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Items: 1 to 20 of 111

1.

Benchmarking regulatory network reconstruction with GRENDEL.

Haynes BC, Brent MR.

Bioinformatics. 2009 Mar 15;25(6):801-7. doi: 10.1093/bioinformatics/btp068. Epub 2009 Feb 2.

2.

ReTRN: a retriever of real transcriptional regulatory network and expression data for evaluating structure learning algorithm.

Li Y, Zhu Y, Bai X, Cai H, Ji W, Guo D.

Genomics. 2009 Nov;94(5):349-54. doi: 10.1016/j.ygeno.2009.08.009. Epub 2009 Aug 25.

3.

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.

4.

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods.

Schaffter T, Marbach D, Floreano D.

Bioinformatics. 2011 Aug 15;27(16):2263-70. doi: 10.1093/bioinformatics/btr373. Epub 2011 Jun 22.

5.

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.

6.

Reconstructing directed signed gene regulatory network from microarray data.

Qiu P, Plevritis SK.

IEEE Trans Biomed Eng. 2011 Dec;58(12):3518-21. doi: 10.1109/TBME.2011.2163188. Epub 2011 Jul 29.

PMID:
21803675
7.

A network synthesis model for generating protein interaction network families.

Sahraeian SM, Yoon BJ.

PLoS One. 2012;7(8):e41474. doi: 10.1371/journal.pone.0041474. Epub 2012 Aug 13.

8.

Empirical Bayes conditional independence graphs for regulatory network recovery.

Mahdi R, Madduri AS, Wang G, Strulovici-Barel Y, Salit J, Hackett NR, Crystal RG, Mezey JG.

Bioinformatics. 2012 Aug 1;28(15):2029-36. doi: 10.1093/bioinformatics/bts312. Epub 2012 Jun 8.

9.

A single source k-shortest paths algorithm to infer regulatory pathways in a gene network.

Shih YK, Parthasarathy S.

Bioinformatics. 2012 Jun 15;28(12):i49-58. doi: 10.1093/bioinformatics/bts212.

10.

Revealing strengths and weaknesses of methods for gene network inference.

Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.

Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91. doi: 10.1073/pnas.0913357107. Epub 2010 Mar 22.

11.

Gene regulatory networks modelling using a dynamic evolutionary hybrid.

Maraziotis IA, Dragomir A, Thanos D.

BMC Bioinformatics. 2010 Mar 18;11:140. doi: 10.1186/1471-2105-11-140.

12.

Reconstructing transcriptional regulatory networks using three-way mutual information and Bayesian networks.

Luo W, Woolf PJ.

Methods Mol Biol. 2010;674:401-18. doi: 10.1007/978-1-60761-854-6_23.

PMID:
20827604
13.

Structural systems identification of genetic regulatory networks.

Xiong H, Choe Y.

Bioinformatics. 2008 Feb 15;24(4):553-60. doi: 10.1093/bioinformatics/btm623. Epub 2008 Jan 5.

14.

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
15.

Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism.

Nemenman I, Escola GS, Hlavacek WS, Unkefer PJ, Unkefer CJ, Wall ME.

Ann N Y Acad Sci. 2007 Dec;1115:102-15. Epub 2007 Oct 9.

PMID:
17925356
16.

Comparison of evolutionary algorithms in gene regulatory network model inference.

Sîrbu A, Ruskin HJ, Crane M.

BMC Bioinformatics. 2010 Jan 27;11:59. doi: 10.1186/1471-2105-11-59.

17.

GeNGe: systematic generation of gene regulatory networks.

Hache H, Wierling C, Lehrach H, Herwig R.

Bioinformatics. 2009 May 1;25(9):1205-7. doi: 10.1093/bioinformatics/btp115. Epub 2009 Feb 27.

18.

Refining regulatory networks through phylogenetic transfer of information.

Zhang X, Moret BM.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1032-45. doi: 10.1109/TCBB.2012.62.

PMID:
22547434
19.

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
20.

Differential dependency network analysis to identify condition-specific topological changes in biological networks.

Zhang B, Li H, Riggins RB, Zhan M, Xuan J, Zhang Z, Hoffman EP, Clarke R, Wang Y.

Bioinformatics. 2009 Feb 15;25(4):526-32. doi: 10.1093/bioinformatics/btn660. Epub 2008 Dec 26.

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