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Items: 1 to 20 of 120

1.

Modular analysis of gene networks by linear temporal logic.

Ito S, Ichinose T, Shimakawa M, Izumi N, Hagihara S, Yonezaki N.

J Integr Bioinform. 2013 Mar 25;10(2):216. doi: 10.2390/biecoll-jib-2013-216.

PMID:
23525897
2.

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
3.

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
4.

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.

5.

Learning a Markov Logic network for supervised gene regulatory network inference.

Brouard C, Vrain C, Dubois J, Castel D, Debily MA, d'Alché-Buc F.

BMC Bioinformatics. 2013 Sep 12;14:273. doi: 10.1186/1471-2105-14-273.

6.

On the basic computational structure of gene regulatory networks.

Rodríguez-Caso C, Corominas-Murtra B, Solé RV.

Mol Biosyst. 2009 Dec;5(12):1617-29. doi: 10.1039/B904960f. Epub 2009 Jul 21.

PMID:
19763330
7.
8.

Comprehensive analysis of gene-environmental interactions with temporal gene expression profiles in Pseudomonas aeruginosa.

Duan K, McCullough WM, Surette MG, Ware T, Song J.

PLoS One. 2012;7(4):e35993. doi: 10.1371/journal.pone.0035993. Epub 2012 Apr 27.

9.

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.

10.

Periodic oscillation in delayed gene networks with SUM regulatory logic and small perturbations.

Wang Y, Ma Z, Shen J, Liu Z, Chen L.

Math Biosci. 2009 Jul;220(1):34-44. doi: 10.1016/j.mbs.2009.03.010. Epub 2009 Apr 17.

PMID:
19376139
11.

Prediction of pairwise gene interaction using threshold logic.

Gowda T, Vrudhula S, Kim S.

Ann N Y Acad Sci. 2009 Mar;1158:276-86. doi: 10.1111/j.1749-6632.2008.03763.x.

PMID:
19348649
12.

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
13.

Elementary network reconstruction: a framework for the analysis of regulatory networks in biological systems.

Dharmadi Y, Gonzalez R.

J Theor Biol. 2010 Apr 21;263(4):499-509. doi: 10.1016/j.jtbi.2009.12.007. Epub 2009 Dec 22.

PMID:
20004670
14.

Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology.

Pasotti L, Quattrocelli M, Galli D, De Angelis MG, Magni P.

Biotechnol J. 2011 Jul;6(7):784-95. doi: 10.1002/biot.201100080. Epub 2011 Jun 17.

PMID:
21681964
15.
16.

Ranking of network elements based on functional substructures.

Koschützki D, Schwöbbermeyer H, Schreiber F.

J Theor Biol. 2007 Oct 7;248(3):471-9. Epub 2007 Jun 6.

PMID:
17644116
17.

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
18.

Algebraic model checking for Boolean gene regulatory networks.

Tran QN.

Adv Exp Med Biol. 2011;696:113-22. doi: 10.1007/978-1-4419-7046-6_12.

PMID:
21431552
19.

Selection Shapes Transcriptional Logic and Regulatory Specialization in Genetic Networks.

Fogelmark K, Peterson C, Troein C.

PLoS One. 2016 Feb 29;11(2):e0150340. doi: 10.1371/journal.pone.0150340. eCollection 2016.

20.

Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm.

Wang M, Augusto Benedito V, Xuechun Zhao P, Udvardi M.

Mol Biosyst. 2010 Jun;6(6):988-98. doi: 10.1039/b917571g. Epub 2010 Feb 19.

PMID:
20485743
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