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Results: 1 to 20 of 54

1.

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM.

Nat Genet. 2014 Apr;46(4):318-9. doi: 10.1038/ng.2932. No abstract available.

PMID:
24675517
[PubMed - in process]
2.

Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching.

Chang H, Nayak N, Spellman PT, Parvin B.

Med Image Comput Comput Assist Interv. 2013;16(Pt 2):91-8.

PMID:
24579128
[PubMed - indexed for MEDLINE]
3.

Integrated analysis of germline and somatic variants in ovarian cancer.

Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L.

Nat Commun. 2014;5:3156. doi: 10.1038/ncomms4156.

PMID:
24448499
[PubMed - in process]
4.

Modeling precision treatment of breast cancer.

Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, van't Veer LJ, Spellman PT, Gray JW.

Genome Biol. 2013;14(10):R110.

PMID:
24176112
[PubMed - in process]
Free PMC Article
5.

A robust prognostic signature for hormone-positive node-negative breast cancer.

Griffith OL, Pepin F, Enache OM, Heiser LM, Collisson EA, Spellman PT, Gray JW.

Genome Med. 2013 Oct 11;5(10):92. [Epub ahead of print]

PMID:
24112773
[PubMed - as supplied by publisher]
Free PMC Article
6.

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma.

Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M; Cancer Genome Atlas Research Network.

J Clin Invest. 2013 Jan 2;123(1):517-25. doi: 10.1172/JCI65833. Epub 2012 Dec 21.

PMID:
23257362
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

ATM suppresses SATB1-induced malignant progression in breast epithelial cells.

Ordinario E, Han HJ, Furuta S, Heiser LM, Jakkula LR, Rodier F, Spellman PT, Campisi J, Gray JW, Bissell MJ, Kohwi Y, Kohwi-Shigematsu T.

PLoS One. 2012;7(12):e51786. doi: 10.1371/journal.pone.0051786. Epub 2012 Dec 10.

PMID:
23251624
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association.

Chang H, Han J, Borowsky A, Loss L, Gray JW, Spellman PT, Parvin B.

IEEE Trans Med Imaging. 2013 Apr;32(4):670-82. doi: 10.1109/TMI.2012.2231420. Epub 2012 Dec 4.

PMID:
23221815
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme.

Chang H, Han J, Spellman PT, Parvin B.

IEEE Trans Biomed Eng. 2012 Dec;59(12):3460-7. doi: 10.1109/TBME.2012.2218107. Epub 2012 Sep 10.

PMID:
22987497
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Xenografts faithfully recapitulate breast cancer-specific gene expression patterns of parent primary breast tumors.

Petrillo LA, Wolf DM, Kapoun AM, Wang NJ, Barczak A, Xiao Y, Korkaya H, Baehner F, Lewicki J, Wicha M, Park JW, Spellman PT, Gray JW, van't Veer L, Esserman LJ.

Breast Cancer Res Treat. 2012 Oct;135(3):913-22. doi: 10.1007/s10549-012-2226-y. Epub 2012 Sep 2.

PMID:
22941572
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Bayesian inference of signaling network topology in a cancer cell line.

Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S.

Bioinformatics. 2012 Nov 1;28(21):2804-10. doi: 10.1093/bioinformatics/bts514. Epub 2012 Aug 24.

PMID:
22923301
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib.

Daemen A, Wolf DM, Korkola JE, Griffith OL, Frankum JR, Brough R, Jakkula LR, Wang NJ, Natrajan R, Reis-Filho JS, Lord CJ, Ashworth A, Spellman PT, Gray JW, van't Veer LJ.

Breast Cancer Res Treat. 2012 Sep;135(2):505-17. doi: 10.1007/s10549-012-2188-0. Epub 2012 Aug 9.

PMID:
22875744
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma.

Collisson EA, Trejo CL, Silva JM, Gu S, Korkola JE, Heiser LM, Charles RP, Rabinovich BA, Hann B, Dankort D, Spellman PT, Phillips WA, Gray JW, McMahon M.

Cancer Discov. 2012 Aug;2(8):685-93. Epub 2012 May 24.

PMID:
22628411
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing.

Corless CL, Spellman PT.

Cancer Discov. 2012 Jan;2(1):23-4. doi: 10.1158/2159-8290.CD-11-0319.

PMID:
22585165
[PubMed - indexed for MEDLINE]
15.

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology.

Hill SM, Neve RM, Bayani N, Kuo WL, Ziyad S, Spellman PT, Gray JW, Mukherjee S.

BMC Bioinformatics. 2012 May 11;13:94. doi: 10.1186/1471-2105-13-94.

PMID:
22578440
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma.

Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH; Cancer Genome Atlas Research Network.

PLoS One. 2012;7(3):e34546. doi: 10.1371/journal.pone.0034546. Epub 2012 Mar 29.

PMID:
22479643
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Morphometic analysis of TCGA glioblastoma multiforme.

Chang H, Fontenay GV, Han J, Cong G, Baehner FL, Gray JW, Spellman PT, Parvin B.

BMC Bioinformatics. 2011 Dec 20;12:484. doi: 10.1186/1471-2105-12-484.

PMID:
22185703
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma.

Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, Gordon PB, Jakkula L, Pennypacker S, Zou Y, Sharma M, North JP, Vemula SS, Mauro TM, Neuhaus IM, Leboit PE, Hur JS, Park K, Huh N, Kwok PY, Arron ST, Massion PP, Bale AE, Haussler D, Cleaver JE, Gray JW, Spellman PT, South AP, Aster JC, Blacklow SC, Cho RJ.

Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17761-6. doi: 10.1073/pnas.1114669108. Epub 2011 Oct 17.

PMID:
22006338
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Subtype and pathway specific responses to anticancer compounds in breast cancer.

Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2724-9. doi: 10.1073/pnas.1018854108. Epub 2011 Oct 14.

PMID:
22003129
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Temporal dissection of tumorigenesis in primary cancers.

Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, Pons J, Chan SW, Lam ET, Chu C, Park K, Hong SW, Hur JS, Huh N, Neuhaus IM, Yu SS, Grekin RC, Mauro TM, Cleaver JE, Kwok PY, LeBoit PE, Getz G, Cibulskis K, Aster JC, Huang H, Purdom E, Li J, Bolund L, Arron ST, Gray JW, Spellman PT, Cho RJ.

Cancer Discov. 2011 Jul;1(2):137-43. doi: 10.1158/2159-8290.CD-11-0028. Epub 2011 Jun 29.

PMID:
21984974
[PubMed - indexed for MEDLINE]
Free PMC Article

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