CS Library

2018

La présidentielle 2017 au prisme de Twitter. (2018, September 19). Retrieved September 19, 2018, from https://lejournal.cnrs.fr/articles/la-presidentielle-2017-au-prisme-de-twitter
Wilmet, A., Viard, T., Latapy, M., & Lamarche-Perrin, R. (2018). Degree-based Outliers Detection within IP Traffic Modelled as a Link Stream. Retrieved from http://www.complexnetworks.fr/wp-content/uploads/2018/06/accepted_version_article.pdf
Sénécat, A. (2018, September 19). Intox, polarisation, risques de manipulation : les leçons de la présidentielle vue de Twitter. Le Monde.fr. Retrieved from https://www.lemonde.fr/le-blog-du-decodex/article/2018/09/19/intox-polarisation-risques-de-manipulation-les-lecons-de-la-presidentielle-vue-de-twitter_5357508_5095029.html
La Dépeche. (2018, September 19). Fake news : ce sont les pro-Fillon qui en auraient partagé le plus pendant la Présidentielle. Retrieved September 21, 2018, from https://www.ladepeche.fr/article/2018/09/20/2872449-fake-news-sont-pro-fillon-auraient-partage-plus-pendant-presidentielle.html
L’Express. (2018, September 21). Fillonistes, mélenchonistes ou macronistes, qui a fait quoi sur Twitter pendant la présidentielle 2017. Retrieved September 21, 2018, from https://www.lexpress.fr/actualite/politique/fillonistes-melenchonistes-ou-macronistes-qui-a-fait-quoi-sur-twitter-pendant-la-presidentielle-2017_2036143.html
Gaumont, N., Panahi, M., & Chavalarias, D. (2018). Reconstruction of the socio-semantic dynamics of political activist Twitter networks—Method and application to the 2017 French presidential election. PLOS ONE, 13(9), e0201879. https://doi.org/10.1371/journal.pone.0201879
Chavalarias, D. (2018, November 7). Fake news : l’arbre qui cache la forêt. Retrieved November 7, 2018, from https://aoc.media/analyse/2018/11/07/fake-news-larbre-cache-foret/
Albert, S., Michl, M., Lunkenheimer, P., Loidl, A., Déjardin, P. M., & Ladieu, F. (2018). Third and Fifth Harmonic Responses in Viscous Liquids. In Nonlinear Dielectric Spectroscopy (pp. 219–260). Springer, Cham. https://doi.org/10.1007/978-3-319-77574-6_7

2017

Vibert, J., & Thomas-Vaslin, V. (2017). Modelling T cell proliferation: Dynamics heterogeneity depending on cell differentiation, age, and genetic background. PLOS Computational Biology, 13(3), e1005417. https://doi.org/10.1371/journal.pcbi.1005417
Thomas-Vaslin, V. (2017). Questionnements et connaissance de la complexité. Editions Matériologiques. Retrieved from https://hal.archives-ouvertes.fr/hal-01499478
Thomas-Vaslin, V. (2017). Le rôle des traces dans le système immunitaire : des anticorps au corps. (Paris CNRS éditions, Vol. 4). Retrieved from http://www.cnrseditions.fr/sociologie-ethnologie-anthropologie/7489-l-homme-trace.html%7D
Latapy, M., & Chavalarias, D. (2017). L’analyse à grande échelle de nos traces numériques. In Les Big Data à Découvert (CNRS Éditions).
Julien Delile, M. H., & Nadine Peyriéras, R. D. (2017). A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation. Nature Communication, (13929). https://doi.org/doi: 10.1038/ncomms13929

2016

Villoutreix, P., Delile, J., Rizzi, B., Duloquin, L., Savy, T., Bourgine, P., … Peyri’eras, N. (2016). An integrated modelling framework from cells to organism based on a cohort of digital embryos. Scientific Reports, 6, 37438. Retrieved from http://www.nature.com/articles/srep37438
Véronique Thomas-Vaslin, & Frédéric Jacquemart. (2016). Approche de la résilience et perturbations des systèmes complexes par une évaluation globale. Presented at the Congrès mondial pour la pensée complexe: Les défis d’un monde globalisé, Paris, France. Retrieved from https://hal.archives-ouvertes.fr/hal-01427233
Véronique Thomas-Vaslin, & Frédéric Jacquemart. (2016). L’évaluation globale des technologies. In La Fièvre de l’évaluation (Presses Universitaires du Septentrion, 2016, p. 196 p.). Bertrand Bocquet. Retrieved from https://hal.archives-ouvertes.fr/hal-01298219
Mathieu Le Goc, Lawrence H. Kim, Ali Parsaei, Jean-Daniel Fekete, Pierre Dragicevic, & Sean Follmer. (2016). Zooids: Building Blocks for Swarm User Interfaces. Presented at the UIST ’16 Proceedings of the 29th Annual Symposium on User Interface Software and Technology, Tokyo, Japan: ACM. https://doi.org/10.1145/2984511.2984547
Kowaliw, T., & Doursat, R. (2016). Bias-variance decomposition in Genetic Programming. Open Mathematics, (14), 62–80. https://doi.org/http://doursat.free.fr/docs/Kowaliw_Doursat_2016_bvgp_OpenMath.pdf
Chavalarias, D., Wallach, J. D., Li, A. H. T., & Ioannidis, J. P. A. (2016). Evolution of Reporting P Values in the Biomedical Literature, 1990-2015. JAMA, 315(11), 1141. https://doi.org/10.1001/jama.2016.1952
Chavalarias, D. (2016). What’s wrong with Science? Scientometrics, 1–23. https://doi.org/10.1007/s11192-016-2109-9
Chavalarias, D. (2016). The unlikely encounter between von Foerster and Snowden: When second-order cybernetics sheds light on societal impacts of Big Data. Big Data & Society, 3(1), 2053951715621086. https://doi.org/10.1177/2053951715621086
Bouyrie, M., Cornuéjols, A., Manfredotti, C., & Peyriéras, N. (2016). Denoising 3D microscopy images of cell nuclei using shape priors on an anisotropic grid. In Proc. of ICPRAM-2016. Rome, Italy.
Albert, S., Bauer, T., Michl, M., Biroli, G., Bouchaud, J.-P., Loidl, A., … Ladieu, F. (2016). Fifth-order susceptibility unveils growth of thermodynamic amorphous order in glass-formers. Science, 352(6291), 1308–1311. https://doi.org/10.1126/science.aaf3182

2015

Varenne, F., Chaigneau, P., Petitot, J., & Doursat, R. (2015). Programming the Emergence in Morphogenetically Architected Complex Systems. Acta Biotheoretica, 63(3), 295–308. https://doi.org/10.1007/s10441-015-9262-z
Thomas-Vaslin, V. (2015). Complexité multi-échelle du système immunitaire: Evolution, du chaos aux fractales. In Le vivant critique et chaotique (1re édition, p. 424). Retrieved from http://materiologiques.com/modelisations-simulations-systemes-complexes-2425-5661/206-le-vivant-critique-et-chaotique-9782919694938.html
Schmitt, C., Rey, S., Reuillon, R., & Pumain, D. (2015). Half a billion simulations: Evolutionary algorithms and distributed computing for calibrating the SimpopLocal geographical model. Environment and Planning B., 42(2), 300–315.
Rule, A., Cointet, J.-P., & Bearman, P. S. (2015). Lexical shifts, substantive changes, and continuity in State of the Union discourse, 1790–2014. Proceedings of the National Academy of Sciences, 112(35), 10837–10844. https://doi.org/10.1073/pnas.1512221112
Rouquier, J.-B., Alvarez, I., Reuillon, R., & Wuillemin, P.-H. (2015). A kd-tree algorithm to discover the boundary of a black box hypervolume. Annals of Mathematics and Artificial Intelligence, 1–16. https://doi.org/10.1007/s10472-015-9456-8
Rioult, M., Datta, S., Stanescu, D., Stanescu, S., Belkhou, R., Maccherozzi, F., … Barbier, A. (2015). Tailoring the photocurrent in BaTiO3/Nb:SrTiO3 photoanodes by controlled ferroelectric polarization. Applied Physics Letters, 107(10), 103901. https://doi.org/10.1063/1.4930814
Reuillon, R., Schmitt, C., De Aldama, R., & Mouret, J.-B. (2015). A New Method to Evaluate Simulation Models: The Calibration Profile (CP) Algorithm. Journal of Artificial Societies and Social Simulation, 18(1), 12. Retrieved from http://jasss.soc.surrey.ac.uk/18/1/12.html
Reuillon, R., Leclaire, M., & Passerat-Palmbach, J. (2015). Model Exploration Using OpenMOLE - a workflow engine for large scale distributed design of experiments and parameter tuning. CoRR, abs/1506.04182. Retrieved from http://dblp.uni-trier.de/db/journals/corr/corr1506.html#ReuillonLP15
Mesmoudi, S., Rodic, M., Cioli, C., Cointet, J.-P., Yarkoni, T., & Burnod, Y. (2015). LinkRbrain: Multi-scale data integrator of the brain. Journal of Neuroscience Methods, 241(0), 44–52. https://doi.org/http://dx.doi.org/10.1016/j.jneumeth.2014.12.008
Lopez-Rincon, A., Bendahmane, M., & Ainseba, B. (2015). On 3D numerical inverse problems for the bidomain model in electrocardiology. Computers  Mathematics with Applications, 69(4), 255–274. https://doi.org/http://dx.doi.org/10.1016/j.camwa.2014.09.022
Glade, N., & Stephanou, A. (Eds.). (2015). Le vivant critique et chaotique. In Véronique Thomas-Vaslin, Le vivant critique et chaotique. Paris: Editions Matériologiques.
Faure, E., Campana, M., Cunderlik, R., Drblikova, O., Duloquin, L., Keller, R., … Bourgine, P. (2015). From 3D+time imaging of developing model organisms to the reconstruction and analysis of their digital lineage trees with the BioEmergences workflow. Nature Methods, p. (In Press).
Ducruet, C., & Itoh, H. (2015). Regions and material flows: investigating the regional branching and industry relatedness of port traffics in a global perspective. Journal of Economic Geography. https://doi.org/10.1093/jeg/lbv010
Deffuant, G., Banos, A., Chavalarias, D., Bertelle, C., Brodu, N., Jensen, P., … Varenne, F. (2015). Visions de la complexité. Le démon de Laplace dans tous ses états. Natures Sciences Sociétés, 23(1), 42–53. https://doi.org/10.1051/nss/2015007
De Domenico, M., Sole-Ribalta, A., Omodei, E., Gomez, S., & Arenas, A. (2015). Ranking in interconnected multilayer networks reveals versatile nodes. Nat Commun, 6. Retrieved from http://dx.doi.org/10.1038/ncomms7868
Darmon, D., Omodei, E., & Garland, J. (2015). Followers Are Not Enough: A Multifaceted Approach to Community Detection in Online Social Networks. PLOS ONE, 10(8), e0134860. https://doi.org/10.1371/journal.pone.0134860
Cottineau, C., Chapron, P., & Reuillon, R. (2015). Growing Models from the Bottom Up. an Evaluation-Based Incremental Modelling Method (EBIMM) Applied to the Simulation of Systems of Cities. Journal of Artificial Societies and Social Simulation, 18(4). https://doi.org/10.18564/jasss.2828
Cottineau, C., Chapron, P., & Reuillon, R. (2015). An incremental method for building and evaluating agent-based models of systems of cities. Journal of Artificial Societies and Social Simulation (JASSS).
Chérel, G., Cottineau, C., & Reuillon, R. (2015). Beyond Corroboration: Strengthening Model Validation by Looking for Unexpected Patterns. PLOS ONE, 10(9), e0138212. https://doi.org/10.1371/journal.pone.0138212
Barbier, A., Aghavnian, T., Badjeck, V., Mocuta, C., Stanescu, D., Magnan, H., … Jedrecy, N. (2015). Antiferromagnetic long-range spin ordering in Fe- and NiFe2-doped BaTiO3 multiferroic layers. PHYSICAL REVIEW B, 91(3). https://doi.org/10.1103/PhysRevB.91.035417

2014

Thomas-Vaslin, V. (2014). A Complex Immunological Idiotypic Network for Maintenance of Tolerance. Frontiers in Immunology, 5. https://doi.org/10.3389/fimmu.2014.00369
Rincon, A. L., Bendahmane, M., & Ainseba, B. (2014). Two-step genetic algorithm to solve the inverse problem in electrocardiography for cardiac sources. Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 2(3), 129–137. https://doi.org/10.1080/21681163.2013.814295
Omodei, E., Bazzani, A., Rambaldi, S., Michieletto, P., & Giorgini, B. (2014). The physics of the city: pedestrians dynamics and crowding panic equation in Venezia. Quality  Quantity, 48(1), 347–373. https://doi.org/10.1007/s11135-012-9773-5
Ng, A. K. Y., & Ducruet, C. (2014). The changing tides of port geography (1950-2012). Progress in Human Geography, 38(6), 785–823. https://doi.org/10.1177/0309132513516178
Mesmoudi, S., Alvarez, I., Martin, S., Reuillon, R., Sicard, M., & Perrot, N. (2014). Coupling geometric analysis and viability theory for system exploration: Application to a living food system. JOURNAL OF PROCESS CONTROL, 24(12, SI), 18–28. https://doi.org/10.1016/j.jprocont.2014.09.013
Longo, G., & Montévil, M. (2014). From Physics to Biology by Extending Criticality and Symmetry Breakings. In G. Longo & M. Montévil, Perspectives on Organisms (pp. 161–185). Berlin, Heidelberg: Springer Berlin Heidelberg. Retrieved from http://link.springer.com/10.1007/978-3-642-35938-5_7
Lerbet, J., Aldowaji, M., Challamel, N., Kirillov, O. N., Nicot, F., & Darve, F. (2014). Geometric degree of nonconservativity. Math. Mech. Compl. Sys., 2(2), 123–139. https://doi.org/10.2140/memocs.2014.2.123
Doursat, R., & Sánchez, C. (2014). Growing Fine-Grained Multicellular Robots. Soft Robotics, 1(2), 110–121. https://doi.org/10.1089/soro.2014.0014
Demery, V., Lecomte, V., & Rosso, A. (2014). The effect of disorder geometry on the critical force in disordered elastic systems. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT. https://doi.org/10.1088/1742-5468/2014/03/P03009
Delanoë, A., Chavalarias, D., & Anglade, A. (2014). Dematerialization and Environment: a text-mining landscape on academic, blog and press publications. In Processing of The international conferences ICT4S – ICT for Sustainability. Stockholm.
Delanoë, A., & Galam, S. (2014). Modeling a controversy in the press: The case of abnormal bee deaths. Physica A: Statistical Mechanics and Its Applications, 402(0), 93–103. https://doi.org/http://dx.doi.org/10.1016/j.physa.2014.01.054
Cioli, C., Abdi, H., Beaton, D., Burnod, Y., & Mesmoudi, S. (2014). Differences in Human Cortical Gene Expression Match the Temporal Properties of Large-Scale Functional Networks. PLoS ONE, 9(12), e115913. https://doi.org/10.1371/journal.pone.0115913
Castro-González, C., Luengo-Oroz, M. A., Duloquin, L., Savy, T., Rizzi, B., Desnoulez, S., … Santos, A. (2014). A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis. PLoS Computational Biology, 10(6), e1003670. https://doi.org/10.1371/journal.pcbi.1003670
Barbieri, D., Citti, G., & Sarti, A. (2014). How Uncertainty Bounds the Shape Index of Simple Cells. The Journal of Mathematical Neuroscience, 4(1), 5. https://doi.org/10.1186/2190-8567-4-5
Barbieri, D., Citti, G., Cocci, G., & Sarti, A. (2014). A Cortical-Inspired Geometry for Contour Perception and Motion Integration. Journal of Mathematical Imaging and Vision, 49(3), 511–529. https://doi.org/10.1007/s10851-013-0482-z

2013

Generation of Potential Fields and Route Simulation Based on the Household Travel Survey. (2013). In M. Thériault & F. D. Rosiers, Modeling Urban Dynamics (pp. 83–101). Hoboken, NJ, USA: John Wiley & Sons, Inc. Retrieved from http://doi.wiley.com/10.1002/9781118558041.ch4
Thomas-Vaslin, V., Six, A., Bellier, B., & Klatzmann, D. (2013). Lymphocyte Dynamics and Repertoires, Biological Methods. In W. Dubitzky, O. Wolkenhauer, K.-H. Cho, & H. Yokota (Eds.), Encyclopedia of Systems Biology (pp. 1145–1149). New York, NY: Springer New York. Retrieved from http://link.springer.com/10.1007/978-1-4419-9863-7_95
Thomas-Vaslin, V., Six, A., Ganascia, J.-G., & Bersini, H. (2013). Dynamical and Mechanistic Reconstructive Approaches of T Lymphocyte Dynamics: Using Visual Modeling Languages to Bridge the Gap between Immunologists, Theoreticians, and Programmers. Frontiers in Immunology, 4. https://doi.org/10.3389/fimmu.2013.00300
Tarissan, F., Quoitin, B., Mérindol, P., Donnet, B., Pansiot, J.-J., & Latapy, M. (2013). Towards a bipartite graph modeling of the internet topology. Computer Networks, 57(11), 2331–2347. https://doi.org/http://dx.doi.org/10.1016/j.comnet.2013.04.007
Reuillon, R., Leclaire, M., & Rey-Coyrehourcq, S. (2013). OpenMOLE, a workflow engine specifically tailored for the distributed exploration of simulation models. Future Generation Computer Systems, 29(8), 1981–1990. https://doi.org/http://dx.doi.org/10.1016/j.future.2013.05.003
Peschanski, D., Maréchal, D., Burnod, Y., Dauchot, K., & Deroy, O. (2013). Les chantiers de la mémoire. Bry-sur-Marne: INA éd.
Peschanski, D. (Ed.). (2013). Mémoire et mémorialisation. Paris: Hermann.
Passerat-Palmbach, J., Reuillon, R., Mazel, C., & Hill, D. R. C. (2013). Prototyping parallel simulations on manycore architectures using Scala: A case study. In High Performance Computing and Simulation (HPCS), 2013 International Conference (pp. 405–412). https://doi.org/10.1109/HPCSim.2013.6641447
Passerat-Palmbach, J., Caux, J., Le Pennec, Y., Reuillon, R., Junier, I., Kepes, F., & Hill, D. R. C. (2013). Parallel Stepwise Stochastic Simulation: Harnessing GPUs to Explore Possible Futures States of a Chromosome Folding Model Thanks to the Possible Futures Algorithm (PFA). In Proceedings of the 2013 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (pp. 169–178). New York, NY, USA: ACM. https://doi.org/10.1145/2486092.2486114
Mesmoudi, S., Perlbarg, V., Rudrauf, D., Messe, A., Pinsard, B., Hasboun, D., … Burnod, Y. (2013). Resting State Networks’ Corticotopy: The Dual Intertwined Rings Architecture. PLoS ONE, 8(7), e67444. https://doi.org/10.1371/journal.pone.0067444
Doursat, R., Sayama, H., & Michel, O. (2013). A review of morphogenetic engineering. Natural Computing, 12(4), 517–535. Retrieved from http://dblp.uni-trier.de/db/journals/nc/nc12.html#DoursatSM13
Demery, V. (2013). Diffusion of a particle quadratically coupled to a thermally fluctuating field. PHYSICAL REVIEW E, 87(5). https://doi.org/10.1103/PhysRevE.87.052105
Chavalarias, D., & Cointet, J.-P. (2013). Phylomemetic Patterns in Science EvolutiontextemdashThe Rise and Fall of Scientific Fields. PLoS ONE, 8(2), e54847. https://doi.org/10.1371/journal.pone.0054847
Borghesi, C., Hernández, L., Louf, R., & Caparros, F. (2013). Universal size effects for populations in group-outcome decision-making problems. Physical Review E, 88(6). https://doi.org/10.1103/PhysRevE.88.062813
Bernardes, D., Latapy, M., & Tarissan, F. (2013). Inadequacy of SIR model to reproduce key properties of real-world spreading cascades: experiments on a large-scale P2P system. Social Network Analysis and Mining, 3(4), 1195–1208. https://doi.org/10.1007/s13278-013-0121-0
Bellier, B., Six, A., Thomas-Vaslin, V., & Klatzmann, D. (2013). Systems Immunology, Novel Evaluation of Vaccine. In W. Dubitzky, O. Wolkenhauer, K.-H. Cho, & H. Yokota (Eds.), Encyclopedia of Systems Biology (pp. 2089–2092). New York, NY: Springer New York. Retrieved from http://link.springer.com/10.1007/978-1-4419-9863-7_107
Alvarez, I., Aldama, R. D., Martin, S., & Reuillon, R. (2013). Assessing the Resilience of Socio-ecosystems: Coupling Viability Theory and Active Learning with Kd-trees. Application to Bilingual Societies. In Proceedings of the Twenty-Third International Joint Conference on Artificial Intelligence (pp. 2776–2782). Beijing, China: AAAI Press.

2012

Zhang, P., Krzakala, F., Reichardt, J., & Zdeborova, L. (2012). Comparative study for inference of hidden classes in stochastic block models. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT. https://doi.org/10.1088/1742-5468/2012/12/P12021
Tonda, A., Lutton, E., & Squillero, G. (2012). A benchmark for cooperative coevolution. MEMETIC COMPUTING, 4(4, SI), 263–277. https://doi.org/10.1007/s12293-012-0095-x
Smetacek, V., Klaas, C., Strass, V. H., Assmy, P., Montresor, M., Cisewski, B., … Wolf-Gladrow, D. (2012). Deep carbon export from a Southern Ocean iron-fertilized diatom bloom. Nature, 487(7407), 313–319. https://doi.org/10.1038/nature11229
Roth, C., Kang, S. M., Batty, M., & Barthelemy, M. (2012). A long-time limit for world subway networks. JOURNAL OF THE ROYAL SOCIETY INTERFACE, 9(75), 2540–2550. https://doi.org/10.1098/rsif.2012.0259
Perna, A., Granovskiy, B., Garnier, S., Nicolis, S. C., Labédan, M., Theraulaz, G., … Sumpter, D. J. T. (2012). Individual Rules for Trail Pattern Formation in Argentine Ants (Linepithema humile). PLoS Computational Biology, 8(7), e1002592. https://doi.org/10.1371/journal.pcbi.1002592
Omodei, E., Poibeau, T., & Cointet, J. (2012). Multi-level Modeling of Quotation Families Morphogenesis. In Privacy, Security, Risk and Trust (PASSAT), 2012 International Conference on and 2012 International Confernece on Social Computing (SocialCom) (pp. 392–401). https://doi.org/10.1109/SocialCom-PASSAT.2012.114
Liò, P., & Verma, D. C. (Eds.). (2012). Biologically inspired networking and sensing: algorithms and architectures. Hershey PA: Medical Information Science Reference.
Lesne, A., Bécavin, C., & Victor, J. (2012). The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing. Physical Biology, 9(1), 013001. https://doi.org/10.1088/1478-3975/9/1/013001
Junier, I., Dale, R. K., Hou, C., Kepes, F., & Dean, A. (2012). CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the beta-globin locus. NUCLEIC ACIDS RESEARCH, 40(16), 7718–7727. https://doi.org/10.1093/nar/gks536
Giavitto, J.-L., Klaudel, H., & Pommereau, F. (2012). Integrated regulatory networks (IRNs): Spatially organized biochemical modules. Theoretical Computer Science, 431, 219–234. https://doi.org/10.1016/j.tcs.2011.12.054
Giavitto, J.-L. (2012). The Modeling and the Simulation of the Fluid Machines of Synthetic Biology. In M. Gheorghe, G. Păun, G. Rozenberg, A. Salomaa, & S. Verlan (Eds.), Membrane Computing (Vol. 7184, pp. 19–34). Berlin, Heidelberg: Springer Berlin Heidelberg. Retrieved from http://link.springer.com/10.1007/978-3-642-28024-5_3
Foucquier, J., Chantoiseau, E., Le Feunteun, S., Flick, D., Gaucel, S., & Perrot, N. (2012). Toward an integrated modeling of the dairy product transformations, a review of the existing mathematical models. Food Hydrocolloids, 27(1), 1–13. https://doi.org/10.1016/j.foodhyd.2011.08.002
Doursat, R., Sayama, H., & Michel, O. (Eds.). (2012). Morphogenetic engineering: toward programmable complex systems. Heidelberg ; New York: Springer.
Doursat, R., Sánchez, C., Dordea, R., Fourquet, D., & Kowaliw, T. (2012). Embryomorphic Engineering: Emergent Innovation Through Evolutionary Development. In R. Doursat, H. Sayama, & O. Michel (Eds.), Morphogenetic Engineering (pp. 275–311). Springer Berlin Heidelberg. Retrieved from http://dx.doi.org/10.1007/978-3-642-33902-8_11
Doursat, R. (2012). The Self-Made Puzzle: Integrating Self-Assembly and Pattern Formation Under Non-Random Genetic Regulation. In A. A. Minai, D. Braha, & Y. Bar-Yam (Eds.), Unifying Themes in Complex Systems VII (pp. 54–67). Berlin, Heidelberg: Springer Berlin Heidelberg. Retrieved from http://link.springer.com/10.1007/978-3-642-18003-3_6
Barbieri, D., Citti, G., Sanguinetti, G., & Sarti, A. (2012). An uncertainty principle underlying the functional architecture of V1. Journal of Physiology-Paris, 106(5–6), 183–193. https://doi.org/10.1016/j.jphysparis.2012.03.001
Banos, A., & Genre-Grandpierre, C. (2012). Towards New Metrics for Urban Road Networks: Some Preliminary Evidence from Agent-Based Simulations. In A. J. Heppenstall, A. T. Crooks, L. M. See, & M. Batty (Eds.), Agent-Based Models of Geographical Systems (pp. 627–641). Dordrecht: Springer Netherlands. Retrieved from http://www.springerlink.com/index/10.1007/978-90-481-8927-4_31
Banos, A. (2012). Network effects in Schelling’s model of segregation: new evidence from agent-based simulation. Environment and Planning B: Planning and Design, 39(2), 393–405. https://doi.org/10.1068/b37068

2011

Ulieru, M., & Doursat, R. (2011). Emergent engineering: a radical paradigm shift. International Journal of Autonomous and Adaptive Communications Systems, 4(1), 39. https://doi.org/10.1504/IJAACS.2011.037748
Sicard, M., Baudrit, C., Leclerc-Perlat, M. N., Wuillemin, P. H., & Perrot, N. (2011). Expert knowledge integration to model complex food processes. Application on the camembert cheese ripening process. Expert Systems with Applications, 38(9), 11804–11812. https://doi.org/10.1016/j.eswa.2011.03.068
Salze, P., Banos, A., Oppert, J.-M., Charreire, H., Casey, R., Simon, C., … Weber, C. (2011). Estimating spatial accessibility to facilities on the regional scale: an extended commuting-based interaction potential model. International Journal of Health Geographics, 10(1), 2. https://doi.org/10.1186/1476-072X-10-2
Salze, P., Banos, A., Oppert, J.-M., Charreire, H., Casey, R., Simon, C., … Weber, C. (2011). Estimating spatial accessibility to facilities on the regional scale: an extended commuting-based interaction potential model. International Journal of Health Geographics, 10(1), 2. https://doi.org/10.1186/1476-072X-10-2
Roth, C., Kang, S. M., Batty, M., & Barthélemy, M. (2011). Structure of Urban Movements: Polycentric Activity and Entangled Hierarchical Flows. PLoS ONE, 6(1), e15923. https://doi.org/10.1371/journal.pone.0015923
Perrot, N., Trelea, I. C., Baudrit, C., Trystram, G., & Bourgine, P. (2011). Modelling and analysis of complex food systems: State of the art and new trends. Trends in Food Science & Technology, 22(6), 304–314. https://doi.org/10.1016/j.tifs.2011.03.008
Perna, A., Kuntz, P., & Douady, S. (2011). Characterization of spatial networklike patterns from junction geometry. Physical Review E, 83(6). https://doi.org/10.1103/PhysRevE.83.066106
Devert, A., Bredeche, N., & Schoenauer, M. (2011). Robustness and the Halting Problem for Multicellular Artificial Ontogeny. IEEE Transactions on Evolutionary Computation, 15(3), 387–404. https://doi.org/10.1109/TEVC.2011.2125969
Crespelle, C., & Tarissan, F. (2011). Evaluation of a new method for measuring the internet degree distribution: Simulation results. Computer Communications, 34(5), 635–648. https://doi.org/10.1016/j.comcom.2010.06.006
Chavalarias, David, Cointet J-P., & Cornilleau L., Duong T-K, Mogoutov A., Villard  L., Roth C., Savy T. (2011). Streams of Media Issues - Monitoring World Food Security. UN GLobal Pulse, Presented at United Nations, Oct.
Banos, A., & Thévenin, T. (Eds.). (2011). Geographical information and urban transport systems. London : Hoboken, NJ: ISTE ; Wiley.

2010

Zanella, C., Campana, M., Rizzi, B., Melani, C., Sanguinetti, G., Bourgine, P., … Sarti, A. (2010). Cells Segmentation From 3-D Confocal Images of Early Zebrafish Embryogenesis. IEEE Transactions on Image Processing, 19(3), 770–781. https://doi.org/10.1109/TIP.2009.2033629
Roth, C., & Cointet, J.-P. (2010). Social and semantic coevolution in knowledge networks. Social Networks, 32(1), 16–29. https://doi.org/10.1016/j.socnet.2009.04.005
Reuillon, R., Chuffart, F., Leclaire, M., Faure, T., Dumoulin, N., & Hill, D. R. C. (2010). Declarative task delegation in OpenMOLE. In W. W. Smari & J. P. McIntire (Eds.), HPCS (pp. 55–62). IEEE. Retrieved from http://dblp.uni-trier.de/db/conf/ieeehpcs/ieeehpcs2010.html#ReuillonCLFDH10
Phan, D., & Varenne, F. (2010). Agent-Based Models and Simulations in Economics and Social Sciences: From Conceptual Exploration to Distinct Ways of Experimenting. Journal of Artificial Societies and Social Simulation, 13(1), 5. Retrieved from http://jasss.soc.surrey.ac.uk/13/1/5.html
Olivier, N., Luengo-Oroz, M. A., Duloquin, L., Faure, E., Savy, T., Veilleux, I., … Beaurepaire, E. (2010). Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy. Science, 329(5994), 967–971. https://doi.org/10.1126/science.1189428
Junier, I., Martin, O., & Képès, F. (2010). Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization. PLoS Computational Biology, 6(2), e1000678. https://doi.org/10.1371/journal.pcbi.1000678
Junier, I., Herisson, J., & Kepes, F. (2010). Periodic pattern detection in sparse boolean sequences. Algorithms for Molecular Biology, 5(1), 31. https://doi.org/10.1186/1748-7188-5-31
Ginelli, F., Peruani, F., Bär, M., & Chaté, H. (2010). Large-Scale Collective Properties of Self-Propelled Rods. Physical Review Letters, 104(18). https://doi.org/10.1103/PhysRevLett.104.184502
Chavalarias, D., & Ioannidis, J. P. A. (2010). Science mapping analysis characterizes 235 biases in biomedical research. Journal of Clinical Epidemiology, 63(11), 1205–1215. https://doi.org/10.1016/j.jclinepi.2009.12.011
Baudrit, C., Sicard, M., Wuillemin, P. H., & Perrot, N. (2010). Towards a global modelling of the Camembert-type cheese ripening process by coupling heterogeneous knowledge with dynamic Bayesian networks. Journal of Food Engineering, 98(3), 283–293. https://doi.org/10.1016/j.jfoodeng.2009.12.012
Barthélemy, M., Nadal, J.-P., & Berestycki, H. (2010). Disentangling collective trends from local dynamics. Proceedings of the National Academy of Sciences, 107(17), 7629–7634. https://doi.org/10.1073/pnas.0910259107

2009

Yang, H., Takeuchi, K. A., Ginelli, F., Chaté, H., & Radons, G. (2009). Hyperbolicity and the Effective Dimension of Spatially Extended Dissipative Systems. Physical Review Letters, 102(7). https://doi.org/10.1103/PhysRevLett.102.074102
Takeuchi, K. A., Ginelli, F., & Chaté, H. (2009). Lyapunov Analysis Captures the Collective Dynamics of Large Chaotic Systems. Physical Review Letters, 103(15). https://doi.org/10.1103/PhysRevLett.103.154103
Shuckburgh, E., d’Ovidio, F., & Legras, B. (2009). Local Mixing Events in the Upper Troposphere and Lower Stratosphere. Part II: Seasonal and Interannual Variability. Journal of the Atmospheric Sciences, 66(12), 3695–3706. https://doi.org/10.1175/2009JAS2983.1
Nicolau, M., & Schoenauer, M. (2009). On the evolution of scale-free topologies with a gene regulatory network model. Biosystems, 98(3), 137–148. https://doi.org/10.1016/j.biosystems.2009.06.006
Lavelle, C., Recouvreux, P., Wong, H., Bancaud, A., Viovy, J.-L., Prunell, A., & Victor, J.-M. (2009). Right-Handed Nucleosome: Myth or Reality? Cell, 139(7), 1216–1217. https://doi.org/10.1016/j.cell.2009.12.014
Lavelle, C. (2009). Forces and torques in the nucleus: chromatin under mechanical constraintsThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process. Biochemistry and Cell Biology, 87(1), 307–322. https://doi.org/10.1139/O08-123
Junier, I., Mossa, A., Manosas, M., & Ritort, F. (2009). Recovery of Free Energy Branches in Single Molecule Experiments. Physical Review Letters, 102(7). https://doi.org/10.1103/PhysRevLett.102.070602
Institute of Electrical and Electronics Engineers (Ed.). (2009). IEEE INFOCOM 2009 - IEEE Conference on Computer Communications workshops: Rio de Janeiro, Brazil, 19 - 25 April 2009. Piscataway, NJ: IEEE.
Ginelli, F., Cencini, M., & Torcini, A. (2009). Synchronization of spatio-temporal chaos as an absorbing phase transition: a study in 2+1 dimensions. Journal of Statistical Mechanics: Theory and Experiment, 2009(12), P12018. https://doi.org/10.1088/1742-5468/2009/12/P12018
El Boustani, S., Marre, O., Béhuret, S., Baudot, P., Yger, P., Bal, T., … Frégnac, Y. (2009). Network-State Modulation of Power-Law Frequency-Scaling in Visual Cortical Neurons. PLoS Computational Biology, 5(9), e1000519. https://doi.org/10.1371/journal.pcbi.1000519
d’Ovidio, F., Isern-Fontanet, J., López, C., Hernández-García, E., & García-Ladona, E. (2009). Comparison between Eulerian diagnostics and finite-size Lyapunov exponents computed from altimetry in the Algerian basin. Deep Sea Research Part I: Oceanographic Research Papers, 56(1), 15–31. https://doi.org/10.1016/j.dsr.2008.07.014
d’Ovidio, F., Shuckburgh, E., & Legras, B. (2009). Local Mixing Events in the Upper Troposphere and Lower Stratosphere. Part I: Detection with the Lyapunov Diffusivity. Journal of the Atmospheric Sciences, 66(12), 3678–3694. https://doi.org/10.1175/2009JAS2982.1
D’Ovidio, F., Taillandier, V., Mortier, L., & Taupier-Letage, I. (2009). Lagrangian validation of the Mediterranean mean dynamic topography by extraction of tracer frontal structures. Mercator Ocean Q. Newslett, 32, 24Á32.
Banos, A., & Paré, A. (2009). Simuler les déplacements de piétons dans une station de métro Une approche à base d’agents. Revue Internationale de Géomatique, 19(3), 277–302. https://doi.org/10.3166/geo.19.277-302
Bailly, F., & Longo, G. (2009). BIOLOGICAL ORGANIZATION AND ANTI-ENTROPY. Journal of Biological Systems, 17(01), 63–96. https://doi.org/10.1142/S0218339009002715

2008

Spicher, A., Michel, O., Cieslak, M., Giavitto, J.-L., & Prusinkiewicz, P. (2008). Stochastic P systems and the simulation of biochemical processes with dynamic compartments. Biosystems, 91(3), 458–472. https://doi.org/10.1016/j.biosystems.2006.12.009
Roth, C., Obiedkov, S., & Kourie, D. G. (2008). ON SUCCINCT REPRESENTATION OF KNOWLEDGE COMMUNITY TAXONOMIES WITH FORMAL CONCEPT ANALYSIS. International Journal of Foundations of Computer Science, 19(02), 383–404. https://doi.org/10.1142/S0129054108005735
Roth, C. (2008). Coévolution des auteurs et des concepts dans les réseaux épistémiques : le cas de la communauté « zebrafish». Revue française de sociologie, 49(3), 523. https://doi.org/10.3917/rfs.493.0523
Peruani, F., Deutsch, A., & Bär, M. (2008). A mean-field theory for self-propelled particles interacting by velocity alignment mechanisms. The European Physical Journal Special Topics, 157(1), 111–122. https://doi.org/10.1140/epjst/e2008-00634-x
Peruani, F., & Sibona, G. J. (2008). Dynamics and Steady States in Excitable Mobile Agent Systems. Physical Review Letters, 100(16). https://doi.org/10.1103/PhysRevLett.100.168103
Mitra, B., Ghose, S., Ganguly, N., & Peruani, F. (2008). Stability analysis of peer-to-peer networks against churn. Pramana, 71(2), 263–273. https://doi.org/10.1007/s12043-008-0159-0
Jensen, P., Rouquier, J.-B., Kreimer, P., & Croissant, Y. (2008). Scientists who engage with society perform better academically. Science and Public Policy, 35(7), 527–541. https://doi.org/10.3152/030234208X329130
Hoelzer, G. A., Drewes, R., Meier, J., & Doursat, R. (2008). Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences. PLoS Computational Biology, 4(7), e1000126. https://doi.org/10.1371/journal.pcbi.1000126
Giavitto, J.-L., & Spicher, A. (2008). Topological rewriting and the geometrization of programming. Physica D: Nonlinear Phenomena, 237(9), 1302–1314. https://doi.org/10.1016/j.physd.2008.03.039
Fuchs, J., Schelter, J., Ginelli, F., & Hinrichsen, H. (2008). Local persistence in the directed percolation universality class. Journal of Statistical Mechanics: Theory and Experiment, 2008(04), P04015. Retrieved from http://stacks.iop.org/1742-5468/2008/i=04/a=P04015
Doursat, R., & Ulieru, M. (2008). Emergent engineering for the management of complex situations. In A. Manzalini (Ed.), Autonomics (p. 14). ICST. Retrieved from http://dblp.uni-trier.de/db/conf/autonomics/autonomics2008.html#DoursatU08
Doursat, R. (2008). Organically Grown Architectures: Creating Decentralized, Autonomous Systems by Embryomorphic Engineering. In Organic Computing (pp. 167–199). Springer Berlin Heidelberg. Retrieved from http://dx.doi.org/10.1007/978-3-540-77657-4_8
Chavalarias, David, & Cointet, Jean-Philippe. (2008). Multi-level Science mapping with asymmetric co-occurrence analysis: Methodology and case study. Networks and Heterogeneous Media, pp. 267–276.
Chavalarias, D., & Cointet, J.-P. (2008). Bottom-up scientific field detection for dynamical and hierarchical science mapping, methodology and case study. Scientometrics, 75(1), 37–50. https://doi.org/10.1007/s11192-007-1825-6
Chaté, H., Ginelli, F., Grégoire, G., & Raynaud, F. (2008). Collective motion of self-propelled particles interacting without cohesion. Physical Review E, 77(4). https://doi.org/10.1103/PhysRevE.77.046113
Chaté, H., Ginelli, F., Grégoire, G., Peruani, F., & Raynaud, F. (2008). Modeling collective motion: variations on the Vicsek model. The European Physical Journal B, 64(3–4), 451–456. https://doi.org/10.1140/epjb/e2008-00275-9

2007

Takeuchi, K. A., Kuroda, M., Chaté, H., & Sano, M. (2007). Directed Percolation Criticality in Turbulent Liquid Crystals. Physical Review Letters, 99(23). https://doi.org/10.1103/PhysRevLett.99.234503
Spicher, A., & Michel, O. (2007). Declarative modeling of a neurulation-like process. Biosystems, 87(2–3), 281–288. https://doi.org/10.1016/j.biosystems.2006.09.024
Roth, C. (2007). Empiricism for descriptive social network models. Physica A: Statistical Mechanics and Its Applications, 378(1), 53–58. https://doi.org/10.1016/j.physa.2006.11.045
Ginelli, F., Poggi, P., Turchi, A., Chaté, H., Livi, R., & Politi, A. (2007). Characterizing Dynamics with Covariant Lyapunov Vectors. Physical Review Letters, 99(13). https://doi.org/10.1103/PhysRevLett.99.130601
Chaté, H., Ginelli, F., & Grégoire, G. (2007). Comment on “Phase Transitions in Systems of Self-Propelled Agents and Related Network Models.” Physical Review Letters, 99(22). https://doi.org/10.1103/PhysRevLett.99.229601

2006

Shalizi, C. R., Haslinger, R., Rouquier, J.-B., Klinkner, K. L., & Moore, C. (2006). Automatic filters for the detection of coherent structure in spatiotemporal systems. Physical Review E, 73(3). https://doi.org/10.1103/PhysRevE.73.036104
Chavalarias, D. (2006). Metamimetic Games: Modeling Metadynamics in Social Cognition. Journal of Artificial Societies and Social Simulation, 9(2), 5. Retrieved from http://jasss.soc.surrey.ac.uk/9/2/5.html
Chaté, H., Ginelli, F., & Montagne, R. (2006). Simple Model for Active Nematics: Quasi-Long-Range Order and Giant Fluctuations. Physical Review Letters, 96(18). https://doi.org/10.1103/PhysRevLett.96.180602

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