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Fabien CRAUSTE

CNRS Senior Research Scientist
PhD in Applied Mathematics
Habilité à Diriger des Recherches


MAP5 UMR 8541
Université Paris Cité
45 rue des Saints Pères
75270 Paris cedex 06, France
website


Coordinator of Réseau Thématique Math Bio Santé.
Organiser of Modeling, Analysis, Simulation (MAS) team seminar at MAP5.
Co-organiser of the Joint Seminar on Mathematical Modeling in Life Sciences and Health (seminar of LAGA, LJLL, and MAP5 laboratories).

Member of the 'Comité de Programme' of PEPR Maths-Vives.
Member of the steering committee of AMIES (French Agency for Mathematics in Interaction with Companies and Society).
Member of the MAP5 laboratory initiative MAP1.5, workgroup devoted to the analysis of lab habits and their impact on the environment, relying on the Labos 1point5 initiative.
DEI contact of MAP5.


Research Themes:
 - Biomathematics, Modeling, Delay Equations, Structured Equations, Agent-Based Models
 - Mathematical Immunology (CD8 T cell response, B cell response)
 - Modeling in Medicine (treatments of LLC, atopic dermatitis)
 - Cell Population Dynamics
 - Stochasticity and interindividual variability
 - Parameter estimation anf experimental and medical data fitting


Research Projects:

Project AI4scMED
Multiscale AI for single-cell based precision medicine
Funded by PEPR Santé Numérique and France 2030

Project DCComm
Analysis of communication systems between human dendritic cells and T cells
Funded by ANR


Project Digi-DermA
Modeling interactions between mast cells and sensory neurons in atopic dermatitis
FUnded by Mission pour les Initiatives Transverses et Interdisciplinaires (CNRS)


Ongoing supervisions:
Pawan Kumar : postdoc (2024 - 2026) on the AI4scMED project.
Thi Nhu Thao Nguyen: postdoc (2024 - 2025) on the AI4scMED project.
Lucie Brolon: PhD thesis (2023 - 2026, co-supervised by Marie Perrot-Dockès) on Modeling and statistical analysis of T cell-DC communication.
Clémence Fournié: PhD thesis (2023 - 2026, co-supervised by Olivier Gandrillon) on Optimal Transport and Cellular Differentiation.

Former supervisions:
Thi Nhu Thao Nguyen: postdoc (2022 - 2024)
Madge Martin: postdoc (2021)
Alexey Koshkin (PhD thesis, 2018-2021)
Ronan Duchesne (PhD thesis, 2016-2019)
Simon Girel (PhD thesis, 2015-2018)
Chloé Audebert (postdoc, 2017-2018)
Marine Jacquier (PhD thesis, 2012-2016)
Xuefeng Gao (postdoc, 2014-2015)
Sotiris Prokopiou (postdoc, 2013-2014)
Floriane Lignet (postdoc, 2013-2014)
Emmanuelle Terry (PhD thesis, 2009-2012)


Publications:
  1. T.N.T. Nguyen, M. Martin, C. Arpin, S. Bernard, O. Gandrillon, F. Crauste. In silico modelling of CD8 T cell immune response links genetic regulation to population dynamics. ImmunoInformatics, 15, 100043 (2024).
    HAL preprint  article
  2. S. Cadot, C. Audebert, C. Dion, S. Ken, L. Dupre, L. Largeaud, C. Laurent, L. Ysebaert, F. Crauste, A. Quillet-Mary. New pharmacodynamic parameters linked with ibrutinib responses in chronic lymphocytic leukemia : Prospective study in real-world patients and mathematical modeling. PLoS Med., 21(7), e1004430 (2024).
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  3. S. Wang, M. Prieux, S. de Bernard, M. Dubois, D. Laubreton, S. Djebali, M. Zala, C. Arpin, L. Genestier, Y. Leverrier, O. Gandrillon, F. Crauste, W. Jiang, J. Marvel. Exogenous IL-2 delays memory precursors generation and is essential for enhancing memory cells effector functions. iScience, 27(4), 109411 (2024).
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  4. S. Bernard, F. Crauste, O. Gandrillon, C. Knibbe, D. Parsons. Simuscale: A Modular Framework for Multiscale Single-Cell Modelling. RT-0520, Inria Lyon (2024).
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  5. A. Koshkin, U. Herbach, M. Rodríguez Martínez, O. Gandrillon, F. Crauste. Stochastic modeling of a gene regulatory network driving B cell development in germinal centers. PLoS ONE, 19 (3), pp.e0301022 (2024).
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  6. H. Todorov, M. Prieux, D. Laubreton, M. Bouvier, S. Wang, S. de Bernard, et al. CD8 memory precursor cell generation is a continuous process. iScience 25 (9), pp.104927 (2022).
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  7. R. Duchesne, A. Guillemin, O. Gandrillon, F. Crauste. Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis . BMC Bioinformatics 22 (478) (2021).
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  8. E. Merino Tejero, D. Lashgari, R. Garcia-Valiente, X. Gao, F. Crauste, P. Robert, M. Meyer-Hermann, M. Rodríguez Martínez, S.M. van Ham, J. Guikema, H. Hoefsloot, A. van Kampen. Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help. Front. Immunol. 11, 3805 (2021).
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  9. C. Audebert, D. Laubreton, C. Arpin, O. Gandrillon, J. Marvel, F. Crauste. Investigation of Inter-Individual Variability in CD8 T Cell Responses with Nonlinear Mixed Effects Models. In Silico Biology 14(1-2), 13-39 (2020).
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  10. I. Balelli, C. Pasin, M. Prague, F. Crauste, T. Van Effelterre, V. Bockstal, L. Solforosi, R. Thiébaut. A model for establishment, maintenance and reactivation of the immune response after vaccination against Ebola virus. J. Theor. Biol. 495, 110254 (2020).
    HAL preprint  article
  11. A. Guillemin, R. Duchesne, F. Crauste, S. Gonin-Giraud, O. Gandrillon. Drugs modulating stochastic gene expression affect the erythroid differentiation process. PLoS ONE 14(11): e0225166 (2019).
    HAL preprint  article
  12. R. Duchesne, A. Guillemin, F. Crauste, O. Gandrillon. Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts. In Silico Biology. 13, 55-69 (2019).
    HAL preprint  article
  13. S. Girel, C. Arpin, J. Marvel, O. Gandrillon, F. Crauste. Model-based assessment of the role of uneven partitioning of molecular content on heterogeneity and regulation of differentiation in CD8 T-cell immune responses. Front. Immunol. 10, 230 (2019).
    HAL preprint  article
  14. K. Grzesik, K. Eng, F. Crauste, S. Battaglia. In Silico Methods for Studying T Cell Biology. Int. Rev. Cell. Mol. Biol. 342, 265-304 (2019).
    HAL preprint  article
  15. L. Boullu, M. Adimy, F. Crauste, L. Pujo-Menjouet. Oscillations and asymptotic convergence for a delay differential equation modeling platelet production. Discrete & Continuous Dynamical Systems - B, 24 (6), 2417-2442 (2019).
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  16. S. Girel, F. Crauste. Existence and stability of periodic solutions of an impulsive differential equation and application to CD8 T-cell differentiation. J. Math. Biol. 76 (7), 1765-1795 (2018).
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  17. L. Barbarroux, Ph. Michel, M. Adimy, F. Crauste. A multiscale model of the CD8 T cell immune response structured by intracellular content. Discrete and Continuous Dynamical Systems Series B 23 (9), 3969-4002 (2018).
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  18. O. Angulo, O. Gandrillon, F. Crauste. Investigating the role of the experimental protocol in phenylhydrazine-induced anemia on mice recovery. J. Theoret. Biol. 437, 286-298 (2018).
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  19. O. Angulo, F. Crauste, JC Lopez-Marcos. Numerical integration of an erythropoiesis model with explicit growth factor dynamics. Journal of Computational and Applied Mathematics 330, 770-782 (2018).
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  20. F. Crauste, J. Mafille, L. Boucinha, S. Djebali, O. Gandrillon, J. Marvel, C. Arpin. Identification of nascent Memory CD8 T cells and modeling of their ontogeny. Cell Systems 4(3), 306-317 (2017).
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  21. L. Barbarroux, P. Michel, M. Adimy, F. Crauste. Multi-scale modeling of the CD8 immune response. AIP Conference Proceedings 1738 (1), 320002 (2016).
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  22. X. Gao, C. Arpin, J. Marvel, S. Prokopiou, O. Gandrillon, F. Crauste. IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC: a multiscale modeling study. BMC Systems Biology, 10, 77 (2016).
    HAL preprint  article
  23. M. Jacquier, H.A. Soula, F. Crauste. A mathematical model of leptin resistance. Mathematical Biosciences, 267, 10-23 (2015).
    HAL preprint  article
  24. S. Bernard, F. Crauste. Optimal linear stability condition for scalar differential equations with distributed delay. Discrete and Continuous Dynamical Systems Series B, 20 (7), 1855-1876 (2015).
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  25. F. Crauste, E. Terry, I. Le Mercier, J. Mafi lle, S. Djebali, T. Andrieu, B. Mercier, G. Kaneko, C. Arpin, J. Marvel, O. Gandrillon. Predicting Pathogen-Speci c CD8 T Cell Immune Responses from a Modeling Approach. J. Theor. Biol., 374, 66-82 (2015).
    HAL preprint  article
  26. S. Prokopiou, L. Barbarroux, S. Bernard, J. Mafille, Y. Leverrier, C. Arpin, J. Marvel, O. Gandrillon, F. Crauste. Multiscale modeling of the early CD8 T cell immune response in lymph nodes: an integrative study. Computation, 2(4), 159-181 (2014).
    HAL preprint  article
  27. M. Jacquier, F. Crauste, Ch. Soulage, H. Soula. A predictive model of the dynamics of body weight and food intake in rats submitted to caloric restrictions. PLoS ONE, 9(6): e100073 (2014).
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  28. M. Adimy, F. Crauste. Delay Differential Equations and Autonomous Oscillations in Hematopoietic Stem Cell Dynamics Modeling. Mathematical Modelling of Natural Phenomena, 7 (6), 1-22 (2012).
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  29. E. Terry, J. Marvel, C. Arpin, O. Gandrillon, F. Crauste. Mathematical Model of the primary CD8 T Cell Immune Response: Stability Analysis of a Nonlinear Age-Structured System. Journal of Mathematical Biology, 65, 263-291 (2012).
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  30. S. Fischer, P. Kurbatova, N. Bessonov, O. Gandrillon, V. Volpert, F. Crauste. Modelling erythroblastic islands: using a hybrid model to assess the function of central macrophage. J. Theo. Biol., 298, 92-106 (2012).
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  31. F. Crauste. Equations aux dérivées partielles structurées en âge et équations à retard : Deux exemples d'applications en biologie, MATAPLI, 96, 73-95 (2011).
    article
  32. N. Bessonov, F. Crauste, S. Fischer, P. Kurbatova, V. Volpert. Application of Hybrid Models to Blood Cell Production in the Bone Marrow. Math. Model. Nat. Phenom., 6 (7), 2-12 (2011).
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  33. N. Bessonov, F. Crauste, V. Volpert. Modelling of Plant Growth with Apical or Basal Meristem. Math. Model. Nat. Phenom., 6 (2), 107-132 (2011).
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  34. P. Kurbatova, S. Bernard, N. Bessonov, F. Crauste, I. Demin, C. Dumontet, S. Fischer, V. Volpert. Hybrid model of erythropoiesis and leukemia treatment with cytosine arabinoside. SIAM J. App. Math., 71 (6), 2246-2268 (2011).
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  35. F. Crauste. A review on local asymptotic stability analysis for mathematical models of hematopoietic with delay and delay-dependent coefficients. Annals of the Tiberiu Popoviciu Seminar of functionnal equations, approximation and convexity, 9, 121-143 (2011).
    HAL preprint  journal
  36. M. Adimy, F. Crauste, A. El Abdllaoui. Boundedness and Lyapunov Function for a Nonlinear System of Hematopoietic Stem Cell Dynamics. Comptes Rendus Mathematique, 348 (7-8), 373-377 (2010).
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  37. M. Adimy, F. Crauste, C. Marquet. Asymptotic behavior and stability switch for a mature-immature model of cell differentiation. Nonlinear Analysis: Real World Applications, 11 (4), 2913-2929 (2010).
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  38. F. Crauste. Stability and Hopf bifurcation for a first-order linear delay differential equation with distributed delay, in Complex Time Delay Systems (Ed. F. Atay), Springer, 1st edition, 320p., ISBN: 978-3-642-02328-6 (2010).
    HAL preprint  book chapter
  39. F. Crauste, I. Demin, O. Gandrillon, V. Volpert. Mathematical study of feedback control roles and relevance in stress erythropoiesis. Journal of Theoretical Biology, 263 (3), 303-316 (2010).
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  40. M. Adimy, F. Crauste, My L. Hbid, R. Qesmi. Stability and Hopf bifurcation for a cell population model with state-dependent delay. SIAM J. Appl. Math, 70 (5), 1611-1633 (2010).
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  41. I. Demin, F. Crauste, O. Gandrillon, V. Volpert. A multi-scale model of erythropoiesis. Journal of Biological Dynamics, 4 (1), 59-70 (2010).
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  42. N. Bessonov, F. Crauste, I. Demin, V. Volpert. Dynamics of erythroid progenitors and erythroleukemia. Mathematical Modeling of Natural Phenomena, 4 (3), 210-232 (2009).
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  43. F. Crauste. Delay Model of Hematopoietic Stem Cell Dynamics: Asymptotic Stability and Stability Switch. Mathematical Modeling of Natural Phenomena, 4 (2), 28-47 (2009).
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  44. M. Adimy, F. Crauste. Mathematical model of hematopoiesis dynamics with growth factor-dependent apoptosis and proliferation regulation. Mathematical and Computer Modelling, 49, 2128-2137 (2009).
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  45. F. Crauste, M.L. Hbid, A. Kacha. A delay reaction-diffusion model of the dynamics of botulinum in fish. Mathematical Biosciences, 216, 17-29 (2008).
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  46. M. Adimy, F. Crauste, A. El Abdllaoui. Discrete maturity-structured model of cell differentiation with applications to acute myelogenous leukemia. Journal of Biological Systems, 16 (3),  395-424 (2008).
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  47. M. Adimy, S. Bernard, J. Clairambault, F. Crauste, S. Génieys, L. Pujo-Menjouet. Modélisation de la dynamique de l'hématopoïèse normale et pathologique. Hématologie, 14 (5), 339-350 (2008).
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  48. M. Adimy, O. Angulo, F. Crauste, J.C. Lopez-Marcos. Numerical integration of a mathematical model of hematopoietic stem cell dynamics. Computer and Mathematics with Applications, 56, 594-606 (2008).
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  49. F. Crauste, L. Pujo-Menjouet, S. Génieys, C. Molina, O. Gandrillon. Adding Self-Renewal in Committed Erythroid Progenitors Improves the Biological Relevance of a Mathematical Model of Erythropoiesis. Journal of Theoretical Biology, 250, 322-338 (2008).
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  50. M. Adimy, F. Crauste. Modelling and asymptotic stability of  a growth factor-dependent stem cells dynamics model with distributed delay. Discrete and Continuous Dynamical Systems Series B, 8 (1), 19-38 (2007).
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  51. M. Adimy, F. Crauste, A. El Abdllaoui. Asymptotic Behavior of a Discrete Maturity Structured System of Hematopoietic Stem Cells Dynamics with Several Delays. Mathematical Modelling of Natural Phenomena, Vol 1 (2), 1-22 (2006).
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  52. M. Adimy, F. Crauste, S. Ruan. Modelling hematopoiesis mediated by growth factors with applications to periodic hematological diseases. Bulletin of Mathematical Biology, 68 (8), 2321-2351 (2006).
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  53. M. Adimy, F. Crauste, S. Ruan. Periodic Oscillations in Leukopoiesis Models with Two Delays. Journal of Theoretical Biology, 242, 288-299 (2006).
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  54. F. Crauste. Global Asymptotic Stability and Hopf Bifurcation for a Blood Cell Production Model. Mathematical Biosciences and Engineering, 3 (2), 325-346 (2006).
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  55. M. Adimy, F. Crauste, A. Halanay, M. Neamţu, D. Opriş. Stability of limit cycles in a pluripotent stem cell dynamics model. Chaos, Solitons and Fractals, 27 (4), 1091-1107 (2006).
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  56. M. Adimy, F. Crauste, S. Ruan. A mathematical study of the hematopoiesis process with applications to chronic myelogenous leukemia. SIAM J. Appl. Math., 65 (4), 1328-1352 (2005).
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  57. M. Adimy, F. Crauste, S. Ruan. Stability and Hopf bifurcation in a mathematical model of pluripotent stem cell dynamics. Nonlinear Analysis: Real World Applications, 6 (4), 651-670 (2005).
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  58. M. Adimy, F. Crauste. Existence, positivity and stability for a nonlinear model of cellular proliferation. Nonlinear Analysis: Real World Applications, 6 (2), 337-366 (2005).
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  59. M. Adimy, F. Crauste, L. Pujo-Menjouet. On the stability of a maturity structured model of cellular proliferation. Dis. Cont. Dyn. Sys. Ser. A, 12 (3), 501-522 (2005).
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  60. F. Crauste, M. Adimy. Bifurcation dans un modèle non-linéaire de production du sang. Comptes-rendus de la 7ième Rencontre du Non-Linéaire, Non-Linéaire Publications, Paris, 73-78 (2004).
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  61. M. Adimy, F. Crauste. Stability and instability induced by time delay in an erythropoiesis model. Monografias del Seminario Matematico Garcia de Galdeano, 31, 3-12 (2004).
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  62. M. Adimy, F. Crauste. Global stability of a partial differential equation with distributed delay due to cellular replication. Nonlinear Analysis, 54 (8), 1469-1491 (2003).
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  63. M. Adimy, F. Crauste. Un modèle non-linéaire de prolifération cellulaire : extinction des cellules, invariance. Comptes Rendus Mathématiques, 336, 559-564 (2003).
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Habilitation à Diriger des Recherches (HDR): Delay Equations and Models of Cell Population Dynamics.    manuscript

PhD Thesis: Mathematical study of hyperbolic partial differential equations modelling blood cells regulation processes - Applications to periodic hematological diseases.    manuscript (in french)