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Items: 1 to 20 of 179

1.

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.

Leiserson MD, Vandin F, Wu HT, Dobson JR, Eldridge JV, Thomas JL, Papoutsaki A, Kim Y, Niu B, McLellan M, Lawrence MS, Gonzalez-Perez A, Tamborero D, Cheng Y, Ryslik GA, Lopez-Bigas N, Getz G, Ding L, Raphael BJ.

Nat Genet. 2015 Feb;47(2):106-14. doi: 10.1038/ng.3168. Epub 2014 Dec 15.

2.

Discovery of mutated subnetworks associated with clinical data in cancer.

Vandin F, Clay P, Upfal E, Raphael BJ.

Pac Symp Biocomput. 2012:55-66.

3.

The mutational landscape of phosphorylation signaling in cancer.

Reimand J, Wagih O, Bader GD.

Sci Rep. 2013 Oct 2;3:2651. doi: 10.1038/srep02651.

4.

Algorithms for detecting significantly mutated pathways in cancer.

Vandin F, Upfal E, Raphael BJ.

J Comput Biol. 2011 Mar;18(3):507-22. doi: 10.1089/cmb.2010.0265.

PMID:
21385051
5.

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.

6.

De novo discovery of mutated driver pathways in cancer.

Vandin F, Upfal E, Raphael BJ.

Genome Res. 2012 Feb;22(2):375-85. doi: 10.1101/gr.120477.111. Epub 2011 Jun 7.

7.

Prediction of oncogenic interactions and cancer-related signaling networks based on network topology.

Acencio ML, Bovolenta LA, Camilo E, Lemke N.

PLoS One. 2013 Oct 25;8(10):e77521. doi: 10.1371/journal.pone.0077521. eCollection 2013.

8.

A scalable approach for discovering conserved active subnetworks across species.

Deshpande R, Sharma S, Verfaillie CM, Hu WS, Myers CL.

PLoS Comput Biol. 2010 Dec 9;6(12):e1001028. doi: 10.1371/journal.pcbi.1001028.

9.

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer.

Narayan S, Bader GD, Reimand J.

Genome Med. 2016 May 12;8(1):55. doi: 10.1186/s13073-016-0311-2.

10.

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.

11.

Genetics: HotNet2-see the wood for the trees.

Killock D.

Nat Rev Clin Oncol. 2015 Feb;12(2):66. doi: 10.1038/nrclinonc.2014.234. Epub 2015 Jan 6. No abstract available.

PMID:
25560530
12.

Finding co-mutated genes and candidate cancer genes in cancer genomes by stratified false discovery rate control.

Wang J, Zhang Y, Shen X, Zhu J, Zhang L, Zou J, Guo Z.

Mol Biosyst. 2011 Apr;7(4):1158-66. doi: 10.1039/c0mb00211a. Epub 2011 Jan 28.

PMID:
21279201
13.

SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis.

Pulido-Tamayo S, Weytjens B, De Maeyer D, Marchal K.

Sci Rep. 2016 Nov 3;6:36257. doi: 10.1038/srep36257.

14.

Co-occurrence of MYC amplification and TP53 mutations in human cancer.

Ulz P, Heitzer E, Speicher MR.

Nat Genet. 2016 Feb;48(2):104-6. doi: 10.1038/ng.3468. No abstract available.

PMID:
26813759
15.

Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer.

Leiserson MD, Vandin F, Wu HT, Raphael BJ.

Nat Genet. 2016 Feb;48(2):106-8. doi: 10.1038/ng.3491. No abstract available.

PMID:
26813760
16.

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.

Cho A, Shim JE, Kim E, Supek F, Lehner B, Lee I.

Genome Biol. 2016 Jun 23;17(1):129. doi: 10.1186/s13059-016-0989-x.

17.

Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data.

Raphael BJ, Vandin F.

J Comput Biol. 2015 Jun;22(6):510-27. doi: 10.1089/cmb.2014.0161. Epub 2015 Mar 18.

18.

Characterizing mutation-expression network relationships in multiple cancers.

Ghazanfar S, Yang JYH.

Comput Biol Chem. 2016 Aug;63:73-82. doi: 10.1016/j.compbiolchem.2016.02.009. Epub 2016 Feb 12.

PMID:
26935398
19.

Detection of driver pathways using mutated gene network in cancer.

Li F, Gao L, Ma X, Yang X.

Mol Biosyst. 2016 Jun 21;12(7):2135-41. doi: 10.1039/c6mb00084c.

PMID:
27118146
20.

Shared and unique mutational gene co-occurrences in cancers.

Liu J, Zhao D, Fan R.

Biochem Biophys Res Commun. 2015 Oct 2;465(4):777-83. doi: 10.1016/j.bbrc.2015.08.086. Epub 2015 Aug 24.

PMID:
26315265

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