Network Dynamics as an Interface between Modeling and Experiment in Systems Biology

[1]  Ulrich Lüttge,et al.  The interplay of synchronization and fluctuations reveals connectivity levels in networks of nonlinear oscillators , 2005 .

[2]  M P Young,et al.  Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the cat. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

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

[4]  S. Mangan,et al.  Structure and function of the feed-forward loop network motif , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Peter Andras,et al.  Simulation of robustness against lesions of cortical networks , 2007, The European journal of neuroscience.

[6]  Herbert W. Hethcote,et al.  The Mathematics of Infectious Diseases , 2000, SIAM Rev..

[7]  R. Guimerà,et al.  Functional cartography of complex metabolic networks , 2005, Nature.

[8]  B. Palsson,et al.  Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.

[9]  Marc-Thorsten Hütt,et al.  Organization of Excitable Dynamics in Hierarchical Biological Networks , 2008, PLoS Comput. Biol..

[10]  Marc-Thorsten Huett,et al.  Similar impact of topological and dynamic noise on complex patterns , 2006 .

[11]  S. Strogatz.  Exploring complex networks , 2001, Nature.

[12]  Sanjay Jain,et al.  The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response , 2007 .

[13]  L. Amaral,et al.  The web of human sexual contacts , 2001, Nature.

[14]  R. Sharan,et al.  A genome-scale computational study of the interplay between transcriptional regulation and metabolism , 2007, Molecular systems biology.

[15]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[16]  V. Viasnoff,et al.  Encoding folding paths of RNA switches , 2006, Nucleic acids research.

[17]  Y. Moreno,et al.  Epidemic outbreaks in complex heterogeneous networks , 2001, cond-mat/0107267.

[18]  Julio Collado-Vides,et al.  RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 , 2004, Nucleic Acids Res..

[19]  E. Ruppin,et al.  Regulatory on/off minimization of metabolic flux changes after genetic perturbations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Olaf Sporns,et al.  Network structure of cerebral cortex shapes functional connectivity on multiple time scales , 2007, Proceedings of the National Academy of Sciences.

[21]  Masanori Arita.  The metabolic world of Escherichia coli is not small. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  J. Ferrell,et al.  Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions , 2005, Science.

[23]  Marc-Thorsten Hütt,et al.  Topology regulates the distribution pattern of excitations in excitable dynamics on graphs. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[24]  M. Gerstein,et al.  Genomic analysis of the hierarchical structure of regulatory networks , 2006, Proceedings of the National Academy of Sciences.

[25]  Daniel Durstewitz,et al.  The computational role of dopamine D1 receptors in working memory , 2002, Neural Networks.

[26]  A. Barabasi,et al.  The topology of the transcription regulatory network in the yeast , 2002, cond-mat/0205181.

[27]  Vic Norris,et al.  The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli , 2007, BMC Systems Biology.

[28]  Felix Tretter,et al.  Einführung in die Psychopharmakotherapie: Grundlagen - Praxis - Anwendung , 2004 .

[29]  Kirill Evlampiev,et al.  Conservation and topology of protein interaction networks under duplication-divergence evolution , 2008, Proceedings of the National Academy of Sciences.

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

[31]  T. Sejnowski,et al.  Neurocomputational models of working memory , 2000, Nature Neuroscience.

[32]  D. Fell,et al.  The small world inside large metabolic networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[33]  S. Shen-Orr,et al.  Superfamilies of Evolved and Designed Networks , 2004, Science.

[34]  B. Palsson,et al.  The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Marc-Thorsten Huett,et al.  Topology regulates pattern formation capacity of binary cellular automata on graphs , 2005 .

[36]  D. Fell,et al.  The small world of metabolism , 2000, Nature Biotechnology.

[37]  A. Zeng,et al.  An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. , 2004, Nucleic acids research.

[38]  Mark E. J. Newman,et al.  The Structure and Function of Complex Networks , 2003, SIAM Rev..

[39]  Jürgen Kurths,et al.  Synchronization: Phase locking and frequency entrainment , 2001 .

[40]  J. Miners,et al.  “Phase I and Phase II” Drug Metabolism: Terminology that we Should Phase Out? , 2005, Drug metabolism reviews.

[41]  S. Bornholdt.  Modeling Genetic Networks and Their Evolution: A Complex Dynamical Systems Perspective , 2001, Biological chemistry.

[42]  Alex Arenas,et al.  Synchronization reveals topological scales in complex networks. , 2006, Physical review letters.

[43]  Julio R. Banga,et al.  Optimization in computational systems biology , 2008, BMC Systems Biology.

[44]  A. Barabasi,et al.  Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.

[45]  Kirill Evlampiev,et al.  Modeling protein network evolution under genome duplication and domain shuffling , 2007, BMC Systems Biology.

[46]  S. Bornholdt,et al.  Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast , 2007, PloS one.

[47]  Araceli M. Huerta,et al.  Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. , 2003, Genome research.

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

[49]  S. Teichmann,et al.  Gene regulatory network growth by duplication , 2004, Nature Genetics.

[50]  Joel E. Cohen,et al.  Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better , 2004, PLoS biology.

[51]  Robert Urbanczik.  SNA – a toolbox for the stoichiometric analysis of metabolic networks , 2005, BMC Bioinformatics.

[52]  Marc-Thorsten Hütt,et al.  Regularizing capacity of metabolic networks. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[53]  Sanjay Jain,et al.  Low degree metabolites explain essential reactions and enhance modularity in biological networks , 2005, BMC Bioinformatics.

[54]  Jason A. Papin,et al.  Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. , 2002, Genome research.

[55]  A. Barabasi,et al.  Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.

[56]  O. Sporns,et al.  Identification and Classification of Hubs in Brain Networks , 2007, PloS one.

[57]  S. Brahmachari,et al.  Boolean network analysis of a neurotransmitter signaling pathway. , 2007, Journal of theoretical biology.

[58]  Fiona E. N. LeBeau,et al.  Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. , 2005, Journal of neurophysiology.

[59]  An-Ping Zeng,et al.  The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks , 2003, Bioinform..

[60]  O. Sporns,et al.  Motifs in Brain Networks , 2004, PLoS biology.

[61]  A. Motter,et al.  Synchronization is optimal in nondiagonalizable networks. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[62]  S. Kauffman.  Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[63]  M P Young,et al.  Non-metric multidimensional scaling in the analysis of neuroanatomical connection data and the organization of the primate cortical visual system. , 1995, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[64]  R. Traub,et al.  Cellular mechanism of neuronal synchronization in epilepsy. , 1982, Science.

[65]  Reply to ``Comment on `Regularizing capacity of metabolic networks' '' , 2007, 0709.0823.

[66]  F. Tretter,et al.  REVIEW: The systems view in addiction research , 2008, Addiction biology.

[67]  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.

[68]  S. Bornholdt,et al.  The transition from differential equations to Boolean networks: a case study in simplifying a regulatory network model. , 2008, Journal of theoretical biology.

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

[70]  M. Weigt,et al.  On the properties of small-world network models , 1999, cond-mat/9903411.

[71]  Hildegard Meyer-Ortmanns,et al.  Synchronization of Rössler oscillators on scale-free topologies , 2006 .

[72]  Eric Bullinger,et al.  Approximations and their consequences for dynamic modelling of signal transduction pathways. , 2007, Mathematical biosciences.

[73]  Jason A. Papin,et al.  Reconstruction of cellular signalling networks and analysis of their properties , 2005, Nature Reviews Molecular Cell Biology.

[74]  R. Milo,et al.  Topological generalizations of network motifs. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[75]  H. Möller,et al.  Towards systemic theories in biological psychiatry. , 2006, Pharmacopsychiatry.

[76]  Stephen Wolfram,et al.  Universality and complexity in cellular automata , 1983 .

[77]  Marcus Kaiser,et al.  Criticality of spreading dynamics in hierarchical cluster networks without inhibition , 2007, 0802.2508.

[78]  Markus J. Herrgård,et al.  Reconciling gene expression data with known genome-scale regulatory network structures. , 2003, Genome research.

[79]  Albert-László Barabási,et al.  The Activity Reaction Core and Plasticity of Metabolic Networks , 2005, PLoS Comput. Biol..

[80]  Lan V. Zhang,et al.  Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.

[81]  G. Friedlander,et al.  Regulation of gene expression by small non-coding RNAs: a quantitative view , 2007, Molecular systems biology.

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

[83]  C. Matthai,et al.  Investigation of the forest-fire model on a small-world network. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[84]  Kim Sneppen,et al.  NEUTRAL MUTATIONS AND PUNCTUATED EQUILIBRIUM IN EVOLVING GENETIC NETWORKS , 1997, physics/9708026.

[85]  Alessandro Vespignani,et al.  Velocity and hierarchical spread of epidemic outbreaks in scale-free networks. , 2003, Physical review letters.

[86]  Sheng-You Huang,et al.  Network-induced nonequilibrium phase transition in the "game of Life". , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

[88]  T. Geisel,et al.  Forecast and control of epidemics in a globalized world. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[89]  S. Wolfram.  Statistical mechanics of cellular automata , 1983 .

[90]  O. Alter.  Discovery of principles of nature from mathematical modeling of DNA microarray data , 2006, Proceedings of the National Academy of Sciences.

[91]  M E J Newman,et al.  Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[92]  Albert-László Barabási,et al.  Statistical mechanics of complex networks , 2001, ArXiv.

[93]  A. van Oudenaarden,et al.  MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. , 2007, Molecular cell.

[94]  M Madan Babu,et al.  Adaptive evolution by optimizing expression levels in different environments. , 2006, Trends in microbiology.

[95]  Stefan Bornholdt,et al.  Less Is More in Modeling Large Genetic Networks , 2005, Science.

[96]  Alessandro Vespignani,et al.  Epidemic spreading in scale-free networks. , 2000, Physical review letters.

[97]  Albert-László Barabási,et al.  Internet: Diameter of the World-Wide Web , 1999, Nature.

[98]  Alessandro Vespignani,et al.  Dynamical Patterns of Epidemic Outbreaks in Complex Heterogeneous Networks , 1999 .

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

[100]  Kenneth J. Kauffman,et al.  Advances in flux balance analysis. , 2003, Current opinion in biotechnology.

[101]  Nicolas Le Novère,et al.  DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals , 2006, PLoS Comput. Biol..

[102]  Zeba Wunderlich,et al.  Using the topology of metabolic networks to predict viability of mutant strains. , 2006, Biophysical journal.

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

[104]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[105]  P. Goldman-Rakic,et al.  Division of labor among distinct subtypes of inhibitory neurons in a cortical microcircuit of working memory. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[106]  Philip M. Kim,et al.  Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.

[107]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[108]  B. Kholodenko.  Cell-signalling dynamics in time and space , 2006, Nature Reviews Molecular Cell Biology.

[109]  F. Tretter,et al.  “Computational Neuropsychiatry” of Working Memory Disorders in Schizophrenia: The Network Connectivity in Prefrontal Cortex - Data and Models , 2007 .

[110]  F. Tretter,et al.  Schizophrenia, neurobiology and the methodology of systemic modeling. , 2006, Pharmacopsychiatry.

[111]  U. Alon,et al.  Search for computational modules in the C. elegans brain , 2004, BMC Biology.

[112]  B. Palsson,et al.  Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 , 1994, Applied and environmental microbiology.

[113]  Fatihcan M Atay,et al.  Graph operations and synchronization of complex networks. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[114]  O. Sporns.  Small-world connectivity, motif composition, and complexity of fractal neuronal connections. , 2006, Bio Systems.

[115]  Jeanette Kotaleski,et al.  Transient Calcium and Dopamine Increase PKA Activity and DARPP-32 Phosphorylation , 2006, PLoS Comput. Biol..

[116]  Changsong Zhou,et al.  Hierarchical organization unveiled by functional connectivity in complex brain networks. , 2006, Physical review letters.

[117]  M. Aldana.  Boolean dynamics of networks with scale-free topology , 2003 .

[118]  S. Solla,et al.  Self-sustained activity in a small-world network of excitable neurons. , 2003, Physical review letters.

[119]  Z. N. Oltvai,et al.  Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[120]  Mikael Huss,et al.  Comment on "Regularizing capacity of metabolic networks". , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[121]  James Smith,et al.  SPORCalc: A development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design , 2009, Comput. Biol. Chem..

[122]  M. Newman,et al.  The structure of scientific collaboration networks. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[123]  M. Cosentino Lagomarsino,et al.  Hierarchy and feedback in the evolution of the Escherichia coli transcription network , 2007, Proceedings of the National Academy of Sciences.

[124]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.

[125]  Markus J. Herrgård,et al.  Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.

[126]  Gary D Bader,et al.  Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.

[127]  G. Church,et al.  Analysis of optimality in natural and perturbed metabolic networks , 2002 .

[128]  M. Young,et al.  Computational analysis of functional connectivity between areas of primate cerebral cortex. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[129]  U. an der Heiden.  Schizophrenia as a dynamical disease. , 2006 .

[130]  Christopher G. Langton,et al.  Computation at the edge of chaos: Phase transitions and emergent computation , 1990 .

[131]  Albert-László Barabási,et al.  Hierarchical organization in complex networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[132]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

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