Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Robert Gentleman, Ph.D.

Other Positions

The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01EB008400 (GOTTARDO, RAPHAEL) May 1, 2008 - Dec 31, 2016
    The Statistical and Computational Analysis of Flow Cytometry Data
    Role: Co-Principal Investigator
  2. P41HG004059 (MORGAN, MARTIN) Sep 28, 2006 - Sep 25, 2011
    Bioconductor: an open computing resource for genomics
    Role: Co-Principal Investigator
  3. R33HG002708 (GENTLEMAN, ROBERT C) Sep 30, 2003 - Jun 30, 2008
    A Statistical Computing Framework for Genomic Data
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Fontanillas P, Alipanahi B, Furlotte NA, Johnson M, Wilson CH, Pitts SJ, Gentleman R, Auton A. Disease risk scores for skin cancers. Nat Commun. 2021 01 08; 12(1):160. PMID: 33420020; PMCID: PMC7794415.
    Citations: 10     Fields:    Translation:Humans
  2. Shelton JF, Cameron B, Aslibekyan S, Gentleman R. Demographic, spatial and temporal dietary intake patterns among 526 774 23andMe research participants. Public Health Nutr. 2021 07; 24(10):2952-2963. PMID: 32597744.
    Citations: 1     Fields:    Translation:HumansAnimals
  3. Wu S, Pollard J, Chowdry A, Scheller R, Gentleman R. Addressing the accuracy of direct-to-consumer genetic testing. Genet Med. 2019 03; 21(3):758-759. PMID: 29955106.
    Citations: 1     Fields:    Translation:Humans
  4. Lawrence M, Gentleman R. VariantTools: an extensible framework for developing and testing variant callers. Bioinformatics. 2017 Oct 15; 33(20):3311-3313. PMID: 29028267; PMCID: PMC5860039.
    Citations: 5     Fields:    
  5. 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. Creating a data resource: what will it take to build a medical information commons? Genome Med. 2017 09 22; 9(1):84. PMID: 28938910; PMCID: PMC5610432.
    Citations: 23     Fields:    Translation:Humans
  6. 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. Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers. Cell Rep. 2016 09 06; 16(10):2605-2617. PMID: 27568559.
    Citations: 81     Fields:    Translation:HumansCells
  7. Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R. Prediction and Quantification of Splice Events from RNA-Seq Data. PLoS One. 2016; 11(5):e0156132. PMID: 27218464; PMCID: PMC4878813.
    Citations: 41     Fields:    Translation:HumansCells
  8. Huntley MA, Lou M, Goldstein LD, Lawrence M, Dijkgraaf GJ, Kaminker JS, Gentleman R. Complex regulation of ADAR-mediated RNA-editing across tissues. BMC Genomics. 2016 Jan 15; 17:61. PMID: 26768488.
    Citations: 32     Fields:    Translation:HumansAnimalsCells
  9. 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. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015 Feb; 12(2):115-21. PMID: 25633503; PMCID: PMC4509590.
    Citations: 1305     Fields:    
  10. 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. A comprehensive transcriptional portrait of human cancer cell lines. Nat Biotechnol. 2015 Mar; 33(3):306-12. PMID: 25485619.
    Citations: 294     Fields:    Translation:HumansCells
  11. 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. Integrative analysis of two cell lines derived from a non-small-lung cancer patient--a panomics approach. Pac Symp Biocomput. 2014; 75-86. PMID: 24297535.
    Citations: 4     Fields:    Translation:HumansCells
  12. Yao Z, Macquarrie KL, Fong AP, Tapscott SJ, Ruzzo WL, Gentleman RC. Discriminative motif analysis of high-throughput dataset. Bioinformatics. 2014 Mar 15; 30(6):775-83. PMID: 24162561.
    Citations: 15     Fields:    Translation:HumansCells
  13. Sandmann T, Kummerfeld SK, Gentleman R, Bourgon R. gCMAP: user-friendly connectivity mapping with R. Bioinformatics. 2014 Jan 01; 30(1):127-8. PMID: 24132929.
    Citations: 11     Fields:    Translation:HumansAnimalsCells
  14. Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. The anatomy of successful computational biology software. Nat Biotechnol. 2013 Oct; 31(10):894-7. PMID: 24104757.
    Citations: 10     Fields:    
  15. Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9(8):e1003118. PMID: 23950696.
    Citations: 1371     Fields:    Translation:HumansAnimals
  16. Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ. Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites. Skelet Muscle. 2013 Apr 08; 3(1):8. PMID: 23566431.
    Citations: 14     Fields:    
  17. 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 and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Res. 2012 Dec; 22(12):2315-27. PMID: 23033341.
    Citations: 104     Fields:    Translation:HumansCells
  18. 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. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet. 2012 Oct; 44(10):1111-6. PMID: 22941189.
    Citations: 465     Fields:    Translation:HumansCells
  19. 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. Recurrent R-spondin fusions in colon cancer. Nature. 2012 Aug 30; 488(7413):660-4. PMID: 22895193; PMCID: PMC3690621.
    Citations: 461     Fields:    Translation:HumansCells
  20. Fong AP, Yao Z, Zhong JW, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ. Genetic and epigenetic determinants of neurogenesis and myogenesis. Dev Cell. 2012 Apr 17; 22(4):721-35. PMID: 22445365.
    Citations: 70     Fields:    Translation:AnimalsCells
  21. 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. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res. 2012 Apr; 22(4):593-601. PMID: 22267523.
    Citations: 140     Fields:    Translation:HumansCells
  22. Segal MR, Xiong H, Bengtsson H, Bourgon R, Gentleman R. Querying genomic databases: refining the connectivity map. Stat Appl Genet Mol Biol. 2012 Jan 06; 11(2). PMID: 22499690.
    Citations: 7     Fields:    Translation:Humans
  23. Le Meur N, Gentleman R. Analyzing biological data using R: methods for graphs and networks. Methods Mol Biol. 2012; 804:343-73. PMID: 22144163.
    Citations: 12     Fields:    Translation:Cells
  24. Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R, Tapscott SJ. DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev Cell. 2012 Jan 17; 22(1):38-51. PMID: 22209328.
    Citations: 231     Fields:    Translation:HumansCells
  25. 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. An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. Nucleic Acids Res. 2012 Jan; 40(2):499-510. PMID: 21917857.
    Citations: 39     Fields:    Translation:HumansCells
  26. 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. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). 2011; 2011:baq027. PMID: 21205783; PMCID: PMC3017395.
    Citations: 12     Fields:    
  27. 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. Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages. EMBO J. 2011 Feb 02; 30(3):494-509. PMID: 21179004.
    Citations: 74     Fields:    Translation:HumansCells
  28. 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. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 2011 Jan; 39(Database issue):D7-10. PMID: 21097465; PMCID: PMC3013734.
    Citations: 22     Fields:    
  29. Risk MC, Knudsen BS, Coleman I, Dumpit RF, Kristal AR, LeMeur N, Gentleman RC, True LD, Nelson PS, Lin DW. Differential gene expression in benign prostate epithelium of men with and without prostate cancer: evidence for a prostate cancer field effect. Clin Cancer Res. 2010 Nov 15; 16(22):5414-23. PMID: 20935156.
    Citations: 25     Fields:    Translation:Humans
  30. 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. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature. 2010 May 27; 465(7297):473-7. PMID: 20505728.
    Citations: 260     Fields:    Translation:Humans
  31. Bourgon R, Gentleman R, Huber W. Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci U S A. 2010 May 25; 107(21):9546-51. PMID: 20460310.
    Citations: 320     Fields:    
  32. Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell. 2010 Apr 20; 18(4):662-74. PMID: 20412780.
    Citations: 253     Fields:    Translation:AnimalsCells
  33. 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. Per-channel basis normalization methods for flow cytometry data. Cytometry A. 2010 Feb; 77(2):121-31. PMID: 19899135.
    Citations: 45     Fields:    Translation:HumansCells
  34. Lee K, Hahne F, Sarkar D, Gentleman R. iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor. Adv Bioinformatics. 2009; 103839. PMID: 20049160.
    Citations: 4     
  35. Bankhead A, Sach I, Ni C, LeMeur N, Kruger M, Ferrer M, Gentleman R, Rohl C. Knowledge based identification of essential signaling from genome-scale siRNA experiments. BMC Syst Biol. 2009 Aug 05; 3:80. PMID: 19653913.
    Citations: 8     Fields:    Translation:HumansCells
  36. Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics. 2009 Oct 01; 25(19):2607-8. PMID: 19654119.
    Citations: 240     Fields:    
  37. Lawrence M, Gentleman R, Carey V. rtracklayer: an R package for interfacing with genome browsers. Bioinformatics. 2009 Jul 15; 25(14):1841-2. PMID: 19468054.
    Citations: 257     Fields:    
  38. Hahne F, LeMeur N, Brinkman RR, Ellis B, Haaland P, Sarkar D, Spidlen J, Strain E, Gentleman R. flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinformatics. 2009 Apr 09; 10:106. PMID: 19358741.
    Citations: 195     Fields:    
  39. Carey VJ, Davis AR, Lawrence MF, Gentleman R, Raby BA. Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x. Bioinformatics. 2009 Jun 01; 25(11):1447-8. PMID: 19349284.
    Citations: 11     Fields:    
  40. Landsman D, Gentleman R, Kelso J, Francis Ouellette BF. DATABASE: A new forum for biological databases and curation. Database (Oxford). 2009; 2009:bap002. PMID: 20157475.
    Citations: 5     Fields:    
  41. Kauffmann A, Gentleman R, Huber W. arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics. 2009 Feb 01; 25(3):415-6. PMID: 19106121.
    Citations: 447     Fields:    
  42. Le Meur N, Gentleman R. Modeling synthetic lethality. Genome Biol. 2008; 9(9):R135. PMID: 18789146.
    Citations: 30     Fields:    Translation:Animals
  43. Oron AP, Jiang Z, Gentleman R. Gene set enrichment analysis using linear models and diagnostics. Bioinformatics. 2008 Nov 15; 24(22):2586-91. PMID: 18790795.
    Citations: 31     Fields:    Translation:HumansCells
  44. 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. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A. 2008 Jul 29; 105(30):10513-8. PMID: 18663219.
    Citations: 3290     Fields:    Translation:HumansAnimals
  45. 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. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells. 2008 Oct; 26(10):2496-505. PMID: 18583537.
    Citations: 167     Fields:    Translation:HumansCells
  46. Scholtens D, Chiang T, Huber W, Gentleman R. Estimating node degree in bait-prey graphs. Bioinformatics. 2008 Jan 15; 24(2):218-24. PMID: 18025006.
    Citations: 8     Fields:    Translation:Cells
  47. Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W. Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics. 2008 Apr 15; 24(8):1100-1. PMID: 17989096.
    Citations: 3     Fields:    
  48. Huber W, Carey VJ, Long L, Falcon S, Gentleman R. Graphs in molecular biology. BMC Bioinformatics. 2007 Sep 27; 8 Suppl 6:S8. PMID: 17903289.
    Citations: 38     Fields:    Translation:Cells
  49. Le Meur N, Rossini A, Gasparetto M, Smith C, Brinkman RR, Gentleman R. Data quality assessment of ungated flow cytometry data in high throughput experiments. Cytometry A. 2007 Jun; 71(6):393-403. PMID: 17366638.
    Citations: 15     Fields:    Translation:HumansCells
  50. Gentleman R, Huber W. Making the most of high-throughput protein-interaction data. Genome Biol. 2007; 8(10):112. PMID: 18001486.
    Citations: 17     Fields:    Translation:Cells
  51. Chiang T, Scholtens D, Sarkar D, Gentleman R, Huber W. Coverage and error models of protein-protein interaction data by directed graph analysis. Genome Biol. 2007; 8(9):R186. PMID: 17845715; PMCID: PMC2375024.
    Citations: 15     Fields:    Translation:Animals
  52. Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R. GGtools: analysis of genetics of gene expression in bioconductor. Bioinformatics. 2007 Feb 15; 23(4):522-3. PMID: 17158513.
    Citations: 4     Fields:    
  53. Jiang Z, Gentleman R. Extensions to gene set enrichment. Bioinformatics. 2007 Feb 01; 23(3):306-13. PMID: 17127676.
    Citations: 114     Fields:    
  54. Shi Q, Harris LN, Lu X, Li X, Hwang J, Gentleman R, Iglehart JD, Miron A. Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery. J Proteome Res. 2006 Nov; 5(11):2947-55. PMID: 17081046.
    Citations: 10     Fields:    Translation:HumansCells
  55. Yao J, Weremowicz S, Feng B, Gentleman RC, Marks JR, Gelman R, Brennan C, Polyak K. Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression. Cancer Res. 2006 Apr 15; 66(8):4065-78. PMID: 16618726.
    Citations: 73     Fields:    Translation:HumansCells
  56. Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Top-down standards will not serve systems biology. Nature. 2006 Mar 02; 440(7080):24. PMID: 16511469.
    Citations: 6     Fields:    
  57. Spidlen J, Gentleman RC, Haaland PD, Langille M, Le Meur N, Ochs MF, Schmitt C, Smith CA, Treister AS, Brinkman RR. Data standards for flow cytometry. OMICS. 2006; 10(2):209-14. PMID: 16901228.
    Citations: 11     Fields:    
  58. Chiaretti S, Li X, Gentleman R, Vitale A, Wang KS, Mandelli F, Foà R, Ritz J. Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation. Clin Cancer Res. 2005 Oct 15; 11(20):7209-19. PMID: 16243790.
    Citations: 48     Fields:    Translation:Humans
  59. Scholtens D, Vidal M, Gentleman R. Local modeling of global interactome networks. Bioinformatics. 2005 Sep 01; 21(17):3548-57. PMID: 15998662.
    Citations: 24     Fields:    Translation:Cells
  60. Tadesse MG, Ibrahim JG, Gentleman R, Chiaretti S, Ritz J, Foa R. Bayesian error-in-variable survival model for the analysis of GeneChip arrays. Biometrics. 2005 Jun; 61(2):488-97. PMID: 16011696.
    Citations: 5     Fields:    Translation:Humans
  61. Gurvich N, Berman MG, Wittner BS, Gentleman RC, Klein PS, Green JB. Association of valproate-induced teratogenesis with histone deacetylase inhibition in vivo. FASEB J. 2005 Jul; 19(9):1166-8. PMID: 15901671.
    Citations: 52     Fields:    Translation:AnimalsCells
  62. Tadesse MG, Ibrahim JG, Vannucci M, Gentleman R. Wavelet thresholding with bayesian false discovery rate control. Biometrics. 2005 Mar; 61(1):25-35. PMID: 15737075.
    Citations: 5     Fields:    Translation:Humans
  63. Gentleman R. Reproducible research: a bioinformatics case study. Stat Appl Genet Mol Biol. 2005; 4:Article2. PMID: 16646837.
    Citations: 58     Fields:    
  64. Scholtens D, Gentleman R. Making sense of high-throughput protein-protein interaction data. Stat Appl Genet Mol Biol. 2004; 3:Article39. PMID: 16646819.
    Citations: 6     Fields:    
  65. 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. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMID: 15461798; PMCID: PMC545600.
    Citations: 6289     Fields:    
  66. Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M. Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments. Nucleic Acids Res. 2004 Aug 25; 32(15):e121. PMID: 15329383; PMCID: PMC516078.
    Citations: 9     Fields:    Translation:HumansCells
  67. Carey VJ, Gentry J, Whalen E, Gentleman R. Network structures and algorithms in Bioconductor. Bioinformatics. 2005 Jan 01; 21(1):135-6. PMID: 15297301.
    Citations: 32     Fields:    Translation:Cells
  68. Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R. A graph-theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics. 2004 Dec 12; 20(18):3353-62. PMID: 15256415.
    Citations: 11     Fields:    Translation:Animals
  69. Huber W, Gentleman R. matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. Bioinformatics. 2004 Jul 10; 20(10):1651-2. PMID: 14988118.
    Citations: 17     Fields:    
  70. Chiaretti S, Li X, Gentleman R, Vitale A, Vignetti M, Mandelli F, Ritz J, Foa R. Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood. 2004 Apr 01; 103(7):2771-8. PMID: 14684422.
    Citations: 74     Fields:    Translation:HumansCells
  71. Christopher K, Mueller TF, DeFina R, Liang Y, Zhang J, Gentleman R, Perkins DL. The graft response to transplantation: a gene expression profile analysis. Physiol Genomics. 2003 Sep 29; 15(1):52-64. PMID: 14517350.
    Citations: 4     Fields:    Translation:AnimalsCells
  72. Dudoit S, Gentleman RC, Quackenbush J. Open source software for the analysis of microarray data. Biotechniques. 2003 Mar; Suppl:45-51. PMID: 12664684.
    Citations: 116     Fields:    
  73. Zhang J, Carey V, Gentleman R. An extensible application for assembling annotation for genomic data. Bioinformatics. 2003 Jan; 19(1):155-6. PMID: 12499308.
    Citations: 15     Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.