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Results: 1 to 20 of 144

1.

Modeling mechanistic biological networks: an advanced Boolean approach.

Handorf T, Klipp E.

Bioinformatics. 2012 Feb 15;28(4):557-63. doi: 10.1093/bioinformatics/btr697. Epub 2011 Dec 22.

PMID:
22199382
[PubMed - indexed for MEDLINE]
Free Article
2.

Reduction of Boolean network models.

Veliz-Cuba A.

J Theor Biol. 2011 Nov 21;289:167-72. doi: 10.1016/j.jtbi.2011.08.042. Epub 2011 Sep 5.

PMID:
21907211
[PubMed - indexed for MEDLINE]
3.

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]
4.

The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.

Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US.

Bioinformatics. 2003 Feb 12;19(3):408-15.

PMID:
12584128
[PubMed - indexed for MEDLINE]
Free Article
5.

Boolean modeling in systems biology: an overview of methodology and applications.

Wang RS, Saadatpour A, Albert R.

Phys Biol. 2012 Oct;9(5):055001. doi: 10.1088/1478-3975/9/5/055001. Epub 2012 Sep 25. Review.

PMID:
23011283
[PubMed - indexed for MEDLINE]
6.

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.

Saez-Rodriguez J, Gayer S, Ginkel M, Gilles ED.

Bioinformatics. 2008 Aug 15;24(16):i213-9. doi: 10.1093/bioinformatics/btn289.

PMID:
18689828
[PubMed - indexed for MEDLINE]
Free Article
7.

Odefy--from discrete to continuous models.

Krumsiek J, Pölsterl S, Wittmann DM, Theis FJ.

BMC Bioinformatics. 2010 May 7;11:233. doi: 10.1186/1471-2105-11-233.

PMID:
20459647
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A SAT-based algorithm for finding attractors in synchronous Boolean networks.

Dubrova E, Teslenko M.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1393-9. doi: 10.1109/TCBB.2010.20.

PMID:
21778527
[PubMed - indexed for MEDLINE]
9.

Intervention in a family of Boolean networks.

Choudhary A, Datta A, Bittner ML, Dougherty ER.

Bioinformatics. 2006 Jan 15;22(2):226-32. Epub 2005 Nov 12.

PMID:
16286362
[PubMed - indexed for MEDLINE]
Free Article
10.

An analysis of the class of gene regulatory functions implied by a biochemical model.

Grefenstette J, Kim S, Kauffman S.

Biosystems. 2006 May;84(2):81-90. Epub 2005 Dec 27.

PMID:
16384633
[PubMed - indexed for MEDLINE]
11.

Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study.

Hu X, Ng M, Wu FX, Sokhansanj BA.

IEEE Trans Inf Technol Biomed. 2009 Mar;13(2):184-94. doi: 10.1109/TITB.2008.2007649.

PMID:
19272861
[PubMed - indexed for MEDLINE]
12.

Discrete dynamic modeling of cellular signaling networks.

Albert R, Wang RS.

Methods Enzymol. 2009;467:281-306. doi: 10.1016/S0076-6879(09)67011-7.

PMID:
19897097
[PubMed - indexed for MEDLINE]
13.

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 Article
14.

Algebraic models of biochemical networks.

Laubenbacher R, Jarrah AS.

Methods Enzymol. 2009;467:163-96. doi: 10.1016/S0076-6879(09)67007-5.

PMID:
19897093
[PubMed - indexed for MEDLINE]
15.

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]
Free PMC Article
16.

Implicit methods for qualitative modeling of gene regulatory networks.

Garg A, Mohanram K, De Micheli G, Xenarios I.

Methods Mol Biol. 2012;786:397-443. doi: 10.1007/978-1-61779-292-2_22.

PMID:
21938638
[PubMed - indexed for MEDLINE]
17.

Modelling gene and protein regulatory networks with answer set programming.

Fayruzov T, Janssen J, Vermeir D, Cornelis C, De Cock M.

Int J Data Min Bioinform. 2011;5(2):209-29.

PMID:
21544955
[PubMed - indexed for MEDLINE]
18.

Network legos: building blocks of cellular wiring diagrams.

Murali TM, Rivera CG.

J Comput Biol. 2008 Sep;15(7):829-44. doi: 10.1089/cmb.2007.0139.

PMID:
18707557
[PubMed - indexed for MEDLINE]
19.

Simulation study in Probabilistic Boolean Network models for genetic regulatory networks.

Zhang SQ, Ching WK, Ng MK, Akutsu T.

Int J Data Min Bioinform. 2007;1(3):217-40.

PMID:
18399072
[PubMed - indexed for MEDLINE]
20.

The transition from differential equations to Boolean networks: a case study in simplifying a regulatory network model.

Davidich M, Bornholdt S.

J Theor Biol. 2008 Dec 7;255(3):269-77. doi: 10.1016/j.jtbi.2008.07.020. Epub 2008 Jul 23.

PMID:
18692073
[PubMed - indexed for MEDLINE]

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