Bibliography

Major publications by the team in recent years

• 1B. Perthame.
  Transport equations in biology, Frontiers in Mathematics, Birkhäuser Verlag, Basel, 2007, x+198 p.

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 2M. Doumic.
  Etudes de modèles de croissance et fragmentation et applications en biologie, Université Pierre et Marie Curie (Paris VI), June 2013, Habilitation thesis (HDR).
  http://hal.inria.fr/tel-00844123

Articles in International Peer-Reviewed Journals

• 3Juan Carlos L. Alfonso, N. Jagiella, L. Núñez, Miguel Angel. Herrero, D. Drasdo.
  Estimating dose painting effects in radiotherapy: a mathematica model, 2014, PloS One (accepted for publication).
• 4A. Ballesta, J. Clairambault.
  Physiologically Based Mathematical Models to Optimize Therapies Against Metastatic Colorectal Cancer: a Mini-Review, in: Current Pharmaceutical Design, March 2013.
  http://hal.inria.fr/hal-00849018
• 5A. Ballesta, J. Clairambault, S. Dulong, F. Lévi.
  A systems biomedicine approach for chronotherapeutics optimization: focus on the anticancer drug Irinotecan, in: New Challenges for Cancer Systems Biomedicine, 2013, vol. 1, pp. 301–327.
  http://annabelle.ballesta.fr/sites/default/files/4-Ballesta_chronotherapeutics-springer.pdf
• 6A. Ballesta, J. Lopez, N. Popgeorgiev, P. Gonzalo, M. Doumic, G. Gillet.
  Data-driven modeling of SRC control on the mitochondrial pathway of apoptosis: implication for anticancer therapy optimization, in: PLoS Computational Biology, April 2013, vol. 9, n^o 4. [ DOI : 10.1371/journal.pcbi.1003011 ]
  http://hal.inria.fr/hal-00849021
• 7F. Billy, J. Clairambault.
  Designing proliferating cell population models with functional targets for control by anti-cancer drugs, in: Discrete and Continuous Dynamical Systems - Series B, Jun 2013, vol. 18, n^o 4, pp. 865-889.
  http://dx.doi.org/10.3934/dcdsb.2013.18.865
• 8F. Billy, J. Clairambault, F. Delaunay, C. Feillet, N. Robert.
  Age-structured cell population model to study the influence of growth factors on cell cycle dynamics, in: Mathematical Biosciences and Engineering, 2013, vol. 10, pp. 1–17.
  http://hal.inria.fr/hal-00730457/
• 9F. Billy, J. Clairambault, O. Fercoq, S. Gaubert, T. Lepoutre, T. Ouillon, S. Saito.
  Synchronisation and control of proliferation in cycling cell population models with age structure, in: Mathematics and Computers in Simulation, 2014, vol. 96, pp. 66–94.
  http://dx.doi.org/10.1016/j.matcom.2012.03.005
• 10T. Bourgeron, M. Doumic, M. Escobedo.
  Estimating the Division Rate of the Self-Similar Growth-Fragmentation Equation, in: Inverse Problems, 2014, in press.
  http://hal.archives-ouvertes.fr/hal-00858488
• 11T. Cabana, J. Touboul.
  Large Deviations, Dynamics and Phase Transitions in Large Stochastic and Disordered Neural Networks, in: Journal of Statistical Physics, 2013, vol. 153, n^o 2, pp. 211–269.
• 12M. Doumic, M. Hoffmann, N. Krell, L. Robert.
  Statistical estimation of a growth-fragmentation model observed on a genealogical tree, in: Bernoulli, January 2014, 46 p, under revision.
  http://hal.archives-ouvertes.fr/hal-00763601
• 13M. Doumic, L. M. Tine.
  Estimating the Division Rate for the Growth-Fragmentation Equation, in: Journal of Mathematical Biology, July 2013, vol. 67, n^o 1, pp. 69-103. [ DOI : 10.1007/s00285-012-0553-6 ]
  http://hal.inria.fr/hal-00634539
• 14J. Eliaš, L. Dimitrio, J. Clairambault, R. Natalini.
  The p53 protein and its molecular network: modelling a missing link between DNA damage and cell fate, in: BBA-Biochimica et Biophysica Acta-Proteins and Proteomics, 2014, vol. 1844, pp. 232–247.
  http://hal.archives-ouvertes.fr/hal-00822308/
• 15M. N. Galtier, J. Touboul.
  Macroscopic Equations Governing Noisy Spiking Neuronal Populations with Linear Synapses, in: PloS One, 2013, vol. 8, n^o 11.
• 16P. Godoy, N. J. Hewitt, U. Albrecht, M. E. Andersen, N. Ansari, S. Bhattacharya, J. G. Bode, J. Bolleyn, C. Borner, J. Böttger, A. Braeuning, R. A. Budinsky, B. Burkhardt, N. R. Cameron, G. Camussi, C.-S. Cho, Y.-J. Choi, J. Craig Rowlands, U. Dahmen, G. Damm, O. Dirsch, M. T. Donato, J. Dong, S. Dooley, D. Drasdo, R. Eakins, K. S. Ferreira, V. Fonsato, J. Fraczek, R. Gebhardt, A. Gibson, M. Glanemann, C. E. P. Goldring, M. J. Gómez-Lechón, G. M. M. Groothuis, L. Gustavsson, C. Guyot, D. Hallifax, S. Hammad, A. Hayward, D. Häussinger, C. Hellerbrand, P. Hewitt, S. Hoehme, H.-G. Holzhütter, J. B. Houston, J. Hrach, K. Ito, H. Jaeschke, V. Keitel, J. M. Kelm, B. Kevin Park, C. Kordes, G. A. Kullak-Ublick, E. L. LeCluyse, P. Lu, J. Luebke-Wheeler, A. Lutz, D. J. Maltman, M. Matz-Soja, P. McMullen, I. Merfort, S. Messner, C. Meyer, J. Mwinyi, D. J. Naisbitt, A. K. Nussler, P. Olinga, F. Pampaloni, J. Pi, L. Pluta, S. A. Przyborski, A. Ramachandran, V. Rogiers, C. Rowe, C. Schelcher, K. Schmich, M. Schwarz, B. Singh, E. H. K. Stelzer, B. Stieger, R. Stöber, Y. Sugiyama, C. Tetta, W. E. Thasler, T. Vanhaecke, M. Vinken, T. S. Weiss, A. Widera, C. G. Woods, J. J. Xu, K. M. Yarborough, J. G. Hengstler.
  Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME, in: Arch Toxicol, Aug 2013, vol. 87, n^o 8, pp. 1315–1530.
  http://dx.doi.org/10.1007/s00204-013-1078-5
• 17F. James, N. Vauchelet.
  Chemotaxis: from kinetic equations to aggregate dynamics, in: Nonlinear Differ. Equ. Appl., 2013, vol. 20, pp. 101–127.
  http://hal.archives-ouvertes.fr/hal-00605479
• 18A. Lorz, T. Lorenzi, M. E. Hochberg, J. Clairambault, B. Perthame.
  Populational adaptive evolution, chemotherapeutic resistance and multiple anti-cancer therapies, in: Mathematical Modelling and Numerical Analysis, 2013, vol. 47, pp. 377–399.
  http://hal.archives-ouvertes.fr/hal-00714274
• 19T. Odenthal, B. Smeets, P. Van Liedekerke, E. Tijskens, H. Ramon, H. Van Oosterwijck.
  Analysis of initial cell spreading using mechanistic contact formulations for a deformable cell model., in: PLoS Computational Biology, October 2013, vol. 9, n^o 10. [ DOI : 10.1371/journal.pcbi.1003267 ]
  http://hal.inria.fr/hal-00909485
• 20F. Schliess, S. Hoehme, S. Henkel, A. Ghallab, D. Driesch, J. Boettger, R. Guthke, M. Pfaff, J. G. Hengstler, R. Gebhardt, D. Haeussinger, D. Drasdo, S. Zellmer.
  Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration, 2014, Hepatology (accepted for publication).
• 21M. Tang, N. Vauchelet, I. Cheddadi, I. Vignon-Clementel, D. Drasdo, B. Perthame.
  Composite waves for a cell population system modelling tumor growth and invasion, in: Chinese Annals of Mathematics - Series B, 2013, vol. 34B, n^o 2, pp. 295-318. [ DOI : 10.1007/s11401-007-0001-x ]
  http://hal.inria.fr/hal-00685063
• 22F. Thomas, D. Fisher, P. Fort, J.-P. Marie, S. Daoust, B. Roche, C. Grunau, C. Cosseau, G. Mitta, S. Baghdiguian, F. Rousset, P. Lassus, E. Assenat, D. Grégoire, D. Missé, A. Lorz, F. Billy, W. Vainchenker, F. Delhommeau, S. Koscielny, R. Itzykson, R. Tang, F. Fava, A. Ballesta, T. Lepoutre, L. Krasinska, V. Dulic, P. Raynaud, P. Blache, C. Quittau-Prevostel, E. Vignal, H. Trauchessec, B. Perthame, J. Clairambault, V. Volpert, E. Solary, U. Hibner, M. Hochberg.
  Applying ecological and evolutionary theory to cancer: a long and winding road, in: Evolutionary applications, 2013, vol. 6, n^o 1, pp. 1–10.
  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567465/pdf/eva0006-0001.pdf
• 23P. Van Liedekerke, B. Smeets, T. Odenthal, E. Tijskens, H. Ramon.
  Solving microscopic flow problems using Stokes equations in SPH, in: Computer Physics Communications, February 2013. [ DOI : 10.1016/j.cpc.2013.02.013 ]
  http://hal.inria.fr/hal-00802400
• 24G. Wainrib, J. Touboul.
  Topological and Dynamical Complexity of Random Neural Networks, in: Physical Review Letters, 2013, vol. 110, n^o 11.
• 25L. C. G. del Molino, K. Pakdaman, J. Touboul, G. Wainrib.
  Synchronization in random balanced networks, in: Physical Review E, 2013, vol. 88, n^o 4, 042824 p.

Scientific Books (or Scientific Book chapters)

• 26J. L. Avila Alonso, C. Bonnet, J. Clairambault, H. Özbay, S.-I. Niculescu, F. Merhi, A. Ballesta, R. Tang, J.-P. Marie.
  Analysis of a New Model of Cell Population Dynamics in Acute Myeloid Leukemia, in: Delay Systems : From Theory to Numerics and Applications, T. Vyhlídal, J.-F. Lafay, R. Sipahi (editors), Advances in Delays and Dynamics, Springer, January 2014, vol. 1, pp. 315–328. [ DOI : 10.1007/978-3-319-01695-5_23 ]
  http://hal.inria.fr/hal-00932779
• 27F. Billy, J. Clairambault, O. Fercoq.
  Optimisation of cancer drug treatments using cell population dynamics, in: Mathematical Methods and Models in Biomedicine, Springer, 2013, pp. 265–309.
  http://link.springer.com/chapter/10.1007/978-1-4614-4178-6_10

Other Publications

• 28J. L. Avila Alonso, C. Bonnet, H. Ozbay, J. Clairambault, S.-I. Niculescu.
  A coupled model for healthy and cancer cells dynamics in Acute Myeloid Leukemia, January 2014, The paper has been submitted to the 19th IFAC World Congress.
  http://hal.inria.fr/hal-00940245
• 29J. L. Avila Alonso, C. Bonnet, H. Ozbay, J. Clairambault, S.-I. Niculescu.
  A discrete-maturity Interconnected Model of Healthy and Cancer Cell Dynamics in Acute Myeloid Leukemia, January 2014, The paper has been submitted to the 21st International Symposium on Mathematical Theory of Networks and Systems (MTNS 2014).
  http://hal.inria.fr/hal-00940305
• 30J. Clairambault.
  Deterministic mathematical modelling for cancer chronotherapeutics: cell population dynamics and treatment optimisation, 2014, To appear in “Mathematical Oncology 2013”, A. d'Onofrio and A. Gandolfi Eds., Birkhäuser, New York..
  http://hal.inria.fr/hal-00858032
• 31J. Clairambault, O. Fercoq.
  Physiologically structured cell population dynamic models with applications to combined drug delivery optimisation in oncology, 2014, To appear in “Mathematical modelling of cancer growth and treatment”, Mostafa Bachar, Jerry Batzel, and Mark Chaplain Eds., Springer Lecture Notes in Mathematics Biosciences (LNMBIOS subseries).
  http://hal.archives-ouvertes.fr/hal-00750633
• 32J. Eliaš, L. Dimitrio, J. Clairambault, R. Natalini.
  Dynamics of p53 in single cells: physiologically based ODE and reaction-diffusion PDE models, 2013, Submitted to IOP Physical Biology.
  http://hal.inria.fr/hal-00859412
• 33F. James, N. Vauchelet.
  Equivalence between duality and gradient flow solutions for one-dimensional aggregation equations, March 2013.
  http://hal.archives-ouvertes.fr/hal-00803709
• 34F. James, N. Vauchelet.
  Numerical simulation of a hyperbolic model for chemotaxis after blow up, 2013.
  http://hal.inria.fr/hal-00772653
• 35A. Lorz, T. Lorenzi, J. Clairambault, A. Escargueil, B. Perthame.
  Effects of space structure and combination therapies on phenotypic heterogeneity and drug resistance in solid tumors, December 2013, Submitted.
  http://hal.upmc.fr/docs/00/92/12/66/PDF/AABJT1812.pdf

References in notes

• 36V. Calvez, M. Doumic Jauffret, P. Gabriel.
  Self-similarity in a General Aggregation-Fragmentation Problem; Application to Fitness Analysis, in: J. Math. Pures Appl., 2012, vol. 98, pp. 1–27.
  http://perso.ens-lyon.fr/vincent.calvez/publis/Calvez-Doumic-Gabriel-2011.pdf
• 37L. Dimitrio.
  Modelling nucleocytoplasmic transport with aplication to the intracellular dynamics of the tumor suppressor protein p53, Université Pierre et Marie Curie - Paris VI; Università degli studi di Roma I, September 2012.
  http://tel.archives-ouvertes.fr/tel-00769901
• 38M. Doumic, M. Hoffmann, P. Reynaud-Bouret, V. Rivoirard.
  Nonparametric Estimation of the Division Rate of a Size-Structured Population, in: SIAM Journal on Numerical Analysis, 2012, vol. 50, pp. 925–950.
  http://hal.archives-ouvertes.fr/hal-00578694
• 39M. Doumic, B. Perthame, J. P. Zubelli.
  Numerical Solution of an Inverse Problem in Size-Structured Population Dynamics, in: Inverse Problems, April 2009, vol. 25, n^o 4.
  http://hal.archives-ouvertes.fr/hal-00327151
• 40X. Dupuis.
  Optimal control of leukemic cell population dynamics, Inria, August 2013, n^o RR-8356, 25 p, Accepted for publication in 2014 in Mathematical Modelling of Natural Phenomena.
  http://hal.inria.fr/hal-00858208
• 41S. Hoehme, M. Brulport, A. Bauer, E. Bedawy, W. Schormann, R. Gebhardt, S. Zellmer, M. Schwarz, E. Bockamp, T. Timmel, J. Hengstler, D. Drasdo.
  Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration, in: Proc. Natl. Acad. Sci. (USA), 2010, vol. 107, n^o 23, pp. 10371–10376.
• 42F. James, N. Vauchelet.
  On the hydrodynamical limit for a one dimensional kinetic model of cell aggregation by chemotaxis, in: Riv. Mat. Univ. Parma, 2012, vol. 3, n^o 1, pp. 91–113.
  http://hal.archives-ouvertes.fr/hal-00527338
• 43B. Perthame, J. P. Zubelli.
  On the inverse problem for a size-structured population model, in: Inverse Problems, 2007, vol. 23, n^o 3, pp. 1037–1052.
  http://hal.archives-ouvertes.fr/hal-00110904
• 44S. Prigent, A. Ballesta, F. Charles, N. Lenuzza, P. Gabriel, L. M. Tine, H. Rezaei, M. Doumic.
  An Efficient Kinetic Model for Assemblies of Amyloid Fibrils and Its Application to Polyglutamine Aggregation, in: PLoS One, 2012, vol. 7(11).
  http://dx.doi.org/10.1371/journal.pone.0043273