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1.

Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration.

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

PLoS One. 2010 Apr 21;5(4):e10268. doi: 10.1371/journal.pone.0010268.

2.

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.

3.

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.

4.
5.

Integrating multiple types of data to predict novel cell cycle-related genes.

Wang L, Hou L, Qian M, Li F, Deng M.

BMC Syst Biol. 2011 Jun 20;5 Suppl 1:S9. doi: 10.1186/1752-0509-5-S1-S9.

6.

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells.

Zhu M, Deng X, Joshi T, Xu D, Stacey G, Cheng J.

BMC Genomics. 2012 Aug 31;13:437. doi: 10.1186/1471-2164-13-437.

7.

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.

8.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.

Genome Res. 2012 Jul;22(7):1334-49. doi: 10.1101/gr.127191.111. Epub 2012 Mar 28.

9.

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.

Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.

J Mol Biol. 2001 May 25;309(1):99-120.

PMID:
11491305
10.

Systematic identification of yeast cell cycle transcription factors using multiple data sources.

Wu WS, Li WH.

BMC Bioinformatics. 2008 Dec 5;9:522. doi: 10.1186/1471-2105-9-522.

11.

Finding microRNA regulatory modules in human genome using rule induction.

Tran DH, Satou K, Ho TB.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S5. doi: 10.1186/1471-2105-9-S12-S5.

12.

Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology.

Santra T, Kolch W, Kholodenko BN.

BMC Syst Biol. 2013 Jul 6;7:57. doi: 10.1186/1752-0509-7-57.

13.

Expression-based network biology identifies immune-related functional modules involved in plant defense.

Tully JP, Hill AE, Ahmed HM, Whitley R, Skjellum A, Mukhtar MS.

BMC Genomics. 2014 Jun 3;15:421. doi: 10.1186/1471-2164-15-421.

14.

A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells.

Jung M, Peterson H, Chavez L, Kahlem P, Lehrach H, Vilo J, Adjaye J.

PLoS One. 2010 May 21;5(5):e10709. doi: 10.1371/journal.pone.0010709.

15.

Inferring microRNA and transcription factor regulatory networks in heterogeneous data.

Le TD, Liu L, Liu B, Tsykin A, Goodall GJ, Satou K, Li J.

BMC Bioinformatics. 2013 Mar 11;14:92. doi: 10.1186/1471-2105-14-92.

16.

Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks.

Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y.

Plant Physiol. 2009 Jun;150(2):535-46. doi: 10.1104/pp.109.136028. Epub 2009 Apr 8.

17.

Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling.

Gao S, Hartman JL 4th, Carter JL, Hessner MJ, Wang X.

BMC Syst Biol. 2010 Dec 3;4:167. doi: 10.1186/1752-0509-4-167.

18.

An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data.

Ruan J, Deng Y, Perkins EJ, Zhang W.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S8. doi: 10.1186/1471-2164-10-S1-S8.

19.

Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model.

Youn A, Reiss DJ, Stuetzle W.

Bioinformatics. 2010 Aug 1;26(15):1879-86. doi: 10.1093/bioinformatics/btq289. Epub 2010 Jun 4.

20.

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.

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