Robert Gentleman

Senior Director, Bioinformatics & Computational Biology

POSTDOC MENTOR

"It is very rewarding to be a computational scientist at Genentech, where there are so many great biologists."

• 4
  years at Genentech
• 6
  publications (2010-12)
• 3
  awards & honors

I came to Genentech in 2009 to be the Senior Director of the Bioinformatics Department. The opportunity to take my training and use it to help design therapeutics was very tempting. I had worked at two major cancer centers and while immensely satisfying the research done there is still fairly distant from the patient and I wanted to take a more patient centric approach.

Genentech Research is that rare blend of academia and industry that manages to capture most of the best aspects of both. The department carries out a blend of software engineering, collaborative research and independent research in bioinformatics and computational biology. This was very appealing because of my background in software engineering (through the R language) and my interests in computational biology.

• My Focus

  My lab is working on a number of different projects, mostly centered around the use of high throughput sequencing to advance our knowledge of many basic biological mechanisms. Of particular interest is developing methods for understanding transcriptional regulation through the use of careful experimentation and ChIP-seq data. My group is also interested in helping to develop a better understanding of the role that transposable elements play in human disease. Much of human genome consists of repetitive DNA, much of it in the form of transposable elements (or the artifacts thereof) and it is likely that some of these elements are associated with specific diseases.

  And perhaps the most important current direction is collaboration. It is very rewarding to be a computational scientist at Genentech, where there are so many great biologists to interact with. This gives us a rich and rewarding set of collaborations to engage in. The challenges and rewards come both in my role as a manager and in my role as a scientist.

• 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

  • 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

  • Genetic and Epigenetic Determinants of Neurogenesis and Myogenesis

    Developmental Cell, 2012, ISSN: 1534-5807

    Fong, Abraham P; Yao, Zizhen; Zhong, Jun Wen; Cao, Yi; Ruzzo, Walter L; Gentleman, Robert C; Tapscott, Stephen 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

  • DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy

    Developmental Cell, 2012, ISSN: 1534-5807

    Geng, Linda N.; Snider, Lauren; Fong, Abraham P.; Cech, Jennifer N.; Young, Janet M.; Tapscott, Stephen J.; Yao, Zizhen; vanderMaarel, Silvere M.; Ruzzo, Walter L.; Gentleman, Robert C.; Tawil, Rabi

     View on PubMed

• Education
  • University of Washington, Ph.D. Statistics – 1988
  • University of Washington, M.Sc. Statistics – 1986
  • University of British Columbia, B.Sc. (Hons.) Mathematics – 1984
• Awards & Honors
  • Statistical Computing and Graphics Award – 2010
  • Ross L. Prentice Professor of Biostatistics – 2009
  • Benjamin Franklin Award – 2008