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.

• Publications

  • Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events

    Genome Research, 2012, ISSN: 1088-9051

    Liu, Jinfeng; Lee, William; Jiang, Zhaoshi; Chen, Zhongqiang; Jhunjhunwala, Suchit; Haverty, Peter M; Gnad, Florian; Guan, Yinghui; Gilbert, Houston; Stinson, Jeremy; Klijn, Christiaan; Guillory, Joseph; Bhatt, Deepali; Vartanian, Steffan; Walter, Kimberly; Chan, Jocelyn; Holcomb, Thomas; Dijkgraaf, Peter; Johnson, Stephanie; Koeman, Julie; Minna, John D; Gazdar, Adi F; Stern, Howard M; Hoeflich, Klaus P; Wu, Thomas D; Settleman, Jeff; de Sauvage, Frederic J; Gentleman, Robert C; Neve, Richard M; Stokoe, David; Modrusan, Zora; Seshagiri, Somasekar; Shames, David S; Zhang, Zemin

     View on PubMed

  • Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers

    Proceedings of the National Academy of Sciences, 2012, ISSN: 0027-8424

    Parikh, Chaitali; Janakiraman, Vasantharajan; Wu, Wen-I; Foo, Catherine K; Kljavin, Noelyn M; Chaudhuri, Subhra; Stawiski, Eric; Lee, Brian; Lin, Jie; Li, Hong; Lorenzo, Maria N; Yuan, Wenlin; Guillory, Joseph; Jackson, Marlena; Rondon, Jesus; Franke, Yvonne; Bowman, Krista K; Sagolla, Meredith; Stinson, Jeremy; Wu, Thomas D; Wu, Jiansheng; Stokoe, David; Stern, Howard M; Brandhuber, Barbara J; Lin, Kui; Skelton, Nicholas J; Seshagiri, Somasekar

     View on PubMed

  • Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer

    Nature Genetics, 2012, ISSN: 1061-4036

    Rudin, Charles M.; Durinck, Steffen; Stawiski, Eric W.; Poirier, John T.; Modrusan, Zora; Shames, David S.; Bergbower, Emily A.; Guan, Yinghui; Shin, James; Guillory, Joseph; Rivers, Celina Sanchez; Foo, Catherine K.; Bhatt, Deepali; Stinson, Jeremy; Gnad, Florian; Haverty, Peter M.; Gentleman, Robert; Chaudhuri, Subhra; Janakiraman, Vasantharajan; Jaiswal, Bijay S.; Parikh, Chaitali; Yuan, Wenlin; Zhang, Zemin; Koeppen, Hartmut; Wu, Thomas D.; Stern, Howard M.; Yauch, Robert L.; Huffman, Kenneth E.; Paskulin, Diego D.; Illei, Peter B.; Varella-Garcia, Marileila; Gazdar, Adi F.; De Sauvage, Frederic J.; Bourgon, Richard; Minna, John D.; Brock, Malcolm V.; Seshagiri, Somasekar

     View on PubMed

  • Recurrent R-spondin fusions in colon cancer

    Nature, 2012, ISSN: 0028-0836

    Seshagiri, Somasekar; Stawiski, Eric W. ; Durinck, Steffen; Modrusan, Zora; Storm, Elaine E.; Conboy, Caitlin B.; Chaudhuri, Subhra; Guan, Yinghui; Janakiraman, Vasantharajan; Jaiswal, Bijay S.; Guillory, Joseph; Ha, Connie; Dijkgraaf, Gerrit J. P. ;Stinson, Jeremy; Gnad, Florian; Huntley, Melanie A.; Degenhardt, Jeremiah D.; Haverty, Peter M.; Bourgon, Richard; Wang, Weiru ; Koeppen, Hartmut; Gentleman, Robert; Starr, Timothy K.; Zhang, Zemin; Largaespada, David A.; Wu, Thomas D. ; de Sauvage, Frederic J.

     View on PubMed

  • The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

    Genome Research, 2012, ISSN: 1088-9051

    Jiang, Zhaoshi; Jhunjhunwala, Suchit; Liu, Jinfeng; Haverty, Peter M; Kennemer, Michael I; Guan, Yinghui; Lee, William; Carnevali, Paolo; Stinson, Jeremy; Johnson, Stephanie; Diao, Jingyu; Yeung, Stacy; Jubb, Adrian; Ye, Weilan; Wu, Thomas D; Kapadia, Sharookh B; de Sauvage, Frederic J; Gentleman, Robert C; Stern, Howard M; Seshagiri, Somasekar; Pant, Krishna P; Modrusan, Zora; Ballinger, Dennis G; Zhang, Zemin

     View on PubMed

  • Influence of 17β-estradiol on gene expression of paracoccidioides during mycelia-to-yeast transition

    PLoS ONE, 2011, ISSN: 1932-6203

    Shankar, Jata; Clemons, Karl V.; Monteiro, Jomar P.; Mirels, Laurence F.; Stevens, David A.; Wu, Thomas D.

     View on PubMed

  • Proteolytic activation of pro-macrophage-stimulating protein by hepsin

    Molecular Cancer Research, 29 Aug 2011, ISSN: 1557-3125.

    Ganesan, Rajkumar; Kolumam, Ganesh A; Lin, S Jack; Xie, Ming Hong; Santell, Lydia; Wu, Thomas D; Lazarus, Robert A; Chaudhuri, Amitabha; Kirchhofer, Daniel

     View on PubMed

• Education
  • Stanford University, Department of Biochemistry, Postdoctoral Fellow – 1999
  • Massachusetts Institute of Technology, Department of Computer Science, Ph.D. – 1992
  • Harvard University Medical School, M.D. – 1992
  • Stanford University, Department of Electrical Engineering, M.S. – 1984
  • Stanford University, Department of Electrical Engineering and Biological Sciences, B.S. – 1983
• 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 Laureate Award – 1983
  • Tau Beta Pi National Engineering Fellowship – 1983-1984