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Towards reconstruction of gene networks from expression data by supervised learning.

Soinov LA, Krestyaninova MA, Brazma A.

Genome Biol. 2003;4(1):R6. Epub 2003 Jan 6.PMID: 12540298 [PubMed - indexed for MEDLINE]Related articlesFree article

A novel model-free approach for reconstruction of time-delayed gene regulatory networks.

Jiang W, Li X, Guo Z, Li C, Wang L, Rao S.

Sci China C Life Sci. 2006 Apr;49(2):190-200.PMID: 16704123 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 19594885 [PubMed - indexed for MEDLINE]Related articlesFree article

A copula method for modeling directional dependence of genes.

Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I.

BMC Bioinformatics. 2008 May 1;9:225.PMID: 18447957 [PubMed - indexed for MEDLINE]Related articlesFree article

A classification-based framework for predicting and analyzing gene regulatory response.

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

BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S5.PMID: 16723008 [PubMed - indexed for MEDLINE]Related articlesFree article

Reconstructing genetic networks from time ordered gene expression data using Bayesian method with global search algorithm.

Wang SC.

J Bioinform Comput Biol. 2004 Sep;2(3):441-58.PMID: 15359420 [PubMed - indexed for MEDLINE]Related articles

A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data.

Zou M, Conzen SD.

Bioinformatics. 2005 Jan 1;21(1):71-9. Epub 2004 Aug 12.PMID: 15308537 [PubMed - indexed for MEDLINE]Related articlesFree article

Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory.

Luo F, Yang Y, Zhong J, Gao H, Khan L, Thompson DK, Zhou J.

BMC Bioinformatics. 2007 Aug 14;8:299.PMID: 17697349 [PubMed - indexed for MEDLINE]Related articlesFree article

A bi-dimensional regression tree approach to the modeling of gene expression regulation.

Ruan J, Zhang W.

Bioinformatics. 2006 Feb 1;22(3):332-40. Epub 2005 Nov 22.PMID: 16303796 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle.

Wu WS, Li WH, Chen BS.

BMC Bioinformatics. 2006 Sep 29;7:421.PMID: 17010188 [PubMed - indexed for MEDLINE]Related articlesFree article

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle.

Chen HC, Lee HC, Lin TY, Li WH, Chen BS.

Bioinformatics. 2004 Aug 12;20(12):1914-27. Epub 2004 Mar 25.PMID: 15044243 [PubMed - indexed for MEDLINE]Related articlesFree article

Knowledge-assisted recognition of cluster boundaries in gene expression data.

Okada Y, Sahara T, Mitsubayashi H, Ohgiya S, Nagashima T.

Artif Intell Med. 2005 Sep-Oct;35(1-2):171-83.PMID: 16054350 [PubMed - indexed for MEDLINE]Related articles

Supervised classification for gene network reconstruction.

Soinov LA.

Biochem Soc Trans. 2003 Dec;31(Pt 6):1497-502.PMID: 14641098 [PubMed - indexed for MEDLINE]Related articles

Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae.

Kim H, Hu W, Kluger Y.

BMC Bioinformatics. 2006 Mar 21;7:165.PMID: 16551355 [PubMed - indexed for MEDLINE]Related articlesFree article

A hybrid Bayesian network learning method for constructing gene networks.

Wang M, Chen Z, Cloutier S.

Comput Biol Chem. 2007 Oct;31(5-6):361-72. Epub 2007 Aug 19.PMID: 17889617 [PubMed - indexed for MEDLINE]Related articles

Inferring adaptive regulation thresholds and association rules from gene expression data through combinatorial optimization learning.

Ponzoni I, Azuaje F, Augusto J, Glass D.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):624-34.PMID: 17975273 [PubMed - indexed for MEDLINE]Related articles

Clustering of gene expression data using a local shape-based similarity measure.

Balasubramaniyan R, Hüllermeier E, Weskamp N, Kämper J.

Bioinformatics. 2005 Apr 1;21(7):1069-77. Epub 2004 Oct 28.PMID: 15513997 [PubMed - indexed for MEDLINE]Related articlesFree article

Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks.

Kim CS.

BMC Bioinformatics. 2007 Jul 13;8:251.PMID: 17626641 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene networks reconstruction and time-series prediction from microarray data using recurrent neural fuzzy networks.

Maraziotis IA, Dragomir A, Bezerianos A.

IET Syst Biol. 2007 Jan;1(1):41-50.PMID: 17370428 [PubMed - indexed for MEDLINE]Related articles

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.PMID: 15113405 [PubMed - indexed for MEDLINE]Related articlesFree article