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Items: 1 to 50 of 80

1.

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

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

Genet Med. 2019 Mar;21(3):758-759. doi: 10.1038/s41436-018-0094-5. Epub 2018 Jun 29. No abstract available.

PMID:
29955106
2.

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

Lawrence M, Gentleman R.

Bioinformatics. 2017 Oct 15;33(20):3311-3313. doi: 10.1093/bioinformatics/btx450.

3.

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

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 Sep 22;9(1):84. doi: 10.1186/s13073-017-0476-3.

4.

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

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 Sep 6;16(10):2605-2617. doi: 10.1016/j.celrep.2016.08.010. Epub 2016 Aug 25.

5.

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

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

PLoS One. 2016 May 24;11(5):e0156132. doi: 10.1371/journal.pone.0156132. eCollection 2016.

6.

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

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

BMC Genomics. 2016 Jan 15;17:61. doi: 10.1186/s12864-015-2291-9.

7.

Orchestrating high-throughput genomic analysis with Bioconductor.

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, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

8.

A comprehensive transcriptional portrait of human cancer cell lines.

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. doi: 10.1038/nbt.3080. Epub 2014 Dec 8.

PMID:
25485619
9.

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

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.

10.

Discriminative motif analysis of high-throughput dataset.

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

Bioinformatics. 2014 Mar 15;30(6):775-83. doi: 10.1093/bioinformatics/btt615. Epub 2013 Oct 25.

11.

gCMAP: user-friendly connectivity mapping with R.

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

Bioinformatics. 2014 Jan 1;30(1):127-8. doi: 10.1093/bioinformatics/btt592. Epub 2013 Oct 15.

PMID:
24132929
12.

The anatomy of successful computational biology software.

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. doi: 10.1038/nbt.2721. No abstract available.

13.

Software for computing and annotating genomic ranges.

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

PLoS Comput Biol. 2013;9(8):e1003118. doi: 10.1371/journal.pcbi.1003118. Epub 2013 Aug 8.

14.

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

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

Skelet Muscle. 2013 Apr 8;3(1):8. doi: 10.1186/2044-5040-3-8.

15.

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

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. doi: 10.1101/gr.140988.112. Epub 2012 Oct 2.

16.

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

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. doi: 10.1038/ng.2405. Epub 2012 Sep 2.

17.

Recurrent R-spondin fusions in colon cancer.

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. doi: 10.1038/nature11282.

18.

Querying genomic databases: refining the connectivity map.

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

Stat Appl Genet Mol Biol. 2012 Jan 6;11(2). pii: /j/sagmb.2012.11.issue-2/1544-6115.1715/1544-6115.1715.xml. doi: 10.2202/1544-6115.1715.

PMID:
22499690
19.

Genetic and epigenetic determinants of neurogenesis and myogenesis.

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

Dev Cell. 2012 Apr 17;22(4):721-35. doi: 10.1016/j.devcel.2012.01.015. Epub 2012 Mar 22.

20.

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

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. doi: 10.1101/gr.133926.111. Epub 2012 Jan 20.

21.

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

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. doi: 10.1016/j.devcel.2011.11.013. Epub 2011 Dec 29.

22.

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

Le Meur N, Gentleman R.

Methods Mol Biol. 2012;804:343-73. doi: 10.1007/978-1-61779-361-5_19.

PMID:
22144163
23.

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

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. doi: 10.1093/nar/gkr731. Epub 2011 Sep 14.

24.

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

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; BioDBCore Working Group.

Database (Oxford). 2011 Jan 4;2011:baq027. doi: 10.1093/database/baq027. Print 2011.

25.

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

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 2;30(3):494-509. doi: 10.1038/emboj.2010.342. Epub 2010 Dec 21.

26.

Identification of aberrant pathway and network activity from high-throughput data.

Ochs MF, Karchin R, Ressom H, Gentleman R.

Pac Symp Biocomput. 2011:364-8.

27.

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

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; BioDBCore Working Group.

Nucleic Acids Res. 2011 Jan;39(Database issue):D7-10. doi: 10.1093/nar/gkq1173. Epub 2010 Nov 18.

28.

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

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. doi: 10.1158/1078-0432.CCR-10-0272. Epub 2010 Oct 8.

29.

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

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. doi: 10.1038/nature09004.

PMID:
20505728
30.

Independent filtering increases detection power for high-throughput experiments.

Bourgon R, Gentleman R, Huber W.

Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-51. doi: 10.1073/pnas.0914005107. Epub 2010 May 11.

31.

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

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. doi: 10.1016/j.devcel.2010.02.014.

32.

DATABASE: A new forum for biological databases and curation.

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

Database (Oxford). 2009;2009:bap002. Epub 2009 Mar 16. No abstract available.

33.

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

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

Adv Bioinformatics. 2009:103839. doi: 10.1155/2009/103839. Epub 2009 Nov 12.

34.

Per-channel basis normalization methods for flow cytometry data.

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. doi: 10.1002/cyto.a.20823.

35.

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

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

Bioinformatics. 2009 Oct 1;25(19):2607-8. doi: 10.1093/bioinformatics/btp450. Epub 2009 Aug 3.

36.

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

Bankhead A 3rd, Sach I, Ni C, LeMeur N, Kruger M, Ferrer M, Gentleman R, Rohl C.

BMC Syst Biol. 2009 Aug 5;3:80. doi: 10.1186/1752-0509-3-80.

37.

rtracklayer: an R package for interfacing with genome browsers.

Lawrence M, Gentleman R, Carey V.

Bioinformatics. 2009 Jul 15;25(14):1841-2. doi: 10.1093/bioinformatics/btp328. Epub 2009 May 25.

38.

flowCore: a Bioconductor package for high throughput flow cytometry.

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

BMC Bioinformatics. 2009 Apr 9;10:106. doi: 10.1186/1471-2105-10-106.

39.

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

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

Bioinformatics. 2009 Jun 1;25(11):1447-8. doi: 10.1093/bioinformatics/btp169. Epub 2009 Apr 5.

40.
41.

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

Kauffmann A, Gentleman R, Huber W.

Bioinformatics. 2009 Feb 1;25(3):415-6. doi: 10.1093/bioinformatics/btn647. Epub 2008 Dec 23.

42.

Quality assessment and data analysis for microRNA expression arrays.

Sarkar D, Parkin R, Wyman S, Bendoraite A, Sather C, Delrow J, Godwin AK, Drescher C, Huber W, Gentleman R, Tewari M.

Nucleic Acids Res. 2009 Feb;37(2):e17. doi: 10.1093/nar/gkn932. Epub 2008 Dec 22.

43.

Gene set enrichment analysis using linear models and diagnostics.

Oron AP, Jiang Z, Gentleman R.

Bioinformatics. 2008 Nov 15;24(22):2586-91. doi: 10.1093/bioinformatics/btn465. Epub 2008 Sep 11.

44.

Modeling synthetic lethality.

Le Meur N, Gentleman R.

Genome Biol. 2008;9(9):R135. doi: 10.1186/gb-2008-9-9-r135. Epub 2008 Sep 12.

45.

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

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. doi: 10.1073/pnas.0804549105. Epub 2008 Jul 28.

46.

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

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. doi: 10.1634/stemcells.2008-0356. Epub 2008 Jun 26.

47.

Using flowViz to visualize flow cytometry data.

Sarkar D, Le Meur N, Gentleman R.

Bioinformatics. 2008 Mar 15;24(6):878-9. doi: 10.1093/bioinformatics/btn021. Epub 2008 Feb 1.

48.

Estimating node degree in bait-prey graphs.

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

Bioinformatics. 2008 Jan 15;24(2):218-24. Epub 2007 Nov 19.

PMID:
18025006
49.

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

Gentleman R, Huber W.

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

50.

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

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

Bioinformatics. 2008 Apr 15;24(8):1100-1. Epub 2007 Nov 7.

PMID:
17989096

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