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Sparse combinatorial inference with an application in cancer biology.
Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spellman PT, Gray JW, Speed TP. Mukherjee S, et al. Among authors: speed tp. Bioinformatics. 2009 Jan 15;25(2):265-71. doi: 10.1093/bioinformatics/btn611. Epub 2008 Nov 27. Bioinformatics. 2009. PMID: 19038985 Free PMC article.
A genotype calling algorithm for affymetrix SNP arrays.
Rabbee N, Speed TP. Rabbee N, et al. Among authors: speed tp. Bioinformatics. 2006 Jan 1;22(1):7-12. doi: 10.1093/bioinformatics/bti741. Epub 2005 Nov 2. Bioinformatics. 2006. PMID: 16267090
A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.
Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW. Neve RM, et al. Cancer Cell. 2006 Dec;10(6):515-27. doi: 10.1016/j.ccr.2006.10.008. Cancer Cell. 2006. PMID: 17157791 Free PMC article.
Network inference using informative priors.
Mukherjee S, Speed TP. Mukherjee S, et al. Among authors: speed tp. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14313-8. doi: 10.1073/pnas.0802272105. Epub 2008 Sep 17. Proc Natl Acad Sci U S A. 2008. PMID: 18799736 Free PMC article.
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.
Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN; Cancer Genome Atlas Research Network. Verhaak RG, et al. Among authors: speed tp. Cancer Cell. 2010 Jan 19;17(1):98-110. doi: 10.1016/j.ccr.2009.12.020. Cancer Cell. 2010. PMID: 20129251 Free PMC article.
Exon-level microarray analyses identify alternative splicing programs in breast cancer.
Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW. Lapuk A, et al. Mol Cancer Res. 2010 Jul;8(7):961-74. doi: 10.1158/1541-7786.MCR-09-0528. Epub 2010 Jul 6. Mol Cancer Res. 2010. PMID: 20605923 Free PMC article.
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. Heiser LM, et al. Among authors: speed tp. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2724-9. doi: 10.1073/pnas.1018854108. Epub 2011 Oct 14. Proc Natl Acad Sci U S A. 2012. PMID: 22003129 Free PMC article.
271 results