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Results: 1 to 20 of 92

1.

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.

Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, Huntsman DG, Caldas C, Aparicio SA, Shah SP.

Genome Biol. 2012 Dec 22;13(12):R124. doi: 10.1186/gb-2012-13-12-r124.

PMID:
23383675
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
23717195
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine.

Raphael BJ, Dobson JR, Oesper L, Vandin F.

Genome Med. 2014 Jan 30;6(1):5. doi: 10.1186/gm524. eCollection 2014. Review.

PMID:
24479672
[PubMed]
Free PMC Article
4.

Identification of druggable cancer driver genes amplified across TCGA datasets.

Chen Y, McGee J, Chen X, Doman TN, Gong X, Zhang Y, Hamm N, Ma X, Higgs RE, Bhagwat SV, Buchanan S, Peng SB, Staschke KA, Yadav V, Yue Y, Kouros-Mehr H.

PLoS One. 2014 May 29;9(5):e98293. doi: 10.1371/journal.pone.0098293. eCollection 2014.

PMID:
24874471
[PubMed - in process]
Free PMC Article
5.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.

Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP.

Bioinformatics. 2012 Apr 1;28(7):907-13. doi: 10.1093/bioinformatics/bts053. Epub 2012 Jan 27.

PMID:
22285562
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Inferring causal genomic alterations in breast cancer using gene expression data.

Tran LM, Zhang B, Zhang Z, Zhang C, Xie T, Lamb JR, Dai H, Schadt EE, Zhu J.

BMC Syst Biol. 2011 Aug 1;5:121. doi: 10.1186/1752-0509-5-121.

PMID:
21806811
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Finding driver pathways in cancer: models and algorithms.

Vandin F, Upfal E, Raphael BJ.

Algorithms Mol Biol. 2012 Sep 6;7(1):23. doi: 10.1186/1748-7188-7-23.

PMID:
22954134
[PubMed]
Free PMC Article
8.

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer.

Udyavar AR, Hoeksema MD, Clark JE, Zou Y, Tang Z, Li Z, Li M, Chen H, Statnikov A, Shyr Y, Liebler DC, Field J, Eisenberg R, Estrada L, Massion PP, Quaranta V.

BMC Syst Biol. 2013;7 Suppl 5:S1. doi: 10.1186/1752-0509-7-S5-S1. Epub 2013 Dec 9.

PMID:
24564859
[PubMed - in process]
Free PMC Article
9.

Predicting the functional consequences of cancer-associated amino acid substitutions.

Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR.

Bioinformatics. 2013 Jun 15;29(12):1504-10. doi: 10.1093/bioinformatics/btt182. Epub 2013 Apr 25.

PMID:
23620363
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Predicting the functional consequences of somatic missense mutations found in tumors.

Carter H, Karchin R.

Methods Mol Biol. 2014;1101:135-59. doi: 10.1007/978-1-62703-721-1_8.

PMID:
24233781
[PubMed - indexed for MEDLINE]
11.

Trastuzumab and beyond: sequencing cancer genomes and predicting molecular networks.

Roukos DH.

Pharmacogenomics J. 2011 Apr;11(2):81-92. doi: 10.1038/tpj.2010.81. Epub 2010 Oct 26. Review.

PMID:
20975737
[PubMed - indexed for MEDLINE]
12.

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.

Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP.

Bioinformatics. 2012 Jan 15;28(2):167-75. doi: 10.1093/bioinformatics/btr629. Epub 2011 Nov 13.

PMID:
22084253
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
21653252
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level.

Li W, Wang R, Bai L, Yan Z, Sun Z.

BMC Syst Biol. 2012 Jun 12;6:64. doi: 10.1186/1752-0509-6-64.

PMID:
22691569
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
24565034
[PubMed - in process]
Free PMC Article
16.

DrGaP: a powerful tool for identifying driver genes and pathways in cancer sequencing studies.

Hua X, Xu H, Yang Y, Zhu J, Liu P, Lu Y.

Am J Hum Genet. 2013 Sep 5;93(3):439-51. doi: 10.1016/j.ajhg.2013.07.003. Epub 2013 Aug 15.

PMID:
23954162
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Using passenger mutations to estimate the timing of driver mutations and identify mutator alterations.

Youn A, Simon R.

BMC Bioinformatics. 2013 Dec 13;14:363. doi: 10.1186/1471-2105-14-363.

PMID:
24330428
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.

Yuan Y, Rueda OM, Curtis C, Markowetz F.

Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.

PMID:
21804112
[PubMed - indexed for MEDLINE]
Free Article
19.

Domain landscapes of somatic mutations in cancer.

Nehrt NL, Peterson TA, Park D, Kann MG.

BMC Genomics. 2012 Jun 18;13 Suppl 4:S9. doi: 10.1186/1471-2164-13-S4-S9.

PMID:
22759657
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
20169195
[PubMed - indexed for MEDLINE]
Free PMC Article

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