Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

1A. Ballesta.

Approche combinée expérimentale et mathématique pour la personnalisation sur base moléculaire des thérapies anticancéreuses standards et chronomodulées, Université Paris Sud - Paris XI, June 2011.

http://hal.inria.fr/tel-00628629/en
2P. Gabriel.

Équations de transport-fragmentation et applications aux maladies à prions, Université Pierre et Marie Curie - Paris VI, June 2011.

Articles in International Peer-Reviewed Journal

3M. Artzrouni, C.B. Begg, R. Chabiniok, J. Clairambault, AJ.E. Foss, J. Hargrove, E.K. Lee, J.H. Siggers, M. Tindall.

The First International Workshop on the Role and Impact of Mathematics in Medicine: A collective account, in: Amer. J. Transl. Res., 2011, vol. 3, p. 492–497.
4E. Audusse, F. Benkhaldoun, J. Sainte-Marie, M. Seaid.

Multilayer Saint-Venant Equations over movable beds., in: DCDS-B, 2011, vol. 15, p. 917–934.
5E. Audusse, M.-O. Bristeau, M. Pelanti, J. Sainte-Marie.

Approximation of the hydrostatic Navier-Stokes system for density stratified flows by a multilayer model. Kinetic interpretation and numerical validation., in: J. Comp. Phys., 2011, vol. 230, p. 3453-3478. [ DOI : 10.1016/j.jcp.2011.01.042 ]

http://hal.inria.fr/hal-00654642/en/
6E. Audusse, M.-O. Bristeau, B. Perthame, J. Sainte-Marie.

A multilayer Saint-Venant system with mass exchanges for Shallow Water flows. Derivation and numerical validation., in: ESAIM : M2AN, 2011, vol. 45, p. 169-200. [ DOI : 10.1051/m2an/2010036 ]

http://hal.inria.fr/inria-00551428/en/
7A. Ballesta, J. Clairambault, S. Dulong, F. Lévi.

Theoretical Optimization of Irinotecan-based Anticancer Strategies in case of Drug-induced Efflux, in: Appl. Math. Lett., 2011, vol. 24, p. 1251–1256.
8A. Ballesta, S. Dulong, C. Abbara, B. Cohen, A. Okyar, J. Clairambault, F. Lévi.

A Combined Experimental and Mathematical Approach for Molecular-based Optimization of Irinotecan Circadian Delivery, in: PLoS Comp. Biol., 2011, vol. 7, e1002143 p. [ DOI : 10.1371/journal.pcbi.1002143, 2011 ]
9M.-O. Bristeau, N. Goutal, J. Sainte-Marie.

Numerical simulations of a non-hydrostatic Shallow Water model, in: Computers & fluids, 2011, vol. 47, n^o 1, p. 51-64. [ DOI : 10.1016/j.compfluid.2011.02.013 ]

http://hal.inria.fr/hal-00654634/en/
10M. J. Caceres, J. A. Carrillo, B. Perthame.

Analysis of Nonlinear Noisy Integrate and Fire Neuron Models: blow-up and steady states, in: Journal of Mathematical Neuroscience, 2011, vol. 1, n^o 7.

http://www.mathematical-neuroscience.com/content/1/1/7
11V. Calvez, M. Doumic Jauffret, P. Gabriel.

Self-similarity in a General Aggregation-Fragmentation Problem; Application to Fitness Analysis, in: J. Math. Pures Appl., November 2011, accepted.

http://hal.archives-ouvertes.fr/hal-00539279/fr/
12F. Cerreti, B. Perthame, C. Schmeiser, M. Tang, N. Vauchelet.

Waves for an hyperbolic Keller-Segel model and branching instabilities, in: Mathematical Models and Methods in Applied Sciences, 2011, vol. 21, n^o Suppl., p. 825–842.

http://arxiv.org/abs/0912.1792
13I. Cheddadi, P. Saramito, B. Dollet, C. Raufaste, F. Graner.

Understanding and predicting viscous, elastic, plastic flows, in: Eur. Phys. J. E. Soft matter, 2011, vol. 34, 11001 p. [ DOI : 10.1140/epje/i2011-11001-4 ]
14J. Clairambault.

Commitment of mathematicians in medicine. A personal experience, and generalisations, in: Acta Biotheoretica, 2011, vol. 59, p. 201–211. [ DOI : 10.1007/s10441-011-9140-2 ]
15J. Clairambault.

Optimising cancer pharmacotherapeutics using mathematical modelling and a systems biology approach, in: Personalized Medicine, 2011, vol. 8, p. 271–286.
16J. Clairambault, S. Gaubert, T. Lepoutre.

Circadian rhythm and cell population growth, in: Mathematical and Computer Modelling, 2011, vol. 53, p. 1558–1567.
17M. Doumic, M. Hoffmann, P. Reynaud, V. Rivoirard.

Nonparametric estimation of the division rate of a size-structured population, in: SIAM J. Appl. Math., 2011, vol. 71, n^o 6, p. 1918–1940.
18M. Doumic, M. Hoffmann, P. Reynaud, V. Rivoirard.

Nonparametric estimation of the division rate of a size-structured population, in: SIAM J. Num. Anal., 2011, accepted.

http://hal.archives-ouvertes.fr/hal-00578694/fr/
19D. Drasdo, S. Höhme.

Pushing, Pulling and the possible effect of a granular or cellular embedding medium on the growth of cell populations, in: New Journal of Physics, 2011, re-submitted.
20P. Gabriel.

Long-time asymptotics for nonlinear growth-fragmentation equations, in: Comm. Math. Sci., 2011, accepted.
21P. Gabriel.

The shape of the polymerization rate in the prion equation, in: Math. Comput. Modelling, 2011, vol. 53, n^o 7-8, p. 1451–1456, Submitted.
22N. Goutal, J. Sainte-Marie.

A kinetic interpretation of the section-averaged Saint-Venant system for natural river hydraulics., in: International Journal for Numerical Methods in Fluids, 2011, vol. 67, n^o 7, p. 914-938. [ DOI : 10.1002/fld.2401 ]

http://hal.inria.fr/inria-00551487/en/
23H.-G. Holzhuetter, D. Drasdo, T. Preusser, J. Lippert, A. M. Henney.

A remark on duality solutions for some weakly nonlinear scalar conservation laws, in: WIRES, 2011, in press.
24F. James, N. Vauchelet.

A remark on duality solutions for some weakly nonlinear scalar conservation laws, in: Comptes Rendus de l Académie des Sciences - Series I - Mathematics, June 2011, vol. 349, p. 657-661, 6 pages. [ DOI : 10.1016/j.crma.2011.05.004 ]

http://hal.inria.fr/hal-00591119/en
25C. Jourdana, N. Vauchelet.

Analysis of a diffusive effective mass model for nanowires, in: Kinetic and Related Models, 2011, vol. 4, n^o 4, p. 1121–1142.

http://hal.inria.fr/hal-00593984/en
26A. Lorz.

A coupled Keller–Segel–Stokes model: global existence for small initial data and blow-up delay, in: Commun. Math. Sci., 2012, vol. 10, n^o 2, p. 555–574.

http://www.intlpress.com/CMS/p/2012/issue10-2/CMSV10-2-a07-lorz.pdf
27A. Lorz, S. Mirrahimi, B. Perthame.

Dirac mass dynamics in multidimensional nonlocal parabolic equations, in: Comm. Partial Differential Equations, 2011, vol. 36, n^o 6, p. 1071–1098.

http://dx.doi.org/10.1080/03605302.2010.538784, http://arxiv.org/abs/1011.1768
28S. Mirrahimi, B. Perthame, J.Y. Wakano.

Evolution of species trait through resource competition, in: J. Math. Biol., 2011, Published on line, June 2011.

http://dx.doi.org/10.1007/s00285-011-0447-z
29G. Nadin, B. Perthame, M. Tang.

Can a traveling wave connect two unstable states? The case of the nonlocal Fisher equation, in: C. R. Math. Acad. Sci. Paris, 2011, vol. 349, n^o 9-10, p. 553–557.

http://dx.doi.org/10.1016/j.crma.2011.03.008, http://arxiv.org/abs/1011.4561
30M. Pelanti, F. Bouchut, A. Mangeney.

A Riemann Solver for Single-Phase and Two-Phase Shallow Flow Models based on Relaxation. Relations with Roe and VFRoe Solvers., in: J. Comput. Phys., 2011, vol. 230, n^o 3, p. 515-550.
31B. Perthame, C. Schmeiser, M. Tang, N. Vauchelet.

Traveling plateaus for a hyperbolic Keller-Segel system with attraction and repulsion: existence and branching instabilities, in: Nonlinearity, 2011, vol. 24, p. 1253–1270.

http://hal.inria.fr/inria-00522131
32B. Perthame, P. E. Souganidis.

A homogenization approach to flashing ratchets, in: NoDEA Nonlinear Differential Equations Appl., 2011, vol. 18, n^o 1, p. 45–58.

http://dx.doi.org/10.1007/s00030-010-0083-0
33I. Ramis-Conde, D. Drasdo.

From Genotypes to Phenotypes: classification of the tumour profiles in the cadherin adhesion pathway., in: Physical Biology, 2011, in revision.
34J. Sainte-Marie.

Vertically averaged models for the free surface Euler system. Derivation and kinetic interpretation., in: Mathematical Models and Methods in Applied Sciences, 2011, vol. 21, p. 459-490. [ DOI : 10.1142/S0218202511005118 ]

http://hal.inria.fr/inria-00551484/en/
35J. Saragosti, V. Calvez, N. Bournaveas, A. Buguin, P. Silberzan, B. Perthame.

Directional persistence of chemotactic bacteria in a traveling concentration wave, in: PNAS, 2011, vol. 108, n^o 39, p. 16235–16240.

http://www.mathematical-neuroscience.com/content/1/1/7
36H. Özbay, C. Bonnet, H. Benjelloun, J. Clairambault.

Stability analysis of cell dynamics in leukemia, in: Mathematical Modelling of Natural Phenomena, 2012, Accepted.

International Conferences with Proceedings

37F. Billy, J. Clairambault, O. Fercoq, S. Gaubert, T. Lepoutre, T. Ouillon.

Proliferation in cell population models with age structure, in: Proceedings of ICNAAM 2011, Kallithea Chalkidis (Greece), American Institute of Physics, 2011, p. 1212–1215.

http://dx.doi.org/10.1063/1.3637834
38L. Dimitrio, R. Natalini, L. Milanesi.

A Mathematical Model for the Enhanced Cytoplasmic Transport - How to Get (Faster) to the Nucleus, in: BIOINFORMATICS, 2011, p. 39-46.

Scientific Books (or Scientific Book chapters)

39F. Billy, J. Clairambault, O. Fercoq.

Optimisation of Cancer Drug Treatments Using Cell Population Dynamics, in: Mathematical Methods and Models in Biomedicine, U. Ledzewicz, H. Schättler, A. Friedman, E. Kashdan (editors), Springer, 2012, p. 257–299, in press.
40D. Drasdo, S. Höhme, J. Hengstler.

A quantitative mathematical modeling approach to liver regeneration, in: Liver regeneration, D. Häussinger (editor), De Gruyter, Boston, 2011.
41D. Drasdo, S. Höhme, J. Hengstler.

Systems biology to model liver regeneration, in: Encyclopedia of Systems Biology, O. Wolkenhauer, H. Yokota, K. Cho (editors), Springer, 2011.
42J. Hengstler, M. Gehrmann, S. Höhme, D. Drasdo, J. Steward, M. Schmidt.

Systems biology, bioinformatics and medicine approaches to cancer progression outcomes, in: Cancer Systems Biology, Bioinformatics and Medicine, A. Cesario, F. Marcus (editors), Springer, 2011, p. 297–308.
43J. Hengstler, P. Godoy, R. Reif, J. Steward, M. Schug, T. Heise, A. Oberemm, A. Bräuning, S. Zellmer, J. Boettger, R. Gebhardt, S. Höhme, D. Drasdo, M. Schwarz.

The virtual liver. Spatial-temporal modelling of tissue damage and regeneration, in: Alternative testing strategies & AXLR8-2 Workshop report on a Roadmap to innovative toxicity testing, Berlin: AXLR8 Consortium 2011, T. Seidle, H. Spielmann (editors), Springer, 2011, p. 218 – 225.
44S. Höhme, S. Hammad, A. Othman, I. von Recklinghausen, J. Boettger, R. Gebhardt, O. Dirsch, J. Hengstler, D. Drasdo.

Modeling liver regeneration in a virtual lobe, in: Medical Springer Edition, Springer, 2011.

Other Publications

45E. Audusse, C. Chalons, O. Delestre, J. Giesselmann, N. Goutal, M. Jodeau, G. Sadaka, J. Sainte-Marie.

Sediment transport modelling : relaxation schemes for Saint-Venant - Exner and three layers models., 2011, submitted.
46S. Ayata, M. Lévy, O. Aumont, O. Bernard, J. Sainte-Marie, A. Sciandra, A. Tagliabue.

Phytoplankton growth formulation in marine ecosystem models: should we take into account photo-adaptation and variable stochiometry in oligotrophic areas, 2011, submitted.
47A. Ballesta, M. Doumic Jauffret, G. Gillet.

Modelling Src control on the mitochondrial pathway of apoptosis, implications for cancer therapeutics, 2011, submitted.
48F. 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, 2012, In revision.
49A.-C. Boulanger, J. Sainte-Marie.

A 2D model for the coupling of hydrodynamics and biology. Kinetic interpretation and numerical validation within the framework of algae growth in raceways., 2011, submitted.
50A.-C. Boulanger, J. Sainte-Marie.

Analytical solutions for the free surface hydrostatic Euler equations, 2011, submitted.
51I. Cheddadi, P. Saramito, F. Graner.

Stationary Couette flows of elastoviscoplastic fluids are non-unique, 2011, Version 2, November 2011.

http://hal.inria.fr/hal-00616273/en
52M. Doumic Jauffret, M. Hoffmann, P. Reynaud-Bouret, V. Rivoirard.

Nonparametric estimation of the division rate of a size-structured population, 2011, Version1, March 2011.

http://hal.inria.fr/hal-00578694/en
53M. Doumic Jauffret, L. M. Tine.

A General Inverse Problem for the Growth-Fragmentation Equation, 2011.

http://hal.inria.fr/hal-00634539/en
54P. Gabriel, S.P. Garbett, D.R. Tyson, G.F. Webb.

The contribution of age structure to cell population responses to targeted therapeutics, 2011.

http://hal.archives-ouvertes.fr/hal-00649178/en/
55F. James, N. Vauchelet.

Chemotaxis: from kinetic equations to aggregate dynamics, 2011, 25 pages.

http://hal.inria.fr/hal-00605479/en
56A. Krinner, M. Zscharnack, A. Bader, D. Drasdo, A. Stolzing, M. Loeffler, J. Galle.

Heterogeneity of mesenchymal Stem Cell Populations emerges from Differentiation and Aging, May 2011.
57J. Touboul.

On the dynamics of mean-field equations for stochastic neural fields with delays, 2011, Arxiv 1108.2407.

http://arxiv.org/abs/1108.2407
58J. Touboul.

The propagation of chaos in Neural Fields, 2011, Arxiv 1108.2414.

http://arxiv.org/abs/1108.2414
59M. Tournus, A. Edwards, N. Seguin, B. Perthame.

Analysis of a simplified model of the urine concentration mechanism, 2011, Version 1, September 2011.

http://hal.inria.fr/hal-00605109/en

References in notes

60E. Audusse, M.-O. Bristeau.

A well-balanced positivity preserving second-order scheme for shallow water flows on unstructured meshes, in: J. Comp. Phys., 2005, vol. 206, p. 311-333.
61M. Block, E. Schöll, D. Drasdo.

Classifying the growth kinetics and surface dynamics in growing cell populations, in: Phys. Rev. Lett., 2008, vol. 99, n^o 24, p. 248101–104.
62A. Bräuning, Y. Singh, B. Rignall, A. Buchmann, S. Hammad, A. Othman, I. von Recklinghausen, P. Godoy, S. Höhme, D. Drasdo, J. Hengstler, M. Schwarz.

Phenotype and growth behavior of residual $β$ -catenin-positive hepatocytes in livers of $β$ -catenin-deficient mice, in: Histochemistry and cell biology, 2010, vol. 134, n^o 5, p. 469–481.
63H. Byrne, D. Drasdo.

Individual-based and continuum models of growing cell populations: a comparison, in: J. Math. Biol., 2009, vol. 58, n^o 4-5, p. 657–687.
64A. Decoene.

Modèle hydrostatique pour les écoulements à surface libre tridimensionnels et schémas numériques, Université Pierre et Marie Curie, Paris 6, May 2006.
65Y. Dolak, C. Schmeiser.

Kinetic models for chemotaxis: hydrodynamic limits and spatio-temporal mechanisms, in: J. Math. Biol., 2006, vol. 51, p. 595–615.
66M. Doumic, P. Maia, J. Zubelli.

On the Calibration of a Size-Structured Population Model from Experimental Data, in: Acta Biotheoretica, 2010.

http://dx.doi.org/10.1007/s10441-010-9114-9
67M. Doumic, B. Perthame, J. Zubelli.

Numerical Solution of an Inverse Problem in Size-Structured Population Dynamics, in: Inverse Problems, 2009, vol. 25, n^o electronic version, 045008 p.
68D. Drasdo.

Coarse Graining in Simulated Cell Populations, in: Adv. Complex Syst., 2005, vol. 2 & 3, p. 319–363.
69D. Drasdo, S. Höhme, M. Block.

On the Role of Physics in the Growth and Pattern Formation of Multi-Cellular Systems: What can we Learn from Individual-Cell Based Models?, in: Journal of Statistical Physics, 2007, vol. 128, n^o 1-2, p. 287–345.
70D. Drasdo, S. Höhme.

A single-cell-based model of tumor growth in vitro: monolayers and spheroids, in: Phys. Biol., 2005, vol. 2, p. 133–147.
71D. Drasdo, N. Jagiella, I. Ramis-Conde, I. Vignon-Clémentel, W. Weens.

Modeling steps from a benign tumor to an invasive cancer: examples of intrinsically multi-scale problems, in: From single scale-based models to multiscale modeling, Eds. Chauvière, A. and Preziozi, L. and Verdier, C., 2009.
72D. Drasdo, M. Kruspe.

Emergence of regulatory networks in simulated evolutionary processes, in: Adv. Complex Syst., 2005, vol. 2 & 3, p. 285–318.
73J. Galle, A. Krinner, P. Buske, D. Drasdo, M. Loeffler.

On the impact of single cell biomechanics on the spatio-temporal organization of regenerative tissue, in: World Congress on Medical Physics and Biomedical Engineering, 2009, p. 185–188.
74J. Galle, M. Loeffler, D. Drasdo.

Modelling the effect of deregulated proliferation and apoptosis on the growth dynamics of epithelial cell populations in vitro, in: Biophys. J., 2005, vol. 88, p. 62–75.
75J.-F. Gerbeau, B. Perthame.

Derivation of Viscous Saint-Venant System for Laminar Shallow Water; Numerical Validation, in: Discrete and Continuous Dynamical Systems, Ser. B, 2001, vol. 1, n^o 1, p. 89-102.
76S. Höhme, 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, p. 10371–10376.
77S. Höhme, D. Drasdo.

A cell-based simulation software for multi-cellular systems, in: Bioinformatics, 2010, vol. 26, n^o 20, p. 2641–2642.
78S. Höhme, D. Drasdo.

Biomechanical versus nutrient control: what determines the growth dynamics of mammalian cell population?, in: Mathematical Population Studies, 2010, vol. 17, n^o 3, p. 166–187.
79S. Höhme, J.G. Hengstler, M. Brulport, A. Bauer, D. Drasdo.

Towards modeling liver lobule regeneration in 3D, in: Proceedings of the Fifth International Workshop on Computational Systems Biology, Leipzig, 2008, p. 61–64.
80S. Höhme, J. Hengstler, M. Brulport, M. Schäfer, A. Bauer, R. Gebhardt, D. Drasdo.

Mathematical modelling of liver regeneration after intoxication with CC14, in: Chemico-Biological Interaction, 2007, vol. 168, p. 74–93.
81S. Höhme.

Agent-based modeling of growing cell populations and the regenerating liver based on image processing, Doctoral School, Faculty of Mathematics and Computer Science, University of Leipzig, April 2010.
82F. James, N. Vauchelet.

On the hydrodynamical limit for a one dimensional kinetic model of cell aggregation by chemotaxis, in: Rivista di Matematica dell' Università di Parma, Special Issue, 2010, accepted.

http://hal.archives-ouvertes.fr/hal-00527338/fr/
83A. Krinner, M. Hoffmann, M. Loeffler, D. Drasdo, J. Galle.

Individual fates of mesenchymal stem cells in vitro, in: BMC Systems Biology, May 2010, vol. 4, n^o 73.

http://dx.doi.org/10.1186/1752-0509-4-73
84A. Krinner.

Multi-scale individual-based models, Doctoral School, Faculty of Mathematics and Computer Science, University of Leipzig, June 2010.
85A. Krinner, M. Zscharnack, A. Bader, D. Drasdo, J. Galle.

The impact of the oxygen environment on mesenchyma stem cell expansion and chondrogenic differentiation, in: Cell Proliferation, 2009.
86F. Lévi, A. Okyar, S. Dulong, P. Innominato, J. Clairambault.

Circadian Timing in Cancer Treatments., in: Annual Review of Pharmacology and Toxicology, 2010, vol. 50, p. 377–421.
87K. Missal, M. Cross, D. Drasdo.

Reverse engineering of gene regulatory networks for incomplete expression data: Transciptional control of haemopoietic commitment, in: Bioinformatics, 2006, vol. 22, p. 731–738.
88B. Perthame, J. Zubelli.

On the inverse problem for a size-structured population model, in: Inverse Problems, 2007, vol. 23, n^o 3, p. 1037–1052.
89M. Radszuweit, M. Block, J. Hengstler, E. Schöll, D. Drasdo.

Comparing the growth kinetics of cell populations in two and three dimensions, in: Phys. Rev. E, 2009, vol. 79, n^o 051907.
90I. Ramis-Conde, M.A.J. Chaplain, A.R.A. Anderson, D. Drasdo.

Modelling the influence of E-cadherin- $β$ -catenin pathway in cancer cell invasion: A multi-scale approach, in: Biophys., 2008, vol. 95, p. 155-165.
91I. Ramis-Conde, M. Chaplain, A. Anderson, D. Drasdo.

Multi-scale modelling of cell intravasation: role of cadherins in metastasis, in: Phys. Biol., 2009, vol. 6, n^o 1, p. 16008-16020.
92M. Rohrschneider, G. Scheuermann, S. Höhme, D. Drasdo.

Shape Characterization of Extracted and Simulated Tumor Samples using Topological and Geometric Measures, in: IEEE Engineering in Medicine and Biology Conference 2007, 2007, p. 6271–6277.
93N. Vauchelet.

Numerical simulation of a kinetic model for chemotaxis, in: Kin. Rel. Models, 2010, vol. 3, n^o 3, p. 501–528.

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