Large Causal Gene Regulatory Network Inference by Decomposition into Subnetworks

[1]  M. Omair Ahmad,et al.  Inference of Gene Regulatory Networks with Variable Time Delay from Time-Series Microarray Data , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[2]  Gennaro Oliva,et al.  A Parallel Implementation of the Network Identification by Multiple Regression (NIR) Algorithm to Reverse-Engineer Regulatory Gene Networks , 2010, PloS one.

[3]  J. Stelling,et al.  A tunable synthetic mammalian oscillator , 2009, Nature.

[4]  Julian Lewis Autoinhibition with Transcriptional Delay A Simple Mechanism for the Zebrafish Somitogenesis Oscillator , 2003, Current Biology.

[5]  Kwong-Sak Leung,et al.  Inferring Time-Delayed Causal Gene Network Using Time-Series Expression Data , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[6]  George J. Pappas,et al.  Genetic network identification using convex programming. , 2009, IET systems biology.

[7]  Isabel M. Tienda-Luna,et al.  Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization , 2007, EURASIP J. Bioinform. Syst. Biol..

[8]  Dan Wu,et al.  Modeling Multiple Time Units Delayed Gene Regulatory Network Using Dynamic Bayesian Network , 2006, Sixth IEEE International Conference on Data Mining - Workshops (ICDMW'06).

[9]  M. Ehrenberg,et al.  Rate of translation of natural mRNAs in an optimized in vitro system. , 1996, Archives of biochemistry and biophysics.

[10]  J. Pearl Causality: Models, Reasoning and Inference , 2000 .

[11]  Zheng Li,et al.  Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis , 2011, Bioinform..

[12]  Frank Emmert-Streib,et al.  Inferring the conservative causal core of gene regulatory networks , 2010, BMC Systems Biology.

[13]  Jeff Hasty,et al.  Delay-induced degrade-and-fire oscillations in small genetic circuits. , 2009, Physical review letters.

[14]  Ian A. Swinburne,et al.  Intron delays and transcriptional timing during development. , 2008, Developmental cell.

[15]  Paul P. Wang,et al.  Advances to Bayesian network inference for generating causal networks from observational biological data , 2004, Bioinform..

[16]  Harri Lähdesmäki,et al.  Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics , 2009, Bioinform..

[17]  Diego di Bernardo,et al.  Inference of gene regulatory networks and compound mode of action from time course gene expression profiles , 2006, Bioinform..

[18]  Alvis Brazma,et al.  Current approaches to gene regulatory network modelling , 2007, BMC Bioinformatics.

[19]  Trevor I. Dix,et al.  Causal Modeling of Gene Regulatory Network , 2006, 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

[20]  Chris Wiggins,et al.  ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.

[21]  Hans A. Kestler,et al.  Inferring Boolean network structure via correlation , 2011, Bioinform..

[22]  Vassily Hatzimanikatis,et al.  The Origins of Time-Delay in Template Biopolymerization Processes , 2010, PLoS Comput. Biol..

[23]  R. Tibshirani Regression Shrinkage and Selection via the Lasso , 1996 .

[24]  Mark J. van der Laan,et al.  A causal inference approach for constructing transcriptional regulatory networks , 2005, Bioinform..

[25]  Guy Karlebach,et al.  Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.

[26]  M. Newman,et al.  Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[27]  Huang-Cheng Kuo,et al.  Finding Time-Delayed Gene Regulation Patterns from Microarray Data , 2009, 2009 Ninth International Conference on Hybrid Intelligent Systems.

[28]  Michele Ceccarelli,et al.  articleTimeDelay-ARACNE : Reverse engineering of gene networks from time-course data by an information theoretic approach , 2010 .

[29]  K. Aihara,et al.  Stability of genetic regulatory networks with time delay , 2002 .

[30]  D. di Bernardo,et al.  How to infer gene networks from expression profiles , 2007, Molecular systems biology.