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1.

Reverse engineering module networks by PSO-RNN hybrid modeling.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S15. doi: 10.1186/1471-2164-10-S1-S15.

2.

Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization.

Xu R, Wunsch Ii D, Frank R.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):681-92.

PMID:
17975278
3.

Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks.

Chaitankar V, Ghosh P, Perkins EJ, Gong P, Zhang C.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S19. doi: 10.1186/1471-2105-11-S6-S19.

4.

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach.

Zoppoli P, Morganella S, Ceccarelli M.

BMC Bioinformatics. 2010 Mar 25;11:154. doi: 10.1186/1471-2105-11-154.

5.

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203. doi: 10.1186/1471-2105-9-203.

6.

A swarm intelligence framework for reconstructing gene networks: searching for biologically plausible architectures.

Kentzoglanakis K, Poole M.

IEEE/ACM Trans Comput Biol Bioinform. 2012;9(2):358-71. doi: 10.1109/TCBB.2011.87. Epub 2011 Apr 29.

PMID:
21576756
7.

Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data.

Gao S, Wang X.

BMC Bioinformatics. 2011 Aug 31;12:359. doi: 10.1186/1471-2105-12-359.

8.

RMaNI: Regulatory Module Network Inference framework.

Madhamshettiwar PB, Maetschke SR, Davis MJ, Ragan MA.

BMC Bioinformatics. 2013;14 Suppl 16:S14. doi: 10.1186/1471-2105-14-S16-S14. Epub 2013 Oct 22.

9.

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
10.

Generating realistic in silico gene networks for performance assessment of reverse engineering methods.

Marbach D, Schaffter T, Mattiussi C, Floreano D.

J Comput Biol. 2009 Feb;16(2):229-39. doi: 10.1089/cmb.2008.09TT.

PMID:
19183003
12.

A novel gene network inference algorithm using predictive minimum description length approach.

Chaitankar V, Ghosh P, Perkins EJ, Gong P, Deng Y, Zhang C.

BMC Syst Biol. 2010 May 28;4 Suppl 1:S7. doi: 10.1186/1752-0509-4-S1-S7.

13.

Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis.

Li Z, Li P, Krishnan A, Liu J.

Bioinformatics. 2011 Oct 1;27(19):2686-91. doi: 10.1093/bioinformatics/btr454. Epub 2011 Aug 4.

14.

Construction of gene regulatory networks using biclustering and Bayesian networks.

Alakwaa FM, Solouma NH, Kadah YM.

Theor Biol Med Model. 2011 Oct 22;8:39. doi: 10.1186/1742-4682-8-39.

15.
16.

Inference of gene regulatory subnetworks from time course gene expression data.

Liang XJ, Xia Z, Zhang LW, Wu FX.

BMC Bioinformatics. 2012 Jun 11;13 Suppl 9:S3. doi: 10.1186/1471-2105-13-S9-S3.

17.

An integrative approach to infer regulation programs in a transcription regulatory module network.

Qi J, Michoel T, Butler G.

J Biomed Biotechnol. 2012;2012:245968. doi: 10.1155/2012/245968. Epub 2012 Apr 11.

18.

Modeling of gene regulatory networks with hybrid differential evolution and particle swarm optimization.

Xu R, Venayagamoorthy GK, Wunsch DC 2nd.

Neural Netw. 2007 Oct;20(8):917-27. Epub 2007 Jul 22.

PMID:
17714912
19.

Module network inference from a cancer gene expression data set identifies microRNA regulated modules.

Bonnet E, Tatari M, Joshi A, Michoel T, Marchal K, Berx G, Van de Peer Y.

PLoS One. 2010 Apr 14;5(4):e10162. doi: 10.1371/journal.pone.0010162.

20.

Reverse engineering gene regulatory networks: coupling an optimization algorithm with a parameter identification technique.

Hsiao YT, Lee WP.

BMC Bioinformatics. 2014;15 Suppl 15:S8. doi: 10.1186/1471-2105-15-S15-S8. Epub 2014 Dec 3.

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