Adrien Richard
CNRS Researcher
Head of MC3 team
Laboratoire I3S - UMR CNRS 7271
Université Côte d'Azur, France.

Phone: +33 4 89 15 43 61
Address: Laboratoire I3S
Address: 2000, route des Lucioles
Address: Les Algorithmes - bât. Euclide B
Address: 06900 Sophia Antipolis - France

Research interests

I'm interested in finite dynamical systems (Boolean networks mainly) and their application for the modeling of biological networks (gene networks mainly). The transversal question of interest, behind almost all my works, is the following: What can be said on a finite dynamical system according to the interaction graph of the system (that describes under the form of a graph the interaction between the component of the system)?

Below, I use this color for works concerning mainly the theory of finite dynamical systems, this color for works concerning mainly methods for the modeling of gene networks, and this color for works concerning mainly the modeling of particular biological networks.

Articles submitted
  1. J. Aracena, F. Bridoux, M. Gadouleau, P. Guillon, K. Perrot, A. Richard, G. Theyssier
    On the Dynamics of Bounded-Degree Automata Networks.
    Submitted, 2024.

  2. F. Bridoux, A. Richard, A. Picard Marchetto.
    Asynchronous dynamics of isomorphic Boolean networks.
    Submitted, 2024.

  3. J. Aracena, L. Cabrera-Crot, A. Richard, L. Salinas
    Dynamically equivalent disjunctive networks.
    Submitted, 2023.

Articles in journals
  1. A. Naldi, A. Richard, E. Tonello.
    Linear cuts in Boolean networks.
    Natural Computing, 1-21, 2023.

  2. F. Bridoux, K. Perrot, A. Picard Marchetto, A. Richard.
    Interaction graphs of isomorphic automata networks I: complete digraph and minimum in-degree (slides).
    Journal of Computer and System Sciences, 138:103458, 2023.

  3. J. Aracena, A. Richard, L. Salinas.
    Synchronizing Boolean networks asynchronously (slides).
    Journal of Computer and System Sciences, 136:249-279, 2023.

  4. A. Richard, E. Tonello.
    Attractor separation and signed cycles in asynchronous Boolean networks.
    Theoretical Computer Science, 947:113706, 2023.

  5. F. Bridoux, A. Durbec, K. Perrot, A. Richard.
    Complexity of fixed point counting problems in Boolean Networks (slides).
    Journal of Computer and System Sciences, 226:138-164, 2022.

  6. J. Aracena, M. Gadouleau, A. Richard, L. Salinas.
    Fixing Boolean networks asynchronously (slides).
    Information and Computation, 214:104540, 2020.

  7. A. Richard.
    Positive and negative cycles in Boolean networks.
    Journal of Theoretical Biology, 463:67-76, 2019.

  8. A. Richard.
    Nilpotent dynamics on signed interaction graphs and weak converses of Thomas' rules.
    Discrete Applied Mathematics, 267:160-175, 2019.

  9. G. Bernot, J.-P. Comet, Z. Khalis, A. Richard, O. Roux.
    A Genetically Modified Hoare Logic.
    Theoretical Computer Science, 765:145-157, 2019.

  10. A. Richard.
    Fixed points and connections between positive and negative cycles in Boolean networks.
    Discrete Applied Mathematics, 243:1-10, 2018.

  11. J. Aracena, A. Richard, L. Salinas.
    Number of fixed points and disjoint cycles in monotone Boolean networks (slides).
    SIAM Journal on Discrete Mathematics, 31(3):1702-1725, 2017.

  12. J. Aracena, A. Richard, Lilian Salinas.
    Fixed points in conjunctive networks and maximal independent sets in graph contractions (slides).
    Journal of Computer and System Sciences, 88:145-163, 2017.

  13. M. Gadouleau, A. Richard, E. Fanchon.
    Reduction and Fixed Points of Boolean Networks and Linear Network Coding Solvability (slides).
    IEEE Transaction on Information Theory, 62(5):2504-2519, 2016.

  14. M. Gadouleau, A. Richard.
    Simple dynamics on graphs (slides).
    Theoretical Computer Science, 628:62-77, 2016.

  15. M. Gadouleau, A. Richard, S. Riis.
    Fixed points of Boolean networks, guessing graphs, and coding theory.
    SIAM Journal on Discrete Mathematics, 29(4):2312-2335, 2015.

  16. A. Richard.
    Fixed point theorems for Boolean networks expressed in terms of forbidden subnetworks (slides).
    Theoretical Computer Science, 583:1-26, 2015.

  17. J. Aracena, A. Richard, L. Salinas.
    Maximum number of fixed points in AND-OR-NOT networks.
    Journal of Computer and System Sciences, 80(7):1175-1190, 2014.

  18. S. Laurent, A. Richard, O. Mulner-Lorillon, J. Morales, D. Flament, V. Glippa, J. Bourdon, P. Gosselin, A. Siegel, P. Cormier, R. Bellé.
    Modelisation of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive.
    Frontiers in Genetics, 5(117), 2014.

  19. J.-P. Comet, A. Richard, M. Noual, J. Aracena, L. Calzone, J. Demongeot, M. Kaufman, A. Naldi, E.H. Snoussi, D. Thieffry.
    On circuit functionality in Boolean networks.
    Bulletin of Mathematical Biology, 75(6):906-919, 2013.

  20. A. Richard, P. Ruet.
    From kernels in directed graphs to fixed points and negative cycles in boolean networks.
    Discrete Applied Mathematics, 161(7-8):1106-1117, 2013.

  21. A. Richard, G. Rossignol, J.-P. Comet, G. Bernot, J. Guespin-Michel, A. Merieau.
    Boolean models of biosurfactants production in Pseudomonas fluorescens.
    PLoS ONE, 7(1):e24651, 2012.

  22. M. Mabrouki, M. Aiguier, J.-P. Comet, P. Le Gall, A. Richard.
    Embedding of biological regulatory networks and properties preservation.
    Mathematics in Computer Science , 5(3):263-288, 2011.

  23. A. Richard, J.-P. Comet.
    Stable periodicities and negative circuits in differential systems.
    Journal of Mathematical Biology, 63:593-600, 2011.
    Here is an ERRATUM to this article.

  24. A. Richard.
    Local negative circuits and fixed points in non-expansive boolean networks.
    Discrete Applied Mathematics, 159(11):1085-1093, 2011.

  25. L. Paulevé, A. Richard.
    Topological Fixed Points in Boolean Networks.
    Comptes Rendus de l'Académie des Sciences - Series I - Mathematics, 348(15-16):825 - 828, 2010.

  26. A. Richard.
    Negative circuits and sustained oscillations in asynchronous automata networks.
    Advances in Applied Mathematics, 44(4):378-392, 2010.

  27. A. Richard.
    Positive circuits and maximal number of fixed points in discrete dynamical systems.
    Discrete Applied Mathematics, 157(15):3281-3288, 2009.

  28. Z. Khalis, J.-P. Comet, A. Richard, G. Bernot.
    The smbionet method for discovering models of gene regulatory networks.
    Genes, Genomes and Genomics, 3:15-22, 2009.
  29. A. Richard.
    An extension of a combinatorial fixed point theorem of Shih and Dong.
    Advances in Applied Mathematics, 41(4):620-627, 2008.

  30. J. Ahmad, O. Roux, G. Bernot, J.-P. Comet, A. Richard.
    Analysing Formal Models of Genetic Regulatory Networks with Delays: Applications to Lambda phage and T-cell Activation Systems.
    International Journal of Bioinformatics Research and Applications, 4(3):240-262, 2008.

  31. A. Richard, J.-P. Comet.
    Necessary conditions for multistationarity in discrete dynamical systems.
    Discrete Applied Mathematics, 155(18):2403-2413, 2007.

  32. A. Richard, J.-P. Comet, G. Bernot.
    R. Thomas' modeling of biological regulatory networks: introduction of singular states in the qualitative dynamics.
    Fundamenta Informaticae, 65(4):373-392, 2005.

  33. G. Bernot, J.-P. Comet, A. Richard, J. Guespin-Michel.
    Application of Formal Methods to Biological Regulatory Networks: Extending Thomas' Asynchronous Logical Approach with Temporal Logic.
    Journal of Theoretical Biology, 229(3):339-347, 2004.

  34. J. Guespin-Michel, G. Bernot, J.-P. Comet, A. Mérieau, A. Richard, C. Hulen, B. Polack.
    Epigenesis and dynamic similarity in two regulatory networks in Pseudomonas aeruginosa.
    Acta Biotheoretica. 52 (4): 379-390, 2004.

Articles in conference proceedings
  1. F. Bridoux, C. Crespelle, T. H. D. Phan, A. Richard
    Dividing permutations in the semiring of functional digraphs .
    to appear in AUTOMATA 2024.

  2. J. Aracena, F. Bridoux, P. Guillon, K. Perrot, A. Richard, G. Theyssier.
    On the Dynamics of Bounded-Degree Automata Networks .
    In AUTOMATA 2023, Exploratory Papers collection, 2023.

  3. A. Picard Marchetto, A. Richard.
    Isomorphic Boolean networks and dense interaction graphs (slides).
    In AUTOMATA 2021, Exploratory Papers collection, 2021.

  4. F. Bridoux, N. Durbec, K. Perrot, A. Richard.
    Complexity of Maximum Fixed Point Problem in Boolean Networks (slides).
    Proceedings of CiE'2019, Springer, LNCS 11558, 132-143, 2019.

  5. M. Gadouleau, A. Richard.
    On fixable families of Boolean networks.
    Proceeding of ACRI 2018, Springer, LNCS 11115, 396-405, 2018.

  6. T. Melliti, D. Regnault, A. Richard, S. Sené.
    Asynchronous simulation of Boolean networks by monotone Boolean networks (slides).
    Proceeding of ACRI 2016, Springer, LNCS 9853, 182-191, 2016.

  7. T. Melliti, D. Regnault, A. Richard, S. Sené.
    On the convergence of Boolean automata networks without negative cycles (slides).
    Proceeding of AUTOMATA 2013, Springer, LNCS 8155, 124-138, 2013.

  8. H. Gruber, A. Richard, C. Soulé.
    How to Knock out Feedback Circuits in Gene Networks?
    In V. Capasso, M. Gromov, A. Harel-Bellan, N. Morozova, L. Pritchard, editors, Pattern Formation in Morphogenesis - Problems and Mathematical Issues, volume 15 of Springer Proceedings in Mathematics, pages 175-178, Springer, 2013.

  9. A. Richard.
    A fixed point theorem for boolean networks expressed in terms of forbidden subnetworks (slides).
    Proceeding of the 17th International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA 2011), DMTCS Proceedings AP , 1-16, 2012.

  10. L. Paulevé, A. Richard.
    Static analysis of boolean networks based on interaction graphs: a survey.
    Proceedings of The Second International Workshop on Static Analysis and Systems Biology (SASB 2011), ENTCS 284, 93-104, 2012.

  11. J. Bahi, J.-F. Couchot, C. Guyeux, A. Richard.
    On the link between strongly connected iteration graphs and chaotic Boolean discrete-time dynamical systems.
    Proceeding of the 18th International Symposium on Fundamentals of Computation Theory (FCT 2011), Lecture Note in Computer Science (LNCS), 6914, pp. 126-137, 2011.

  12. M. Dénès, B. Lesage, Y. Bertot, A. Richard.
    Formal proof of theorems on genetic regulatory networks.
    Synasc'09, IEEEXplore Digital Library, 2009.

  13. A. Richard.
    On the link between oscillations and negative circuits in discrete genetic regulatory networks (slides).
    Proceedings of JOBIM 2007, pp. 613-618, 2007.

  14. J. Ahmad, A. Richard, G. Bernot, J.-P. Comet, O. Roux.
    Delays in Biological Regulatory Networks.
    In IWBRA 2006 / ICCS 2006: 6th International Conference, Proceedings, Part II , volume 3992 of LNCS, 887-894, May 2006.

  15. A. Richard, J.-P. Comet, G. Bernot.
    Graph-based Modeling of Biological Regulatory Networks : Introduction of Singular States (slides).
    International workshop on Computational Methods in Systems Biology (CMSB), Paris, France, May 26-28,2004. In Proceedings CMSB 2004, LNBI 3082, pp. 58-72, 2005.

Book chapters
  1. E. Formenti, C. Papazian, A. Richard, P.-A. Scribot.
    From Additive Flowers to Additive Automata Networks
    In Automata and Complexity: Essays Presented to Eric Goles on the Occasion of His 70th Birthday, Automata and Complexity. Emergence, Complexity and Computation, vol 42. Springer, pp 323-343, 2020.

  2. A. Richard, L. Paulevé.
    Analyse statique des réseaux Booléens (slides).
    In Mathématique et Informatique. Une photographie en 2018, CNRS Editions, 2018.

  3. G. Bernot, J.-P. Comet, A. Richard, M. Chaves, J.-L. Gouzé, F. Dayan.
    Modeling and Analysis of Gene Regulatory Networks.
    In Modeling in Computational Biology and Biomedicine, F. Cazals and P. Kornprobst (Ed.), Springer, pp 47-80, 2013.

  4. A. Richard, J.-P. Comet, G. Bernot.
    Formal methods for modeling biological regulatory networks.
    In Modern Formal Methods and Applications, Gabbar Hossam A. (Ed.), pp. 83-122, Springer, 2006.

Dissertation and Thesis
  1. Modèles formels pour les réseaux de régulation génétiques et influence des circuits de rétroaction
    PhD Dissertation in Computer Science, University of Evry Val d'Essonne, France, september 2006.

Organization of scientific events
  1. International Workshop on Boolean Networks (IWBN 2020)
    Concepción, Chile, January 7-10 2020.

  2. Workshop sur la Théorie des réseaux booléens et ses applications en biologie
    Nice, 4-7 novembre 2014.

  3. Ecole thématique CNRS Modélisation Formelle de Réseaux de Régulation Biologique
    Ile de Porquerolles, 24-28 juin 2013.

PhD Students

  1. Florian Bridoux, 2016-2019.
  2. Aymeric Picard Marchetto, started in 2021.