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Fabien CRAUSTE

CNRS Senior Research Scientist
Habilité à Diriger des Recherches

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

Coordinator of Réseau Thématique Math Bio Santé.
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.
Organization of the seminar of mathematical modeling in life sciences and health (joint seminar with LAGA, LJLL, MAP5 laboratories).


Research Themes:
 - Biomathematics, Modeling, Delay Equations, Structured Equations, Agent-Based Models
 - Mathematical Immunology (CD8 T cell response, B cell response)
 - Cell Population Dynamics

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 TROPIC
Optimal Transport and Cellular Differentiation
Funded by Mission pour les Initiatives Transverses et Interdisciplinaires, CNRS


Ongoing supervisions:
Thi Nhu Thao Nguyen: postdoc (2024 - 2025) on the AI4scMED project.
Lucie Brolon: PhD thesis (2023 - ..., co-supervised by Marie Perrot-Dockès) on Modeling and statistical analysis of T cell-DC communication.
Clémence Fournié: PhD thesis (2023 - ..., 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. HAL (2024).
    HAL preprint 
  2. S. Bernard, F. Crauste, O. Gandrillon, C. Knibbe, D. Parsons. Simuscale: A Modular Framework for Multiscale Single-Cell Modelling. RT-0520, Inria Lyon (2024).
    HAL preprint 
  3. 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. HAL (2024).
    HAL preprint 
  4. 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).
    HAL preprint  article
  5. 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).
    HAL preprint  article
  6. 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).
    HAL preprint  article
  7. 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).
    HAL preprint  article
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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).
    HAL preprint  article
  14. 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).
    HAL preprint  article
  15. 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).
    HAL preprint  article
  16. 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).
    HAL preprint  article
  17. 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).
    HAL preprint  article
  18. 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).
    HAL preprint  article
  19. L. Barbarroux, P. Michel, M. Adimy, F. Crauste. Multi-scale modeling of the CD8 immune response. AIP Conference Proceedings 1738 (1), 320002 (2016).
    HAL preprint  article
  20. 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
  21. M. Jacquier, H.A. Soula, F. Crauste. A mathematical model of leptin resistance. Mathematical Biosciences, 267, 10-23 (2015).
    HAL preprint  article
  22. 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).
    HAL preprint  article
  23. 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
  24. 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
  25. 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).
    HAL preprint  article
  26. 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).
    HAL preprint  article
  27. 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).
    HAL preprint  article
  28. 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).
    HAL preprint  article
  29. 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
  30. 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).
    HAL preprint  article
  31. N. Bessonov, F. Crauste, V. Volpert. Modelling of Plant Growth with Apical or Basal Meristem. Math. Model. Nat. Phenom., 6 (2), 107-132 (2011).
    HAL preprint  article
  32. 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).
    HAL preprint  article
  33. 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
  34. 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).
    HAL preprint  article
  35. 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).
    HAL preprint  article
  36. 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
  37. 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).
    HAL preprint  article
  38. 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).
    HAL preprint  article
  39. I. Demin, F. Crauste, O. Gandrillon, V. Volpert. A multi-scale model of erythropoiesis. Journal of Biological Dynamics, 4 (1), 59-70 (2010).
    HAL preprint  article
  40. N. Bessonov, F. Crauste, I. Demin, V. Volpert. Dynamics of erythroid progenitors and erythroleukemia. Mathematical Modeling of Natural Phenomena, 4 (3), 210-232 (2009).
    HAL preprint  article
  41. F. Crauste. Delay Model of Hematopoietic Stem Cell Dynamics: Asymptotic Stability and Stability Switch. Mathematical Modeling of Natural Phenomena, 4 (2), 28-47 (2009).
    HAL preprint  article
  42. 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).
    HAL preprint  article
  43. 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).
    HAL preprint  article
  44. 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).
    HAL preprint  article
  45. 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).
    HAL preprint
  46. 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).
    HAL preprint  article
  47. 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).
    HAL preprint  article
  48. 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).
    HAL preprint  article
  49. 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).
    HAL preprint  article
  50. 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).
    HAL preprint  article
  51. M. Adimy, F. Crauste, S. Ruan. Periodic Oscillations in Leukopoiesis Models with Two Delays. Journal of Theoretical Biology, 242, 288-299 (2006).
    HAL preprint  article
  52. F. Crauste. Global Asymptotic Stability and Hopf Bifurcation for a Blood Cell Production Model. Mathematical Biosciences and Engineering, 3 (2), 325-346 (2006).
    HAL preprint  article
  53. 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).
    HAL preprint  article
  54. 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).
    HAL preprint  article
  55. 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).
    HAL preprint  article
  56. 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).
    HAL preprint  article
  57. 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).
    HAL preprint  article
  58. 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).
    HAL preprint
  59. 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).
    HAL preprint
  60. 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).
    HAL preprint  article
  61. M. Adimy, F. Crauste. Un modèle non-linéaire de prolifération cellulaire : extinction des cellules, invariance. Comptes Rendus Mathématiques, 336, 559-564 (2003).
    HAL preprint  article

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)