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Results: 1 to 20 of 72

1.

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.

PMID:
24297535
[PubMed - in process]
Free Article
2.

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.

PMID:
24162561
[PubMed - indexed for MEDLINE]
3.

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
[PubMed - indexed for MEDLINE]
4.

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.

PMID:
24104757
[PubMed - indexed for MEDLINE]
5.

Software for computing and annotating genomic ranges.

Lawrence M, Huber W, Pag├Ęs 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.

PMID:
23950696
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23566431
[PubMed]
Free PMC Article
7.

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.

PMID:
23033341
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22941189
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22895193
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
22445365
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22267523
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
22209328
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
[PubMed - indexed for MEDLINE]
15.

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.

PMID:
21917857
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
21205783
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
21179004
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
21121064
[PubMed - indexed for MEDLINE]
Free Article
19.

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.

PMID:
21097465
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
20935156
[PubMed - indexed for MEDLINE]
Free PMC Article

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