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Results: 1 to 20 of 84

1.

Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure.

Thomas R, Gohlke JM, Stopper GF, Parham FM, Portier CJ.

Genome Biol. 2009;10(4):R44. doi: 10.1186/gb-2009-10-4-r44. Epub 2009 Apr 24.

PMID:
19393085
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Molecular networks in microarray analysis.

Sivachenko AY, Yuryev A, Daraselia N, Mazo I.

J Bioinform Comput Biol. 2007 Apr;5(2B):429-56. Review.

PMID:
17636854
[PubMed - indexed for MEDLINE]
3.

Precedence Temporal Networks to represent temporal relationships in gene expression data.

Sacchi L, Larizza C, Magni P, Bellazzi R.

J Biomed Inform. 2007 Dec;40(6):761-74. Epub 2007 Jun 10.

PMID:
17644489
[PubMed - indexed for MEDLINE]
Free Article
4.

Reconstructing biological networks using conditional correlation analysis.

Rice JJ, Tu Y, Stolovitzky G.

Bioinformatics. 2005 Mar;21(6):765-73. Epub 2004 Oct 14.

PMID:
15486043
[PubMed - indexed for MEDLINE]
Free Article
5.

An empirical Bayes approach to inferring large-scale gene association networks.

Schäfer J, Strimmer K.

Bioinformatics. 2005 Mar;21(6):754-64. Epub 2004 Oct 12.

PMID:
15479708
[PubMed - indexed for MEDLINE]
Free Article
6.

Discovering gene networks with a neural-genetic hybrid.

Keedwell E, Narayanan A.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):231-42.

PMID:
17044186
[PubMed - indexed for MEDLINE]
7.

Mining pathway signatures from microarray data and relevant biological knowledge.

Panteris E, Swift S, Payne A, Liu X.

J Biomed Inform. 2007 Dec;40(6):698-706. Epub 2007 Feb 22.

PMID:
17395545
[PubMed - indexed for MEDLINE]
Free Article
8.

Gene co-expression network topology provides a framework for molecular characterization of cellular state.

Carter SL, Brechbühler CM, Griffin M, Bond AT.

Bioinformatics. 2004 Sep 22;20(14):2242-50. Epub 2004 May 6.

PMID:
15130938
[PubMed - indexed for MEDLINE]
Free Article
9.

Prediction of regulatory pathways using mRNA expression and protein interaction data: application to identification of galactose regulatory pathway.

Darvish A, Najarian K.

Biosystems. 2006 Feb-Mar;83(2-3):125-35. Epub 2005 Dec 27.

PMID:
16384635
[PubMed - indexed for MEDLINE]
10.

Signal transduction pathway profiling of individual tumor samples.

Breslin T, Krogh M, Peterson C, Troein C.

BMC Bioinformatics. 2005 Jun 29;6:163.

PMID:
15987529
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

GAGE: generally applicable gene set enrichment for pathway analysis.

Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ.

BMC Bioinformatics. 2009 May 27;10:161. doi: 10.1186/1471-2105-10-161.

PMID:
19473525
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Increasing feasibility of optimal gene network estimation.

Hansen A, Ott S, Koentges G.

Genome Inform. 2004;15(2):141-50.

PMID:
15706500
[PubMed - indexed for MEDLINE]
13.

Inferring connectivity of genetic regulatory networks using information-theoretic criteria.

Zhao W, Serpedin E, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):262-74. doi: 10.1109/TCBB.2007.1067.

PMID:
18451435
[PubMed - indexed for MEDLINE]
14.

Inferring gene regulatory networks from multiple microarray datasets.

Wang Y, Joshi T, Zhang XS, Xu D, Chen L.

Bioinformatics. 2006 Oct 1;22(19):2413-20. Epub 2006 Jul 24.

PMID:
16864593
[PubMed - indexed for MEDLINE]
Free Article
15.

Using directed information to build biologically relevant influence networks.

Rao A, Hero AO 3rd, States DJ, Engel JD.

Comput Syst Bioinformatics Conf. 2007;6:145-56.

PMID:
17951820
[PubMed - indexed for MEDLINE]
Free Article
16.

Bayesian sparse hidden components analysis for transcription regulation networks.

Sabatti C, James GM.

Bioinformatics. 2006 Mar 15;22(6):739-46. Epub 2005 Dec 20.

PMID:
16368767
[PubMed - indexed for MEDLINE]
Free Article
17.

Challenges and prospects in the analysis of large-scale gene expression data.

Ihmels JH, Bergmann S.

Brief Bioinform. 2004 Dec;5(4):313-27.

PMID:
15606968
[PubMed - indexed for MEDLINE]
Free Article
18.

Inference of gene regulatory networks using boolean-network inference methods.

Hickman GJ, Hodgman TC.

J Bioinform Comput Biol. 2009 Dec;7(6):1013-29. Review.

PMID:
20014476
[PubMed - indexed for MEDLINE]
19.

Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.

Ott S, Hansen A, Kim SY, Miyano S.

Bioinformatics. 2005 Jan 15;21(2):227-38. Epub 2004 Sep 17.

PMID:
15377501
[PubMed - indexed for MEDLINE]
Free Article
20.

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

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