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Items: 1 to 20 of 245

1.

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.

Batt G, Besson B, Ciron PE, de Jong H, Dumas E, Geiselmann J, Monte R, Monteiro PT, Page M, Rechenmann F, Ropers D.

Methods Mol Biol. 2012;804:439-62. doi: 10.1007/978-1-61779-361-5_22.

PMID:
22144166
2.

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.

Batt G, Ropers D, de Jong H, Geiselmann J, Mateescu R, Page M, Schneider D.

Bioinformatics. 2005 Jun;21 Suppl 1:i19-28.

PMID:
15961457
3.

Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.

de Jong H, Geiselmann J, Hernandez C, Page M.

Bioinformatics. 2003 Feb 12;19(3):336-44.

PMID:
12584118
4.

Qualitative simulation of genetic regulatory networks using piecewise-linear models.

De Jong H, Gouzé JL, Hernandez C, Page M, Sari T, Geiselmann J.

Bull Math Biol. 2004 Mar;66(2):301-40.

PMID:
14871568
5.

Logical modelling of gene regulatory networks with GINsim.

Chaouiya C, Naldi A, Thieffry D.

Methods Mol Biol. 2012;804:463-79. doi: 10.1007/978-1-61779-361-5_23.

PMID:
22144167
6.

Comparing Boolean and piecewise affine differential models for genetic networks.

Chaves M, Tournier L, Gouzé JL.

Acta Biotheor. 2010 Sep;58(2-3):217-32. doi: 10.1007/s10441-010-9097-6. Epub 2010 Jul 28.

PMID:
20665073
7.

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.

Monteiro PT, Dumas E, Besson B, Mateescu R, Page M, Freitas AT, de Jong H.

BMC Bioinformatics. 2009 Dec 30;10:450. doi: 10.1186/1471-2105-10-450.

8.

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.

9.

Search for steady states of piecewise-linear differential equation models of genetic regulatory networks.

de Jong H, Page M.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):208-22. doi: 10.1109/TCBB.2007.70254.

PMID:
18451430
10.

Gene expression complex networks: synthesis, identification, and analysis.

Lopes FM, Cesar RM, Costa Lda F.

J Comput Biol. 2011 Oct;18(10):1353-67. doi: 10.1089/cmb.2010.0118. Epub 2011 May 6.

PMID:
21548810
11.

BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks.

Longabaugh WJ.

Methods Mol Biol. 2012;786:359-94. doi: 10.1007/978-1-61779-292-2_21.

PMID:
21938637
12.

Preservation of dynamic properties in qualitative modeling frameworks for gene regulatory networks.

Jamshidi S, Siebert H, Bockmayr A.

Biosystems. 2013 May;112(2):171-9. doi: 10.1016/j.biosystems.2013.03.001. Epub 2013 Mar 14.

PMID:
23499821
13.

Petri nets in Snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks.

Marwan W, Rohr C, Heiner M.

Methods Mol Biol. 2012;804:409-37. doi: 10.1007/978-1-61779-361-5_21.

PMID:
22144165
14.

On the transient and steady-state estimates of interval genetic regulatory networks.

Li P, Lam J, Shu Z.

IEEE Trans Syst Man Cybern B Cybern. 2010 Apr;40(2):336-49. doi: 10.1109/TSMCB.2009.2022402. Epub 2009 Oct 23.

PMID:
19858029
15.

MAVisto: a tool for biological network motif analysis.

Schwöbbermeyer H, Wünschiers R.

Methods Mol Biol. 2012;804:263-80. doi: 10.1007/978-1-61779-361-5_14.

PMID:
22144158
16.

Modeling of gene regulatory network dynamics using threshold logic.

Gowda T, Vrudhula S, Kim S.

Ann N Y Acad Sci. 2009 Mar;1158:71-81. doi: 10.1111/j.1749-6632.2008.03754.x.

PMID:
19348633
17.

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.

Batt G, Page M, Cantone I, Goessler G, Monteiro P, de Jong H.

Bioinformatics. 2010 Sep 15;26(18):i603-10. doi: 10.1093/bioinformatics/btq387.

18.

Reconstruction of transcriptional network from microarray data using combined mutual information and network-assisted regression.

Wang XD, Qi YX, Jiang ZL.

IET Syst Biol. 2011 Mar;5(2):95-102. doi: 10.1049/iet-syb.2010.0041.

PMID:
21405197
19.

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. doi: 10.1186/1471-2105-10-S12-S14.

20.

GeNESiS: gene network evolution simulation software.

Kratz A, Tomita M, Krishnan A.

BMC Bioinformatics. 2008 Dec 16;9:541. doi: 10.1186/1471-2105-9-541.

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