Robert Gentleman, PhD

Robert Gentleman, PhD

Executive Director

Center for Computational Biomedicine

Harvard Medical School

Pronouns: he/him/his

Dr. Robert Gentleman is the founding executive director of Harvard Medical School’s Center for Computational Biomedicine. An accomplished statistician and bioinformatician, Dr. Gentleman is one of the creators of the R programming language and a founder of the Bioconductor project, an open-source collaborative software tool to promote statistical analysis of biological data. He has served as vice president of 23andMe, where he helped launch their therapeutic division, and as senior director for bioinformatics and computational biology at Genentech. He was head of computational biology at the Fred Hutchinson Cancer Research Center and held academic positions at Harvard University, University of Auckland and the University of Waterloo. Dr. Gentleman’s research interests are related to genomics, machine learning, data visualization, and the application of statistical and computational methods to study human disease.

  • Disease risk scores for skin cancers.

    Authors: Fontanillas P, Alipanahi B, Furlotte NA, Johnson M, Wilson CH, Pitts SJ, Gentleman R, Auton A.

    Nat Commun. 2021 01 08; 12(1):160.

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  • Demographic, spatial and temporal dietary intake patterns among 526 774 23andMe research participants.

    Authors: Shelton JF, Cameron B, Aslibekyan S, Gentleman R.

    Public Health Nutr. 2021 07; 24(10):2952-2963.

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  • Addressing the accuracy of direct-to-consumer genetic testing.

    Authors: Wu S, Pollard J, Chowdry A, Scheller R, Gentleman R.

    Genet Med. 2019 03; 21(3):758-759.

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  • VariantTools: an extensible framework for developing and testing variant callers.

    Authors: Lawrence M, Gentleman R.

    Bioinformatics. 2017 Oct 15; 33(20):3311-3313.

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  • Creating a data resource: what will it take to build a medical information commons?

    Authors: Deverka PA, Majumder MA, Villanueva AG, Anderson M, Bakker AC, Bardill J, Boerwinkle E, Bubela T, Evans BJ, Garrison NA, Gibbs RA, Gentleman R, Glazer D, Goldstein MM, Greely H, Harris C, Knoppers BM, Koenig BA, Kohane IS, La Rosa S, Mattison J, O'Donnell CJ, Rai AK, Rehm HL, Rodriguez LL, Shelton R, Simoncelli T, Terry SF, Watson MS, Wilbanks J, Cook-Deegan R, McGuire AL.

    Genome Med. 2017 09 22; 9(1):84.

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  • Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers.

    Authors: Goldstein LD, Lee J, Gnad F, Klijn C, Schaub A, Reeder J, Daemen A, Bakalarski CE, Holcomb T, Shames DS, Hartmaier RJ, Chmielecki J, Seshagiri S, Gentleman R, Stokoe D.

    Cell Rep. 2016 09 06; 16(10):2605-2617.

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  • Prediction and Quantification of Splice Events from RNA-Seq Data.

    Authors: Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R.

    PLoS One. 2016; 11(5):e0156132.

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  • Complex regulation of ADAR-mediated RNA-editing across tissues.

    Authors: Huntley MA, Lou M, Goldstein LD, Lawrence M, Dijkgraaf GJ, Kaminker JS, Gentleman R.

    BMC Genomics. 2016 Jan 15; 17:61.

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  • Orchestrating high-throughput genomic analysis with Bioconductor.

    Authors: Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oles AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

    Nat Methods. 2015 Feb; 12(2):115-21.

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  • A comprehensive transcriptional portrait of human cancer cell lines.

    Authors: Klijn C, Durinck S, Stawiski EW, Haverty PM, Jiang Z, Liu H, Degenhardt J, Mayba O, Gnad F, Liu J, Pau G, Reeder J, Cao Y, Mukhyala K, Selvaraj SK, Yu M, Zynda GJ, Brauer MJ, Wu TD, Gentleman RC, Manning G, Yauch RL, Bourgon R, Stokoe D, Modrusan Z, Neve RM, de Sauvage FJ, Settleman J, Seshagiri S, Zhang Z.

    Nat Biotechnol. 2015 Mar; 33(3):306-12.

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  • Integrative analysis of two cell lines derived from a non-small-lung cancer patient--a panomics approach.

    Authors: Mayba O, Gnad F, Peyton M, Zhang F, Walter K, Du P, Huntley MA, Jiang Z, Liu J, Haverty PM, Gentleman RC, Li R, Minna JD, Li Y, Shames DS, Zhang Z.

    Pac Symp Biocomput. 2014; 75-86.

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  • Discriminative motif analysis of high-throughput dataset. Bioinformatics.

    Authors: Yao Z, Macquarrie KL, Fong AP, Tapscott SJ, Ruzzo WL, Gentleman RC.

    Bioinformatics. 2014 Mar 15; 30(6):775-83.

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  • gCMAP: user-friendly connectivity mapping with R.

    Authors: Sandmann T, Kummerfeld SK, Gentleman R, Bourgon R.

    Bioinformatics. 2014 Jan 01; 30(1):127-8.

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  • The anatomy of successful computational biology software.

    Authors: Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C.

    Nat Biotechnol. 2013 Oct; 31(10):894-7.

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  • Software for computing and annotating genomic ranges. PLoS Comput Biol.

    Authors: Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ.

    PLoS Comput Biol. 2013; 9(8):e1003118.

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  • Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.

    Authors: Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.

    Skelet Muscle. 2013 Apr 08; 3(1):8.

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

    Authors: Liu J, Lee W, Jiang Z, Chen Z, Jhunjhunwala S, Haverty PM, Gnad F, Guan Y, Gilbert HN, Stinson J, Klijn C, Guillory J, Bhatt D, Vartanian S, Walter K, Chan J, Holcomb T, Dijkgraaf P, Johnson S, Koeman J, Minna JD, Gazdar AF, Stern HM, Hoeflich KP, Wu TD, Settleman J, de Sauvage FJ, Gentleman RC, Neve RM, Stokoe D, Modrusan Z, Seshagiri S, Shames DS, Zhang Z.

    Genome Res. 2012 Dec; 22(12):2315-27.

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

    Authors: Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS, Bergbower EA, Guan Y, Shin J, Guillory J, Rivers CS, Foo CK, Bhatt D, Stinson J, Gnad F, Haverty PM, Gentleman R, Chaudhuri S, Janakiraman V, Jaiswal BS, Parikh C, Yuan W, Zhang Z, Koeppen H, Wu TD, Stern HM, Yauch RL, Huffman KE, Paskulin DD, Illei PB, Varella-Garcia M, Gazdar AF, de Sauvage FJ, Bourgon R, Minna JD, Brock MV, Seshagiri S.

    Nat Genet. 2012 Oct; 44(10):1111-6.

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  • Recurrent R-spondin fusions in colon cancer.

    Authors: Seshagiri S, Stawiski EW, Durinck S, Modrusan Z, Storm EE, Conboy CB, Chaudhuri S, Guan Y, Janakiraman V, Jaiswal BS, Guillory J, Ha C, Dijkgraaf GJ, Stinson J, Gnad F, Huntley MA, Degenhardt JD, Haverty PM, Bourgon R, Wang W, Koeppen H, Gentleman R, Starr TK, Zhang Z, Largaespada DA, Wu TD, de Sauvage FJ.

    Nature. 2012 Aug 30; 488(7413):660-4.

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  • Genetic and epigenetic determinants of neurogenesis and myogenesis.

    Authors: Fong AP, Yao Z, Zhong JW, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.

    Dev Cell. 2012 Apr 17; 22(4):721-35.

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

    Authors: Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, Kennemer MI, Guan Y, Lee W, Carnevali P, Stinson J, Johnson S, Diao J, Yeung S, Jubb A, Ye W, Wu TD, Kapadia SB, de Sauvage FJ, Gentleman RC, Stern HM, Seshagiri S, Pant KP, Modrusan Z, Ballinger DG, Zhang Z.

    Genome Res. 2012 Apr; 22(4):593-601.

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  • Querying genomic databases: refining the connectivity map.

    Authors: Segal MR, Xiong H, Bengtsson H, Bourgon R, Gentleman R.

    Stat Appl Genet Mol Biol. 2012 Jan 06; 11(2).

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  • Analyzing biological data using R: methods for graphs and networks.

    Authors: Le Meur N, Gentleman R.

    Methods Mol Biol. 2012; 804:343-73.

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  • DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy.

    Authors: Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R, Tapscott SJ.

    Dev Cell. 2012 Jan 17; 22(1):38-51.

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  • An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.

    Authors: Knouf EC, Garg K, Arroyo JD, Correa Y, Sarkar D, Parkin RK, Wurz K, O'Briant KC, Godwin AK, Urban ND, Ruzzo WL, Gentleman R, Drescher CW, Swisher EM, Tewari M.

    Nucleic Acids Res. 2012 Jan; 40(2):499-510.

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  • Towards BioDBcore: a community-defined information specification for biological databases.

    Authors: Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C.

    Database (Oxford). 2011; 2011:baq027.

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  • Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages.

    Authors: Palii CG, Perez-Iratxeta C, Yao Z, Cao Y, Dai F, Davison J, Atkins H, Allan D, Dilworth FJ, Gentleman R, Tapscott SJ, Brand M.

    EMBO J. 2011 Feb 02; 30(3):494-509.

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  • Towards BioDBcore: a community-defined information specification for biological databases.

    Authors: Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C.

    Nucleic Acids Res. 2011 Jan; 39(Database issue):D7-10.

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  • Differential gene expression in benign prostate epithelium of men with and without prostate cancer: evidence for a prostate cancer field effect.

    Authors: Risk MC, Knudsen BS, Coleman I, Dumpit RF, Kristal AR, LeMeur N, Gentleman RC, True LD, Nelson PS, Lin DW.

    Clin Cancer Res. 2010 Nov 15; 16(22):5414-23.

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  • The mutation spectrum revealed by paired genome sequences from a lung cancer patient.

    Authors: 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.

    Nature. 2010 May 27; 465(7297):473-7.

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  • Independent filtering increases detection power for high-throughput experiments.

    Authors: Bourgon R, Gentleman R, Huber W.

    Proc Natl Acad Sci U S A. 2010 May 25; 107(21):9546-51.

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  • Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

    Authors: Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ.

    Dev Cell. 2010 Apr 20; 18(4):662-74.

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  • Per-channel basis normalization methods for flow cytometry data.

    Authors: Hahne F, Khodabakhshi AH, Bashashati A, Wong CJ, Gascoyne RD, Weng AP, Seyfert-Margolis V, Bourcier K, Asare A, Lumley T, Gentleman R, Brinkman RR.

    Cytometry A. 2010 Feb; 77(2):121-31.

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  • iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor.

    Authors: Lee K, Hahne F, Sarkar D, Gentleman R.

    Adv Bioinformatics. 2009; 103839.

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  • Knowledge based identification of essential signaling from genome-scale siRNA experiments.

    Authors: Bankhead A, Sach I, Ni C, LeMeur N, Kruger M, Ferrer M, Gentleman R, Rohl C.

    BMC Syst Biol. 2009 Aug 05; 3:80.

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  • ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.

    Authors: Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R.

    Bioinformatics. 2009 Oct 01; 25(19):2607-8.

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  • rtracklayer: an R package for interfacing with genome browsers.

    Authors: Lawrence M, Gentleman R, Carey V.

    Bioinformatics. 2009 Jul 15; 25(14):1841-2.

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  • flowCore: a Bioconductor package for high throughput flow cytometry.

    Authors: Hahne F, LeMeur N, Brinkman RR, Ellis B, Haaland P, Sarkar D, Spidlen J, Strain E, Gentleman R.

    BMC Bioinformatics. 2009 Apr 09; 10:106.

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  • Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.

    Authors: Carey VJ, Davis AR, Lawrence MF, Gentleman R, Raby BA.

    Bioinformatics. 2009 Jun 01; 25(11):1447-8.

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  • DATABASE: A new forum for biological databases and curation.

    Authors: Landsman D, Gentleman R, Kelso J, Francis Ouellette BF.

    Database (Oxford). 2009; 2009:bap002.

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  • arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.

    Authors: Kauffmann A, Gentleman R, Huber W.

    Bioinformatics. 2009 Feb 01; 25(3):415-6.

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  • Modeling synthetic lethality.

    Authors: Le Meur N, Gentleman R.

    Genome Biol. 2008; 9(9):R135.

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  • Gene set enrichment analysis using linear models and diagnostics.

    Authors: Oron AP, Jiang Z, Gentleman R.

    Bioinformatics. 2008 Nov 15; 24(22):2586-91.

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  • Circulating microRNAs as stable blood-based markers for cancer detection.

    Authors: Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M.

    Proc Natl Acad Sci U S A. 2008 Jul 29; 105(30):10513-8.

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  • MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.

    Authors: Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M.

    Stem Cells. 2008 Oct; 26(10):2496-505.

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  • Estimating node degree in bait-prey graphs.

    Authors: Scholtens D, Chiang T, Huber W, Gentleman R.

    Bioinformatics. 2008 Jan 15; 24(2):218-24.

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  • Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.

    Authors: Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W.

    Bioinformatics. 2008 Apr 15; 24(8):1100-1.

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  • Graphs in molecular biology.

    Authors: Huber W, Carey VJ, Long L, Falcon S, Gentleman R.

    BMC Bioinformatics. 2007 Sep 27; 8 Suppl 6:S8.

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  • Data quality assessment of ungated flow cytometry data in high throughput experiments.

    Authors: Le Meur N, Rossini A, Gasparetto M, Smith C, Brinkman RR, Gentleman R.

    Cytometry A. 2007 Jun; 71(6):393-403.

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  • Making the most of high-throughput protein-interaction data.

    Authors: Gentleman R, Huber W.

    Genome Biol. 2007; 8(10):112.

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  • Coverage and error models of protein-protein interaction data by directed graph analysis.

    Authors: Chiang T, Scholtens D, Sarkar D, Gentleman R, Huber W.

    Genome Biol. 2007; 8(9):R186.

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  • GGtools: analysis of genetics of gene expression in bioconductor.

    Authors: Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R.

    Bioinformatics. 2007 Feb 15; 23(4):522-3.

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  • Extensions to gene set enrichment.

    Authors: Jiang Z, Gentleman R.

    Bioinformatics. 2007 Feb 01; 23(3):306-13.

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  • Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery.

    Authors: Shi Q, Harris LN, Lu X, Li X, Hwang J, Gentleman R, Iglehart JD, Miron A.

    J Proteome Res. 2006 Nov; 5(11):2947-55.

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  • Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression.

    Authors: Yao J, Weremowicz S, Feng B, Gentleman RC, Marks JR, Gelman R, Brennan C, Polyak K.

    Cancer Res. 2006 Apr 15; 66(8):4065-78.

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  • Top-down standards will not serve systems biology.

    Authors: Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N.

    Nature. 2006 Mar 02; 440(7080):24.

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  • Data standards for flow cytometry.

    Authors: Spidlen J, Gentleman RC, Haaland PD, Langille M, Le Meur N, Ochs MF, Schmitt C, Smith CA, Treister AS, Brinkman RR.

    OMICS. 2006; 10(2):209-14.

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  • Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation.

    Authors: Chiaretti S, Li X, Gentleman R, Vitale A, Wang KS, Mandelli F, Foà R, Ritz J.

    Clin Cancer Res. 2005 Oct 15; 11(20):7209-19.

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  • Local modeling of global interactome networks.

    Authors: Scholtens D, Vidal M, Gentleman R.

    Bioinformatics. 2005 Sep 01; 21(17):3548-57.

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  • Bayesian error-in-variable survival model for the analysis of GeneChip arrays.

    Authors: Tadesse MG, Ibrahim JG, Gentleman R, Chiaretti S, Ritz J, Foa R.

    Biometrics. 2005 Jun; 61(2):488-97.

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  • Association of valproate-induced teratogenesis with histone deacetylase inhibition in vivo.

    Authors: Gurvich N, Berman MG, Wittner BS, Gentleman RC, Klein PS, Green JB.

    FASEB J. 2005 Jul; 19(9):1166-8.

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  • Wavelet thresholding with bayesian false discovery rate control.

    Authors: Tadesse MG, Ibrahim JG, Vannucci M, Gentleman R.

    Biometrics. 2005 Mar; 61(1):25-35.

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  • Reproducible research: a bioinformatics case study.

    Authors: Gentleman R.

    Stat Appl Genet Mol Biol. 2005; 4:Article2.

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  • Making sense of high-throughput protein-protein interaction data.

    Authors: Scholtens D, Gentleman R.

    Stat Appl Genet Mol Biol. 2004; 3:Article39.

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  • Bioconductor: open software development for computational biology and bioinformatics.

    Authors: Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J.

    Genome Biol. 2004; 5(10):R80.

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  • Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.

    Authors: Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M.

    Nucleic Acids Res. 2004 Aug 25; 32(15):e121.

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  • Network structures and algorithms in Bioconductor.

    Authors: Carey VJ, Gentry J, Whalen E, Gentleman R.

    Bioinformatics. 2005 Jan 01; 21(1):135-6.

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  • A graph-theoretic approach to testing associations between disparate sources of functional genomics data.

    Authors: Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R.

    Bioinformatics. 2004 Dec 12; 20(18):3353-62.

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  • matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.

    Authors: Huber W, Gentleman R.

    Bioinformatics. 2004 Jul 10; 20(10):1651-2.

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  • Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.

    Authors: Chiaretti S, Li X, Gentleman R, Vitale A, Vignetti M, Mandelli F, Ritz J, Foa R.

    Blood. 2004 Apr 01; 103(7):2771-8.

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  • The graft response to transplantation: a gene expression profile analysis.

    Authors: Christopher K, Mueller TF, DeFina R, Liang Y, Zhang J, Gentleman R, Perkins DL.

    Physiol Genomics. 2003 Sep 29; 15(1):52-64.

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  • Open source software for the analysis of microarray data.

    Authors: Dudoit S, Gentleman RC, Quackenbush J.

    Biotechniques. 2003 Mar; Suppl:45-51.

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  • An extensible application for assembling annotation for genomic data.

    Authors: Zhang J, Carey V, Gentleman R.

    Bioinformatics. 2003 Jan; 19(1):155-6.

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