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Scientist Profile

Robert Gentleman

Senior Director, Bioinformatics & Computational Biology
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"It is very rewarding to be a computational scientist at Genentech, where there are so many great biologists."
 

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.

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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.

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Publications & Recognition
  • Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming
  • Dev Cell 2010 Apr 20;18(4):662-74
  • Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ
  • View Abstract on Pubmed
  • Independent filtering increases detection power for high-throughput experiments
  • Proc Natl Acad Sci U S A. 2010; 107(21):9546-51
  • Bourgon R, Gentleman R, Huber W
  • View Abstract on Pubmed
  • The mutation spectrum revealed by paired genome sequences from a lung cancer patient
  • Nature 2010; 465(7297):473-7
  • Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, Yue P, Zhang Y, Pant KP, Bhatt D, Ha C, Johnson S, Kennemer MI, Mohan S, Nazarenko I, Watanabe C, Sparks AB, Shames DS, Gentleman R, de Sauvage FJ, Stern H, Pandita A, Ballinger DG, Drmanac R, Modrusan Z, Seshagiri S, Zhang Z
  • View Abstract on Pubmed
 
View All Publications & Recognition
 
  • Bioinformatics and Computational Biology, Genentech
  • Senior Director
  • 2009-present
  • Fred Hutchinson Cancer Research Center, Seattle, WA
  • Member
  • 2004-2009
  • Department of Statistics, University of Washington, Seattle WA
  • Adjunct Professor
  • 2004-2009
  • Department of Biostatistics, Harvard University, Boston, MA
  • Adjunct Associate Professor
  • 2005-2008
  • University of Ghent, Ghent, Belgium
  • Visiting Professor
  • 2005-2006
  • Department of Biostatistical Science, Dana-Farber Cancer Institute and Harvard University, Department of Biostatistics
  • Assoc. Prof
  • 2000-2004
  • Department of Biostatistics, Harvard School of Public Health
  • Visiting Scholar
  • 1999-2000
  • Clinical Trials Research Unit, Department of Medicine, University of Auckland (Tenured)
  • Senior Research Fellow
  • 1998-2000
  • Department of Statistics, University of Auckland (Tenured)
  • Senior Lecturer
  • 1996-2000
  • Department of Mathematics and Statistics, University of Auckland
  • Lecturer
  • 1992-1996
  • Department of Statistics and Actuarial Science, University of Waterloo
  • Assistant Professor
  • 1988-1992
  • Statistics University of Washington
  • Ph.D.
  • 1988
  • Statistics University of Washington
  • M.Sc.
  • 1986
  • Mathematics University of British Columbia
  • B.Sc. (Hons.)
  • 1984
Publications & Recognition
  • Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming
  • Dev Cell 2010 Apr 20;18(4):662-74
  • Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ
  • View Abstract on Pubmed
  • Independent filtering increases detection power for high-throughput experiments
  • Proc Natl Acad Sci U S A. 2010; 107(21):9546-51
  • Bourgon R, Gentleman R, Huber W
  • View Abstract on Pubmed
  • The mutation spectrum revealed by paired genome sequences from a lung cancer patient
  • Nature 2010; 465(7297):473-7
  • Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, Yue P, Zhang Y, Pant KP, Bhatt D, Ha C, Johnson S, Kennemer MI, Mohan S, Nazarenko I, Watanabe C, Sparks AB, Shames DS, Gentleman R, de Sauvage FJ, Stern H, Pandita A, Ballinger DG, Drmanac R, Modrusan Z, Seshagiri S, Zhang Z
  • View Abstract on Pubmed
  • Dierential Gene Expression in Benign Prostate Epithelium of Men with and without Prostate Cancer: Evidence for a Prostate Cancer Field Eect
  • Clin Cancer Res. 2010
  • Risk MC, Knudsen BS, Coleman I, Dumpit R, Kristal AR, Le Meur N, Gentleman R, True LD, Nelson PS, Lin DW
  • Per-Channel Basis Normalization Methods for Flow Cytometry Data
  • Cytometry A 2010; 77:121-31
  • Seifert-Margolis V, Bourcier K, Asare A, Lumley T, Gentleman R, Brinkman RR
  • View Abstract on Pubmed
  • DATABASE: A new forum for biological databases and curation
  • Database (Oxford) 2009:bap002
  • Landsman D, Gentleman R, Kelso J, Ouellette BF
  • View Abstract on Pubmed
  • arrayQualityMetrics -a Bioconductor package for quality assessment of microarray data
  • Bioinformatics 2009
  • Kaumann A, Gentleman R, Huber W
  • View Abstract on Pubmed
  • Interpreting genetics of gene expression: integrative architecture in Bioconductor
  • Proceedings of the Pacific Symposium on Biocomputing 2009
  • Carey VJ, Gentleman R
  • View Abstract on Pubmed
  • flowCore: a Bioconductor package for high throughput flow cytometry
  • BMC Bioinformatics 2009; 10:106
  • Hahne F, Le Meur N, Brinkman RR, Byron E, Haaland PD, Sarkar D, Spidlen J, Strain E, Gentleman R
  • View Abstract on Pubmed
  • Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x
  • Bioinformatics 2009; 25:1447-1448
  • Carey V, Davis A, Lawrence MF, Gentleman R, AR Benjamin
  • View Abstract on Pubmed
  • an R package for interfacing with genome browsers
  • Bioinformatics 2009, 25, 1841-1842
  • Lawrence MF, Carey VJ, Gentleman R. rtracklayer
  • View Abstract on Pubmed
  • Knowledge based identification of essential signaling from genome-scale siRNA experiments
  • BMC Systems Biology 2009; 4;3:80
  • Bankhead A, Sach I, Ni C, LeMeur N, Kruger M, Ferrer M, Gentleman R, Rohl C
  • View Abstract on Pubmed
  • ShortRead: A Bioconductor package for input, quality assessment, and exploration of high throughput sequence data
  • Bioinformatics 2009; 25:2607-2608
  • Morgan MT, Anders S, Lawrence MF, Aboyoun P, Pages H, Gentleman R
  • View Abstract on Pubmed
  • iFlow: a graphical user interface for flow cytometry tools in Bioconductor
  • Advances in Bioinformatics 2009, 103839. Epub 2009 Nov 12
  • Lee K, Hahne F, Sarkar D, Gentleman R
  • Estimating node degree in bait-prey graphs
  • Bioinformatics 2008
  • Scholtens D, Chiang T, Huber W, Gentleman R
  • Using flowViz to Visualize Flow Cytometry Data
  • Bioinformatics 2008
  • Sarkar D, Le Meur N, Gentleman R
  • View Abstract on Pubmed
  • SGDI: System for Genomic Data Integration
  • Proceedings of the Pacific Symposium on Biocomputing 2008; 141-152
  • Carey VJ, Gentry J, Sarkar D, Gentleman R, Ramaswamy S
  • View Abstract on Pubmed
  • Circulating microRNAs as stable blood-based markers for cancer detection
  • PNAS 2008; 105:10513-10518
  • Mitchell P, Parkin R, Kroh E, Fritz B, Wyman S, Pogosova-Agadjanyan E, Peterson A, Noteboom J, O'Briant K, Allen A, Lin D, Urban N, Drescher C, Knudsen B, Stirewalt D, Gentleman R, Vessella R, Nelson P, Martin D, Tewari M
  • View Abstract on Pubmed
  • MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries
  • Stem Cells 2008; Oct;26(10):2496-505
  • Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson A, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M
  • View Abstract on Pubmed
  • Modeling Synthetic Lethality
  • Genome Biology 2008; doi:10.1186/gb-2008-9-9-r135
  • Le Meur N, Gentleman R
  • View Abstract on Pubmed
  • Gene Set Enrichment Analysis using Linear Models and Diagnostics
  • Bioinformatics 2008; 24:2586-91
  • Oron A, Jiang Z, Gentleman R
  • View Abstract on Pubmed
  • Quality Assessment and Data Analysis for microRNA Expression Arrays
  • Nucleic Acids Research 2008
  • Sarkar D, Parkin R, Wyman S, Bendoraite A, Sather C, Delrow J, Godwin AK, Drescher C, Huber W, Gentleman R, Tewari M
  • View Abstract on Pubmed
  • Statistical Analyses and Reproducible Research
  • Journal of Computational and Graphical Statistics 2007; 16:1-24
  • Gentleman R, Temple LD
  • Using GOstats to test gene lists for GO term association
  • Bioinformatics 2007; 23:257-258
  • Falcon S, Gentleman R
  • View Abstract on Pubmed
  • GGtools: flexible genetical genomics in Bioconducto
  • Bioinformatics 2007; 23:522-523
  • Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R
  • Data Quality Assessment of Ungated Flow Cytometry Data in High Throughput Experiments
  • Cytometry Part A 2007; 71A:393-403
  • Le Meur N, Rossini A, Gasparetto M, Smith C, Brinkman RR, Gentleman R
  • View Abstract on Pubmed
  • Graphs in molecular biology, BMC
  • Bioinformatics 2007; 8(Suppl 6):S8
  • Huber W, Carey VJ, Li L, Falcon S, Gentleman R
  • View Abstract on Pubmed
  • Coverage and Error Models of Protein-Protein Interaction Data by Directed Graph Analysis
  • Genome Biology 2007
  • Chiang T, Scholtens D, Sarkar D, Gentleman R, Huber W
  • View Abstract on Pubmed
  • Top-down standards will not serve systems biology
  • Nature, 440(7080): 24
  • Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N
  • View Abstract on Pubmed
  • Rintact: a direct link between molecular interaction data and methods in proteomic analysis
  • Bioinformatics 2007
  • Chiang T, Li N, Orchard S, Kerrin S, Hermjakob H, Gentleman R, Huber W
  • Combined cDNA array CGH and SAGE analysis of breast tumor progression
  • Cancer Reasearch 2006; 66:4065-4078
  • Yao J, Weremowicz S, Feng B, Gentleman RC, Marks JR, Gelman R, Brennan C, Polyak K
  • View Abstract on Pubmed
  • Data Standards for Flow Cytometry
  • Omics 2006; 10:209-214
  • Spidlen J, Gentleman RC, Haaland PD, Langille M, Le Meur N, Ochs MF, Schmitt C, Smith CA, TreiSter AS, Brinkman RR
  • View Abstract on Pubmed
  • Declining Plasma Fibrinogen Alpha Fragment Identifies HER2-Positive Breast Cancer Patients and Reverts to Normal Levels after Surgery
  • J. Proteome Res 2006; 5:2947-2955
  • Shi Q, Harris LN, Lu X, Li X, Hwang J, Gentleman R, Iglehart JD, Miron A
  • View Abstract on Pubmed
  • Reproducible Research: A Bioinformatics Case Study
  • Statistical Applications in Genetics and Molecular Biology 2005; Vol. 4: No. 1, Article 2
  • Gentleman, R
  • Wavelet thresholding with Bayesian false discovery rate control
  • Biometrics 2005; 61:26-36
  • Tadesse, M, Ibrahim JG, Vannucci M, Gentleman R
  • View Abstract on PubMed
  • Constrained estimation and likelihood intervals for censored data
  • The Canadian Journal of Statistics 2005; 33:71-84
  • Vandal, A, Gentleman, R and Liu, X
  • Network structures and algorithms in Bioconductor
  • Bioinformatics 2005; 21:135-136
  • Carey V, Gentry J, Whalen E, Gentleman, R
  • View Abstract on Pubmed
  • Classification Using Generalized Partial Least Squares
  • Journal of Computational and Graphical Statistics 2005; 14:280-298
  • Ding B, Gentleman R
  • BB. Association of Valproate-induced Teratogenesis with Histone Deacetylase Inhibition in vivo
  • The FASB Journal 2005; 19:1166-1168
  • Gurvich N, Berman M, Wittner BS, Gentleman RC, Klein, Peter S, Green J
  • View Abstract on Pubmed
  • Local dynamic modeling of global interactome networks
  • Bioinformatics 2005; 21:3548-3557
  • Scholtens D, Vidal M, Gentleman R
  • View Abstract on Pubmed
  • Gene Expression Profiles of B-lineage Adult Acute Lymphocytic Leukemia Reveal Genetic Patterns that Identify Lineage Derivation and Distinct Mechanisms of Transformation
  • Clinical Cancer Research 2005; 11:7209-7219
  • Chiaretti S, Li X, Gentleman R, Vitale A, Wang KS, Mandelli F, Foa R, Ritz J
  • View Abstract on Pubmed
  • On the synthesis of microarray experiments
  • Journal de la Societe Francaises de Statistique 2005; 146(1-2):173-194
  • Gentleman R, Ruschhaupt M, Huber W
  • Bayesian error-in-variable survival model for the analysis of GeneChip arrays
  • Biometrics 2005; 61:488-497
  • Tadesse MG, Ibrahim JG, Gentleman R, Chiaretti S, Ritz J, Foa R
  • View Abstract on Pubmed
  • Making Sense of High-Throughput Protein-Protein Interaction Data
  • Statistical Applications in Genetics and Molecular Biology, Vol. 3: No. 1, Article 39, 2005
  • Scholtens D, Gentleman R
  • View Abstract on Pubmed
  • A graph theoretic approach to testing associations between disparate sources of functional genomics data
  • Bioinformatics 2004; 20:3353-3362
  • Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R
  • Analyzing Factorial Designed Microarray Experiments
  • Journal of Multivariate Analysis 2004; 90:19-43
  • Scholtens D, Miron A, Merchant F, Miller A, Miron P, Iglehart JD, Gentleman, R
  • matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements
  • Bioinformatics, 2004; 20:1651-1652
  • Huber W, Gentleman R
  • View Abstract on PubMed
  • Gene expression Profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival
  • Blood 2004; 103:2771-2778
  • Chiaretti S, Li X, Gentleman R
  • View Abstract on PubMed
  • Some perspectives on statistical computing
  • Canadian Journal of Statistics 2004; 32:209-226
  • Gentleman R
  • A Model Based Background Adjustment for Oligonucleotide Expression Arrays
  • JASA 2004 99:909-917
  • Zhijin Wu, Irizarry RA, Gentleman R, Martinez M, Spencer F
  • Bioconductor: Open software development for computational biology and bioinformatics
  • Genome Biology 2004; 5:R80
  • Gentleman R, Carey V
  • View Abstract on Pubmed
  • Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
  • Nucleic Acids Research 2004; 32:e121
  • Tengs T, LaFramboise T, Den R, Hayes D, Zhang J, DebRoy S, Gentleman R, O'Neill K, Birren B, Meyerson M
  • View Abstract on Pubmed
  • An extensible application for assembling annotation for genomic data
  • Bioinformatics 2003; 19:155-56
  • Zhang J, Carey V, Gentleman R
  • View Abstract on PubMed
  • Open Source Software for the analysis of Microarray Data
  • BioTechniques Supplements 2003; 45-51
  • Dudoit S, Gentleman RC, Quackenbush J
  • View Abstract on PubMed
  • The Graft Response to Transplantation: a Gene Expression Profile Analysis
  • Physiological Genomics 2003; 15:52-64
  • Christopher K, Mueller TF, DeFina R, Liang Y, Zhang J, Gentleman R, Perkins DL
  • View Abstract on PubMed
  • An extensible application for assembling annotation for genomic data
  • Bioinformatics 2003; 19:155-56
  • Zhang J, Carey V, Gentleman R
  • View Abstract on PubMed
  • Open Source Software for the analysis of Microarray Data
  • BioTechniques Supplements 2003; 45-51
  • Dudoit S, Gentleman RC, Quackenbush J
  • View Abstract on PubMed
  • A Language for Data Analysis and Graphics
  • Journal of Graphical and Computational Statistics 1996; 5:299-314
  • Ihaka R, Gentleman RR
  • Computational Algorithms for Censored Data Problems Using Intersection Graphs
  • Journal of Computational and Graphical Statistics 2001; 10:403-421
  • Gentleman R, Vandal AC
  • View Abstract on PubMed
  • Nonparametric estimation of the bivariate CDF for arbitrarily censored data
  • Canadian Journal of Statistics 2002; 4:557-571
  • Gentleman R, Vandal AC
  • Nonparametric estimation of the bivariate CDF for arbitrarily censored data
  • Canadian Journal of Statistics 2002; 4:557-571
  • Gentleman R, Vandal AC
  • Global Expression Changes in Constitutive and Hormonally Regulated Genes during Endometrial Neoplastic Transformation
  • Gynecologic Oncology 2001; 83:177-185
  • Baak M, Gentleman RC
  • View Abstract on PubMed
  • Global Expression Changes in Constitutive and Hormonally Regulated Genes during Endometrial Neoplastic Transformation
  • Gynecologic Oncology 2001; 83:177-185
  • Baak M, Gentleman RC
  • View Abstract on PubMed
  • Computational Algorithms for Censored Data Problems Using Intersection Graphs
  • Journal of Computational and Graphical Statistics 2001; 10:403-421
  • Gentleman R, Vandal AC
  • View Abstract on PubMed
  • Lexical Scope and Statistical Computing
  • Journal of Computational and Graphical Statistics 2000; 9:491-508
  • Gentleman R, Ihaka R
  • Lexical Scope and Statistical Computing
  • Journal of Computational and Graphical Statistics 2000; 9:491-508
  • Gentleman R, Ihaka R
  • Java and Dylan
  • Journal of Computational and Graphical Statistics 2000; 9:452-458
  • Gentleman R, Ihaka R.
  • Lexical Scope and Statistical Computing
  • Journal of Computational and Graphical Statistics 2000; 9:491-508
  • Gentleman R, Ihaka R
  • Java and Dylan
  • Journal of Computational and Graphical Statistics 2000; 9:452-458
  • Gentleman R, Ihaka R
  • A Language for Data Analysis and Graphics
  • Journal of Graphical and Computational Statistics 1996; 5:299-314
  • Ihaka R, Gentleman RR
  • Exploratory Methods inSurvival Analysis
  • In IMS Lecture Notes - Monograph Series, HL Koul and JV Deshpande eds 1995; 27:55-78
  • Crowley J, LeBlanc M, Gentleman R, Salmon S
  • Maximum likelihood for interval censored data: consistency and computation
  • Biometrika 1994; 81:618-623
  • Gentleman R, Geyer C
  • Statistical quality control of HIV-1 ELISA test performance
  • Journal of the American Statistical Association 1994; 86:1200-1208
  • Gentleman RC, Hamada MS, Matthews DE, Wilson AR
  • Multi-state Markov models for analyzing incomplete disease history data with illustrations for HIV disease
  • Statistics in Medicine 1994; 13:805-821
  • Gentleman RC, Lawless JF, Lindsey JC, Yan P
  • View Abstract on PubMed
  • Exploratory Methods inSurvival Analysis
  • In IMS Lecture Notes - Monograph Series, HL Koul and JV Deshpande eds 1995; 27:55-78
  • Crowley J, LeBlanc M, Gentleman R, Salmon S
  • Statistical quality control of HIV-1 ELISA test performance
  • Journal of the American Statistical Association 1994; 86:1200-1208
  • Gentleman RC, Hamada MS, Matthews DE, Wilson AR
  • Multi-state Markov models for analyzing incomplete disease history data with illustrations for HIV disease
  • Statistics in Medicine 1994; 13:805-821
  • Gentleman RC, Lawless JF, Lindsey JC, Yan P
  • View Abstract on PubMed
  • Maximum likelihood for interval censored data: consistency and computation
  • Biometrika 1994; 81:618-623
  • Gentleman R, Geyer C
  • A graphical approach to the analysis of censored data
  • Breast Cancer Research and Treatment. 1992; 22:229-240
  • Gentleman RC, Crowley J
  • View Abstract on PubMed
  • Population size estimation for the Bowhead whale, Balaena mysticetus, based on 1985 and 1986 visual and acoustic data
  • Report of the International Whaling Commission SC/39/PS7 1988; 38:349-364
  • Zeh JE, Turet P, Gentleman R, Raftery AE
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Awards & Honors
  • Statistical Computing and Graphics Award, ASA 2010
  • Ross L. Prentice Professor of Biostatistics, U. of Washington 2009
  • Benjamin Franklin Award, by the Bioinformatics Organization 2008
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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.