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    Results: 1 to 20 of 182

    1.

    Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks.

    Michoel T, De Smet R, Joshi A, Van de Peer Y, Marchal K.

    BMC Syst Biol. 2009 May 7;3:49.PMID: 19422680 [PubMed - indexed for MEDLINE]Related articlesFree article

    2.

    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.PMID: 19594874 [PubMed - indexed for MEDLINE]Related articlesFree article

    3.

    Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations.

    Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A.

    BMC Syst Biol. 2009 Apr 14;3:39.PMID: 19366454 [PubMed - indexed for MEDLINE]Related articlesFree article

    4.

    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

    5.

    Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.

    Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS.

    PLoS Biol. 2007 Jan;5(1):e8.PMID: 17214507 [PubMed - indexed for MEDLINE]Related articlesFree article

    6.

    Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development.

    Vermeirssen V, Joshi A, Michoel T, Bonnet E, Casneuf T, Van de Peer Y.

    Mol Biosyst. 2009 Jul 17. [Epub ahead of print]PMID: 19763340 [PubMed - as supplied by publisher]Related articles

    7.

    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

    8.

    ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.

    Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A.

    BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7.PMID: 16723010 [PubMed - indexed for MEDLINE]Related articlesFree article

    9.

    Inference of regulatory gene interactions from expression data using three-way mutual information.

    Watkinson J, Liang KC, Wang X, Zheng T, Anastassiou D.

    Ann N Y Acad Sci. 2009 Mar;1158:302-13.PMID: 19348651 [PubMed - indexed for MEDLINE]Related articles

    10.

    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

    11.

    Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress.

    Taylor RC, Acquaah-Mensah G, Singhal M, Malhotra D, Biswal S.

    PLoS Comput Biol. 2008 Aug 29;4(8):e1000166.PMID: 18769717 [PubMed - indexed for MEDLINE]Related articlesFree article

    12.

    Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms.

    Zampieri M, Soranzo N, Bianchini D, Altafini C.

    PLoS One. 2008 Aug 20;3(8):e2981.PMID: 18714358 [PubMed - indexed for MEDLINE]Related articlesFree article

    13.

    Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.

    Guzmán-Vargas L, Santillán M.

    BMC Syst Biol. 2008 Jan 31;2:13.PMID: 18237429 [PubMed - indexed for MEDLINE]Related articlesFree article

    14.

    A predictive model of the oxygen and heme regulatory network in yeast.

    Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C.

    PLoS Comput Biol. 2008 Nov;4(11):e1000224. Epub 2008 Nov 14.PMID: 19008939 [PubMed - indexed for MEDLINE]Related articlesFree article

    15.

    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.PMID: 19183003 [PubMed - indexed for MEDLINE]Related articles

    16.

    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

    17.

    Computational discovery of gene modules and regulatory networks.

    Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

    Nat Biotechnol. 2003 Nov;21(11):1337-42. Epub 2003 Oct 12.PMID: 14555958 [PubMed - indexed for MEDLINE]Related articles

    18.

    Predicting genetic interactions with random walks on biological networks.

    Chipman KC, Singh AK.

    BMC Bioinformatics. 2009 Jan 12;10:17.PMID: 19138426 [PubMed - indexed for MEDLINE]Related articlesFree article

    19.

    Methods to reconstruct and compare transcriptional regulatory networks.

    Babu MM, Lang B, Aravind L.

    Methods Mol Biol. 2009;541:163-80. Review.PMID: 19381525 [PubMed - indexed for MEDLINE]Related articles

    20.

    Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach.

    Ma HW, Buer J, Zeng AP.

    BMC Bioinformatics. 2004 Dec 16;5:199.PMID: 15603590 [PubMed - indexed for MEDLINE]Related articlesFree article

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