Stability and Flexibility from a System Analysis of Gene Regulatory Networks Based on Ordinary Differential Equations

The inference of large-scale gene regulatory networks from high-throughput data sets has revealed a diverse picture of only partially overlapping descriptions. Nevertheless, several properties in t ...

[1]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[2]  Raj Kumar Pan,et al.  Modular networks emerge from multiconstraint optimization. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[3]  S. Kauffman,et al.  Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms , 2008, PloS one.

[4]  J. Tegnér,et al.  Genome-wide system analysis reveals stable yet flexible network dynamics in yeast. , 2009, IET systems biology.

[5]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[6]  A. Lesne.  Robustness: confronting lessons from physics and biology , 2008, Biological reviews of the Cambridge Philosophical Society.

[7]  D. Pe’er,et al.  Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.

[8]  U. Alon,et al.  Spontaneous evolution of modularity and network motifs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Tomáš Helikar,et al.  Boolean modeling of biochemical networks , 2011 .

[10]  Sitabhra Sinha,et al.  Evidence of universality for the May-Wigner stability theorem for random networks with local dynamics. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[11]  Mika Gustafsson,et al.  Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge , 2010, PloS one.

[12]  Sitabhra Sinha,et al.  Complexity vs. stability in small-world networks , 2004, nlin/0407053.

[13]  Merav Parter,et al.  Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments , 2008, PLoS Comput. Biol..

[14]  U. Alon.  Biological Networks: The Tinkerer as an Engineer , 2003, Science.

[15]  M E J Newman,et al.  Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Massimo Marchiori,et al.  Error and attacktolerance of complex network s , 2004 .

[17]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Kevin Y. Yip,et al.  Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data , 2010, PloS one.

[19]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[20]  H. Kitano,et al.  Computational systems biology , 2002, Nature.

[21]  ROBERT M. MAY,et al.  Will a Large Complex System be Stable? , 1972, Nature.

[22]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[23]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[24]  C. R. Willis,et al.  Discrete Breathers , 1997 .

[25]  Francesco Iorio,et al.  NIRest: A Tool for Gene Network and Mode of Action Inference , 2009, Annals of the New York Academy of Sciences.

[26]  Ming Wu,et al.  Gene module level analysis: identification to networks and dynamics. , 2008, Current opinion in biotechnology.

[27]  Peter Langfelder,et al.  Eigengene networks for studying the relationships between co-expression modules , 2007, BMC Systems Biology.

[28]  Scale-free networks are not robust under neutral evolution , 2001, nlin/0104016.

[29]  Yaniv Ziv,et al.  Revealing modular organization in the yeast transcriptional network , 2002, Nature Genetics.

[30]  A. Califano,et al.  Dialogue on Reverse‐Engineering Assessment and Methods , 2007, Annals of the New York Academy of Sciences.

[31]  Satoru Miyano,et al.  Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data , 2003, CMSB.

[32]  M. Gustafsson,et al.  Constructing and analyzing a large-scale gene-to-gene regulatory network Lasso-constrained inference and biological validation , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[33]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[34]  Katherine C. Chen,et al.  Kinetic analysis of a molecular model of the budding yeast cell cycle. , 2000, Molecular biology of the cell.

[35]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[36]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[37]  Judea Pearl,et al.  Fusion, Propagation, and Structuring in Belief Networks , 1986, Artif. Intell..

[38]  Alberto de la Fuente,et al.  Inferring Gene Networks: Dream or Nightmare? , 2009, Annals of the New York Academy of Sciences.

[39]  J. Collins,et al.  Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling , 2003, Science.

[40]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[41]  Sergei Maslov,et al.  Computational architecture of the yeast regulatory network , 2005, Physical biology.

[42]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[43]  R. Steuer.  Computational approaches to the topology, stability and dynamics of metabolic networks. , 2007, Phytochemistry.

[44]  Mika Gustafsson,et al.  Comparison and validation of community structures in complex networks , 2006 .

[45]  Ravi Iyengar,et al.  Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks , 2008, Proceedings of the National Academy of Sciences.

[46]  Olaf Wolkenhauer,et al.  Principal difference between stability and structural stability (robustness) as used in systems biology. , 2007, Nonlinear dynamics, psychology, and life sciences.

[47]  P. Brazhnik,et al.  Gene networks: how to put the function in genomics. , 2002, Trends in biotechnology.

[48]  Michael Hecker,et al.  Gene regulatory network inference: Data integration in dynamic models - A review , 2009, Biosyst..

[49]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[50]  Mark Ptashne,et al.  A Genetic Switch, Phage Lambda Revisited , 2004 .