PUBLICATIONS

Wilmet, A., & Lamarche-Perrin, R. (2019). Multidimensional Outlier Detection in Interaction Data: Application to Political Communication on Twitter. CompleNet 2019: Complex Networks X, pp 147-155. https://doi.org/https://doi.org/10.1007/978-3-030-14459-3_12

Raimbault, J., Cottineau, C., Le Texier, M., Le Nechet, F., & Reuillon, R. (2019). Space Matters: Extending Sensitivity Analysis to Initial Spatial Conditions in Geosimulation Models. Journal of Artificial Societies and Social Simulation, 22(4). https://doi.org/10.18564/jasss.4136

Raimbault, J. (2019). Second-order control of complex systems with correlated synthetic data. Complex Adaptive Systems Modeling. https://doi.org/https://doi.org/10.1186/s40294-019-0065-y

Raimbault, J. (2019, December). Worldwide estimation of parameters for a simple reaction-diffusion model of urban growth. International Land-use Symposium 2019, Paris, France. https://halshs.archives-ouvertes.fr/halshs-02406539/

Raimbault, J. (2019, Février). Towards multi-scalar models for the co-evolution of transportation networks and territories. Theo Quant 2019, Besançon, France. https://halshs.archives-ouvertes.fr/halshs-02013006/

Chavalarias, D., Panahi, M., & Gaumont, N. (2019). Politoscope. In K. Börner & E. Record (Eds.), 15th Iteration (2019): Macroscopes for Tracking the Flow of Resources. http://scimaps.org

Chavalarias, D., Gaumont, N., & Panahi, M. (2019). Hostilité et prosélytisme des communautés politiques. Reseaux, n° 214-215(2), 67–107. http://www.cairn.info/revue-reseaux-2019-2-page-67.htm

Chavalarias, D. (2019). Les Formes de l’Intelligence Collective. In A. Fleischer & A. Prochiantz (Eds.), Le Rêve des formes. Arts, sciences & Cie (Seuil, pp. 145–152).

Botterman, H.-L., & Lamarche-Perrin, R. (2019, March 6). Combining Path-Constrained Random Walks to Recover Link Weights in Heterogeneous Information Networks. 10th Conference on Complex Networks CompleNet 2019. https://doi.org/https://doi.org/10.1007/978-3-030-14459-3_8

Baudot, P., Tapia, M., Bennequin, D., & Goaillard, J.-M. (2019). Topological Information Data Analysis. Entropy, 21, 869. https://doi.org/10.3390/e21090869

Baudot, P. (2019). Elements of qualitative cognition: An information topology perspective. Physics of Life Reviews. https://doi.org/10.1016/j.plrev.2019.10.003

Baudot, P. (2019). The Poincaré-Shannon Machine: Statistical Physics and Machine Learning Aspects of Information Cohomology. Entropy, 21(9), 881. https://doi.org/10.3390/e21090881

La présidentielle 2017 au prisme de Twitter. (2018, September 19). CNRS Le journal. 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. 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. 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. ladepeche.fr. 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. LExpress.fr. 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., Panahi, M., & Gaumont, N. (2018). Climate Tweetoscope. In K. Börner & E. Record (Eds.), 14th Iteration (2018): Macroscopes for Ensuring our Well-being. http://scimaps.org

Chavalarias, D. (2018, November 14). A l’ère numérique, nos démocraties doivent évoluer pour ne pas mourir. AOC media - Analyse Opinion Critique. https://aoc.media/analyse/2018/11/14/a-lere-numerique-nos-democraties-doivent-evoluer-ne-mourir/

Chavalarias, D. (2018, November 7). Fake news : l’arbre qui cache la forêt. AOC media - Analyse Opinion Critique. 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

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. 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). 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 M. Bouzeghoub & R. Mosseri (Eds.), 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

Villoutreix, P., Delile, J., Rizzi, B., Duloquin, L., Savy, T., Bourgine, P., Doursat, R., & Peyri’eras, N. (2016). An integrated modelling framework from cells to organism based on a cohort of digital embryos. Scientific Reports, 6, 37438. http://www.nature.com/articles/srep37438

Véronique Thomas-Vaslin, & Frédéric Jacquemart. (2016, Décembre). Approche de la résilience et perturbations des systèmes complexes par une évaluation globale. Congrès mondial pour la pensée complexe: Les défis d’un monde globalisé, Paris, France. 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. https://hal.archives-ouvertes.fr/hal-01298219

Mathieu Le Goc, Lawrence H. Kim, Ali Parsaei, Jean-Daniel Fekete, Pierre Dragicevic, & Sean Follmer. (2016, October 16). Zooids: Building Blocks for Swarm User Interfaces. UIST ’16 Proceedings of the 29th Annual Symposium on User Interface Software and Technology, Tokyo, Japan. 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. Proc. of ICPRAM-2016. Int. Conf. on Pattern Recognition Applications and Methods, Rome, Italy.

Albert, S., Bauer, T., Michl, M., Biroli, G., Bouchaud, J.-P., Loidl, A., Lunkenheimer, P., Tourbot, R., Wiertel-Gasquet, C., & 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

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). 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., Magnan, H., & 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. 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. 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. Editions Matériologiques.

Faure, E., Campana, M., Cunderlik, R., Drblikova, O., Duloquin, L., Keller, R., Lombardot, B., Melani, C., Remesikova, M., Rizzi, B., Savy, T., Recher, G., Zanella, C., Kollar, J., Fabrèges, D., Villoutreix, P., Delile, J., Affaticati, P., Maury, B., … 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, (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., Lesne, A., Müller, J.-P., Perrier, É., & 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. 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., Rountree, C. L., Belkhou, R., Ohresser, P., & 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

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). Springer Berlin Heidelberg. 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. Processing of The International Conferences ICT4S – ICT for Sustainability.

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., Doursat, R., Kergosien, Y. L., Ledesma-Carbayo, M. J., Bourgine, P., Peyriéras, N., & 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

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). John Wiley & Sons, Inc. 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). Springer New York. 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. INA éd.

Peschanski, D. (Ed.). (2013). Mémoire et mémorialisation. Hermann.

Passerat-Palmbach, J., Reuillon, R., Mazel, C., & Hill, D. R. C. (2013). Prototyping parallel simulations on manycore architectures using Scala: A case study. High Performance Computing and Simulation (HPCS), 2013 International Conference, 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). Proceedings of the 2013 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, 169–178. https://doi.org/10.1145/2486092.2486114

Mesmoudi, S., Perlbarg, V., Rudrauf, D., Messe, A., Pinsard, B., Hasboun, D., Cioli, C., Marrelec, G., Toro, R., Benali, H., & 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. 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, DanielF., 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). Springer New York. 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. Proceedings of the Twenty-Third International Joint Conference on Artificial Intelligence, 2776–2782.

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., Savoye, N., Webb, A., d’Ovidio, F., Arrieta, J. M., Bathmann, U., Bellerby, R., Berg, G. M., Croot, P., Gonzalez, S., Henjes, J., Herndl, G. J., Hoffmann, L. J., Leach, H., … 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., Fourcassié, V., & 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. Privacy, Security, Risk and Trust (PASSAT), 2012 International Conference on and 2012 International Confernece on Social Computing (SocialCom), 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. 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). Springer Berlin Heidelberg. 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. 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. 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). Springer Berlin Heidelberg. 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). Springer Netherlands. 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

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., Chaix, B., Badariotti, D., & 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., Chaix, B., Badariotti, D., & 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. ISTE ; Wiley.

Zanella, C., Campana, M., Rizzi, B., Melani, C., Sanguinetti, G., Bourgine, P., Mikula, K., Peyrieras, N., & 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. 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. http://jasss.soc.surrey.ac.uk/13/1/5.html

Olivier, N., Luengo-Oroz, M. A., Duloquin, L., Faure, E., Savy, T., Veilleux, I., Solinas, X., Debarre, D., Bourgine, P., Santos, A., Peyrieras, N., & 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

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. 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., Destexhe, A., & 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

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. 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. 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. 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, 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

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

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. 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