PubMed

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]Related articlesFree article

Computing paths and cycles in biological interaction graphs.

Klamt S, von Kamp A.

BMC Bioinformatics. 2009 Jun 15;10:181.PMID: 19527491 [PubMed - indexed for MEDLINE]Related articlesFree article

Structural and functional analysis of cellular networks with CellNetAnalyzer.

Klamt S, Saez-Rodriguez J, Gilles ED.

BMC Syst Biol. 2007 Jan 8;1:2.PMID: 17408509 [PubMed - indexed for MEDLINE]Related articlesFree article

A logical model provides insights into T cell receptor signaling.

Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus UU, Weismantel R, Gilles ED, Klamt S, Schraven B.

PLoS Comput Biol. 2007 Aug;3(8):e163. Epub 2007 Jul 5.PMID: 17722974 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of feedback loops and robustness in network evolution based on Boolean models.

Kwon YK, Cho KH.

BMC Bioinformatics. 2007 Nov 7;8:430.PMID: 17988389 [PubMed - indexed for MEDLINE]Related articlesFree article

Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling.

Kwon YK, Choi SS, Cho KH.

BMC Bioinformatics. 2007 Oct 15;8:384.PMID: 17935633 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article

Specification of spatial relationships in directed graphs of cell signaling networks.

Lipshtat A, Neves SR, Iyengar R.

Ann N Y Acad Sci. 2009 Mar;1158:44-56.PMID: 19348631 [PubMed - indexed for MEDLINE]Related articlesFree article

Incremental and unifying modelling formalism for biological interaction networks.

Yartseva A, Klaudel H, Devillers R, Képès F.

BMC Bioinformatics. 2007 Nov 8;8:433.PMID: 17996051 [PubMed - indexed for MEDLINE]Related articlesFree article

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data.

Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S.

PLoS Comput Biol. 2009 Aug;5(8):e1000438. Epub 2009 Aug 7.PMID: 19662154 [PubMed - indexed for MEDLINE]Related articlesFree article

The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks.

Potapov AP, Goemann B, Wingender E.

BMC Bioinformatics. 2008 May 2;9:227.PMID: 18454847 [PubMed - indexed for MEDLINE]Related articlesFree article

A structural approach for finding functional modules from large biological networks.

Mete M, Tang F, Xu X, Yuruk N.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S19.PMID: 18793464 [PubMed - indexed for MEDLINE]Related articlesFree article

Discovering functional interaction patterns in protein-protein interaction networks.

Turanalp ME, Can T.

BMC Bioinformatics. 2008 Jun 11;9:276.PMID: 18547430 [PubMed - indexed for MEDLINE]Related articlesFree article

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.

Fauré A, Naldi A, Chaouiya C, Thieffry D.

Bioinformatics. 2006 Jul 15;22(14):e124-31.PMID: 16873462 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Dynamic analysis of integrated signaling, metabolic, and regulatory networks.

Lee JM, Gianchandani EP, Eddy JA, Papin JA.

PLoS Comput Biol. 2008 May 23;4(5):e1000086. Erratum in: PLoS Comput Biol. 2008 Jun;4(6). doi: 10.1371/annotation/5594348b-de00-446a-bdd0-ec56e70b3553. Min Lee, Jong [corrected to Lee, Jong Min]. PMID: 18483615 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploration of biological network centralities with CentiBiN.

Junker BH, Koschützki D, Schreiber F.

BMC Bioinformatics. 2006 Apr 21;7:219.PMID: 16630347 [PubMed - indexed for MEDLINE]Related articlesFree article

Visual setup of logical models of signaling and regulatory networks with ProMoT.

Saez-Rodriguez J, Mirschel S, Hemenway R, Klamt S, Gilles ED, Ginkel M.

BMC Bioinformatics. 2006 Nov 17;7:506.PMID: 17109765 [PubMed - indexed for MEDLINE]Related articlesFree article

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

Steggles LJ, Banks R, Shaw O, Wipat A.

Bioinformatics. 2007 Feb 1;23(3):336-43. Epub 2006 Nov 22.PMID: 17121774 [PubMed - indexed for MEDLINE]Related articlesFree article