Staff Scientist, Cancer Immunology
"It is very rewarding to be a computational scientist at Genentech, where there are so many great biologists."
years at Genentech
awards & honors
I joined Genentech in 2009 as Senior Director of the Bioinformatics and Computational Biology Department. I was excited by the opportunity to get involved in drug development and to do work that would directly impact patients. I had worked at two major cancer centers and while immensely satisfying the research done there is still fairly distant from the patient. At Genentech patients are at the forefront of everything we do.
Genentech Research is that rare blend of academia and industry that manages to capture most of the best aspects of both. The advent of genome scale data technologies is revolutionizing molecular biology and is providing us with new and exciting opportunities for drug development. I am very excited by the new opportunities we have to develop methods for computational discovery of potential drug targets. At the same time, these large genomic data sets provide us with opportunities to identify and understand different patient subsets and to help guide us towards much more targeted therapeutics.
Being a post-doc mentor is one of the highlights of being in Research. The ability to work with really talented post-docs who are interested in pushing the boundaries of computational science provides me with an outlet for my blue-skies research ideas.
Bioconductor: open software development for computational biology and bioinformatics
Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.
Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang and Jianhua Zhang
View Abstract on PubMed
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. We have projects on variant calling for detecting mutations in tumors at low frequency as well as for studying RNA editing in different tissues.
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.
Orchestrating high-throughput genomic analysis with BioconductorNature methods, 2015, ISSN: 1548-7091 View on PubMed
A comprehensive transcriptional portrait of human cancer cell linesNature biotechnology, 2014, ISSN: 1087-0156 View on PubMed
Discriminative motif analysis of high-throughput datasetBioinformatics, 2014, ISSN: 1367-4803 View on PubMed
gCMAP: user-friendly connectivity mapping with RBioinformatics, 2013, ISSN: 1367-4803 View on PubMed
The anatomy of successful computational biology softwareNature Biotechnology, 2013, ISSN: 1087-0156 View on PubMed
Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing eventsGenome Research, 2012, ISSN: 1088-9051 View on PubMed
Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancerNature Genetics, 2012, ISSN: 1061-4036 View on PubMed
Recurrent R-spondin fusions in colon cancerNature, 2012, ISSN: 0028-0836 View on PubMed
Genetic and Epigenetic Determinants of Neurogenesis and MyogenesisDevelopmental Cell, 2012, ISSN: 1534-5807 View on PubMed
The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patientsGenome Research, 2012, ISSN: 1088-9051 View on PubMed
DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral DystrophyDevelopmental Cell, 2012, ISSN: 1534-5807 View on PubMed
- 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
- ISCB Fellow, International Society for Computational Biology – 2014
- Statistical Computing and Graphics Award – 2010
- Ross L. Prentice Professor of Biostatistics – 2009
- Benjamin Franklin Award – 2008