Publications (M. Chaves)

Links to:
And also:
Journal articles and book chapters
  1. O. Burckard and M. Chaves. Analytic solutions for the circadian oscillator characterize cycle dynamics and its robustnesss, submitted preprint, 2024.

  2. N. Augier, M. Chaves, and J.-L. Gouzé. Weak synchronization and convergence in coupled genetic regulatory networks: Applications to damped oscillators and multistable circuits, International Journal of Robust and Nonlinear Control, 33(9), pp. 673-688, 2023 (Preprint).

  3. N. Augier, M. Chaves, and J.-L. Gouzé. Qualitative control strategies for synchronization of bistable gene regulatory networks, IEEE Transactions on Automatic Control, 68(2), pp. 673-688, 2023. (Preprint).

  4. O. Burckard, M. Teboul, F. Delaunay, and M. Chaves. Cycle dynamics and synchronization in a coupled network of peripheral circadian clocks, Interface Focus, 12: 20210087, 2022. (Preprint).

  5. M. Chaves, L.C. Gomes-Pereira, and J. Roux. Two-level modeling approach to identify the regulatory dynamics capturing drug response heterogeneity in single-cells, Scientific Reports, 11, pp. 20809, 2021.

  6. M. Chaves and H. de Jong. Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits. In: Menolascina F. (eds) Synthetic Gene Circuits. Methods in Molecular Biology, vol 2229, pp. 1-40. Humana, New York, NY, 2021.

  7. E. Firippi and M. Chaves. Topology-induced dynamics in a network of synthetic oscillators with piecewise affine approximation, Chaos, 30, pp. 113128, 2020. https://doi.org/10.1063/5.0020670 2020.

  8. S. Almeida, M. Chaves, and F. Delaunay. Cell cycle period control through modulation of clock inputs, Journal of Bioinformatics and Computational Biology, 18(3), pp. 2040006, 2020.

  9. S. Almeida, M. Chaves, and F. Delaunay. Control of Synchronization Ratios in Clock/Cell Cycle Coupling by Growth Factors and Glucocorticoids, Royal Society Open Science, 7, pp. 192054, 2020.

  10. S. Almeida, M. Chaves, and F. Delaunay. Transcription-based circadian mechanism controls the duration of molecular clock states in response to signaling inputs, J. Theoretical Biology, 484, pp. 110015, 2020. Available through HAL archives.

  11. M. Chaves, D.A. Oyarzún, and J.-L. Gouzé. Analysis of a genetic-metabolic oscillator with piecewise linear models, J. Theoretical Biology, 462, pp. 259-269, 2019. Online.

  12. M. Chaves and D.A. Oyarzún. Dynamics of complex feedback architectures in metabolic pathways, Automatica, 99, pp. 323-332, 2019.

  13. M. Chaves and D. Figueiredo and M.A. Martins. Boolean dynamics revisited through feedback interconnections, Natural Computing, 19(1), pp. 29-49, 2020.Online (2018).

  14. M. Chaves and L. Tournier. Analysis tools for interconnected Boolean networks with biological applications, Frontiers in Physiology, 9, pp. 586, 2018.

  15. C. Poignard, M. Chaves, and J.-L. Gouzé. A stability result for periodic solutions of some nonmonotonic smooth negative feedback systems, SIAM J. Applied Dynamical Systems, 17(2), pp. 1091-1116, 2018.

  16. D. Figueiredo, M.A. Martins, and M. Chaves. Applying differential dynamic logic to reconfigurable networks, Mathematical Biosciences, 291, pp. 10-20, 2017.

  17. C. Poignard, M. Chaves and J.-L. Gouzé. Periodic oscillations for nonmonotonic smooth negative feedback circuits, SIAM J. Applied Dynamical Systems, 15(1), pp. 257-286, 2016.

  18. D.A. Oyarzún and M. Chaves. Design of a bistable switch to control cellular uptake, J. Royal Society Interface, 12(113), pp. 20150618, 2015.

  19. A. Carta, M. Chaves, and J.-L. Gouzé. Continuous-switch piecewise quadratic models of biological networks: application to bacterial growth, Automatica, 61, pp. 164-172, 2015.

  20. M. Chaves and A. Carta. Attractor computation using interconnected Boolean networks: testing growth rate models in E. Coli, Theoretical Computer Science, 599, pp. 47-63, 2015.

  21. W. Abou-Jaoudé, M. Chaves and J.-L. Gouzé. Links between topology of the transition graph and limit cycles in a two-dimensional piecewise affine biological model, J. Mathematical Biology, 69(6-7), pp.1461-1495, 2014.

  22. M. Chaves and M. Preto. Hierarchy of models: from qualitative to quantitative analysis of circadian rhythms in cyanobacteria, Chaos (Focus issue), 23(2), pp. 025113, 2013.

  23. L. Tournier and M. Chaves. Interconnection of asynchronous Boolean networks, asymptotic and transient dynamics, Automatica, 49(4), pp. 884-893, 2013. DOI.

  24. M. Chaves, E. Farcot, and J.-L. Gouzé. Probabilistic approach for predicting periodic orbits in piecewise affine differential models, Bull. Math. Biology, 75(6), pp. 967-987, 2013, DOI.

  25. G. Bernot, J.-P. Comet, A. Richard, M. Chaves, J.-L. Gouzé, and F. Dayan. Modeling and analysis of gene regulatory networks. In "Modeling in Computational Biology and Biomedicine", F. Cazals and P. Kornprobst Eds, Springer-Verlag Heidelberg (2013), pp. 47-80 (available for download from Springer's website, as Sample pages).

  26. A. Carta, M. Chaves, and J.-L. Gouzé. A simple model to control growth rate of synthetic E. coli during the exponential phase: model analysis and parameter estimation. In "CMBS 2012", D. Gilbert and M. Heiner Eds, Springer-Verlag Heidelberg (2012), Lecture Notes in Computer Science 7605, pp. 107-126.

  27. D.A. Oyarzún, M. Chaves, and M. Hoffmeyer-Zlotnik. Multistability and oscillations in genetic control of metabolism, J. Theoretical Biology, 295(2012), pp. 139-153. (INRIA research report available on HAL archives).

  28. W. Abou-Jaoudé, M. Chaves, and J.-L. Gouzé. A theoretical exploration of birhythmicity in the p53-Mdm2 network. PLoS ONE, 6(2)(2011), pp. e17075. (INRIA research report available on HAL archives).

  29. M. Chaves and J.-L. Gouzé. Exact control of genetic networks in a qualitative framework: the bistable switch example. Automatica, 47(2011), pp. 1105-1112. (INRIA research report available on HAL archives).

  30. M. Chaves and J.-L. Gouzé. Piecewise affine models of regulatory genetic networks: review and probabilistic interpretation. In "Advances in the Theory of Control, Signals and Systems, with Physical Modelling", J. Levine and P. Mullhaupt Eds, Springer-Verlag Heidelberg, LNCIS 470(2010), pp.241-253.

  31. M. Chaves, L. Tournier and J.-L. Gouzé. Comparison between Boolean and piecewise affine differential models for genetic networks. Acta Biotheoretica, 58(2)(2010), pp. 217-232. Supplementary material available. (INRIA research report available on HAL archives).

  32. 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, 4(4)(2010), pp. 263-276. Supplementary material available.

  33. L. Tournier and M. Chaves. Uncovering operational interactions in genetic networks using asynchronous boolean dynamics. J. Theoretical Biology, 260(2)(2009), pp. 196-209. (INRIA research report available on HAL archives).

  34. M. Chaves, A. Sengupta and E.D. Sontag. Geometry and topology of parameter space: investigating measures of robustness in regulatory networks. J. Mathematical Biology, 59(3)(2009), pp. 315-358.

  35. A. Dayarian, M. Chaves, E.D. Sontag and A. Sengupta . Shape, size and robustness: feasible regions in the parameter space of biochemical networks. PLoS Computational Biology, 5(1)(2009), pp. e1000256.

  36. T. Eissing, M. Chaves and F. Allgöwer. Live and let die - a systems biology view on cell death. Computers & Chemical Engineering, 33(3)(2009), pp. 583-589.

  37. M. Chaves, T. Eissing and F. Allgöwer. Regulation of apoptosis via the NFkB pathway: modeling and analysis. In "Dynamics on and of complex networks: applications to biology, computer science and the social sciences", N. Ganguly, A. Deutsch and A. Mukherjee (Eds.), Birkhauser Boston, 2009, pp. 19-34.
    (Available here, as sample chapter.)

  38. M. Chaves, T. Eissing and F. Allgower. Bistable biological systems: a characterization through local compact input-to-state stability. IEEE Trans. Automatic Control, 53(1)(2008), pp. 87-100. (Special issue Systems Biology.)

  39. M. Chaves and R. Albert. Studying the effect of cell division on expression patterns of the segment polarity genes. J. Royal Society Interface, 5(S1)(2008), pp. S71-S84.

  40. E.D. Sontag and M. Chaves. Exact computation of amplification for a class of nonlinear systems arising from cellular signaling pathways. Automatica, 42(11)(2006), pp. 1987-1992.
    (A previous version is available at http://arXiv.org/ as q-bio.QM/0408012.)

  41. M. Chaves, E.D. Sontag and R. Albert. Methods of robustness analysis for Boolean models of gene control networks. IEE Proc. Systems Biology, 153(4)(2006), pp. 154-167.
    (A preliminary version is available at http://arXiv.org/  as q-bio.MN/0605004.)

  42. M. Chaves. Input-to-state stability of rate-controlled biochemical networks. SIAM J. Control and Optimization, 44(2)(2005), pp. 704-727.

  43. M. Chaves, R. Albert and E.D. Sontag. Robustness and fragility of Boolean models for genetic regulatory networks. J. Theoretical Biology, 235(3)(2005), pp. 431-449.
    (A preliminary version is available at http://arXiv.org/ as q-bio.MN/0501037.)

  44. M. Chaves, E.D. Sontag and R.J. Dinerstein. Optimal length and signal amplification in weakly activated signal transduction cascades. J. Physical Chemistry B 108(39)(2004), pp. 15311-15320.
    (A preliminary version is available at http://arXiv.org/ as math.OC/0311357. Also some supplementary material.)

  45. M. Chaves, E.D. Sontag and R.J. Dinerstein. Steady-states of receptor--ligand dynamics: a theoretical framework. J. Theoretical Biology 227(3)(2004), pp. 413-428.

  46. M. Chaves and E.D. Sontag. State-estimators for chemical reaction networks of Feinberg-Horn-Jackson zero deficiency type. European J. Control 8(4)(2002), pp. 343-359.

Conference proceedings - peer reviewed
  1. G. Fiandaca, M. Péré, J. Roux,and M. Chaves Tolerant vs. Sensitive: deciphering heterogeneous cellular response via mathematical modeling of single-cell dynamics. Presentation at a Mini-symposium, 13th European Conference on Mathematical and Theoretical Biology (ECMTB24), Toledo, Spain, July 2024.

  2. [Poster] O. Burckard and M Chaves. Benchmark for for quantitative characterization of circadian clock models. 21st Int Conf Computational Methods in Systems Biology (CMSB 2023), Luxemburg, September 2023.

  3. [Poster] O. Burckard and M. Chaves. Coupling and synchronization of peripheral circadian clocks. 5th Labex Signalife Meeting, Nice, France, November 2022.

  4. [Poster] M. Péré, A. Chalabi, B. Bian, D. Oyarzún, M. Chaves, J. Roux. Integrating machine learning methods to single cell signaling analyses increases throughput and accuracy for target identification in immuno-oncology. 5th Labex Signalife Meeting, Nice, France, November 2022.

  5. M Péré, D. Oyarzún, J. Roux and M. Chaves. Modeling Isogenic Cancer Cell Response upon Varying TRAIL Stimulations to Decipher the Kinetic Determinants of Cell Fate Decision. 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE 2022), Boston, USA, August 2022.

  6. N. Augier, M. Chaves, and J.-L. Gouzé. Control for Synchronization of Bistable Piecewise Affine Genetic Regulatory Networks. 6th IFAC Hybrid Conference on Analysis and Control of Chaotic Systems (CHAOS 2021), Catania, Italy, September 2021.

  7. [Poster] M. Péré, M. Chaves, and J. Roux. TRAIL-induced apoptosis signaling modeling identifies dynamic signs of efficient cell death initiation, enabling an early prediction of the cell response. 19th Int Conf Computational Methods in Systems Biology (CMSB 2021), Bordeaux, France, September 2021.

  8. O. Diop, M. Chaves, and L. Tournier. Qualitative analysis of mammalian circadian oscillations: cycle dynamics and robustness. 18th Int Conf Computational Methods in Systems Biology (CMSB 2020), Germany, September 2020.

  9. M Péré, M. Chaves, and J. Roux. Core models of receptor reactions evaluate basic pathway designs enabling heterogeneous commitments to apoptosis. 18th Int Conf Computational Methods in Systems Biology (CMSB 2020), Germany, September 2020.

  10. L.C. Gomes Pereira, M. Chaves, and J. Roux. A Model of Apoptosis Receptor Reactions to Study Cell Fate Decision. 28th Mediterranean Conference on Control and Automation (MED'2020), France, September 2020.

  11. S. Almeida, M. Chaves, and F. Delaunay. Period control of the coupled clock and cell cycle systems. 10th Int. Conf. Computational Systems-Biology and Bioinformatics (CSBio 2019), Nice, France, December 2019.

  12. M. Chaves, L. Scardovi, and E. Firippi Coupling and synchronization of piecewise linear genetic regulatory systems. 58th IEEE Conference on Decision and Control (CDC19), Nice, France, December 2019, pg. 2826-2831.

  13. E. Firippi and M. Chaves. Period-control in a coupled system of two genetic oscillators for synthetic biology. IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE 2019), Valencia, Spain, October 2019.

  14. D. Figueiredo, E. Rocha, M.A. Martins, and M. Chaves. rPrism - A software for reactive weighted state transition models. 6th Int. Workshop on Hybrid Systems and Biology (HSB19), Prague, Czech Republic, April 2019. In Lecture Notes in Computer Science (LNCS), vol. 11705, pp. 165-174, 2019.

  15. [Poster] L. Pereira, P. Hofman, J.-L. Gouzé, M. Chaves, and J. Roux. Modelling cell-death drug response heterogeneity at the receptor layer. European Conference on Mathematical and Theoretical Biology (ECMTB 2018), Lisbon, Portugal, July 2018.

  16. S. Almeida, M. Chaves, F. Delaunay, and C. Feillet. A comprehensive reduced model of the mammalian cell cycle. Proc. 20th IFAC World Congress, Toulouse, France, Jul. 2017. IFAC-PapersOnLine, 50(1), pp. 12617-12622, 2017.

  17. [Poster] L. Pereira, M. Meyer, P. Hofman, J.-L. Gouzé, M. Chaves, and J. Roux. Modeling cell death dynamics at the receptor level. CompSysBio, Advanced Lecture Course on Computational Systems Biology, Aussois, France, Mar. 2017.

  18. M. Chaves, J.-L. Gouzé. 2D piecewise affine models approximate real continuous dynamics up to invariant sets. Proc. 10th IFAC Symp. on Nonlinear Control Systems (NOLCOS'16), Monterrey, USA, Aug. 2016. IFAC-PapersOnLine, 49(18), pp. 1060-1065, 2016.

  19. C. Poignard, M. Chaves, J.-L. Gouzé. Oscillations for non monotonic smooth negative feedback systems bounded by two hybrid systems. Conference in Open problems in Nonsmooth Dynamics, CRM Barcelona, Spain, Fev. 2016 (abstract).

  20. [Poster] S. Almeida, M. Chaves, and J.-L. Gouzé, F. Delaunay. Modeling and coupling biorhythms. 2nd Labex SIGNALIFE Meeting, Nice, France, Nov. 2015.

  21. M. Chaves and M. Preto. Hybrid models for the interconnection of circadian and genetic cycles in cyanobacteria. Proc. Int. Symp. Mathematical Theory of Networks and Systems (MTNS'14), Groningen, The Netherlands, Jul. 2014 (extended abstract).

  22. C. Breindl, M. Chaves, and F. Allgower. A linear reformulation of Boolean optimization problems and its application to the problem of estimating the structure of gene regulation networks. Proc. 52nd IEEE Conference on Decision and Control (CDC'13), Florence, Italy, Dec. 2013.

  23. A. Carta, M. Chaves, and J.-L. Gouzé. A class of Switched Piecewise Quadratic Systems for coupling gene expression with growth rate in bacteria. Proc. 9th IFAC Symp. on Nonlinear Control Systems (NOLCOS'13), Toulouse, France, Sep 2013.

  24. C. Breindl, M. Chaves, J.-L. Gouzé, and F. Allgower. Structure Estimation for Unate Boolean Models of Gene Regulation Networks. Proc. 16th IFAC Symp. on System Identification, Brussels, Belgium, Jul. 2012.

  25. Xiao-Dong Li, M. Chaves, and J.-L. Gouzé. Robust estimation for hybrid models of genetic networks. Proc. 20th Mediterranean Conf. on Control and Automation, Barcelona, Spain, Jul 2012.

  26. M. Chaves and L. Tournier. Predicting the asymptotic dynamics of large biological networks by interconnections of Boolean modules . Proc. 50th IEEE Conf. Decision and Control and European Control Conf. (CDC/ECC'11), Orlando, USA, Dec. 2011.

  27. Xiao-Dong Li, J.-L. Gouzé and M. Chaves. An observer for a genetic network model with Boolean observations. Proc. 50th IEEE Conf. Decision and Control and European Control Conf. (CDC/ECC'11), Orlando, USA, Dec. 2011.

  28. D.A. Oyarzún and M. Chaves. Global gene regulation in metabolic networks. Proc. 18th IFAC World Congress, Milan, Italy, Aug. 2011.

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

  30. M. Chaves and J.-L. Gouzé. Qualitative control of genetic networks: the bistable switch example. Proc. IFAC Nonlinear Control Systems Symp. (NOLCOS'10), Bologna, Italy, Sep. 2010.

  31. M. Chaves, E. Farcot, and J.-L. Gouzé. Transition probabilities for piecewise affine models of genetic networks. Proc. Int. Symp. Mathematical Theory of Networks and Systems (MTNS'10), Budapest, Hungary, Jul. 2010.

  32. M. Chaves. Methods for qualitative analysis of genetic networks. Proc. 10th European Control Conference (ECC'09), Budapest, Hungary, Aug. 2009, MoB2.4, pp. 671-676 (mini-tutorial).

  33. L. Tournier and M. Chaves. Operational interactions in genetic networks: application to an apoptosis signalling pathway. Proc. 10th European Control Conference (ECC'09), Budapest, Hungary, Aug. 2009, TuA5.6, pp. 1889-1894.

  34. I. Ndiaye, M. Chaves, and J.-L. Gouzé. Study and parameter identification of a model coupling cell signaling and gene expression. Proc. 16th Mediterranean Conf. Control and Automation (MED'08), Ajaccio, France, Jun. 2008, pp. 1711-1716.

  35. I. Ndiaye, M. Chaves, and J.-L. Gouzé. Un petit modele d'interaction entre expression genetique et signalisation. Journee thematique "Reseaux d'Interactions: Analyse, Modelisation et Simulation" (RIAMS'07), Lyon, France, Nov. 2007.

  36. [Poster] M.Chaves, A.Dayarian, A. Sengupta and E.D. Sontag. Geometry, functionality and robustness: exploring the parameter space of the segment polarity network. The 8th Int. Conf. Systems Biology, Long Beach, CA, Oct. 2007.

  37. S. Waldherr, T. Eissing, M. Chaves and F. Allgöwer. Bistability preserving model reduction in apoptosis. Proc. 10th IFAC Symp. on Computer Applications in Biotechnology (CAB'07), Cancun, Mexico, Jun. 2007, vol. 2, pp. 327-332.

  38. M. Chaves. Stability of rate-controlled zero-deficiency networks. Proc. Conf. Decision and Control (CDC'06), San Diego, CA, USA, Dec. 2006, pp. 5766-5771.

  39. M. Chaves, E.D. Sontag and R. Albert. Structure and timescale analysis in genetic regulatory networks. Proc. Conf. Decision and Control (CDC'06), San Diego, CA, USA, Dec. 2006, pp. 2358-2363.

  40. M. Chaves, T. Eissing and F. Allgöwer. Identifying mechanisms for bistability in an apoptosis network. Journee thematique "Reseaux d'Interactions: Analyse, Modelisation et Simulation" (RIAMS'06), Lyon, France, Nov. 2006.

  41. [poster] S. Waldherr, T. Eissing, M. Chaves and F. Allgower. Preservation of bistability in the reduction of an apoptosis model. Genomes to Systems 2006 Conference, Manchester International Convention Centre, U.K., 22-24th March 2006.

  42. E.D. Sontag and M. Chaves. Computation of amplification for systems arising from cellular signaling pathways. Proc. 16th IFAC World Congress, Prague, Czech Republic, July 2005.
    (A version is available at http://arXiv.org/  as q-bio.QM/0408012.)

  43. M. Chaves, E.D. Sontag and R.J. Dinerstein. Gains and optimal design in signaling pathways. Proc. Conf. Decision and Control (CDC'04), Paradise Island, The Bahamas, Dec. 2004.

  44. S. Glavaski, M. Chaves, R. Day, P. Nag, A. Wiliams and  W. Zhang. Vehicle networks: achieving regular formation. Proc. American Control Conf. (ACC'03), Denver, Colorado, June 2003.

  45. M. Chaves. A parameter-robust observer as an application of ISS techniques. Proc. Int. Symp. Mathematical Theory of Networks and Systems (MTNS'02), South Bend, Indiana, Aug. 2002.

  46. M. Chaves and E.D. Sontag. Observers for chemical reaction networks. Proc. European Control Conf. (ECC'01), Porto, Portugal, Sep. 2001.

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

Book edited
  1. M. Chaves and M.A. Martins (Editors). Molecular Logic and Computational Synthetic Biology, First International Symposium, MLCSB 2018, Santiago, Chile, December 17-18, 2018, Springer Switzerland (LNCS vol. 11415).

PhD. thesis and HDR
  1. M. Chaves. Predictive analysis of dynamical systems: combining discrete and continuous formalisms . HDR, Université Nice Sophia Antipolis, France, October 2013. (Also available through HAL/TEL.)

  2. M. Chaves. Observer design for a class of nonlinear systems, with applications to biochemical networks. PhD. thesis, Rutgers University, New Jersey, USA, May 2003.