Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 1A. Bonnaffoux.
  Inferring gene regulatory networks from dynamic multi-scale data, Université de Lyon, October 2018.
  https://hal.archives-ouvertes.fr/tel-01920262
• 2L. Boullu.
  Study of delay differential equations with applications to the regulation of blood platelet production, Université de Lyon, November 2018.
  https://hal.inria.fr/tel-01948726
• 3S. Girel.
  Modeling the CD8 T-cell Immune Response : Mathematical Analysis and Multiscale Models, Université de Lyon, November 2018.
  https://hal.archives-ouvertes.fr/tel-01941850
• 4U. Herbach.
  From stochastic modelling of gene expression to inference of regulatory networks, Université de Lyon, September 2018.
  https://tel.archives-ouvertes.fr/tel-01930398

Articles in International Peer-Reviewed Journals

• 5O. Angulo, F. Crauste, J. López-Marcos.
  Numerical integration of an erythropoiesis model with explicit growth factor dynamics, in: Journal of Computational and Applied Mathematics, March 2018, vol. 330, pp. 770 - 782. [ DOI : 10.1016/j.cam.2017.01.033 ]
  https://hal.inria.fr/hal-01646786
• 6O. Angulo, O. Gandrillon, F. Crauste.
  Investigating the role of the experimental protocol in phenylhydrazine-induced anemia on mice recovery, in: Journal of Theoretical Biology, January 2018, vol. 437, pp. 286 - 298. [ DOI : 10.1016/j.jtbi.2017.10.031 ]
  https://hal.inria.fr/hal-01646792
• 7L. Barbarroux, P. Michel, M. Adimy, F. Crauste.
  A multiscale model of the CD8 T cell immune response structured by intracellular content, in: Discrete and Continuous Dynamical Systems - Series B (DCDS-B), November 2018, vol. 23, n^o 9, pp. 3969-4002.
  https://hal.inria.fr/hal-01969237
• 8V. A. Belyaev, J. L. Dunster, J. M. Gibbins, M. Panteleev, V. Volpert.
  Modeling thrombosis in silico: Frontiers, challenges, unresolved problems and milestones, in: Physics of Life Reviews, November 2018, vol. 26-27, pp. 57-95. [ DOI : 10.1016/j.plrev.2018.02.005 ]
  https://hal.archives-ouvertes.fr/hal-01941469
• 9N. Bessonov, A. Beuter, S. Trofimchuk, V. Volpert.
  Estimate of the travelling wave speed for an integro-differential equation, in: Applied Mathematics Letters, February 2019, vol. 88, pp. 103-110. [ DOI : 10.1016/j.aml.2018.07.037 ]
  https://hal.archives-ouvertes.fr/hal-01941455
• 10N. Bessonov, N. Reinberg, M. Banerjee, V. Volpert.
  The Origin of Species by Means of Mathematical Modelling, in: Acta Biotheoretica, December 2018, vol. 66, n^o 4, pp. 333-344. [ DOI : 10.1007/s10441-018-9328-9 ]
  https://hal.archives-ouvertes.fr/hal-01941452
• 11A. Beuter, A. Balossier, S. Trofimchuk, V. Volpert.
  Modeling of post-stroke stimulation of cortical tissue, in: Mathematical Biosciences, November 2018, vol. 305, pp. 146-159. [ DOI : 10.1016/j.mbs.2018.08.014 ]
  https://hal.archives-ouvertes.fr/hal-01941460
• 12G. Bocharov, A. Meyerhans, N. Bessonov, S. Trofimchuk, V. Volpert.
  Interplay between reaction and diffusion processes in governing the dynamics of virus infections, in: Journal of Theoretical Biology, November 2018, vol. 457, pp. 221-236. [ DOI : 10.1016/j.jtbi.2018.08.036 ]
  https://hal.archives-ouvertes.fr/hal-01941458
• 13L. Boullu, M. Adimy, F. Crauste, L. Pujo-Menjouet.
  Oscillations and asymptotic convergence for a delay differential equation modeling platelet production, in: Discrete and Continuous Dynamical Systems - Series B, 2018, pp. 1-27.
  https://hal.inria.fr/hal-01835435
• 14I. S. Ciuperca, M. Dumont, A. Lakmeche, P. Mazzocco, L. Pujo-Menjouet, H. Rezaei, L. M. Tine.
  Alzheimer's disease and prion: analysis of an in vitro mathematical model, in: Discrete and Continuous Dynamical Systems - Series B (DCDS-B), 2018.
  https://hal.inria.fr/hal-01368862
• 15T. Galochkina, M. Marion, V. Volpert.
  Initiation of reaction–diffusion waves of blood coagulation, in: Physica D: Nonlinear Phenomena, August 2018, vol. 376-377, pp. 160-170. [ DOI : 10.1016/j.physd.2017.11.006 ]
  https://hal.archives-ouvertes.fr/hal-01941465
• 16S. Girel, F. Crauste.
  Existence and stability of periodic solutions of an impulsive differential equation and application to CD8 T-cell differentiation, in: Journal of Mathematical Biology, June 2018, vol. 76, n^o 7, pp. 1765-1795, https://arxiv.org/abs/1803.01674. [ DOI : 10.1007/s00285-018-1220-3 ]
  https://hal.archives-ouvertes.fr/hal-01721728
• 17M. Helal, A. Igel-Egalon, A. Lakmeche, P. Mazzocco, A. Perrillat-Mercerot, L. Pujo-Menjouet, H. Rezaei, L. Matar Tine.
  Stability analysis of a steady state of a model describing Alzheimer’s disease and interactions with prion proteins, in: Journal of Mathematical Biology, August 2018, pp. 1-25. [ DOI : 10.1007/s00285-018-1267-1 ]
  https://hal.archives-ouvertes.fr/hal-01946610
• 18H. B. Huttner, O. Bergmann, M. Salehpour, R. E. Cheikh, M. Nakamura, A. Tortora, P. Heinke, R. Coras, E. Englund, I. Y. Eyüpoglu, J. B. Kuramatsu, S. S. Roeder, S. P. Kloska, I. Muehlen, A. Doerfler, S. Schwab, G. Possnert, S. Bernard, J. Frisén.
  Meningioma growth dynamics assessed by radiocarbon retrospective birth dating, in: EBioMedicine, 2018, vol. 27, pp. 176–181. [ DOI : 10.1016/j.ebiom.2017.12.020 ]
  https://hal.archives-ouvertes.fr/hal-01671339
• 19P. Lemarre, L. Pujo-Menjouet, S. S. Sindi.
  Generalizing a mathematical model of prion aggregation allows strain coexistence and co-stability by including a novel misfolded species, in: Journal of Mathematical Biology, 2018. [ DOI : 10.1007/s00285-018-1280-4 ]
  https://hal.archives-ouvertes.fr/hal-01858724
• 20L. Matar Tine, B. Lèye.
  Analysis and numerical simulation of a polymerization model with aggregation and Ostwald ripening for the growth phenomenon, in: Acta Applicandae Mathematicae, October 2018, pp. 1-28. [ DOI : 10.1007/s10440-018-0222-x ]
  https://hal.archives-ouvertes.fr/hal-01933553
• 21M. Sen, V. Volpert, V. Vougalter.
  Existence of waves for a reaction–diffusion–dispersion system, in: Nonlinear Analysis: Theory, Methods and Applications, March 2019, vol. 180, pp. 52-66. [ DOI : 10.1016/j.na.2018.09.011 ]
  https://hal.archives-ouvertes.fr/hal-01941461
• 22S. Trofimchuk, V. Volpert.
  Traveling Waves for a Bistable Reaction-Diffusion Equation with Delay, in: SIAM Journal on Mathematical Analysis, January 2018, vol. 50, n^o 1, pp. 1175-1199. [ DOI : 10.1137/17M1115587 ]
  https://hal.archives-ouvertes.fr/hal-01941474
• 23G. Vogin, T. Bastogne, L. Bodgi, J. Gillet-Daubin, A. Canet, S. Pereira, N. Foray.
  The pATM Immunofluorescence assay: a high-performance radiosensitivity assay to predict post radiotherapy overreactions, in: International Journal of Radiation Oncology - Biology - Physics, July 2018, vol. 101, n^o 3, pp. 690–693. [ DOI : 10.1016/j.ijrobp.2018.03.047 ]
  https://hal.archives-ouvertes.fr/hal-01757771
• 24V. Vougalter, V. Volpert.
  On the Existence in the Sense of Sequences of Stationary Solutions for Some Systems of Non-Fredholm Integro-differential Equations, in: Mediterranean Journal of Mathematics, October 2018, vol. 15, n^o 5.
  https://hal.archives-ouvertes.fr/hal-01941463
• 25V. Vougalter, V. Volpert.
  Solvability of Some Integro-Differential Equations with Anomalous Diffusion in Two Dimensions, in: Journal of Mathematical Sciences, December 2018, vol. 235, n^o 3, pp. 243-255. [ DOI : 10.1007/978-3-319-47512-7_9 ]
  https://hal.archives-ouvertes.fr/hal-01941457

Scientific Books (or Scientific Book chapters)

• 26G. Bocharov, V. Volpert, B. Ludewig, A. Meyerhans.
  Mathematical Immunology of Virus Infections, Springer International Publishing, 2018, XV, 245 p. [ DOI : 10.1007/978-3-319-72317-4 ]
  https://hal.archives-ouvertes.fr/hal-01941475

Other Publications

• 27I. S. Ciuperca, M. Dumont, A. Lakmeche, P. Mazzocco, L. Pujo-Menjouet, H. Rezaei, L. Matar Tine.
  Alzheimer's disease and prion: an in vitro mathematical model, February 2018, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01708659
• 28T. Lepoutre.
  Improved duality estimates: time discrete case and applications to a class of cross-diffusion systems, September 2018, https://arxiv.org/abs/1812.01296 - working paper or preprint.
  https://hal.inria.fr/hal-01943576

References in notes

• 29A. Besse, G. D. Clapp, S. Bernard, F. E. Nicolini, D. Levy, T. Lepoutre.
  Stability Analysis of a Model of Interaction Between the Immune System and Cancer Cells in Chronic Myelogenous Leukemia, in: Bulletin of Mathematical Biology, 2017, pp. 1–27. [ DOI : 10.1007/s11538-017-0272-7 ]
  https://hal.archives-ouvertes.fr/hal-01539364
• 30A. Besse, T. Lepoutre, S. Bernard.
  Long-term treatment effects in chronic myeloid leukemia, in: Journal of Mathematical Biology, 2017, pp. 1-26. [ DOI : 10.1007/s00285-017-1098-5 ]
  https://hal.archives-ouvertes.fr/hal-01447781
• 31G. D. Clapp, T. Lepoutre, R. El Cheikh, S. Bernard, J. Ruby, H. Labussière-Wallet, F. E. Nicolini, D. Levy.
  Implication of the Autologous Immune System in BCR-ABL Transcript Variations in Chronic Myelogenous Leukemia Patients Treated with Imatinib., in: Cancer Research, October 2015, vol. 75, n^o 19, pp. 4053-62. [ DOI : 10.1158/0008-5472.CAN-15-0611 ]
  https://hal.inria.fr/hal-01251396
• 32F. 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, in: Cell Systems, February 2017, vol. 4, n^o 3, pp. 306-317. [ DOI : 10.1016/j.cels.2017.01.014 ]
  https://hal.inria.fr/hal-01409637
• 33F. 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, in: Journal of theoretical biology, 2008, vol. 250, n^o 2, pp. 322–338.
• 34U. Herbach, A. Bonnaffoux, T. Espinasse, O. Gandrillon.
  Inferring gene regulatory networks from single-cell data: a mechanistic approach, in: BMC Systems Biology, November 2017, vol. 11, n^o 1, 105 p. [ DOI : 10.1186/s12918-017-0487-0 ]
  https://hal.archives-ouvertes.fr/hal-01646910