Members
Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

[1]
W. Haffaf.
Analysis of Protein Aggregation in Amyloid Neurodegenerative Diseases - Case of Prion Diseases, Université Pierre et Marie Curie - Laboratoire Jacques-Louis Lions ; Inria , October 2014.
https://tel.archives-ouvertes.fr/tel-01079779
[2]
N. Vauchelet.
Contributions mathématiques à l'étude de modèles décrivant le mouvement de particules confinées et de micro-organismes, Université Pierre et Marie Curie, December 2014, Habilitation à diriger des recherches.
https://hal.archives-ouvertes.fr/tel-01111810

Articles in International Peer-Reviewed Journals

[3]
F. Bertaux, S. Stoma, D. Drasdo, G. Batt.
Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance, in: PLoS Computational Biology, 2014, vol. 10, no 10, 14 p. [ DOI : 10.1371/journal.pcbi.1003893.s016 ]
https://hal.inria.fr/hal-00942885
[4]
F. 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, February 2014, vol. 96, pp. 66-94. [ DOI : 10.1016/j.matcom.2012.03.005 ]
https://hal.archives-ouvertes.fr/hal-00662885
[5]
T. Bourgeron, M. Doumic-Jauffret, M. Escobedo.
Estimating the Division Rate of the Self-Similar Growth-Fragmentation Equation, in: Inverse Problem, January 2014, vol. 30, no 2, 025007, 28 p.
https://hal.inria.fr/hal-00858488
[6]
D. Drasdo, J. Bode, U. Dahmen, O. Dirsch, S. Dooley, R. Gebhardt, A. Ghallab, P. Godoy, D. Häussinger, S. Hammad, S. Hoehme, H.-G. Holzhütter, U. Klingmüller, L. Kuepfer, J. Timmer, M. Zerial, J. G. Hengstler.
The virtual liver: state of the art and future perspectives, in: Archives of Toxicology, December 2014, pp. 2071-2075. [ DOI : 10.1007/s00204-014-1384-6 ]
https://hal.inria.fr/hal-01110684
[7]
D. Drasdo, S. Hoehme, J. G. Hengstler.
How predictive quantitative modeling of tissue organization can inform liver disease pathogenesis, in: Journal of Hepatology, October 2014, vol. 61, no 4, pp. 951–956. [ DOI : 10.1016/j.jhep.2014.06.013 ]
https://hal.inria.fr/hal-01110644
[8]
J. Eliaš, J. Clairambault.
Reaction-diffusion systems for spatio-temporal intracellular protein networks: a beginner's guide with two examples, in: Computational and structural biotechnology journal, June 2014, 11 p. [ DOI : 10.1016/j.csbj.2014.05.007 ]
https://hal.inria.fr/hal-00957344
[9]
J. Eliaš, L. Dimitrio, J. Clairambault, R. Natalini.
Dynamics of p53 in single cells: physiologically based ODE and reaction-diffusion PDE models, in: Physical Biology, July 2014, 22 p, Phys. Biol. 11 (2014) 045001. [ DOI : 10.1088/1478-3975/11/4/045001 ]
https://hal.inria.fr/hal-00859412
[10]
S. Hammad, S. Hoehme, A. Friebel, I. von Recklinghausen, A. Othman, B. Begher-Tibbe, R. Reif, P. Godoy, T. Johann, A. Vartak, K. Golka, P. O. Bucur, E. Vibert, R. Marchan, B. Christ, S. Dooley, C. Meyer, I. Ilkavets, U. Dahmen, O. Dirsch, J. Böttger, R. Gebhardt, D. Drasdo, J. G. Hengstler.
Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis, in: Archives of Toxicology, May 2014, vol. 88, no 5, pp. 1161-1183. [ DOI : 10.1007/s00204-014-1243-5 ]
https://hal.inria.fr/hal-01110657
[11]
P.-L. Lions, B. Perthame, P. E. Souganidis.
Scalar conservation laws with rough (stochastic) fluxes; the spatially dependent case, in: Stochastic Partial Differential Equations : Analysis and Computations, December 2014, vol. 2, no 4, pp. 517-538. [ DOI : 10.1007/s40072-014-0038-2 ]
https://hal.archives-ouvertes.fr/hal-00960332
[12]
J. C. Lopez Alfonso, N. Jagiella, L. Núñez, M. Herrero, D. Drasdo.
Estimating Dose Painting Effects in Radiotherapy: A Mathematical Model, in: PLoS ONE, February 2014, vol. 9, no 2, 22 p. [ DOI : 10.1371/journal.pone.0089380 ]
https://hal.inria.fr/hal-01109675
[13]
A. Lorz, B. Perthame.
Long-term analysis of phenotypically structured models, in: Proceedings of the Royal Society of London. Series A, Mathematical and physical sciences, April 2014, vol. 470, no 2167, pp. 1-10. [ DOI : 10.1098/rspa.2014.0089 ]
https://hal.archives-ouvertes.fr/hal-00941097
[14]
B. Perthame, N. Seguin, M. Tournus.
A simple derivation of BV bounds for inhomogeneous relaxation systems, in: Communications in Mathematical Sciences, 2014, vol. 13, no 2, pp. 577-586.
https://hal.archives-ouvertes.fr/hal-00974269
[15]
S. Prigent, W. Haffaf, H. T. Banks, M. Hoffmann, H. Rezaei, M. Doumic-Jauffret.
Size distribution of amyloid brils. Mathematical models and experimental data, in: International Journal of Pure and Applied Mathematics, June 2014, vol. 93, no 6, pp. 845-878. [ DOI : 10.12732/ijpam.v93i6.10 ]
http://hal.upmc.fr/hal-00958785
[16]
L. Robert, M. Hoffmann, N. Krell, S. Aymerich, J. Robert, M. Doumic-Jauffret.
Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism, in: BMC Biology, 2014, vol. 12, no 1, 17 p. [ DOI : 10.1186/1741-7007-12-17 ]
https://hal.inria.fr/hal-00981312
[17]
F. Schliess, S. Hoehme, S. Henkel, A. Ghallab, D. Driesch, J. Böttger, R. Guthke, M. Pfaff, J. Hengstler, R. Gebhardt, D. Häussinger, D. Drasdo, S. Zellmer.
Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration, in: Hepatology, December 2014, vol. 60, no 6, pp. 2040–2051.
https://hal.inria.fr/hal-01110646
[18]
B. Smeets, T. Odenthal, J. Keresztes, S. Vanmaercke, P. Van Liedekerke, E. Tijskens, W. Saeys, H. Van Oosterwyck, H. Ramon.
Modeling contact interactions between triangulated rounded bodies for the discrete element method, in: Computer Methods in Applied Mechanics and Engineering, May 2014, vol. 277, pp. 219-238. [ DOI : 10.1016/j.cma.2014.04.017 ]
https://hal.inria.fr/hal-00999663
[19]
O. Wolkenhauer, C. Auffray, O. Brass, J. Clairambault, A. Deutsch, D. Drasdo, F. Gervasio, L. Preziosi, P. Maini, A. Marciniak-Czochra, C. Kossow, L. Kuepfer, K. Rateitschak, I. Ramis-Conde, B. Ribba, A. Schuppert, R. Smallwood, G. Stamatakos, F. Winter, H. Byrne.
Enabling multiscale modeling in systems medicine: From reactions in cells to organ physiology, in: Genome Medicine, May 2014, vol. 6, no 21, 3 p.
https://hal.inria.fr/hal-01109002

Invited Conferences

[20]
B. Perthame.
Some mathematical aspects of tumor growth and therapy, in: ICM 2014 - International Congress of Mathematicians, Seoul, South Korea, August 2014.
http://hal.upmc.fr/hal-01059766

International Conferences with Proceedings

[21]
J. L. Avila Alonso, C. Bonnet, E. Fridman, F. Mazenc, J. Clairambault.
Stability analysis of PDE’s modelling cell dynamics in Acute Myeloid Leukemia , in: 53rd IEEE Conference on Decision and Control, Los Angeles, United States, December 2014.
https://hal.inria.fr/hal-01110304
[22]
J. 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, in: The 19th World Congress of the International Federation of Automatic Control, Groningen, South Africa, August 2014.
https://hal.inria.fr/hal-00940245
[23]
J. 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, in: Mathematical Theory of Networks and Systems, Groningen, Netherlands, July 2014.
https://hal.inria.fr/hal-00940305

Conferences without Proceedings

[24]
C. Bonnet, J. L. Avila Alonso, H. Ozbay, J. Clairambault, S.-I. Niculescu, P. Hirsch.
A Discrete-Maturity Interconnected Model of Healthy and Cancer Cell Dynamics in Acute Myeloid Leukemia, in: The 10th AIMS Conference on Dynamical Systems,Differential Equations and Applications, Madrid, Spain, July 2014.
https://hal.inria.fr/hal-01110309

Scientific Books (or Scientific Book chapters)

[25]
J. L. Avila Alonso, C. Bonnet, J. Clairambault, H. Ozbay, 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 ]
https://hal.inria.fr/hal-00932779

Scientific Popularization

[26]
J. Clairambault.
Perspective on "New and Less New Opportunities For Mathematical Biology as Applied To Biological and Clinical Medicine", in: Society of Mathematical Biology Newsletter, May 2014, vol. 27, no 2, 2 p.
https://hal.inria.fr/hal-01108995
[27]
J. Clairambault.
My Personal Journey In Mathematical Biology & Medicine, in: Society of Mathematical Biology Newsletter, January 2015, vol. 28, no 1, 2 p.
https://hal.inria.fr/hal-01109000

Other Publications

[28]
L. Almeida, C. Emako, N. Vauchelet.
Existence and diffusive limit of a two-species kinetic model of chemotaxis, April 2014.
https://hal.archives-ouvertes.fr/hal-00980594
[29]
H. T. Banks, M. Doumic-Jauffret, C. Kruse.
Efficient Numerical Schemes for Nucleation-Aggregation Models: Early Steps, March 2014.
https://hal.inria.fr/hal-00954437
[30]
L. Boudin, C. Grandmont, A. Lorz, A. Moussa.
Modelling and numerics for respiratory aerosols, July 2014.
https://hal.archives-ouvertes.fr/hal-01044590
[31]
J. A. Carrillo, F. James, F. Lagoutière, N. Vauchelet.
The Filippov characteristic flow for the aggregation equation with mildly singular potentials, September 2014, 33 pages.
https://hal.archives-ouvertes.fr/hal-01061991
[32]
J. Carrillo, B. Perthame, D. Salort, D. Smets.
Qualitative Properties of Solutions for the Noisy Integrate & Fire model in Computational Neuroscience, November 2014.
https://hal.archives-ouvertes.fr/hal-01079381
[33]
R. H. Chisholm, T. Lorenzi, A. Lorz, A. K. Larsen, L. Almeida, A. Escargueil, J. Clairambault.
Emergence of drug tolerance in cancer cell populations: an evolutionary outcome of selection, non-genetic instability and stress-induced adaptation, January 2015, First submitted version.
https://hal.archives-ouvertes.fr/hal-01111271
[34]
M. Doumic-Jauffret, M. Escobedo.
Time Asymptotics for a Critical Case in Fragmentation and Growth-Fragmentation Equations, January 2015.
https://hal.inria.fr/hal-01080361
[35]
J. Haskovec, P. Markowich, B. Perthame.
Mathematical Analysis of a System for Biological Network Formation, May 2014.
http://hal.upmc.fr/hal-00998344
[36]
F. James, N. Vauchelet.
Equivalence between duality and gradient flow solutions for one-dimensional aggregation equations, September 2014.
https://hal.archives-ouvertes.fr/hal-00803709
[37]
F. James, N. Vauchelet.
Numerical methods for one-dimensional aggregation equations, October 2014.
https://hal.archives-ouvertes.fr/hal-00955971
[38]
C. Jourdana, P. Pietra, N. Vauchelet.
A classical-quantum coupling strategy for a hierarchy of one dimensional models for semiconductors, 2014.
https://hal.archives-ouvertes.fr/hal-01052415
[39]
M. Kolwalczyk, B. Perthame, N. Vauchelet.
Transversal instability for the thermodiffusive reaction-diffusion system, January 2014, 13 pages.
https://hal.archives-ouvertes.fr/hal-00939013
[40]
A. Lorz, T. Lorenzi, J. Clairambault, A. Escargueil, B. Perthame.
Modeling the effects of space structure and combination therapies on phenotypic heterogeneity and drug resistance in solid tumors, June 2014.
http://hal.upmc.fr/hal-00921266
[41]
S. Mirrahimi, B. Perthame.
Asymptotic analysis of a selection model with space, July 2014.
https://hal.archives-ouvertes.fr/hal-01030762
[42]
B. Perthame, C. Quiñinao, J. Touboul.
Competition and boundary formation in heterogeneous media: Application to neuronal differentiation, August 2014.
https://hal.archives-ouvertes.fr/hal-01054813
[43]
B. Perthame, M. Tang, N. Vauchelet.
Traveling wave solution of the Hele-Shaw model of tumor growth with nutrient, January 2014, 25 pages.
https://hal.archives-ouvertes.fr/hal-00931399
[44]
B. Perthame, N. Vauchelet.
Incompressible limit of mechanical model of tumor growth with viscosity, September 2014, 17 pages.
https://hal.archives-ouvertes.fr/hal-01066494
[45]
S. Prigent, W. Haffaf.
Modelling and analysis of protein aggregation - completing pathways in prion (PrP) polymerisation, January 2014.
http://hal.upmc.fr/hal-00958804
References in notes
[46]
L. Almeida, P. Bagnerini, A. Habbal.
Modeling actin cable contraction, in: Computer and mathematics with applications, 2012, vol. 64, no 3, pp. 310-321.
https://hal.inria.fr/hal-00648724
[47]
L. Almeida, P. Bagnerini, A. Habbal, S. Noselli, F. Serman.
A Mathematical Model for Dorsal Closure, in: Journal of Theoretical Biology, January 2011, vol. 268, no 1, pp. 105-119. [ DOI : 10.1016/j.jtbi.2010.09.029 ]
https://hal.inria.fr/inria-00544350
[48]
F. 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, 2013, vol. 18, no 4, pp. 865 - 889, 24 pages. [ DOI : 10.3934/dcdsb.2013.18.865 ]
https://hal.archives-ouvertes.fr/hal-00726195
[49]
F. 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), Lecture Notes on Mathematical Modelling in the Life Sciences, Springer New York, January 2013, 265 p. [ DOI : 10.1007/978-1-4614-4178-6_10 ]
https://hal.archives-ouvertes.fr/hal-00770366
[50]
V. Calvez, M. Doumic-Jauffret, P. Gabriel.
Self-similarity in a General Aggregation-Fragmentation Problem ; Application to Fitness Analysis, in: J. Maths Pures Appl., November 2010, vol. 98, pp. 1-27.
https://hal.archives-ouvertes.fr/hal-00539279
[51]
M. Doumic-Jauffret, P. Gabriel.
Eigenelements of a General Aggregation-Fragmentation Model, in: Mathematical Models and Methods in Applied Sciences, May 2010, vol. 20, pp. 757-783.
https://hal.archives-ouvertes.fr/hal-00408088
[52]
M. Doumic-Jauffret, M. Hoffmann, N. Krell, L. Robert.
Statistical estimation of a growth-fragmentation model observed on a genealogical tree, October 2012, 46 pages, 4 figures.
https://hal.archives-ouvertes.fr/hal-00763601
[53]
M. Doumic-Jauffret, M. Hoffmann, P. Reynaud-Bouret, V. Rivoirard.
Nonparametric estimation of the division rate of a size-structured population, in: SIAM Journal on Numerical Analysis, April 2012, vol. 50, no 2, pp. 925–950. [ DOI : 10.1137/110828344 ]
https://hal.archives-ouvertes.fr/hal-00578694
[54]
D. Drasdo, S. Hoehme, 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, no 1-2, pp. 287–345.
http://dx.doi.org/10.1007/s10955-007-9289-x
[55]
J. 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, 2013. [ DOI : 10.1016/j.bbapap.2013.09.019 ]
https://hal.inria.fr/hal-00822308
[56]
J. Galle, G. Aust, G. Schaller, T. Beyer, D. Drasdo.
Individual cell-based models of the spatial-temporal organization of multicellular systems–achievements and limitations., in: Cytometry. Part A : the journal of the International Society for Analytical Cytology, July 2006, vol. 69, no 7, pp. 704–10. [ DOI : 10.1002/cyto.a.20287 ]
http://www.ncbi.nlm.nih.gov/pubmed/16807896
[57]
S. Hoehme, M. Brulport, A. Bauer, E. Bedawy, W. Schormann, M. Hermes, V. Puppe, R. Gebhardt, S. Zellmer, M. Schwarz, E. Bockamp, T. Timmel, J. G. Hengstler, D. Drasdo.
Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration, in: Proceedings of the National Academy of Sciences, 2010, vol. 107, no 23, pp. 10371–10376.
[58]
A. Lorz, T. Lorenzi, M. E. Hochberg, J. Clairambault, B. Perthame.
Populational adaptive evolution, chemotherapeutic resistance and multiple anti-cancer therapies, in: ESAIM: Mathematical Modelling and Numerical Analysis, March 2013, 23 p. [ DOI : 10.1051/m2an/2012031 ]
https://hal.archives-ouvertes.fr/hal-00714274
[59]
A. Lorz, S. Mirrahimi, B. Perthame.
Dirac mass dynamics in a multidimensional nonlocal parabolic equation, in: Communications in Partial Differential Equations, 2011, vol. 36, pp. 1071-1098. [ DOI : 10.1080/03605302.2010.538784 ]
https://hal.archives-ouvertes.fr/hal-00533693
[60]
S. Mirrahimi, B. Perthame, J. Y. Wakano.
Evolution of species trait through resource competition, in: Journal of Mathematical Biology, June 2012, vol. 64, no 7, pp. 1189-1223, 28 pages. [ DOI : 10.1007/s00285-011-0447-z ]
https://hal.archives-ouvertes.fr/hal-00566888
[61]
B. Perthame, F. Quirós, M. Tang, N. Vauchelet.
Derivation of a Hele-Shaw type system from a cell model with active motion, July 2013.
http://hal.upmc.fr/hal-00906168
[62]
M. Radszuweit, M. Block, J. G. Hengstler, E. Schöll, D. Drasdo.
Comparing the growth kinetics of cell populations in two and three dimensions, in: Phys. Rev. E, May 2009, vol. 79, 051907.
http://link.aps.org/doi/10.1103/PhysRevE.79.051907
[63]
M. 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, no 2, pp. 295-318. [ DOI : 10.1007/s11401-007-0001-x ]
https://hal.archives-ouvertes.fr/hal-00685063