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1.

Characterizing regulatory path motifs in integrated networks using perturbational data.

Joshi A, Van Parys T, Peer YV, Michoel T.

Genome Biol. 2010;11(3):R32. doi: 10.1186/gb-2010-11-3-r32. Epub 2010 Mar 11.

2.

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.

Audenaert P, Van Parys T, Brondel F, Pickavet M, Demeester P, Van de Peer Y, Michoel T.

Bioinformatics. 2011 Jun 1;27(11):1587-8. doi: 10.1093/bioinformatics/btr182. Epub 2011 Apr 8.

3.

Integrated module and gene-specific regulatory inference implicates upstream signaling networks.

Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP.

PLoS Comput Biol. 2013;9(10):e1003252. doi: 10.1371/journal.pcbi.1003252. Epub 2013 Oct 17.

4.

Bridge and brick network motifs: identifying significant building blocks from complex biological systems.

Huang CY, Cheng CY, Sun CT.

Artif Intell Med. 2007 Oct;41(2):117-27. Epub 2007 Sep 7.

PMID:
17825540
5.

Genetic reconstruction of a functional transcriptional regulatory network.

Hu Z, Killion PJ, Iyer VR.

Nat Genet. 2007 May;39(5):683-7. Epub 2007 Apr 8.

PMID:
17417638
6.

iRegulon: from a gene list to a gene regulatory network using large motif and track collections.

Janky R, Verfaillie A, Imrichová H, Van de Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Naval Sanchez M, Potier D, Svetlichnyy D, Kalender Atak Z, Fiers M, Marine JC, Aerts S.

PLoS Comput Biol. 2014 Jul 24;10(7):e1003731. doi: 10.1371/journal.pcbi.1003731. eCollection 2014 Jul.

7.

Regulatory patterns in molecular interaction networks.

Murrugarra D, Laubenbacher R.

J Theor Biol. 2011 Nov 7;288:66-72. doi: 10.1016/j.jtbi.2011.08.015. Epub 2011 Aug 24.

PMID:
21872607
8.

Predicting genetic regulatory response using classification.

Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40.

9.

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

Westenberg MA, Roerdink JB, Kuipers OP, van Hijum SA.

Bioinformatics. 2010 Nov 15;26(22):2922-3. doi: 10.1093/bioinformatics/btq535. Epub 2010 Sep 21.

10.

Clustering of genes into regulons using integrated modeling-COGRIM.

Chen G, Jensen ST, Stoeckert CJ Jr.

Genome Biol. 2007;8(1):R4.

11.

The executable pathway to biological networks.

Fisher J, Piterman N.

Brief Funct Genomics. 2010 Jan;9(1):79-92. doi: 10.1093/bfgp/elp054. Review.

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14.

Integration of genomic information with biological networks using Cytoscape.

Bauer-Mehren A.

Methods Mol Biol. 2013;1021:37-61. doi: 10.1007/978-1-62703-450-0_3.

PMID:
23715979
15.

An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury.

Chang LW, Viader A, Varghese N, Payton JE, Milbrandt J, Nagarajan R.

BMC Genomics. 2013 Feb 6;14:84. doi: 10.1186/1471-2164-14-84.

16.

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.

Herrgård MJ, Lee BS, Portnoy V, Palsson BØ.

Genome Res. 2006 May;16(5):627-35. Epub 2006 Apr 10.

17.

Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches.

Teixeira MC, Dias PJ, Monteiro PT, Sala A, Oliveira AL, Freitas AT, Sá-Correia I.

Mol Biosyst. 2010 Dec;6(12):2471-81. doi: 10.1039/c004881j. Epub 2010 Oct 11.

PMID:
20938527
18.

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae.

Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN.

BMC Bioinformatics. 2006 Oct 28;7:478.

19.

Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data.

Vu TT, Vohradsky J.

Genomics. 2009 May;93(5):426-33. doi: 10.1016/j.ygeno.2009.01.006. Epub 2009 Feb 5.

20.

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
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