Regulation of apoptosis via the NFkB pathway: modeling and analysis Dynamics on and of complex networks: applications to biology, computer science and the social sciences, pp.19-34, 2009. ,
Dynamics on and of complex networks: applications to biology, computer science and the social sciences, pp.19-34, 2009. ,
Advances in the Theory of Control, Signals and Systems, with Physical Modelling, pp.241-253, 2010. ,
The topology of the regulatory interactions predicts the expression pattern of the Drosophila segment polarity genes, Bull. Math. Biology J. Theor. Biol, vol.75, issue.223, pp.967-9871, 2003. ,
An Introduction to Systems Biology: Design Principles of Biological Circuits, 2006. ,
Synthetic biology: new engineering rules for an emerging discipline, Molecular Systems Biology, vol.299, pp.0-0, 2006. ,
DOI : 10.1038/msb4100073
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems, Proceedings of the National Academy of Sciences, vol.101, issue.7, pp.1822-1827, 2004. ,
DOI : 10.1073/pnas.0308265100
Monotone control systems, IEEE Transactions on Automatic Control, vol.48, issue.10, pp.481684-1698, 2003. ,
DOI : 10.1109/TAC.2003.817920
URL : http://arxiv.org/abs/math/0206133
Controllability Analysis of Biosystems Based on Piecewise-Affine Systems Approach, IEEE Transactions on Automatic Control, vol.53, issue.Special Issue, pp.139-152, 2008. ,
DOI : 10.1109/TAC.2007.911316
Engineering stability in gene networks by autoregulation, Nature, vol.405, issue.6786, pp.590-593, 2000. ,
DOI : 10.1038/35014651
Application of formal methods to biological regulatory networks: extending Thomas??? asynchronous logical approach with temporal logic, Journal of Theoretical Biology, vol.229, issue.3, pp.339-347, 2004. ,
DOI : 10.1016/j.jtbi.2004.04.003
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement, PLoS Computational Biology, vol.2006, issue.3, p.1000702, 2010. ,
DOI : 10.1371/journal.pcbi.1000702.s008
URL : https://hal.archives-ouvertes.fr/inserm-00704979
Piecewise-linear Models of Genetic Regulatory Networks: Equilibria and their Stability, Journal of Mathematical Biology, vol.52, issue.1, pp.27-56, 2006. ,
DOI : 10.1007/s00285-005-0338-2
URL : https://hal.archives-ouvertes.fr/inria-00071250
Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast, PLoS ONE, vol.11, issue.12, p.1672, 2008. ,
DOI : 10.1371/journal.pone.0001672.t004
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks, Bioinformatics, vol.19, issue.3, pp.336-344, 2003. ,
DOI : 10.1093/bioinformatics/btf851
URL : https://hal.archives-ouvertes.fr/inria-00072325
Graph Clustering Via a Discrete Uncoupling Process, SIAM Journal on Matrix Analysis and Applications, vol.30, issue.1, p.121141, 2008. ,
DOI : 10.1137/040608635
Analysis of continuous-time switching networks, Physica D: Nonlinear Phenomena, vol.146, issue.1-4, pp.165-199, 2000. ,
DOI : 10.1016/S0167-2789(00)00130-5
Combinatorial explosion in model gene networks, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.10, issue.3, pp.691-704, 2000. ,
DOI : 10.1063/1.1286997
Bistability Analyses of a Caspase Activation Model for Receptor-induced Apoptosis, Journal of Biological Chemistry, vol.279, issue.35, pp.36892-36897, 2004. ,
DOI : 10.1074/jbc.M404893200
A synthetic oscillatory network of transcriptional regulators, Nature, vol.403, issue.6767, pp.335-338, 2000. ,
DOI : 10.1038/35002125
Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM, Journal of Biological Physics and Chemistry, vol.4, issue.2, pp.64-73, 2005. ,
DOI : 10.4024/2040402.jbpc.04.02
URL : https://hal.archives-ouvertes.fr/hal-01431345
A mathematical framework for the control of piecewise-affine models of gene networks, Automatica, vol.44, issue.9, pp.2326-2332, 2008. ,
DOI : 10.1016/j.automatica.2007.12.019
URL : https://hal.archives-ouvertes.fr/hal-00831803
Periodic Solutions of Piecewise Affine Gene Network Models with Non Uniform Decay Rates: The Case of a Negative Feedback Loop, Acta Biotheoretica, vol.4, issue.3???4, pp.429-455, 2009. ,
DOI : 10.1007/s10441-009-9086-9
URL : https://hal.archives-ouvertes.fr/hal-00831799
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle, Bioinformatics, vol.22, issue.14, pp.22-124, 2006. ,
DOI : 10.1093/bioinformatics/btl210
Mathematical aspects of mass action kinetics, Chemical Reactor Theory: A Review, pp.1-78, 1977. ,
Chemical reaction network structure and the stability of complex isothermal reactors???I. The deficiency zero and deficiency one theorems, Chemical Engineering Science, vol.42, issue.10, pp.2229-2268, 1987. ,
DOI : 10.1016/0009-2509(87)80099-4
An introduction to probability theory and its applications, 1970. ,
Differential equations with discontinuous righthand-sides, 1988. ,
DOI : 10.1007/978-94-015-7793-9
Construction of a genetic toggle switch in Escherichia coli, Nature, vol.403, pp.339-342, 2000. ,
Planar systems of piecewise linear differential equations with a line of discontinuity, Nonlinearity, vol.14, issue.6, p.16111632, 2001. ,
DOI : 10.1088/0951-7715/14/6/311
Combinatorial and topological methods in nonlinear chemical kinetics, The Journal of Chemical Physics, vol.63, issue.4, pp.1325-1335, 1975. ,
DOI : 10.1063/1.431518
The logical analysis of continuous, non-linear biochemical control networks, Journal of Theoretical Biology, vol.39, issue.1, pp.103-129, 1973. ,
DOI : 10.1016/0022-5193(73)90208-7
Stable oscillations in mathematical models of biological control systems, Journal of Mathematical Biology, vol.11, issue.3, pp.207-223, 1978. ,
DOI : 10.1007/BF02547797
GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks, Biosystems, vol.84, issue.2, pp.91-100, 2006. ,
DOI : 10.1016/j.biosystems.2005.10.003
URL : https://hal.archives-ouvertes.fr/hal-00088152
A class of piecewise linear differential equations arising in biological models, Dynamical Systems, vol.17, issue.4, pp.299-316, 2002. ,
DOI : 10.1080/1468936021000041681
A control problem for affine dynamical systems on a full-dimensional polytope, Automatica, vol.40, issue.1, pp.21-35, 2004. ,
DOI : 10.1016/j.automatica.2003.08.001
The regulation of cellular systems, 1996. ,
DOI : 10.1007/978-1-4613-1161-4
The Ikappa B-NF-kappa B Signaling Module: Temporal Control and Selective Gene Activation, Science, vol.298, issue.5596, pp.1241-1245, 2002. ,
DOI : 10.1126/science.1071914
General mass action kinetics Archive for Rational Mechanics and Analysis, pp.81-116, 1972. ,
Comparing Discrete and Piecewise Affine Differential Equation Models of Gene Regulatory Networks, Information Processign in Cells and Tissues, pp.17-24, 2012. ,
DOI : 10.1007/978-3-642-28792-3_3
Hierarchical clustering schemes, Psychometrika, vol.58, issue.4, p.241254, 1967. ,
DOI : 10.1007/BF02289588
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review, Journal of Computational Biology, vol.9, issue.1, pp.67-103, 2002. ,
DOI : 10.1089/10665270252833208
URL : https://hal.archives-ouvertes.fr/inria-00072606
Mathematical Physiology, 1998. ,
DOI : 10.1007/978-0-387-75847-3
Nonlinear systems, 2002. ,
Biological robustness, Nature Reviews Genetics, vol.37, issue.11, p.826, 2004. ,
DOI : 10.1038/nrg1471
The yeast cell-cycle network is robustly designed, Proceedings of the National Academy of Sciences, vol.101, issue.14, p.47814786, 2004. ,
DOI : 10.1073/pnas.0305937101
Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling, PLoS Biology, vol.34, issue.10, p.312, 2006. ,
DOI : 10.1371/journal.pbio.0040312.sd003
Mathematical model of NF-??B regulatory module, Journal of Theoretical Biology, vol.228, issue.2, pp.195-215, 2004. ,
DOI : 10.1016/j.jtbi.2004.01.001
Reconstruction of cellular signalling networks and analysis of their properties, Nature Reviews Molecular Cell Biology, vol.82, issue.2, pp.99-111, 2005. ,
DOI : 10.1038/nrm1570
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework, Advances in Applied Mathematics, vol.41, issue.3, p.41, 2008. ,
DOI : 10.1016/j.aam.2007.11.003
URL : https://hal.archives-ouvertes.fr/hal-00692086
Positive circuits and maximal number of fixed points in discrete dynamical systems, Discrete Applied Mathematics, vol.157, issue.15, pp.3281-3288, 2009. ,
DOI : 10.1016/j.dam.2009.06.017
Negative circuits and sustained oscillations in asynchronous automata networks, Advances in Applied Mathematics, vol.44, issue.4, pp.378-392, 2010. ,
DOI : 10.1016/j.aam.2009.11.011
Qualitative simulation of the carbon starvation response in Escherichia coli, Biosystems, vol.84, issue.2, pp.124-152, 2006. ,
DOI : 10.1016/j.biosystems.2005.10.005
URL : https://hal.archives-ouvertes.fr/hal-00171698
A Logical Model Provides Insights into T Cell Receptor Signaling, PLoS Computational Biology, vol.284, issue.8, p.163, 2007. ,
DOI : 10.1371/journal.pcbi.0030163.st002
A Logical Analysis of the Drosophila Gap-gene System, Journal of Theoretical Biology, vol.211, issue.2, pp.115-141, 2001. ,
DOI : 10.1006/jtbi.2001.2335
ON/OFF and Beyond - A Boolean Model of Apoptosis, PLoS Computational Biology, vol.122, issue.12, p.1000595, 2009. ,
DOI : 10.1371/journal.pcbi.1000595.s007
Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator, PLoS Computational Biology, vol.253, issue.7, p.1000842, 2010. ,
DOI : 10.1371/journal.pcbi.1000842.t001
Temporal constraints in the logical analysis of regulatory networks, Theoretical Computer Science, vol.391, issue.3, pp.258-275, 2008. ,
DOI : 10.1016/j.tcs.2007.11.010
Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics, vol.27, issue.3, p.431432, 2011. ,
DOI : 10.1093/bioinformatics/btq675
Mathematical Control Theory, 1998. ,
DOI : 10.1007/978-1-4684-0374-9
Some new directions in control theory inspired by systems biology, Systems Biology, vol.1, issue.1, pp.1-18, 2004. ,
DOI : 10.1049/sb:20045006
Boolean formalization of genetic control circuits, Journal of Theoretical Biology, vol.42, issue.3, pp.563-585, 1973. ,
DOI : 10.1016/0022-5193(73)90247-6
Biological feedback, 1990. ,
URL : https://hal.archives-ouvertes.fr/hal-00087681
Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.1, pp.170-179, 2001. ,
DOI : 10.1063/1.1350439
A tunable synthetic mammalian oscillator, Nature, vol.16, issue.7227, pp.309-312, 2009. ,
DOI : 10.1038/nature07616
How to deal with variables with more than two levels, Lecture Notes in Biomathematics, vol.29, pp.326-343, 1979. ,
DOI : 10.1007/978-3-642-49321-8_15
Modular cell biology: Retroactivity and insulation, Molecular Systems Biology, vol.4, p.161, 2008. ,
Synthetic biology: A systems engineering perspective, Control Theory and Systems Biology, pp.101-124, 2009. ,
A tutorial on spectral clustering, Statistics and Computing, vol.21, issue.1, pp.395-416, 2007. ,
DOI : 10.1007/s11222-007-9033-z
Boolean modeling in systems biology: an overview of methodology and applications, Physical Biology, vol.9, issue.5, p.55001, 2012. ,
DOI : 10.1088/1478-3975/9/5/055001
On the Relation between Effector Concentration and the Rate of Induced Enzyme Synthesis, Biophysical Journal, vol.11, issue.1, pp.11-27, 1971. ,
DOI : 10.1016/S0006-3495(71)86192-1
Network model of survival signaling in LGL leukemia, pp.16308-16313, 2008. ,
Hierarchy of models: From qualitative to quantitative analysis of circadian rhythms in cyanobacteria, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.23, issue.2, p.25113, 2013. ,
DOI : 10.1063/1.4810922
URL : https://hal.archives-ouvertes.fr/hal-00850373
Interconnection of asynchronous Boolean networks, asymptotic and transient dynamics, Automatica, vol.49, issue.4, pp.884-893, 2013. ,
DOI : 10.1016/j.automatica.2013.01.015
URL : https://hal.archives-ouvertes.fr/hal-00848450
Probabilistic Approach for Predicting Periodic Orbits in Piecewise Affine Differential Models, Bulletin of Mathematical Biology, vol.228, issue.4, pp.967-987, 2013. ,
DOI : 10.1007/s11538-012-9773-6
URL : https://hal.archives-ouvertes.fr/hal-00828847
Modeling and Analysis of Gene Regulatory Networks, Modeling in Computational Biology and Biomedicine, pp.47-80, 2013. ,
DOI : 10.1007/978-3-642-31208-3_2
URL : https://hal.archives-ouvertes.fr/hal-00848394
A Simple Model to Control Growth Rate of Synthetic E. coli during the Exponential Phase: Model Analysis and Parameter Estimation, CMSB 2012, pp.107-126, 2012. ,
DOI : 10.1007/978-3-642-33636-2_8
URL : https://hal.archives-ouvertes.fr/hal-00848400
Multistability and oscillations in genetic control of metabolism, Journal of Theoretical Biology, vol.295, pp.139-153, 2012. ,
DOI : 10.1016/j.jtbi.2011.11.017
A Theoretical Exploration of Birhythmicity in the p53-Mdm2 Network, PLoS ONE, vol.426, issue.2, p.17075, 2011. ,
DOI : 10.1371/journal.pone.0017075.s012
Exact control of genetic networks in a qualitative framework: The bistable switch example, Automatica, vol.47, issue.6, pp.1105-1112, 2011. ,
DOI : 10.1016/j.automatica.2011.01.071
URL : https://hal.archives-ouvertes.fr/hal-00848406
Oscillations induced by different timescales in signal transduction modules regulated by slowly evolving protein???protein interactions, IET Systems Biology, vol.4, issue.4, pp.263-276, 2010. ,
DOI : 10.1049/iet-syb.2009.0020
Comparing Boolean and Piecewise Affine Differential Models for Genetic Networks, Acta Biotheoretica, vol.11, issue.2, pp.217-232, 2010. ,
DOI : 10.1007/s10441-010-9097-6
URL : https://hal.archives-ouvertes.fr/hal-00847281
Piecewise affine models of regulatory genetic networks: review and probabilistic interpretation Advances in the Theory of Control, Signals and Systems, with Physical Modelling, Lecture Notes in Control and Information Sciences, vol.470, pp.241-253, 2010. ,
Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics, Journal of Theoretical Biology, vol.260, issue.2, pp.196-209, 2009. ,
DOI : 10.1016/j.jtbi.2009.06.006
URL : https://hal.archives-ouvertes.fr/hal-00554625
Live and let die???A systems biology view on cell death, Computers & Chemical Engineering, vol.33, issue.3, pp.583-589, 2009. ,
DOI : 10.1016/j.compchemeng.2008.10.014
Regulation of Apoptosis via the NF??B Pathway: Modeling and Analysis, Dynamics on and of complex networks: applications to biology, computer science and the social sciences, Modeling and Simulation in Science, Engineering and Technology, pp.19-34, 2009. ,
DOI : 10.1007/978-0-8176-4751-3_2
Geometry and topology of parameter space: investigating measures of robustness in regulatory networks, Journal of Mathematical Biology, vol.1, issue.10, pp.315-358, 2009. ,
DOI : 10.1007/s00285-008-0230-y
Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks, PLoS Computational Biology, vol.110, issue.1, p.1000256, 2009. ,
DOI : 10.1371/journal.pcbi.1000256.t002
Studying the effect of cell division on expression patterns of the segment polarity genes, Journal of The Royal Society Interface, vol.68, issue.1-2, pp.71-84, 2008. ,
DOI : 10.1016/S0925-4773(97)00150-0
Bistable Biological Systems: A Characterization Through Local Compact Input-to-State Stability, IEEE Transactions on Automatic Control, vol.53, issue.Special Issue, pp.87-100, 2008. ,
DOI : 10.1109/TAC.2007.911328
Exact computation of amplification for a class of nonlinear systems arising from cellular signaling pathways, Automatica, vol.42, issue.11, pp.1987-1992, 2006. ,
DOI : 10.1016/j.automatica.2006.06.011
Methods of robustness analysis for Boolean models of gene control networks, IEE Proceedings - Systems Biology, vol.153, issue.4, pp.154-167, 2006. ,
DOI : 10.1049/ip-syb:20050079
Input-to-State Stability of Rate-Controlled Biochemical Networks, SIAM Journal on Control and Optimization, vol.44, issue.2, pp.704-727, 2005. ,
DOI : 10.1137/S0363012903437964
Robustness and fragility of Boolean models for genetic regulatory networks, Journal of Theoretical Biology, vol.235, issue.3, pp.431-449, 2005. ,
DOI : 10.1016/j.jtbi.2005.01.023
Steady-states of receptor???ligand dynamics: a theoretical framework, Journal of Theoretical Biology, vol.227, issue.3, pp.413-428, 2004. ,
DOI : 10.1016/j.jtbi.2003.11.019
Optimal Length and Signal Amplification in Weakly Activated Signal Transduction Cascades, The Journal of Physical Chemistry B, vol.108, issue.39, pp.15311-15320, 2004. ,
DOI : 10.1021/jp048935f
Observer design for a class of nonlinear systems, with applications to biochemical networks, 2003. ,
State-estimators for Chemical Reaction Networks of Feinberg-Horn-Jackson Zero Deficiency Type, European Journal of Control, vol.8, issue.4, pp.343-359, 2002. ,
DOI : 10.3166/ejc.8.343-359
A linear reformulation of Boolean optimization problems and its application to the problem of estimating the structure of gene regulation networks, Proc. 52 th Conf. Decision and Control, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00850371
A class of Switched Piecewise Quadratic Systems for coupling gene expression with growth rate in bacteria, Proc. 9 th IFAC Symp. Nonlinear Control Systems (NOLCOS'13), 2013. ,
DOI : 10.3182/20130904-3-FR-2041.00140
URL : https://hal.archives-ouvertes.fr/hal-00850372
Structure estimation for unate Boolean models of gene regulation networks, Proc. 16 th IFAC Symposium on System Identification, 2012. ,
DOI : 10.3182/20120711-3-BE-2027.00278
URL : https://hal.archives-ouvertes.fr/hal-00848397
Robust estimation for hybrid models of genetic networks, 2012 20th Mediterranean Conference on Control & Automation (MED), 2012. ,
DOI : 10.1109/MED.2012.6265629
Predicting the asymptotic dynamics of large biological networks by interconnections of Boolean modules, IEEE Conference on Decision and Control and European Control Conference, 2011. ,
DOI : 10.1109/CDC.2011.6160454
URL : https://hal.archives-ouvertes.fr/hal-00848407
An observer for a genetic network model with boolean observations, Proc. 50 th Conf. Decision and Control and European Control Conf, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00647317
Global Gene Regulation in Metabolic Networks, Proc. 18 th IFAC World Congress, 2011. ,
DOI : 10.3182/20110828-6-IT-1002.01406
Mechanisms for coexistence of two limit cycles in a biochemical model, Proc. 18 th IFAC World Congress, 2011. ,
Qualitative Control of Genetic Networks: the Bistable Switch Example, Proc. 8 th IFAC Symp. Nonlinear Control Systems (NOLCOS'10), 2010. ,
DOI : 10.3182/20100901-3-IT-2016.00166
URL : https://hal.archives-ouvertes.fr/hal-00847280
Transition probabilities for piecewise affine models of genetic networks, Proc. 19 th Int. Symp. Mathematical Theory of Networks and Systems (MTNS'10), 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00831793
Methods for qualitative analysis of genetic networks, Proc. 10 th European Control Conf. (ECC'09), pp.671-676, 2009. ,
Operational interactions in genetic networks: application to an apoptosis signalling pathway, Proc. 10 th European Control Conf. (ECC'09), pp.1889-1894, 2009. ,
Study and parameter identification of a model coupling cell signaling and gene expression, 2008 16th Mediterranean Conference on Control and Automation ,
DOI : 10.1109/MED.2008.4602118
Un petit modèle d'interaction entre expression genétique et signalisation . In Réseaux d'interactions : analyse, modélisation et simulation, Integrative Post-Genomics, 2007. ,
BISTABILITY PRESERVING MODEL REDUCTION IN APOPTOSIS, Proc. 10 th IFAC Symp. on Computer Applications in Biotechnology (CAB'07), pp.327-332, 2007. ,
DOI : 10.3182/20070604-3-MX-2914.00072
Structure and timescale analysis in genetic regulatory networks, Proceedings of the 45th IEEE Conference on Decision and Control, pp.2358-2363, 2006. ,
DOI : 10.1109/CDC.2006.376804
Stability of Rate-Controlled Zero-Deficiency Networks, Proceedings of the 45th IEEE Conference on Decision and Control, pp.5766-5771, 2006. ,
DOI : 10.1109/CDC.2006.377577
Identifying mechanisms for bistability in an apoptosis network . In Réseaux d'interactions : analyse, modélisation et simulation, Integrative Post-Genomics, 2006. ,
COMPUTATION OF AMPLIFICATION FOR SYSTEMS ARISING FROM CELLULAR SIGNALING PATHWAYS, Proc. 16 th IFAC World Congress, 2005. ,
DOI : 10.3182/20050703-6-CZ-1902.02205
Gains and optimal design in signaling pathways The Bahamas, Proc. 43 th Conf. Decision and Control Paradise Island, 2004. ,
Vehicle networks: achieving regular formation, Proceedings of the 2003 American Control Conference, 2003., 2003. ,
DOI : 10.1109/ACC.2003.1240477
A parameter-robust observer as an application of iss techniques, Proc. 15 th Int. Symp. Mathematical Theory of Networks and Systems (MTNS'02), 2002. ,
Observers for chemical reaction networks, Proc. 6 th European Control Conf. (ECC'01), 2001. ,
An alternative observer for zero deficiency chemical networks, Proc. 5 th IFAC Symp. Nonlinear Control Systems (NOLCOS'01), 2001. ,
Shape, size and robustness: feasible regions in the parameter space of biochemical networks, 2007. ,
Vehicle networks: achieving regular formation Mathematical modeling in industry ? IMA Summer program for graduate students, 2002. ,
Some of them are freely accessible. Preliminary versions can also be found in my webpage, http://www-sop.inria. fr/members/Madalena.Chaves. The book chapter Modeling and analysis of gene regulatory networks, Modeling in Computational Biology and Biomedicine, pp.47-80978, 2013. ,