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Results: 1 to 20 of 102

1.

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM.

Bioinformatics. 2013 Nov 1;29(21):2757-64. doi: 10.1093/bioinformatics/btt471. Epub 2013 Aug 27.

PMID:
23986566
[PubMed - indexed for MEDLINE]
2.

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.

Gu J, Xuan J, Riggins RB, Chen L, Wang Y, Clarke R.

Bioinformatics. 2012 Aug 1;28(15):1990-7. doi: 10.1093/bioinformatics/bts296. Epub 2012 May 17. Erratum in: Bioinformatics. 2014 Aug 1;30(15):2242.

PMID:
22595208
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM.

Sedgewick AJ, Benz SC, Rabizadeh S, Soon-Shiong P, Vaske CJ.

Bioinformatics. 2013 Jul 1;29(13):i62-70. doi: 10.1093/bioinformatics/btt229.

PMID:
23813010
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identifying proteins controlling key disease signaling pathways.

Gitter A, Bar-Joseph Z.

Bioinformatics. 2013 Jul 1;29(13):i227-36. doi: 10.1093/bioinformatics/btt241.

PMID:
23812988
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM.

Bioinformatics. 2010 Jun 15;26(12):i237-45. doi: 10.1093/bioinformatics/btq182.

PMID:
20529912
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
7.

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.

Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM.

Bioinformatics. 2012 Sep 15;28(18):i640-i646. doi: 10.1093/bioinformatics/bts402.

PMID:
22962493
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
9.

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
10.

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.

Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW.

Cancer Cell. 2006 Dec;10(6):515-27.

PMID:
17157791
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
12.

The UCSC Interaction Browser: multidimensional data views in pathway context.

Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W218-24. doi: 10.1093/nar/gkt473. Epub 2013 Jun 8.

PMID:
23748957
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.

Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma'ayan A.

Bioinformatics. 2012 Jan 1;28(1):105-11. doi: 10.1093/bioinformatics/btr625. Epub 2011 Nov 10.

PMID:
22080467
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays.

Rodenhiser DI, Andrews J, Kennette W, Sadikovic B, Mendlowitz A, Tuck AB, Chambers AF.

Breast Cancer Res. 2008;10(4):R62. doi: 10.1186/bcr2121. Epub 2008 Jul 18.

PMID:
18638373
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

RIP: the regulatory interaction predictor--a machine learning-based approach for predicting target genes of transcription factors.

Bauer T, Eils R, König R.

Bioinformatics. 2011 Aug 15;27(16):2239-47. doi: 10.1093/bioinformatics/btr366. Epub 2011 Jun 20.

PMID:
21690103
[PubMed - indexed for MEDLINE]
Free Article
16.

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer.

Chari R, Coe BP, Vucic EA, Lockwood WW, Lam WL.

BMC Syst Biol. 2010 May 17;4:67. doi: 10.1186/1752-0509-4-67.

PMID:
20478067
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A modulator based regulatory network for ERα signaling pathway.

Wu HY, Zheng P, Jiang G, Liu Y, Nephew KP, Huang TH, Li L.

BMC Genomics. 2012;13 Suppl 6:S6. doi: 10.1186/1471-2164-13-S6-S6. Epub 2012 Oct 26.

PMID:
23134758
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Characterizing disease states from topological properties of transcriptional regulatory networks.

Tuck DP, Kluger HM, Kluger Y.

BMC Bioinformatics. 2006 May 2;7:236.

PMID:
16670008
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A multi-layer inference approach to reconstruct condition-specific genes and their regulation.

Wu M, Liu L, Hijazi H, Chan C.

Bioinformatics. 2013 Jun 15;29(12):1541-52. doi: 10.1093/bioinformatics/btt186. Epub 2013 Apr 22.

PMID:
23610368
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
22863767
[PubMed - indexed for MEDLINE]
Free PMC Article

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