T. Eissing and F. Allgöwer, 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.

M. Article, T. Chaves, F. Eissing, and . Allgöwer, Dynamics on and of complex networks: applications to biology, computer science and the social sciences, pp.19-34, 2009.

M. Article, J. Chaves, and . Gouzé, Advances in the Theory of Control, Signals and Systems, with Physical Modelling, pp.241-253, 2010.

M. Article, E. Chaves, J. Farcot, R. Gouzé, H. G. Albert et al., 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.

U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, 2006.

E. Andrianantoandro, S. Basu, D. Karig, and R. Weiss, Synthetic biology: new engineering rules for an emerging discipline, Molecular Systems Biology, vol.299, pp.0-0, 2006.
DOI : 10.1038/msb4100073

D. Angeli, J. E. Ferrell, and E. D. Sontag, 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

D. Angeli and E. D. Sontag, 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

S. Azuma, E. Yanagisawa, and J. Imura, 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

A. Becskei and L. Serrano, Engineering stability in gene networks by autoregulation, Nature, vol.405, issue.6786, pp.590-593, 2000.
DOI : 10.1038/35014651

G. Bernot, J. Comet, A. Richard, and J. Guespin, 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

L. Calzone, L. Tournier, S. Fourquet, D. Thieffry, B. Zhivotovsky et al., 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

R. Casey, H. De-jong, and J. L. Gouzé, 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

M. Davidich and S. Bornholdt, 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

H. De-jong, J. Geiselmann, C. Hernandez, and M. Page, 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

S. Van-dongen, 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

R. Edwards, 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

R. Edwards and L. Glass, 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

T. Eissing, H. Conzelmann, E. D. Gilles, F. Allgöwer, E. Bullinger et al., 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

M. B. Elowitz and S. Leibler, A synthetic oscillatory network of transcriptional regulators, Nature, vol.403, issue.6767, pp.335-338, 2000.
DOI : 10.1038/35002125

F. Fages, S. Soliman, and N. Chabrier-rivier, 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

E. Farcot and J. L. Gouzé, 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

E. Farcot and J. L. Gouzé, 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

A. Fauré, A. Naldi, C. Chaouiya, and D. Thieffry, 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

M. Feinberg, Mathematical aspects of mass action kinetics, Chemical Reactor Theory: A Review, pp.1-78, 1977.

M. Feinberg, 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

W. Feller, An introduction to probability theory and its applications, 1970.

A. F. Filippov, Differential equations with discontinuous righthand-sides, 1988.
DOI : 10.1007/978-94-015-7793-9

T. S. Gardner, C. R. Cantor, and J. J. Collins, Construction of a genetic toggle switch in Escherichia coli, Nature, vol.403, pp.339-342, 2000.

F. Giannakopoulos and K. Pliete, 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

L. Glass, 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

L. Glass and S. A. Kauffman, 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

L. Glass and J. S. Pasternak, 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

A. G. Gonzalez, A. Naldi, L. S-`-anchez, D. Thieffry, and C. Chaouiya, 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

J. L. Gouzé and T. Sari, 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

L. C. Habets and J. Van-schuppen, 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

R. Heinrich and S. Schuster, The regulation of cellular systems, 1996.
DOI : 10.1007/978-1-4613-1161-4

A. Hoffmann, A. Levchenko, M. L. Scott, and D. Baltimore, 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

F. Horn and R. Jackson, General mass action kinetics Archive for Rational Mechanics and Analysis, pp.81-116, 1972.

H. Jamshidi, A. Siebert, and . Bockmayr, 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

S. C. Johnson, Hierarchical clustering schemes, Psychometrika, vol.58, issue.4, p.241254, 1967.
DOI : 10.1007/BF02289588

D. Jong, 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

J. Keener and J. Sneyd, Mathematical Physiology, 1998.
DOI : 10.1007/978-0-387-75847-3

H. K. Khalil, Nonlinear systems, 2002.

H. Kitano, Biological robustness, Nature Reviews Genetics, vol.37, issue.11, p.826, 2004.
DOI : 10.1038/nrg1471

F. Li, T. Long, Y. Lu, Q. Ouyang, and C. Tang, 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

S. Li, S. M. Assmann, and R. Albert, 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

T. Lipniacki, P. Paszek, A. R. Brasier, B. Luxon, and M. Kimmel, 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

J. A. Papin, T. Hunter, B. O. Palsson, and S. Subramaniam, 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

E. Remy, P. Ruet, and D. Thieffry, 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

A. Richard, 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

A. Richard, 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

D. Ropers, H. De-jong, M. Page, D. Schneider, and J. Geiselmann, 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

J. Saez-rodriguez, L. Simeoni, J. Lindquist, . Hemenway, . Bommhardt et al., 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

L. Sánchez and D. Thieffry, 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

R. Schlatter, K. Schmich, I. A. Vizcarra, P. Scheurich, and T. Sauter, 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

V. Sevim, X. Gong, and J. E. Socolar, 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

H. Siebert and A. Bockmayr, 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

M. Smoot, K. Ono, J. Ruscheinski, P. Wang, and T. Ideker, Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics, vol.27, issue.3, p.431432, 2011.
DOI : 10.1093/bioinformatics/btq675

E. D. Sontag, Mathematical Control Theory, 1998.
DOI : 10.1007/978-1-4684-0374-9

E. D. Sontag, 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

R. Thomas, 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

R. Thomas and R. D. Ari, Biological feedback, 1990.
URL : https://hal.archives-ouvertes.fr/hal-00087681

R. Thomas and M. Kaufman, 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

M. Tigges, T. T. Marquez-lago, J. Stelling, and M. Fussenegger, A tunable synthetic mammalian oscillator, Nature, vol.16, issue.7227, pp.309-312, 2009.
DOI : 10.1038/nature07616

P. Van-ham, 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

D. , D. Vecchio, A. J. Ninfa, and E. D. Sontag, Modular cell biology: Retroactivity and insulation, Molecular Systems Biology, vol.4, p.161, 2008.

D. , D. Vecchio, and E. D. Sontag, Synthetic biology: A systems engineering perspective, Control Theory and Systems Biology, pp.101-124, 2009.

U. Luxburg, A tutorial on spectral clustering, Statistics and Computing, vol.21, issue.1, pp.395-416, 2007.
DOI : 10.1007/s11222-007-9033-z

R. S. Wang, A. Saadatpour, and R. Albert, 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

G. Yagil and E. Yagil, 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

R. Zhang, M. V. Shah, J. Yang, S. B. Nyland, X. Liu et al., Network model of survival signaling in LGL leukemia, pp.16308-16313, 2008.

M. Chaves and M. Preto, 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

L. Tournier and M. Chaves, 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

M. Chaves, E. Farcot, and J. Gouzé, 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

G. Bernot, J. Comet, A. Richard, M. Chaves, J. Gouzé et al., 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. Carta, M. Chaves, and J. Gouzé, 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

D. A. Oyarzún, M. Chaves, and M. Hoffmeyer-zlotnik, 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

W. Abou-jaoudé, M. Chaves, and J. L. Gouzé, 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

M. Chaves and J. L. Gouzé, 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

I. Ndiaye, M. Chaves, and J. L. Gouzé, 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

M. Chaves, L. Tournier, and J. L. Gouzé, 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

J. L. Gouzé and M. Chaves, 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.

L. Tournier and M. Chaves, 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

T. Eissing, M. Chaves, and F. Allgöwer, 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

M. Chaves, T. Eißing, and F. Allgöwer, 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

M. Chaves, A. Sengupta, and E. D. Sontag, 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

A. Dayarian, M. Chaves, A. Sengupta, and E. D. Sontag, 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

M. Chaves and R. Albert, 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

M. Chaves, T. Eissing, and F. Allgöwer, 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

E. D. Sontag and M. Chaves, 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

M. Chaves, E. D. Sontag, and R. Albert, 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

M. Chaves, 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

M. Chaves, R. Albert, and E. D. Sontag, 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

M. Chaves, E. D. Sontag, and R. J. Dinerstein, 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

M. Chaves, E. D. Sontag, and R. J. Dinerstein, 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

M. Chaves, Observer design for a class of nonlinear systems, with applications to biochemical networks, 2003.

M. Chaves and E. D. Sontag, 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

C. Breindl, M. Chaves, and F. Allgöwer, 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. Carta, M. Chaves, and J. Gouzé, 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

C. Breindl, M. Chaves, J. Gouzé, and F. Allgöwer, 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

X. Li, M. Chaves, and J. Gouzé, Robust estimation for hybrid models of genetic networks, 2012 20th Mediterranean Conference on Control & Automation (MED), 2012.
DOI : 10.1109/MED.2012.6265629

M. Chaves and L. Tournier, 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

X. Li, J. L. Gouzé, and M. Chaves, 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

D. A. Oyarzún and M. Chaves, Global Gene Regulation in Metabolic Networks, Proc. 18 th IFAC World Congress, 2011.
DOI : 10.3182/20110828-6-IT-1002.01406

W. Abou-jaoudé, M. Chaves, and J. L. Gouzé, Mechanisms for coexistence of two limit cycles in a biochemical model, Proc. 18 th IFAC World Congress, 2011.

M. Chaves and J. L. Gouzé, 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

M. Chaves, E. Farcot, and J. L. Gouzé, 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

M. Chaves, Methods for qualitative analysis of genetic networks, Proc. 10 th European Control Conf. (ECC'09), pp.671-676, 2009.

L. Tournier and M. Chaves, Operational interactions in genetic networks: application to an apoptosis signalling pathway, Proc. 10 th European Control Conf. (ECC'09), pp.1889-1894, 2009.

I. Ndiaye, M. Chaves, and J. L. Gouzé, 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

I. Ndiaye, M. Chaves, and J. L. Gouzé, Un petit modèle d'interaction entre expression genétique et signalisation . In Réseaux d'interactions : analyse, modélisation et simulation, Integrative Post-Genomics, 2007.

S. Waldherr, T. Eissing, M. Chaves, and F. Allgöwer, 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

M. Chaves, E. D. Sontag, and R. Albert, 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

M. Chaves, 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

M. Chaves, T. Eißing, and F. Allgöwer, Identifying mechanisms for bistability in an apoptosis network . In Réseaux d'interactions : analyse, modélisation et simulation, Integrative Post-Genomics, 2006.

E. D. Sontag and M. Chaves, 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

M. Chaves, E. D. Sontag, and R. J. Dinerstein, Gains and optimal design in signaling pathways The Bahamas, Proc. 43 th Conf. Decision and Control Paradise Island, 2004.

S. Glavaski, M. Chaves, R. Day, P. Nag, A. Wiliams et al., Vehicle networks: achieving regular formation, Proceedings of the 2003 American Control Conference, 2003., 2003.
DOI : 10.1109/ACC.2003.1240477

M. Chaves, A parameter-robust observer as an application of iss techniques, Proc. 15 th Int. Symp. Mathematical Theory of Networks and Systems (MTNS'02), 2002.

M. Chaves and E. D. Sontag, Observers for chemical reaction networks, Proc. 6 th European Control Conf. (ECC'01), 2001.

M. Chaves and E. D. Sontag, An alternative observer for zero deficiency chemical networks, Proc. 5 th IFAC Symp. Nonlinear Control Systems (NOLCOS'01), 2001.

M. Chaves, E. D. Sontag, and A. Sengupta, Shape, size and robustness: feasible regions in the parameter space of biochemical networks, 2007.

M. Chaves, R. Day, L. Gomez-ramos, P. Nag, A. Wiliams et al., Vehicle networks: achieving regular formation Mathematical modeling in industry ? IMA Summer program for graduate students, 2002.

G. Bernot, J. Comet, A. Richard, M. Chaves, J. Gouzé et al., 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.