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Results: 1 to 20 of 106

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.

A densely interconnected genome-wide network of microRNAs and oncogenic pathways revealed using gene expression signatures.

Ooi CH, Oh HK, Wang HZ, Tan AL, Wu J, Lee M, Rha SY, Chung HC, Virshup DM, Tan P.

PLoS Genet. 2011 Dec;7(12):e1002415. doi: 10.1371/journal.pgen.1002415. Epub 2011 Dec 15.

PMID:
22194702
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer.

Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM.

Breast Cancer Res. 2009;11(4):R55. doi: 10.1186/bcr2344. Epub 2009 Jul 28. Erratum in: Breast Cancer Res. 2011;13(4):406.

PMID:
19638211
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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]
5.

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]
Free Article
6.

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
7.

Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes.

Gatza ML, Kung HN, Blackwell KL, Dewhirst MW, Marks JR, Chi JT.

Breast Cancer Res. 2011 Jun 7;13(3):R62. doi: 10.1186/bcr2899.

PMID:
21672245
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
9.

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
10.

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]
11.

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
12.

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
13.

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
14.

Systems analysis of the NCI-60 cancer cell lines by alignment of protein pathway activation modules with "-OMIC" data fields and therapeutic response signatures.

Federici G, Gao X, Slawek J, Arodz T, Shitaye A, Wulfkuhle JD, De Maria R, Liotta LA, Petricoin EF 3rd.

Mol Cancer Res. 2013 Jun;11(6):676-85. doi: 10.1158/1541-7786.MCR-12-0690. Epub 2013 May 1.

PMID:
23635402
[PubMed - indexed for MEDLINE]
Free Article
15.

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
16.

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
17.

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]
18.

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]
19.

Identifying causal genes and dysregulated pathways in complex diseases.

Kim YA, Wuchty S, Przytycka TM.

PLoS Comput Biol. 2011 Mar;7(3):e1001095. doi: 10.1371/journal.pcbi.1001095. Epub 2011 Mar 3.

PMID:
21390271
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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

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