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Scientist Profile

Thomas D. Wu

Senior Scientist: Bioinformatics & Computational Biology
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"I am inspired by the tremendous resources we have at Genentech, and by the unprecedented volumes of high-throughput data that are now available. Much of our motivation comes from the opportunity to use such data to discover biological phenomena and possible insights to develop new therapeutics."
 

I came to Genentech because it provided an interdisciplinary and open environment where I could apply my background in medicine and computer science to solve challenging and important problems.

 
 
My Focus

Our group is focused primarily on analyzing data from large-scale biological assays and developing new methods for their analysis. Our work in the past has emphasized microarrays, and we have developed a comprehensive infrastructure at Genentech for both laboratory management and scientific analysis of microarray data. Our systems enable researchers to visualize and comprehend large data sets across our entire range of internal and external data sets.

We are now shifting our focus to high-throughput sequencing. I previously developed a genomic alignment program called GMAP, which can rapidly and accurately map and align sequence fragments to entire genomes. This program is distributed publicly and is used widely in the bioinformatics community. To handle the special needs of recent sequencing technologies, I have recently written and released another program called GSNAP, which can detect complex variants and splicing in short reads. These and other associated tools enable us to identify new biological phenomena in genomic and transcriptional sequencing data.

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Publications & Recognition
  • Fast and SNP-tolerant detection of complex variants and splicing in short reads
  • Bioinformatics 2010 Feb 10
  • Wu TD, Nacu S
  • View Abstract on PubMed
  • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
  • Bioinformatics 2005 May 1; 21(9): 1859-75
  • Wu TD, Watanabe CK
  • View Abstract on PubMed
  • Identification of hepatocyte growth factor activator inhibitor-1B as a potential physiological inhibitor of prostasin
  • J Biol Chem 2005 Oct 14; 280(41): 34513-20
  • Fan B, Wu TD, Li W, Kirchhofer D
  • View Abstract on PubMed
 
View All Publications & Recognition
 
  • Stanford University, Department of Biochemistry
  • Postdoctoral Fellow
  • 1994-1999
  • Stanford University Hospital, Department of Internal Medicine
  • Intern/Resident
  • 1992-1994
  • Massachusetts Institute of Technology, Department of Computer Science
  • Ph.D.
  • 1985-1992
  • Harvard University Medical School
  • M.D.
  • 1984-1992
  • Stanford University, Department of Electrical Engineering
  • M.S.
  • 1983-1984
  • Stanford University, Department of Electrical Engineering and Biological Sciences
  • B.S.
  • 1980-1983
Publications & Recognition
  • Fast and SNP-tolerant detection of complex variants and splicing in short reads
  • Bioinformatics 2010 Feb 10
  • Wu TD, Nacu S
  • View Abstract on PubMed
  • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
  • Bioinformatics 2005 May 1; 21(9): 1859-75
  • Wu TD, Watanabe CK
  • View Abstract on PubMed
  • Identification of hepatocyte growth factor activator inhibitor-1B as a potential physiological inhibitor of prostasin
  • J Biol Chem 2005 Oct 14; 280(41): 34513-20
  • Fan B, Wu TD, Li W, Kirchhofer D
  • View Abstract on PubMed
  • Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
  • J Virol 2003 Apr; 77(8): 4836-47
  • Wu TD, Schiffer CA, Gonzales MJ, Taylor J, Kantor R, Chou S, Israelski D, Zolopa AR, Fessel WJ, Shafer RW
  • View Abstract on PubMed
  • In silico data filtering to identify new angiogenesis targets from a large in vitro gene profiling data set
  • Physiol Genomics 2002 Jul 12; 10(1): 13-20
  • Gerritsen ME, Soriano R, Yang S, Ingle G, Zlot C, Toy K, Winer J, Draksharapu A, Peale F, Wu TD, Williams PM
  • View Abstract on PubMed
  • Gene expression profiling in silico: relative expression of candidate angiogenesis associated genes in renal cell carcinomas
  • Exp Nephrol 2002; 10(2): 114-9
  • Gerritsen ME, Peale FV Jr, Wu T
  • View Abstract on PubMed
  • Large-scale analysis of gene expression profiles
  • Brief Bioinform 2002 Mar; 3(1): 7-17
  • Wu TD
  • View Abstract on PubMed
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Awards & Honors
  • Howard Hughes Medical Institute Postdoctoral Physician Fellowship--1996-1999
  • National Library of Medicine Postdoctoral Fellowship--1994-1996
  • George M. Sprowls Dissertation Award, Massachusetts Institute of Technology--1993
  • Martin Epstein Award, American Medical Informatics Association--1990
  • Tau Beta Pi National Engineering Fellowship--1983-1984
  • Tau Beta Pi National Laureate Award--1983
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Ellen Filvaroff, Senior Scientist and Alex Avardo, Receipent of Free Medicine From the Genentech® Access to Care Foundation, on the cover of Genentech's 2006 Annual Report.