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Items: 1 to 20 of 75

1.

Automatic generation of causal networks linking growth factor stimuli to functional cell state changes.

Guziolowski C, Kittas A, Dittmann F, Grabe N.

FEBS J. 2012 Sep;279(18):3462-74. doi: 10.1111/j.1742-4658.2012.08616.x. Epub 2012 May 22.

2.

Directed random walks and constraint programming reveal active pathways in hepatocyte growth factor signaling.

Kittas A, Delobelle A, Schmitt S, Breuhahn K, Guziolowski C, Grabe N.

FEBS J. 2016 Jan;283(2):350-60. doi: 10.1111/febs.13580. Epub 2015 Nov 26.

PMID:
26518250
3.

Fitting a geometric graph to a protein-protein interaction network.

Higham DJ, Rasajski M, Przulj N.

Bioinformatics. 2008 Apr 15;24(8):1093-9. doi: 10.1093/bioinformatics/btn079. Epub 2008 Mar 14.

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Integrating whole-genome expression results into metabolic networks with Pathway Processor.

Cavalieri D, Grosu P.

Curr Protoc Bioinformatics. 2004 May;Chapter 7:Unit 7.6. doi: 10.1002/0471250953.bi0706s05.

PMID:
18428732
6.

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.

7.

NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks.

Kachalo S, Zhang R, Sontag E, Albert R, DasGupta B.

Bioinformatics. 2008 Jan 15;24(2):293-5. Epub 2007 Nov 22.

8.

DEEP--a tool for differential expression effector prediction.

Degenhardt J, Haubrock M, Dönitz J, Wingender E, Crass T.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W619-24. Epub 2007 Jun 21.

9.

Data integration and analysis of biological networks.

Kim TY, Kim HU, Lee SY.

Curr Opin Biotechnol. 2010 Feb;21(1):78-84. doi: 10.1016/j.copbio.2010.01.003. Epub 2010 Feb 6.

PMID:
20138751
10.

M@IA: a modular open-source application for microarray workflow and integrative datamining.

Le Béchec A, Zindy P, Sierocinski T, Petritis D, Bihouée A, Le Meur N, Léger J, Théret N.

In Silico Biol. 2008;8(1):63-9.

PMID:
18430991
11.

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.

Jupiter D, Chen H, VanBuren V.

BMC Bioinformatics. 2009 Oct 14;10:332. doi: 10.1186/1471-2105-10-332.

12.

A methodology for the structural and functional analysis of signaling and regulatory networks.

Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED.

BMC Bioinformatics. 2006 Feb 7;7:56.

13.

Gene expression analysis in clear cell renal cell carcinoma using gene set enrichment analysis for biostatistical management.

Maruschke M, Reuter D, Koczan D, Hakenberg OW, Thiesen HJ.

BJU Int. 2011 Jul;108(2 Pt 2):E29-35. doi: 10.1111/j.1464-410X.2010.09794.x. Epub 2011 Mar 16.

14.

Selective integration of multiple biological data for supervised network inference.

Kato T, Tsuda K, Asai K.

Bioinformatics. 2005 May 15;21(10):2488-95. Epub 2005 Feb 22.

15.

Inferring functional pathways from multi-perturbation data.

Yosef N, Kaufman A, Ruppin E.

Bioinformatics. 2006 Jul 15;22(14):e539-46.

16.

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.

BMC Syst Biol. 2012 May 1;6:29. doi: 10.1186/1752-0509-6-29.

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A framework for mapping, visualisation and automatic model creation of signal-transduction networks.

Tiger CF, Krause F, Cedersund G, Palmér R, Klipp E, Hohmann S, Kitano H, Krantz M.

Mol Syst Biol. 2012 Apr 24;8:578. doi: 10.1038/msb.2012.12.

20.

Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment.

Missal K, Cross MA, Drasdo D.

Bioinformatics. 2006 Mar 15;22(6):731-8. Epub 2005 Dec 6.

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