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Items: 1 to 20 of 103

1.

Using MEMo to discover mutual exclusivity modules in cancer.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N.

Curr Protoc Bioinformatics. 2013 Mar;Chapter 8:Unit 8.17. doi: 10.1002/0471250953.bi0817s41.

PMID:
23504936
2.

Mutual exclusivity analysis identifies oncogenic network modules.

Ciriello G, Cerami E, Sander C, Schultz N.

Genome Res. 2012 Feb;22(2):398-406. doi: 10.1101/gr.125567.111. Epub 2011 Sep 9.

3.

Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data.

Zhang J, Zhang S, Wang Y, Zhang XS.

BMC Syst Biol. 2013;7 Suppl 2:S4. doi: 10.1186/1752-0509-7-S2-S4. Epub 2013 Oct 14.

4.

An information theoretic method to identify combinations of genomic alterations that promote glioblastoma.

Melamed RD, Wang J, Iavarone A, Rabadan R.

J Mol Cell Biol. 2015 Jun;7(3):203-13. doi: 10.1093/jmcb/mjv026. Epub 2015 May 4.

5.

Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets.

Lu S, Lu KN, Cheng SY, Hu B, Ma X, Nystrom N, Lu X.

PLoS Comput Biol. 2015 Aug 28;11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. eCollection 2015 Aug.

6.

Modeling mutual exclusivity of cancer mutations.

Szczurek E, Beerenwinkel N.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003503. doi: 10.1371/journal.pcbi.1003503. eCollection 2014 Mar.

7.

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.

Babur Ö, Gönen M, Aksoy BA, Schultz N, Ciriello G, Sander C, Demir E.

Genome Biol. 2015 Feb 26;16:45. doi: 10.1186/s13059-015-0612-6.

8.

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors.

Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A.

BMC Med Genomics. 2011 Apr 14;4:34. doi: 10.1186/1755-8794-4-34.

9.

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.

Kim YA, Cho DY, Dao P, Przytycka TM.

Bioinformatics. 2015 Jun 15;31(12):i284-92. doi: 10.1093/bioinformatics/btv247.

10.

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.

Li W, Zhang S, Liu CC, Zhou XJ.

Bioinformatics. 2012 Oct 1;28(19):2458-66. Epub 2012 Aug 3.

11.

Combined analysis of gene expression, DNA copy number, and mutation profiling data to display biological process anomalies in individual breast cancers.

Shi W, Balazs B, Györffy B, Jiang T, Symmans WF, Hatzis C, Pusztai L.

Breast Cancer Res Treat. 2014 Apr;144(3):561-8. doi: 10.1007/s10549-014-2904-z. Epub 2014 Mar 12.

PMID:
24619174
12.

On the Sample Complexity of Cancer Pathways Identification.

Vandin F, Raphael BJ, Upfal E.

J Comput Biol. 2016 Jan;23(1):30-41. doi: 10.1089/cmb.2015.0100. Epub 2015 Dec 8.

13.

Simultaneous identification of multiple driver pathways in cancer.

Leiserson MD, Blokh D, Sharan R, Raphael BJ.

PLoS Comput Biol. 2013;9(5):e1003054. doi: 10.1371/journal.pcbi.1003054. Epub 2013 May 23.

15.

IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals.

Ping Y, Zhang H, Deng Y, Wang L, Zhao H, Pang L, Fan H, Xu C, Li F, Zhang Y, Gong Y, Xiao Y, Li X.

Mol Biosyst. 2014 Aug;10(8):2031-42. doi: 10.1039/c4mb00289j.

PMID:
24911613
16.

Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer.

Srihari S, Singla J, Wong L, Ragan MA.

Biol Direct. 2015 Oct 1;10:57. doi: 10.1186/s13062-015-0086-1.

17.

Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers.

Hwang TH, Atluri G, Kuang R, Kumar V, Starr T, Silverstein KA, Haverty PM, Zhang Z, Liu J.

BMC Genomics. 2013 Jul 3;14:440. doi: 10.1186/1471-2164-14-440.

18.

A weighted exact test for mutually exclusive mutations in cancer.

Leiserson MD, Reyna MA, Raphael BJ.

Bioinformatics. 2016 Sep 1;32(17):i736-i745. doi: 10.1093/bioinformatics/btw462.

PMID:
27587696
19.

Expression-based network biology identifies immune-related functional modules involved in plant defense.

Tully JP, Hill AE, Ahmed HM, Whitley R, Skjellum A, Mukhtar MS.

BMC Genomics. 2014 Jun 3;15:421. doi: 10.1186/1471-2164-15-421.

20.

Automated network analysis identifies core pathways in glioblastoma.

Cerami E, Demir E, Schultz N, Taylor BS, Sander C.

PLoS One. 2010 Feb 12;5(2):e8918. doi: 10.1371/journal.pone.0008918.

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