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Research Article
A model of transcriptional regulatory networks based on biases in the observed regulation rules
Article first published online: 14 AUG 2002
DOI: 10.1002/cplx.10022
Copyright © 2002 Wiley Periodicals, Inc.
1099-0526/asset/cover.gif?v=1&s=2daaa4acf3bd7f833d75aa89369b1eb85ebc43bf "Complexity")
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How to Cite
Harris, S. E., Sawhill, B. K., Wuensche, A. and Kauffman, S. (2002), A model of transcriptional regulatory networks based on biases in the observed regulation rules. Complexity, 7: 23–40. doi: 10.1002/cplx.10022
Publication History
- Issue published online: 14 AUG 2002
- Article first published online: 14 AUG 2002
- Manuscript Revised: 19 DEC 2001
- Manuscript Accepted: 19 DEC 2001
- Manuscript Received: 28 JUL 2000
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- 1, , , , A rate-distortion theory for gene regulatory networks and its application to logic gate consistency, Bioinformatics, 2013, 29, 9, 1166
- 2, , , , , Boolean nested canalizing functions: A comprehensive analysis, Theoretical Computer Science, 2013, 481, 24
- 3, , , Mathematical Conditions for Induced Cell Differentiation and Trans-differentiation in Adult Cells, Bulletin of Mathematical Biology, 2013, 75, 5, 819
- 4, , , , , , Properties of Boolean networks and methods for their tests, EURASIP Journal on Bioinformatics and Systems Biology, 2013, 2013, 1, 1
- 5, , , Dynamical Instability in Boolean Networks as a Percolation Problem, Physical Review Letters, 2012, 109, 8
- 6, Emergence of robustness against noise: A structural phase transition in evolved models of gene regulatory networks, Physical Review E, 2012, 85, 4
- 7, Guiding the self-organization of random Boolean networks, Theory in Biosciences, 2012, 131, 3, 181
- 8, , , , , Inferring Boolean functions via higher-order correlations, Computational Statistics, 2012,
- 9, , , , Invalidation of the structure of genetic network dynamics: a geometric approach, International Journal of Robust and Nonlinear Control, 2012, 22, 10Direct Link:
- 10, , , Singleton and 2-periodic attractors of sign-definite Boolean networks, Information Processing Letters, 2012, 112, 1-2, 35
- 11, , , Singular Boolean networks: Semi-tensor product approach, Science China Information Sciences, 2012,
- 12, , , Stability of Boolean networks with generalized canalizing rules, Physical Review E, 2012, 85, 4
- 13, , , Comparing the evolution of canalyzing and threshold networks, The European Physical Journal B, 2011, 80, 2, 195
- 14, , , , Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions, Journal of Computational Biology, 2011, 18, 10, 1275
- 15, , , , , Influence and Dynamic Behavior in Random Boolean Networks, Physical Review Letters, 2011, 107, 10
- 16
- 17, , , , PATHWAY REGULATORY ANALYSIS IN THE CONTEXT OF BAYESIAN NETWORKS USING THE COEFFICIENT OF DETERMINATION, Journal of Biological Systems, 2011, 19, 04, 651
- 18, , Regulatory patterns in molecular interaction networks, Journal of Theoretical Biology, 2011, 288, 66
- 19, , A Linear Representation of Dynamics of Boolean Networks, IEEE Transactions on Automatic Control, 2010, 55, 10, 2251
- 20, , Anomalies in the transcriptional regulatory network of the Yeast Saccharomyces cerevisiae, Journal of Theoretical Biology, 2010, 263, 3, 328
- 21, , , Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks, Journal of Theoretical Biology, 2010, 266, 3, 436
- 22, , Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space, Physical Review E, 2010, 81, 2
- 23, , , , Higher order Boolean networks as models of cell state dynamics, Journal of Theoretical Biology, 2010, 264, 3, 945
- 24, , ROBUSTNESS OF TRANSCRIPTIONAL REGULATION IN YEAST-LIKE MODEL BOOLEAN NETWORKS, International Journal of Bifurcation and Chaos, 2010, 20, 03, 929
- 25, , Sequential operator for filtering cycles in Boolean networks, Advances in Applied Mathematics, 2010, 45, 3, 346
- 26, , , , Structural properties of continuous representations of Boolean functions for gene network modelling, Automatica, 2010, 46, 12, 2047
- 27, , , The Dynamics of Conjunctive and Disjunctive Boolean Network Models, Bulletin of Mathematical Biology, 2010, 72, 6, 1425
- 28, The phase diagram of random Boolean networks with nested canalizing functions, The European Physical Journal B, 2010, 78, 2, 187
- 29, , Controllability and observability of Boolean control networks, Automatica, 2009, 45, 7, 1659
- 30, , Dynamical approaches to modeling developmental gene regulatory networks, Birth Defects Research Part C: Embryo Today: Reviews, 2009, 87, 2Direct Link:
- 31, , SYMBOLIC APPROACHES FOR FINDING CONTROL STRATEGIES IN BOOLEAN NETWORKS, Journal of Bioinformatics and Computational Biology, 2009, 07, 02, 323
- 32, , 2009,
- 33, , Broad edge of chaos in strongly heterogeneous Boolean networks, Journal of Physics A: Mathematical and Theoretical, 2008, 41, 41, 415001
- 34, , , Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length, EURASIP Journal on Bioinformatics and Systems Biology, 2008, 2008, 1
- 35, Maximum Number of Fixed Points in Regulatory Boolean Networks, Bulletin of Mathematical Biology, 2008, 70, 5, 1398
- 36
- 37, , , The cost and capacity of signaling in the Escherichia coli protein reaction network, Journal of Statistical Mechanics: Theory and Experiment, 2008, 2008, 01, P01018
- 38, , Boolean Dynamics of Biological Networks with Multiple Coupled Feedback Loops, Biophysical Journal, 2007, 92, 8, 2975
- 39, , , Boolean networks with biologically relevant rules show ordered behavior, Biosystems, 2007, 90, 1, 40
- 40, , Comparative study of the transcriptional regulatory networks of E. coli and yeast: Structural characteristics leading to marginal dynamic stability, Journal of Theoretical Biology, 2007, 248, 4, 618
- 41, , , , Control of Boolean networks: Hardness results and algorithms for tree structured networks, Journal of Theoretical Biology, 2007, 244, 4, 670
- 42, , Entropy of complex relevant components of Boolean networks, Physical Review E, 2007, 76, 3
- 43, , Evolution of canalizing Boolean networks, The European Physical Journal B, 2007, 56, 4, 373
- 44, , , , Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data, Journal of Theoretical Biology, 2007, 246, 3, 449
- 45, , , An analysis of the class of gene regulatory functions implied by a biochemical model, Biosystems, 2006, 84, 2, 81
- 46, , , , COMBINATORIAL FRACTAL GEOMETRY WITH A BIOLOGICAL APPLICATION, Fractals, 2006, 14, 02, 133
- 47
- 48, , , Perturbation avalanches and criticality in gene regulatory networks, Journal of Theoretical Biology, 2006, 242, 1, 164
- 49, , , , Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks, Signal Processing, 2006, 86, 4, 814
- 50, Reverse Engineering Discrete Dynamical Systems from Data Sets with Random Input Vectors, Journal of Computational Biology, 2006, 13, 8, 1435
- 51
- 52, , Canalizing Kauffman Networks: Nonergodicity and Its Effect on Their Critical Behavior, Physical Review Letters, 2005, 94, 21
- 53, , , , Cell Fates as High-Dimensional Attractor States of a Complex Gene Regulatory Network, Physical Review Letters, 2005, 94, 12
- 54, , , Gene-to-phenotype models and complex trait genetics, Australian Journal of Agricultural Research, 2005, 56, 9, 895
- 55, , , On spectral techniques in analysis of Boolean networks, Physica D: Nonlinear Phenomena, 2005, 206, 1-2, 49
- 56, , On the properties of cycles of simple Boolean networks, The European Physical Journal B, 2005, 43, 1, 115
- 57, , , Stability of functions in Boolean models of gene regulatory networks, Chaos: An Interdisciplinary Journal of Nonlinear Science, 2005, 15, 3, 034101
- 58, , , Tracking perturbations in Boolean networks with spectral methods, Physical Review E, 2005, 72, 2
- 59, A proposal for using the ensemble approach to understand genetic regulatory networks, Journal of Theoretical Biology, 2004, 230, 4, 581
- 60, , Activities and Sensitivities in Boolean Network Models, Physical Review Letters, 2004, 93, 4
- 61, , , Genetic network models and statistical properties of gene expression data in knock-out experiments, Journal of Theoretical Biology, 2004, 227, 1, 149
- 62, , , Inferring models of gene expression dynamics, Journal of Theoretical Biology, 2004, 230, 3, 289
- 63, , , Spectral Methods for Testing Membership in Certain Post Classes and the Class of Forcing Functions, IEEE Signal Processing Letters, 2004, 11, 2, 289
- 64, The ensemble approach to understand genetic regulatory networks, Physica A: Statistical Mechanics and its Applications, 2004, 340, 4, 733
- 65, , , The number and probability of canalizing functions, Physica D: Nonlinear Phenomena, 2004, 197, 3-4, 211
- 66, , , Dynamics of Biomolecular Networks, Encyclopedia of Molecular Cell Biology and Molecular Medicine,Direct Link: