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Results: 1 to 20 of 88

1.

A genomic strategy to elucidate modules of oncogenic pathway signaling networks.

Chang JT, Carvalho C, Mori S, Bild AH, Gatza ML, Wang Q, Lucas JE, Potti A, Febbo PG, West M, Nevins JR.

Mol Cell. 2009 Apr 10;34(1):104-14. doi: 10.1016/j.molcel.2009.02.030.

PMID:
19362539
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Oncogenic pathway signatures in human cancers as a guide to targeted therapies.

Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR.

Nature. 2006 Jan 19;439(7074):353-7. Epub 2005 Nov 6.

PMID:
16273092
[PubMed - indexed for MEDLINE]
3.

An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer.

Dressman HK, Berchuck A, Chan G, Zhai J, Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsburg GS, Potti A, West M, Nevins JR, Lancaster JM.

J Clin Oncol. 2007 Feb 10;25(5):517-25. Retraction in: J Clin Oncol. 2012 Feb 20;30(6):678.

PMID:
17290060
[PubMed - indexed for MEDLINE]
4.

Gene expression signature of human cancer cell lines treated with the ras inhibitor salirasib (S-farnesylthiosalicylic acid).

Blum R, Elkon R, Yaari S, Zundelevich A, Jacob-Hirsch J, Rechavi G, Shamir R, Kloog Y.

Cancer Res. 2007 Apr 1;67(7):3320-8.

PMID:
17409441
[PubMed - indexed for MEDLINE]
Free Article
5.

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.

PMID:
21908773
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression.

Shi Z, Derow CK, Zhang B.

BMC Syst Biol. 2010 May 27;4:74. doi: 10.1186/1752-0509-4-74.

PMID:
20507583
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer.

Xu M, Kao MC, Nunez-Iglesias J, Nevins JR, West M, Zhou XJ.

BMC Genomics. 2008;9 Suppl 1:S12. doi: 10.1186/1471-2164-9-S1-S12.

PMID:
18366601
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Differential oncogenic Ras signaling and senescence in tumor cells.

Bihani T, Mason DX, Jackson TJ, Chen SC, Boettner B, Lin AW.

Cell Cycle. 2004 Sep;3(9):1201-7. Epub 2004 Sep 5.

PMID:
15492501
[PubMed - indexed for MEDLINE]
Free Article
9.

Oncogenic signaling pathways and deregulated target genes.

Schäfer R, Schramme A, Tchernitsa OI, Sers C.

Recent Results Cancer Res. 2007;176:7-24. Review.

PMID:
17607912
[PubMed - indexed for MEDLINE]
10.

Elucidating the altered transcriptional programs in breast cancer using independent component analysis.

Teschendorff AE, Journée M, Absil PA, Sepulchre R, Caldas C.

PLoS Comput Biol. 2007 Aug;3(8):e161. Epub 2007 Jun 29.

PMID:
17708679
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Patterns of cell signaling pathway activation that characterize mammary development.

Andrechek ER, Mori S, Rempel RE, Chang JT, Nevins JR.

Development. 2008 Aug;135(14):2403-13. doi: 10.1242/dev.019018. Epub 2008 Jun 11.

PMID:
18550711
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The Rb/E2F pathway and Ras activation regulate RecQ helicase gene expression.

Liu Y, El-Naggar S, Clem B, Chesney J, Dean DC.

Biochem J. 2008 Jun 1;412(2):299-306. doi: 10.1042/BJ20070975.

PMID:
18215118
[PubMed - indexed for MEDLINE]
Free Article
13.

Simplistic pathways or complex networks?

Jørgensen C, Linding R.

Curr Opin Genet Dev. 2010 Feb;20(1):15-22. doi: 10.1016/j.gde.2009.12.003. Epub 2010 Jan 22. Review.

PMID:
20096559
[PubMed - indexed for MEDLINE]
14.

Cancer systems biology: exploring cancer-associated genes on cellular networks.

Wang E, Lenferink A, O'Connor-McCourt M.

Cell Mol Life Sci. 2007 Jul;64(14):1752-62. Review.

PMID:
17415519
[PubMed - indexed for MEDLINE]
15.

Use of gene expression and pathway signatures to characterize the complexity of human melanoma.

Freedman JA, Tyler DS, Nevins JR, Augustine CK.

Am J Pathol. 2011 Jun;178(6):2513-22. doi: 10.1016/j.ajpath.2011.02.037.

PMID:
21641377
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors.

Loboda A, Nebozhyn M, Klinghoffer R, Frazier J, Chastain M, Arthur W, Roberts B, Zhang T, Chenard M, Haines B, Andersen J, Nagashima K, Paweletz C, Lynch B, Feldman I, Dai H, Huang P, Watters J.

BMC Med Genomics. 2010 Jun 30;3:26. doi: 10.1186/1755-8794-3-26.

PMID:
20591134
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A pathway-based classification of human breast cancer.

Gatza ML, Lucas JE, Barry WT, Kim JW, Wang Q, Crawford MD, Datto MB, Kelley M, Mathey-Prevot B, Potti A, Nevins JR.

Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6994-9. doi: 10.1073/pnas.0912708107. Epub 2010 Mar 24.

PMID:
20335537
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME.

Finocchiaro G, Mancuso FM, Cittaro D, Muller H.

Nucleic Acids Res. 2007;35(7):2343-55. Epub 2007 Mar 27.

PMID:
17389643
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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
20.

Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers.

Lucas JE, Kung HN, Chi JT.

PLoS Comput Biol. 2010 Sep 2;6(9):e1000920. doi: 10.1371/journal.pcbi.1000920.

PMID:
20824128
[PubMed - indexed for MEDLINE]
Free PMC Article

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