PubMed

A method for the generation of standardized qualitative dynamical systems of regulatory networks.

Mendoza L, Xenarios I.

Theor Biol Med Model. 2006 Mar 16;3:13.PMID: 16542429 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Dynamic simulation of regulatory networks using SQUAD.

Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L.

BMC Bioinformatics. 2007 Nov 26;8:462.PMID: 18039375 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

A network model for the control of the differentiation process in Th cells.

Mendoza L.

Biosystems. 2006 May;84(2):101-14. Epub 2005 Dec 28.PMID: 16386358 [PubMed - indexed for MEDLINE]Related citations

RMBNToolbox: random models for biochemical networks.

Aho T, Smolander OP, Niemi J, Yli-Harja O.

BMC Syst Biol. 2007 May 24;1:22.PMID: 17524136 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Modularization of biochemical networks based on classification of Petri net t-invariants.

Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker BH, Grunwald S, Speer A, Winder K, Koch I.

BMC Bioinformatics. 2008 Feb 8;9:90.PMID: 18257938 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

From minimal signed circuits to the dynamics of Boolean regulatory networks.

Remy E, Ruet P.

Bioinformatics. 2008 Aug 15;24(16):i220-6.PMID: 18689829 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

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.PMID: 16464248 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Synchronous versus asynchronous modeling of gene regulatory networks.

Garg A, Di Cara A, Xenarios I, Mendoza L, De Micheli G.

Bioinformatics. 2008 Sep 1;24(17):1917-25. Epub 2008 Jul 9.PMID: 18614585 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

Salis H, Sotiropoulos V, Kaznessis YN.

BMC Bioinformatics. 2006 Feb 24;7:93.PMID: 16504125 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Modeling gene expression regulatory networks with the sparse vector autoregressive model.

Fujita A, Sato JR, Garay-Malpartida HM, Yamaguchi R, Miyano S, Sogayar MC, Ferreira CE.

BMC Syst Biol. 2007 Aug 30;1:39.PMID: 17761000 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

An analytical study of the number of steady states in gene regulatory networks.

Mochizuki A.

J Theor Biol. 2005 Oct 7;236(3):291-310.PMID: 15885706 [PubMed - indexed for MEDLINE]Related citations

The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models.

Madar A, Greenfield A, Ostrer H, Vanden-Eijnden E, Bonneau R.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:5448-51.PMID: 19964678 [PubMed - indexed for MEDLINE]Related citations

A computational framework for qualitative simulation of nonlinear dynamical models of gene-regulatory networks.

Ironi L, Panzeri L.

BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S14.PMID: 19828074 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Modeling of multiple valued gene regulatory networks.

Garg A, Mendoza L, Xenarios I, DeMicheli G.

Conf Proc IEEE Eng Med Biol Soc. 2007;2007:1398-404.PMID: 18002226 [PubMed - indexed for MEDLINE]Related citations

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.

Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ.

BMC Syst Biol. 2009 Sep 28;3:98.PMID: 19785753 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks.

Ispolatov I, Maslov S.

BMC Bioinformatics. 2008 Oct 8;9:424.PMID: 18842147 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Boolean network models of cellular regulation: prospects and limitations.

Bornholdt S.

J R Soc Interface. 2008 Aug 6;5 Suppl 1:S85-94. Review.PMID: 18508746 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

GraphCrunch: a tool for large network analyses.

Milenković T, Lai J, Przulj N.

BMC Bioinformatics. 2008 Jan 30;9:70.PMID: 18230190 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

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

Higham DJ, Rasajski M, Przulj N.

Bioinformatics. 2008 Apr 15;24(8):1093-9. Epub 2008 Mar 14.PMID: 18344248 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method.

Fujita A, Sato JR, Garay-Malpartida HM, Morettin PA, Sogayar MC, Ferreira CE.

Bioinformatics. 2007 Jul 1;23(13):1623-30. Epub 2007 Apr 26.PMID: 17463021 [PubMed - indexed for MEDLINE]Free ArticleRelated citations