-2003 sabbatical year as a Visiting Scientist at the Institute.
4. We have many active collaborations with biologists at the Fred Hutchinson Cancer Research Center. Larry Ruzzo and Ka Yee Yeung have collaborated with members of Brian Reid's Lab on gene expression in the Barrett's esophagus data set. Martin Tompa is collaborating with Barbara Trask on the discovery of regulatory elements in mammalian olfactory receptor genes, with Bruce Edgar on the discovery of regulatory elements in Drosophila melanogaster, and with Barry Stoddard on the uses of engineered homing endonucleases.
5. Amir Ben-Dor at Agilent is an Affiliate Assistant Professor in our department.
6. Martin Tompa collaborated with researchers at The Institute for Genome Research on the discovery of ribosome binding sites in prokaryotic genomes.

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