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Raff R: The Shape of Life. Chicago: University of Chicago Press; 1996.
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The Shape of Life
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Turing A.M. The chemical basis of morphogenesis. Philos Trans Roy Soc London B. 237:1952;37-72.
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Meinhardt H., Gierer A. Pattern formation by local self-activation and lateral inhibition. Bioessays. 22:2000;753-760.
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Meinhardt, H.1
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Modeling and simulation of genetic regulatory systems: A literature review
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An excellent extensive review of many studies modelling gene networks.
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de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 9:2002;67-103 An excellent extensive review of many studies modelling gene networks.
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J Comput Biol
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De Jong, H.1
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Modeling a hox gene network in silico using a stochastic simulation algorithm
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Kastner J., Solomon J., Fraser S. Modeling a hox gene network in silico using a stochastic simulation algorithm. Dev Biol. 246:2002;122-131.
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Dynamical behaviour of biological regulatory networks. I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state
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Thomas R., Thieffry D., Kaufman M. Dynamical behaviour of biological regulatory networks. I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull Math Biol. 57:1995;247-276.
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Thomas, R.1
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From gradients to stripes in Drosophila embryogenesis: Filling in the gaps
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Rivera-Pomar R., Jäckle H. From gradients to stripes in Drosophila embryogenesis: filling in the gaps. Trends Genet. 12:1996;478-483.
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Programming the Drosophila embryo 2: From genotype to phenotype
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Bodnar J.W., Bradley M.K. Programming the Drosophila embryo 2: from genotype to phenotype. Cell Biochem Biophys. 34:2001;153-190.
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Burstein Z. A network model of developmental gene hierarchy. J Theor Biol. 174:1995;1-11.
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Burstein, Z.1
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Modelling the Drosophila-rule pattern by reaction-diffusion: Gap input and pattern control in a 4-morphogen system
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Lacalli T.C. Modelling the Drosophila-rule pattern by reaction-diffusion: gap input and pattern control in a 4-morphogen system. J Theor Biol. 144:1990;171-194.
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Meinhardt H. Hierarchical inductions of cell states: a model for segmentation in Drosophila. J Cell Sci. 4(Suppl):1986;357-381.
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Meinhardt, H.1
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A logical analysis of the Drosophila gap gene system
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Sánchez L., Thieffry D. A logical analysis of the Drosophila gap gene system. J Theor Biol. 211:2001;115-141.
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J Theor Biol
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Sánchez, L.1
Thieffry, D.2
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0036962769
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Alternative epigenetic states understood in terms of specific regulatory structures
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Following up our logical analysis of the gap regulatory module [16], we provide here an extensive set of simulations encompassing single or multiple loss-of-function mutations and cis-regulatory mutations as well as ectopic gene expression. Many of these simulations lead to results that still await experimental testing
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Thieffry D., Sánchez L. Alternative epigenetic states understood in terms of specific regulatory structures. Ann NY Acad Sci. 981:2002;135-153 Following up our logical analysis of the gap regulatory module [16], we provide here an extensive set of simulations encompassing single or multiple loss-of-function mutations and cis-regulatory mutations as well as ectopic gene expression. Many of these simulations lead to results that still await experimental testing.
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Ann NY Acad Sci
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Thieffry, D.1
Sánchez, L.2
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The segment polarity network is a robust developmental module
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Von Dassow G., Meir E., Munro E.M., Odell G.M. The segment polarity network is a robust developmental module. Nature. 406:2000;188-192.
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Nature
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Von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
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19
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0037108607
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Design and constraints of the Drosophila segment polarity module: Robust spatial patterning emerges from intertwined cell state switches
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Pursuing their model analysis of the segment-polarity gene network [18], the authors analyse different variants of the core of this network; their results lead them to understand its organisation in terms of simple dynamical elements such as several 'bistable switches' and an 'homeostat'
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Von Dassow G., Odell G.M. Design and constraints of the Drosophila segment polarity module: robust spatial patterning emerges from intertwined cell state switches. J Exp Zool. 294:2002;179-215 Pursuing their model analysis of the segment-polarity gene network [18], the authors analyse different variants of the core of this network; their results lead them to understand its organisation in terms of simple dynamical elements such as several 'bistable switches' and an 'homeostat'.
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J Exp Zool
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Von Dassow, G.1
Odell, G.M.2
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21
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0036130611
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Temporal classification of Drosophila segmentation gene expression patterns by multi-valued neural recognition method
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This paper describes a computational method that automatically determines the developmental age of an embryo on the basis of knowledge of its gene expression patterns
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Aizenberg I., Mynikova E., Samsonova M., Reinitz J. Temporal classification of Drosophila segmentation gene expression patterns by multi-valued neural recognition method. Math Biosci. 176:2002;145-159 This paper describes a computational method that automatically determines the developmental age of an embryo on the basis of knowledge of its gene expression patterns.
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Math Biosci
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Aizenberg, I.1
Mynikova, E.2
Samsonova, M.3
Reinitz, J.4
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22
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0037075022
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Establishment of developmental precision and proportions in the early Drosophila embryo
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Houchmandzadeh B., Wieschaus E., Leibler S. Establishment of developmental precision and proportions in the early Drosophila embryo. Nature. 415:2002;798-802.
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Nature
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Houchmandzadeh, B.1
Wieschaus, E.2
Leibler, S.3
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23
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0037136555
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Robustness of the BMP morphogen gradient in Drosophila embryonic patterning
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Combining computing and experimental approaches, these authors have studied the gene network responsible for the patterning of the dorsal domain. This patterning involves two morphogens, Screw and Decapentaplegic, belonging to the class of BMPs. They find that the gradient of active BMP is robust to changes in gene dosage, and that this robustness depends on complex formation coupled with the restricted diffusion of BMP ligands
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Eldar A., Dorfman R., Weiss D., Ashe H., Shilo B.Z., Barkai N. Robustness of the BMP morphogen gradient in Drosophila embryonic patterning. Nature. 419:2002;304-308 Combining computing and experimental approaches, these authors have studied the gene network responsible for the patterning of the dorsal domain. This patterning involves two morphogens, Screw and Decapentaplegic, belonging to the class of BMPs. They find that the gradient of active BMP is robust to changes in gene dosage, and that this robustness depends on complex formation coupled with the restricted diffusion of BMP ligands.
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(2002)
Nature
, vol.419
, pp. 304-308
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Eldar, A.1
Dorfman, R.2
Weiss, D.3
Ashe, H.4
Shilo, B.Z.5
Barkai, N.6
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24
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0031583031
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Establishment of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: A logical analysis
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Sánchez L., VanHelden J., Thieffry D. Establishment of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: a logical analysis. J Theor Biol. 189:1997;377-389.
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J Theor Biol
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Sánchez, L.1
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Thieffry, D.3
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25
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0037076210
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Robustness, flexibility, and the role of lateral inhibition in the neurogenic network
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This paper addresses modelling of the gene network that underlies the cell-cell lateral signalling mediated through Notch and Delta. On the basis of three different scenarios with respect to cellular arrangements and expression patterns, the authors analyse different core networks through random recombination and mutation of consistent parameter values
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Meir E., von Dassow G., Munro E., Odell G.M. Robustness, flexibility, and the role of lateral inhibition in the neurogenic network. Curr Biol. 12:2002;778-786 This paper addresses modelling of the gene network that underlies the cell-cell lateral signalling mediated through Notch and Delta. On the basis of three different scenarios with respect to cellular arrangements and expression patterns, the authors analyse different core networks through random recombination and mutation of consistent parameter values.
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(2002)
Curr Biol
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Meir, E.1
Von Dassow, G.2
Munro, E.3
Odell, G.M.4
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26
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0042031453
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The formation of sense organs in Drosophila: A logical analysis
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in press
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Ghysen A, Thomas R: The formation of sense organs in Drosophila: a logical analysis. BioEssays 2003, in press.
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(2003)
BioEssays
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Ghysen, A.1
Thomas, R.2
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27
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0037079015
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Computational approaches to cellular rhythms
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A recent review of the mathematical modelling of oscillating biological systems, including the gene networks involved in the control of circadian rhythms, by a pioneer of the field
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Goldbeter A. Computational approaches to cellular rhythms. Nature. 420:2002;238-245 A recent review of the mathematical modelling of oscillating biological systems, including the gene networks involved in the control of circadian rhythms, by a pioneer of the field.
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(2002)
Nature
, vol.420
, pp. 238-245
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Goldbeter, A.1
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