Gene Expression Complex Networks: Synthesis, Identification, and Analysis
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Roberto Marcondes Cesar Junior | Luciano da Fontoura Costa | Fabrício Martins Lopes | Fabricio M. Lopes | L. Costa | R. M. C. Junior
[1] R. Somogyi,et al. Gene Expression Data Analysis and Modeling , 1999 .
[2] David Correa Martins,et al. W-operator window design by minimization of mean conditional entropy , 2006, Pattern Analysis and Applications.
[3] Hidde de Jong,et al. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks , 2003, Bioinform..
[4] Albert-László Barabási,et al. Statistical mechanics of complex networks , 2001, ArXiv.
[5] Alberto de la Fuente,et al. Discovery of meaningful associations in genomic data using partial correlation coefficients , 2004, Bioinform..
[6] David Correa Martins,et al. Comparative study of GRNS inference methods based on feature selection by mutual information , 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics.
[7] A. Barabasi,et al. The topology of the transcription regulatory network in the yeast , 2002, cond-mat/0205181.
[8] R. Albert,et al. Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling , 2006, PLoS biology.
[9] Raghunathan Rengaswamy,et al. Structural Properties of Gene Regulatory Networks: Definitions and Connections , 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[10] Steffen Klamt,et al. Structural and functional analysis of cellular networks with CellNetAnalyzer , 2007, BMC Systems Biology.
[11] Pedro Mendes,et al. Artificial gene networks for objective comparison of analysis algorithms , 2003, ECCB.
[12] Hidde de Jong,et al. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..
[13] R. Albert. Scale-free networks in cell biology , 2005, Journal of Cell Science.
[14] Roberto Marcondes Cesar Junior,et al. AGN Simulation and Validation Model , 2008, BSB.
[15] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[16] M. Hetzer,et al. Eukaryotic cells. , 2011, Current opinion in cell biology.
[17] Josef Kittler,et al. Floating search methods in feature selection , 1994, Pattern Recognit. Lett..
[18] Michael Hecker,et al. Gene regulatory network inference: Data integration in dynamic models - A review , 2009, Biosyst..
[19] H. Okayama. Mammalian Cell Cycle. , 1993 .
[20] S. Bornholdt,et al. Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast , 2007, PloS one.
[21] Edward R Dougherty,et al. Validation of Inference Procedures for Gene Regulatory Networks , 2007, Current genomics.
[22] David Correa Martins,et al. Feature selection environment for genomic applications , 2008, BMC Bioinformatics.
[23] Alan M. Frieze,et al. Random graphs , 2006, SODA '06.
[24] S Fuhrman,et al. Reveal, a general reverse engineering algorithm for inference of genetic network architectures. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[25] Ilya Shmulevich,et al. Eukaryotic cells are dynamically ordered or critical but not chaotic. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[26] Alvis Brazma,et al. Current approaches to gene regulatory network modelling , 2007, BMC Bioinformatics.
[27] Luciano da Fontoura Costa,et al. Complex networks: The key to systems biology , 2008 .
[28] Joshua M. Stuart,et al. A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.
[29] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[30] P. Bourgine,et al. Topological and causal structure of the yeast transcriptional regulatory network , 2002, Nature Genetics.
[31] Kathleen Marchal,et al. SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms , 2006, BMC Bioinformatics.
[32] Michael R. Brent,et al. Benchmarking regulatory network reconstruction with GRENDEL , 2009, Bioinform..
[33] A. Lehninger. Principles of Biochemistry , 1984 .
[34] Mark E. J. Newman,et al. The Structure and Function of Complex Networks , 2003, SIAM Rev..
[35] Claudio Altafini,et al. Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data , 2007, Bioinform..
[36] H. Othmer,et al. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.
[37] Edward R. Dougherty,et al. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks , 2002, Bioinform..
[38] Duncan J. Watts,et al. Collective dynamics of ‘small-world’ networks , 1998, Nature.
[39] Albert,et al. Emergence of scaling in random networks , 1999, Science.
[40] Stuart A. Kauffman,et al. The origins of order , 1993 .
[41] Michael T. Gastner,et al. The spatial structure of networks , 2006 .
[42] S. Kauffman. Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.
[43] S Bullock,et al. Modelling the evolution of genetic regulatory networks. , 2006, Journal of theoretical biology.
[44] Carsten Peterson,et al. Random Boolean network models and the yeast transcriptional network , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[45] Song Li,et al. Boolean network simulations for life scientists , 2008, Source Code for Biology and Medicine.
[46] L. da F. Costa,et al. Characterization of complex networks: A survey of measurements , 2005, cond-mat/0505185.
[47] M Wahde,et al. Coarse-grained reverse engineering of genetic regulatory networks. , 2000, Bio Systems.
[48] D. Thieffry,et al. A logical analysis of the Drosophila gap-gene system. , 2001, Journal of theoretical biology.
[49] S. Carroll,et al. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design , 2000 .
[50] R. Rengaswamy,et al. Structural Properties of Gene Regulatory Networks: Definitions and Connections , 2009, TCBB.
[51] Roberto Lucchetti,et al. Microarray Data Analysis via Weighted Indices and Weighted Majority Games , 2009, CIBB.
[52] Andrew R. Webb,et al. Statistical Pattern Recognition , 1999 .
[53] V. Latora,et al. Complex networks: Structure and dynamics , 2006 .
[54] Charlie Hodgman,et al. Inference of Gene Regulatory Networks Using Boolean-Network Inference Methods , 2009, J. Bioinform. Comput. Biol..
[55] Yufei Huang,et al. Genomic Signal Processing , 2012, IEEE Signal Processing Magazine.
[56] Edward R. Dougherty,et al. From Boolean to probabilistic Boolean networks as models of genetic regulatory networks , 2002, Proc. IEEE.
[57] Lei M. Li,et al. Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks , 2005, J. Comput. Biol..
[58] David Correa Martins,et al. Constructing Probabilistic Genetic Networks of Plasmodium falciparum from Dynamical Expression Signals of the Intraerythrocytic Development Cycle , 2007 .
[59] Guy Karlebach,et al. Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.
[60] C. Espinosa-Soto,et al. A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profilesw⃞ , 2004, The Plant Cell Online.
[61] Hans C. van Houwelingen,et al. Microarray Data Analysis , 2004 .
[62] Aurélien Naldi,et al. Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle , 2006, ISMB.
[63] M Villani,et al. Genetic network models and statistical properties of gene expression data in knock-out experiments. , 2004, Journal of theoretical biology.
[64] Mark P. Styczynski,et al. Overview of computational methods for the inference of gene regulatory networks , 2005, Comput. Chem. Eng..
[65] Q. Ouyang,et al. The yeast cell-cycle network is robustly designed. , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[66] Patrik D'haeseleer,et al. Genetic network inference: from co-expression clustering to reverse engineering , 2000, Bioinform..
[67] Judea Pearl,et al. Probabilistic reasoning in intelligent systems - networks of plausible inference , 1991, Morgan Kaufmann series in representation and reasoning.
[68] D. di Bernardo,et al. How to infer gene networks from expression profiles , 2007, Molecular systems biology.