BioInfo

Publications

2020

Journal articles

  • Frédérique Bassino, Mathilde Bouvel, Valentin Féray, Lucas Gerin, Mickaël Maazoun, and Adeline Pierrot. Universal limits of substitution-closed permutation classes. Journal of the European Mathematical Society, 2020. 73 pages, 17 figures. doi:10.4171/JEMS/993.
    HAL ] [ Bibtex ]

  • Thomas Chatain, Stefan Haar, Juraj Kolčák, Loïc Paulevé, and Aalok Thakkar. Concurrency in Boolean networks. Natural Computing, 19(1):91–109, 2020. doi:10.1007/s11047-019-09748-4.
    HAL ] [ Bibtex ]

  • Loïc Paulevé, Juraj Kolčák, Thomas Chatain, and Stefan Haar. Reconciling Qualitative, Abstract, and Scalable Modeling of Biological Networks. Nature Communications, 11:4256, 2020. doi:10.1038/s41467-020-18112-5.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Zinovyev, and Loïc Paulevé. Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. In 18th International Conference on Computational Methods in Systems Biology (CMSB). Online, Germany, 2020.
    HAL ] [ Bibtex ]

Reports and working papers

  • Thomas Chatain, Stefan Haar, Juraj Kolčák, and Loïc Paulevé. Most Permissive Semantics of Boolean Networks. Research Report, Univ. Bordeaux, Bordeaux INP, CNRS, LaBRI, UMR5800, F-33400 Talence, France ; LSV, ENS Cachan, CNRS, INRIA, Université Paris-Saclay, Cachan (France), 2020.
    HAL ] [ Bibtex ]

2019

Journal articles

  • Jean-Paul Allouche, S. Choi, Alain Denise, T. Erdélyi, and B. Saffari. Bounds on Autocorrelation Coefficients of Rudin-Shapiro Polynomials. Analysis Mathematica, 45(4):705–726, December 2019. doi:10.1007/s10476-019-0003-4.
    HAL ] [ Bibtex ]

  • Jorgelindo Da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Laurent H Schwartz, Mario Jolicœur, and Sabine Pérès. Metabolic therapies inhibit tumor growth in vivo and in silico. Scientific Reports, December 2019. doi:10.1038/s41598-019-39109-1.
    HAL ] [ Bibtex ]

  • Flora Jay, Simon Boitard, and Frédéric Austerlitz. An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions. Molecular Biology and Evolution, 36(7):1565–1579, July 2019. doi:10.1093/molbev/msz038.
    HAL ] [ Bibtex ]

  • Juraj Kolčák, David Šafránek, Stefan Haar, and Loïc Paulevé. Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. Theoretical Computer Science, 765:120–144, December 2019. doi:10.1016/j.tcs.2018.03.009.
    HAL ] [ Bibtex ]

  • Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia, and Olivier Gascuel. NGPhylogeny.fr: new generation phylogenetic services for non-specialists. Nucleic Acids Research, 47(W1):W260–W265, July 2019. doi:10.1093/nar/gkz303.
    HAL ] [ Bibtex ]

  • Hugues Mandon, Cui Su, Jun Pang, Soumya Paul, Stefan Haar, and Loïc Paulevé. Algorithms for the Sequential Reprogramming of Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(5):1610–1619, 2019. doi:10.1109/TCBB.2019.2914383.
    HAL ] [ Bibtex ]

  • Christophe Pradal, Sarah Cohen-Boulakia, Patrick Valduriez, and Dennis Shasha. VersionClimber: version upgrades without tears. Computing in Science & Engineering, 21(5):87–93, September 2019. doi:10.1109/MCSE.2019.2921898.
    HAL ] [ Bibtex ]

  • Xiaojie Ren, Jean-Sébastien Deschênes, Réjean Tremblay, Sabine Pérès, and Mario Jolicœur. A kinetic metabolic study of lipid production in Chlorella protothecoides under heterotrophic condition. Microbial Cell Factories, December 2019. doi:10.1186/s12934-019-1163-4.
    HAL ] [ Bibtex ]

  • Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, and Alain Denise. CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts. BMC Bioinformatics, January 2019.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Pierre Andrieu, Bryan Brancotte, Laurent Bulteau, Sarah Cohen-Boulakia, Alain Denise, Adeline Pierrot, and Stéphane Vialette. Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data. In 2019 15th International Conference on eScience (eScience), 136–145. San Diego, France, September 2019. IEEE. doi:10.1109/eScience.2019.00022.
    HAL ] [ Bibtex ]

  • Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, and Andrei Zinovyev. Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. In 2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), ICTAI. Portland, Oregon, United States, 2019. IEEE. doi:10.1109/ICTAI.2019.00014.
    HAL ] [ Bibtex ]

  • Stefan Haar, Juraj Kolčák, and Loïc Paulevé. Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics. In VMCAI 2019 - 20th International Conference on Verification, Model Checking, and Abstract Interpretation, volume 11388 of Lecture Notes in Computer Science, 555–576. Lisbon, Portugal, January 2019. Springer. doi:10.1007/978-3-030-11245-5_26.
    HAL ] [ Bibtex ]

  • Maher Mallem, Alain Denise, and Yann Ponty. Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity tests. In SEQBIM 2019 - Séquences en Bioinformatique, Informatique et Mathématiques. Marne-la-Vallée, France, December 2019.
    HAL ] [ Bibtex ]

Book sections

  • Cecile Moulin, Laurent Tournier, and Sabine Pérès. Using a hybrid approach to model central carbon metabolism across the cell cycle. In Hybrid Systems Biology, volume 11705 of Lecture Notes in Computer Science. Češka M., Paoletti N. (eds), 2019. doi:10.1007/978-3-030-28042-0_9.
    HAL ] [ Bibtex ]

Reports and working papers

  • Simon Artzet, Tsu Wei Chen, Jérôme Chopard, Nicolas Brichet, Michael Mielewczik, Sarah Cohen-Boulakia, Llorenç Cabrera Bosquet, Francois Tardieu, Christian Fournier, and Christophe Pradal. <em>Phenomenal</em>: An automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping. working paper or preprint, 2019. doi:10.1101/805739.
    HAL ] [ Bibtex ]

  • Frédérique Bassino, Mathilde Bouvel, Valentin Féray, Lucas Gerin, Mickaël Maazoun, and Adeline Pierrot. Random cographs: Brownian graphon limit and asymptotic degree distribution. 36 pages, 6 figures, July 2019.
    HAL ] [ Bibtex ]

  • Frédérique Bassino, Mathilde Bouvel, Valentin Féray, Lucas Gerin, Mickaël Maazoun, and Adeline Pierrot. Scaling limits of permutation classes with a finite specification: a dichotomy. 72 pages, 27 figures, March 2019.
    HAL ] [ Bibtex ]

  • Olivier François, Séverine Liégeois, Benjamin Demaille, and Flora Jay. Inference of population genetic structure from temporal samples of DNA. biorxiv, December 2019. doi:10.1101/801324.
    HAL ] [ Bibtex ]

  • Burak Yelmen, Aurelien Decelle, Linda Ongaro, Davide Marnetto, Francesco Montinaro, Cyril Furtlehner, Luca Pagani, and Flora Jay. Creating Artificial Human Genomes Using Generative Models. biorxiv, December 2019. doi:10.1101/769091.
    HAL ] [ Bibtex ]

2018

Journal articles

  • Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphaël Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, and Anne Lopes. Meet-U: educating through research immersion. PLoS Computational Biology, 14(3):1–10, March 2018. This is a PLOS Computational Biology Education paper. doi:10.1371/journal.pcbi.1005992.
    HAL ] [ Bibtex ]

  • Frédérique Bassino, Mathilde Bouvel, Valentin Féray, Lucas Gerin, and Adeline Pierrot. The Brownian limit of separable permutations. Annals of Probability, 46(4):2134 – 2189, July 2018. doi:10.1214/17-AOP1223.
    HAL ] [ Bibtex ]

  • Kevin Caye, Flora Jay, Olivier Michel, and Olivier François. Fast inference of individual admixture coefficients using geographic data. Annals Of Applied Statistics, 12(1):586–608, March 2018.
    HAL ] [ Bibtex ]

  • Kevin Caye, Flora Jay, Olivier J.J. Michel, and Olivier François. Fast Inference of Individual Admixture Coefficients Using Geographic Data. Annals of Applied Statistics, 12(1):586–608, March 2018. doi:10.1214/17-AOAS1106.
    HAL ] [ Bibtex ]

  • Alexis Courbet, Patrick Amar, François Fages, Eric Renard, and Franck Molina. Computer-aided biochemical programming of synthetic microreactors as diagnostic devices. Molecular Systems Biology, April 2018. doi:10.15252/msb.20177845.
    HAL ] [ Bibtex ]

  • Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa da Silva, Adrian M Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith Blake, Jesualdo Tomás Fernández Breis, Brigitte Boeckmann, Toni Gabaldon, Erik Sonnhammer, Christophe Dessimoz, Suzanna Lewis, Carla Bello, Sébastien Briois, Edward Chalstrey, Hirokazu Chiba, Oscar Conchillo-Solé, Vincent Daubin, Todd DeLuca, Jean-François Dufayard, Dannie Durand, Jesualdo Tomás Fernández-Breis, Natasha Glover, Alexander Hauser, Davide Heller, Mateus Kaduk, Jan Koch, Eugene Koonin, Evgenia V. Kriventseva, Shigehiro Kuraku, Odile Lecompte, Olivier Lespinet, Jeremy Levy, Benjamin Liebeskind, Benjamin Linard, Marc Marcet-Houben, Martin Kauffmann, Claire McWhite, Sergei Mekhedov, Sebastien Moretti, Steven Müller, El-Mabrouk Nadia, Cedric Notredame, Simon Penel, Ivana Pilizota, Henning Redestig, Marc Robinson-Rechavi, Fabian Schreiber, Kimmen Sjölander, Nives Škunca, Martin Steinegger, Damian Szklarczyk, Paul Thomas, Ernst Thuer, Clément Train, Ikuo Uchiyama, Lucas Wittwer, Ioannis Xenarios, Bethan Yates, Evgeny Zdobnov, and Robert Waterhouse. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics, 34(2):323–329, January 2018. doi:10.1093/bioinformatics/btx542.
    HAL ] [ Bibtex ]

  • Benoît Laflaquière, Gabrielle Leclercq, Chandarong Choey, Jingkui Chen, Sabine Pérès, Caryn Ito, and Mario Jolicœur. Identifying Biomarkers of Wharton's Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect. Metabolites, 8(1):18, March 2018. doi:10.3390/metabo8010018.
    HAL ] [ Bibtex ]

  • Nicolas Levy, Aurélien Naldi, Céline Hernandez, Gautier Stoll, Denis Thieffry, Andrei Zinovyev, Laurence Calzone, and Loïc Paulevé. Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial). Frontiers in Physiology, 9:787, 2018. doi:10.1101/319780.
    HAL ] [ Bibtex ]

  • Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, and Loïc Paulevé. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Frontiers in Physiology, 9:n°680:1–13, June 2018. doi:10.3389/fphys.2018.00680.
    HAL ] [ Bibtex ]

  • Loïc Paulevé. Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4):1167–1179, August 2018. doi:10.1109/TCBB.2017.2749225.
    HAL ] [ Bibtex ]

  • Christophe Pradal, Sarah Cohen-Boulakia, Gaetan Heidsieck, Esther Pacitti, Francois Tardieu, and Patrick Valduriez. Distributed Management of Scientific Workflows for High-Throughput Plant Phenotyping. ERCIM News, pages 36–37, 2018.
    HAL ] [ Bibtex ]

  • Sabine Pérès, Stefan Schuster, and Philippe Dague. Thermodynamic constraints for identifying elementary flux modes. Biochemical Society Transactions, 46:641–647, May 2018. doi:10.1042/BST20170260.
    HAL ] [ Bibtex ]

  • Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, and Carito Guziolowski. Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data. PLoS Computational Biology, 14:1–23, 2018. doi:10.1371/journal.pcbi.1006538.
    HAL ] [ Bibtex ]

  • Vladimir Reinharz, Antoine Soulé, Eric Westhof, Jérôme Waldispühl, and Alain Denise. Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families. Nucleic Acids Research, 2018.
    HAL ] [ Bibtex ]

  • Adrien Rougny, Pauline Gloaguen, Nathalie Langonné, Eric Reiter, Pascale Crepieux, Anne Poupon, and Christine Froidevaux. A logic-based method to build signaling networks and propose experimental plans. Scientific Reports, 8(1):1–11, May 2018. doi:10.1038/s41598-018-26006-2.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Patrick Amar. Metabolic network Boolean bio-computer embedded in an artificial vesicle: timing with an enzymatic oscillator. In Séminaire de la Société Francophone de Biologie Théorique. Saint Flour, France, June 2018.
    HAL ] [ Bibtex ]

  • Thomas Chatain, Stefan Haar, and Loïc Paulevé. Boolean Networks: Beyond Generalized Asynchronicity. In Baetens, Jan M., Kutrib, and Martin, editors, AUTOMATA 2018 - 24th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems, volume 10875 of Lecture Notes in Computer Science, 29–42. Ghent, Belgium, June 2018. Springer. doi:10.1007/978-3-319-92675-9_3.
    HAL ] [ Bibtex ]

  • Stefan Hammer, Yann Ponty, Wei Wang, and Sebastian Will. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. In RECOMB 2018 – 22nd Annual International Conference on Research in Computational Molecular Biology. Paris, France, April 2018.
    HAL ] [ Bibtex ]

  • Robin Milosz, Adeline Pierrot, and Sylvie Hamel. Median of 3 Permutations, 3-Cycles and 3-Hitting Set Problem. In IWOCA (International Workshop on Combinatorial Algorithms) . Singapour, Singapore, 2018.
    HAL ] [ Bibtex ]

  • Sabine Pérès. Metabolic view of tumor growth: a kinetic model to screen potential therapeutic targets. In Computational systems biology for cancer. Paris, France, January 2018.
    HAL ] [ Bibtex ]

  • Karima Rafes, Serge Abiteboul, Sarah Cohen-Boulakia, and Bastien Rance. Designing scientific SPARQL queries using autocompletion by snippets. In 14th IEEE International Conference on eScience. Amsterdam, Netherlands, October 2018.
    HAL ] [ Bibtex ]

Book sections

  • Loïc Paulevé and Adrien Richard. Analyse statique des réseaux booléens. In Emmanuel Jeandel and Laurent Vigneron, editors, Informatique Mathématique, Une photographie en 2018, pages 157–194. CNRS Éditions, March 2018.
    HAL ] [ Bibtex ]

Edited proceedings

  • Patrick Amar, François Képès, Vic Norris, and Attila Csikasz-Nagy, editors. advances in Systems and Synthetic Biology, Evry, France, March 2018. EDP Sciences.
    HAL ] [ Bibtex ]

Thesis

  • Alexandra Zaharia. Mining conserved neighborhood patterns in metabolic and genomic contexts. Theses, Université Paris Saclay, September 2018.
    HAL ] [ Bibtex ]

Other publications

  • Séverine Liégeois, Olivier François, and Flora Jay. Dimension reduction adapted to paleogenomics. Paris-Saclay Junior Conference on Data Science and Engineering, September 2018. Poster.
    HAL ] [ Bibtex ]

Reports and working papers

  • Flora Jay, Simon Boitard, and Frédéric Austerlitz. An ABC method for whole–genome sequence data: inferring paleolithic and neolithic human expansions. working paper or preprint, October 2018.
    HAL ] [ Bibtex ]

2017

Journal articles

  • Frédérique Bassino, Mathilde Bouvel, Adeline Pierrot, Carine Pivoteau, and Dominique Rossin. An algorithm computing combinatorial specifications of permutation classes. Discrete Applied Mathematics, 224:16–44, 2017. doi:10.1016/j.dam.2017.02.013.
    HAL ] [ Bibtex ]

  • Melanie Boudard, Dominique Barth, Julie Bernauer, Alain Denise, and Johanne Cohen. GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization. Bioinformatics, 16:2479–2486, 2017. doi:10.1093/bioinformatics/btx175.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal, and Christophe Blanchet. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems, 75:284–298, October 2017. doi:10.1016/j.future.2017.01.012.
    HAL ] [ Bibtex ]

  • Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, and Loïc Paulevé. Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming. Algorithms for Molecular Biology, 12(1):19, July 2017. doi:10.1186/s13015-017-0110-3.
    HAL ] [ Bibtex ]

  • Michael Martin, Flora Jay, Sergi Castellano, and Montgomery Slatkin. Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations. Molecular Ecology, 26(16):4145 – 4157, August 2017. doi:10.1111/mec.14188.
    HAL ] [ Bibtex ]

  • Vic Norris, François Képès, Patrick Amar, Ina Koch, and Laurent Janniere. Hypothesis: Local variations in the speed of individual DNA replication forks determine the phenotype of daughter cells. Medical Research Archives, December 2017. doi:10.18103/mra.v5i12.1598.
    HAL ] [ Bibtex ]

  • Adeline Pierrot and Dominique Rossin. 2-Stack Sorting is Polynomial. Theory of Computing Systems, 60(3):552 – 579, April 2017. doi:10.1007/s00224-016-9743-8.
    HAL ] [ Bibtex ]

  • Christophe Pradal, Simon Artzet, Jerome Chopard, Dimitri Dupuis, Christian Fournier, Michael Mielewczik, Vincent Negre, Pascal Neveu, Didier Parigot, Patrick Valduriez, and Sarah Cohen-Boulakia. InfraPhenoGrid: A scientific workflow infrastructure for Plant Phenomics on the Grid. Future Generation Computer Systems, 67:341–353, February 2017. doi:10.1016/j.future.2016.06.002.
    HAL ] [ Bibtex ]

  • Sabine Pérès, Mario Jolicœur, Cécile MOULIN, Philippe Dague, and Stefan Schuster. How important is thermodynamics for identifying elementary flux modes? PLoS ONE, February 2017. doi:10.1371/journal.pone.0171440.
    HAL ] [ Bibtex ]

  • Xinhe Zhao, Mayssa Kasbi, Jingkui Chen, Sabine Pérès, and Mario Jolicœur. A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product. Biotechnology and Bioengineering, 114(12):2907 – 2919, December 2017. doi:10.1002/bit.26393.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Frederic Austerlitz, Carla Aimé, and Flora Jay. Inference of past historical events using ABC and MCMC methods on population genomics data sets. Applications to human populations. In ESEB 2017 - Congress of the European Society for Evolutionary Biology. Groningen, Netherlands, August 2017.
    HAL ] [ Bibtex ]

  • Bertrand Beauvoit, Sophie Colombie, Razanne Issa, Jean-Pierre Mazat, Christine Nazaret, and Sabine Pérès. HSM a reduced model of Central Carbon Metabolism: a dynamical approach. In advances in Systems and Synthetic Biology. Lyon, France, March 2017.
    HAL ] [ Bibtex ]

  • Thomas Chatain and Loïc Paulevé. Goal-Driven Unfolding of Petri Nets. In 28th International Conference on Concurrency Theory (CONCUR 2017). Berlin, Germany, September 2017. doi:10.4230/LIPIcs.CONCUR.2017.14.
    HAL ] [ Bibtex ]

  • Flora Jay, Simon S. Boitard, and Frederic Austerlitz. Reconstructing past history from whole-genomes: an ABC approach handling recombining data. In European Mathematical Genetics Meeting. Tartu, Estonia, April 2017.
    HAL ] [ Bibtex ]

  • Hugues Mandon, Stefan Haar, and Loïc Paulevé. Temporal Reprogramming of Boolean Networks. In Jérôme Feret and Heinz Koeppl, editors, CMSB 2017 - 15th conference on Computational Methods for Systems Biology, volume 10545 of Lecture Notes in Computer Science, 179 – 195. Darmstadt, Germany, September 2017. Springer International Publishing. doi:10.1007/978-3-319-67471-1_11.
    HAL ] [ Bibtex ]

  • Loïc Paulevé. Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface. In Jérôme Feret and Heinz Koeppl, editors, CMSB 2017 - 15th conference on Computational Methods for Systems Biology, volume 10545 of Lecture Notes in Computer Science, 370 – 316. Darmstadt, Germany, September 2017. Springer International Publishing. doi:10.1007/978-3-319-67471-1_20.
    HAL ] [ Bibtex ]

  • Sabine Pérès, Philippe Dague, Mario Jolicœur, and Stefan Schuster. Computing EFMs consistent with equilibrium constants. In Metabolic Pathway Analysis MPA 2017. Bozeman, United States, July 2017.
    HAL ] [ Bibtex ]

  • Karima Rafes, Sarah Cohen-Boulakia, and Serge Abiteboul. Une autocomplétion générique de SPARQL dans un contexte multi-services. In BDA 2017 - 33ème conférence sur la “Gestion de Données - Principes, Technologies et Applications”. Nancy, France, November 2017.
    HAL ] [ Bibtex ]

  • Théophile Sanchez, Guillaume Charpiat, and Flora Jay. SPI-DNA: End-to-end Deep Learning Approach for Demographic History Inference. In Paris-Saclay Junior Conference on Data Science and Engineering. Orsay, France, September 2017.
    HAL ] [ Bibtex ]

Edited proceedings

  • Patrick Amar, François Képès, and Vic Norris, editors. advances in Systems and Synthetic Biology, Lyon, France, March 2017. EDP Sciences.
    HAL ] [ Bibtex ]

Other publications

  • Loïc Paulevé and Philippe Dague. Journées BIOSS-IA 2017. July 2017. Bulletin 97 de l'AFIA - Association française pour l'Intelligence Artificielle.
    HAL ] [ Bibtex ]

  • Théophile Sanchez, Guillaume Charpiat, and Flora Jay. End-to-End Deep Learning Approach for Demographic History Inference. Human Evolution: Fossils, Ancient and Modern Genomes 2017, November 2017. Poster.
    HAL ] [ Bibtex ]

2016

Journal articles

  • Adrian M Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutiérrez, Daniel A Dalquen, Todd DeLuca, Kristoffer Forslund, Jaime Huerta-Cepas, Benjamin Linard, Cécile Pereira, Leszek P Pryszcz, Fabian Schreiber, Alan Sousa Da Silva, Damian Szklarczyk, Clément-Marie Train, Peer Bork, Odile Lecompte, Christian Von Mering, Ioannis Xenarios, Kimmen Sjölander, Lars Juhl Jensen, Maria J Martin, Matthieu Muffato, Toni Gabaldon, Suzanna E Lewis, Paul D Thomas, Erik Sonnhammer, and Christophe Dessimoz. Standardized benchmarking in the quest for orthologs. Nature Methods, 13(5):425–430, 2016. doi:10.1038/nMeth.3830.
    HAL ] [ Bibtex ]

  • Erwan Bigan, Loïc Paulevé, Jean-Marc Steyaert, and Stéphane S. Douady. Necessary and sufficient conditions for protocell growth. Journal of Mathematical Biology, April 2016. doi:10.1007/s00285-016-0998-0.
    HAL ] [ Bibtex ]

  • Simon Boitard, Willy Rodríguez, Flora Jay, Stefano Mona, and Frédéric Austerlitz. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. PLoS Genetics, 12(3):e1005877, 2016. doi:10.1371/journal.pgen.1005877.
    HAL ] [ Bibtex ]

  • Jorgelindo Da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Sabine Pérès, Loïc Paulevé, Marcel Levy Nogueira, Jean-Marc Steyaert, and Laurent Schwartz. The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect. Metabolites, 6(4):12 p., October 2016. doi:10.3390/metabo6040033.
    HAL ] [ Bibtex ]

  • David Ellison, Andrew Mugler, Matthew D. Brennan, Sung Hoon Lee, Robert J. Huebner, Eliah R. Shamir, Laura A. Woo, Joseph Kim, Patrick Amar, Ilya Nemenman, Andrew J. Ewald, and Andre Levchenko. Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis. Proceedings of the National Academy of Sciences of the United States of America , 113(6):E679–E688, January 2016. doi:10.1073/pnas.1516503113.
    HAL ] [ Bibtex ]

  • Lirong Huang, Loïc Paulevé, Christoph Zechner, Michael Unger, Anders S. Hansen, and Heinz Koeppl. Reconstructing dynamic molecular states from single-cell time series. Journal of the Royal Society Interface, September 2016. doi:10.1098/rsif.2016.0533.
    HAL ] [ Bibtex ]

  • Emmanuelle Jaillette, Christophe Girault, Guillaume Brunin, Farid Zerimech, Arnaud Chiche, Céline Broucqsault-Dedrie, Cyril Fayolle, Franck Minacori, Isabelle Alves, Stephanie Barrailler, Laurent Robriquet, Emmanuel Delaporte, Damien Thellier, Claire Delcourte, Alain Duhamel, Saad Nseir, Xavier Valette, Isabelle Desmeulles, Benoit Savary, Romain Masson, Amélie Seguin, Cédric Daubin, Bertrand Sauneuf, Pierre Verrier, Véronique Pottier, Marie Orabona, Désiré Samba, Gerald Viquesnel, Mathilde Lermuzeaux, Pascal Hazera, Jean-Luc Hanouz, Jean-Jacques Parienti, Damien Du Cheyron, Alexandre Demoule, Marc Clavel, Camille Rolland-Debord, Sébastien Perbet, Nicolas Terzi, Achille Kouatchet, Florent Wallet, Hadrien Rozé, Frédéric Vargas, Claude Guerin, Jean Dellamonica, Samir Jaber, Thomas Similowski, Jean-Pierre Quenot, Christine Binquet, Christophe Vinsonneau, Saber-Davide Barbar, Sandrine Vinault, Valérie Deckert, Stéphanie Lemaire, Ali Ait Hssain, REMI BRUYERE, Bertrand Souweine, Laurent Lagrost, Christophe Adrie, Boris Jung, Aurélien Daurat, Audrey De Jong, Gerald Chanques, Martin Mahul, Marion Monnin, Nicolas Molinari, Olivier Lheureux, Eric Trépo, Maya Hites, Frederic Cotton, Fleur Wolff, Rudy Surin, Jean-Louis Vincent, Thierry Gustot, Frédérique Jacobs, Fabio Silvio Taccone, Mathilde Neuville, Jean-François Timsit, Najoua El-Helali, Alban Le Monnier, Éric Magalhaes, Aguila Radjou, Roland Smonig, Jean-François Soubirou, Guillaume Voiriot, Romain Sonneville, Lila Bouadma, Bruno Mourvillier, Elodie Gélisse, Alexandre Brasseur, Sandrine Roisin, Daniel De Backer, Valerie Van Ruychevelt, Eric Carlier, Michael Piagnerelli, Michel Vanhaeverbeek, Christine Danguy, Patrick Biston, Siu-Ming Au, Emmanuelle Bégot, François Dalmay, Xavier Repessé, Gwenael Prat, Koceila Bouferrache, Michel Slama, Antoine Vieillard-Baron, Paul Marik, Jean-Louis Teboul, Mathieu Jozwiak, Christian Richard, Jean-Louis Chauvet, Shari El-Dash, Olivier Delastre, Bernard Bouffandeau, Dominique Jusserand, Jean-Baptiste Michot, Fabrice Bauer, François Brazier, Pablo Mercado, Loay Kontar, Dimitri Titeca, Bertand De Cagny, Gaelle Bacari-Risal, Antoine Rivière, Camille Guillot, Claire Le Reun, Marie Lampin, Ahmed Sadik, Astrid Botte, Aurélie Collins, Céline Kempeneers, Nathalie Cajgfinger, Camille Ohlmann, Robin POUYAU, Fabien Subtil, Florent BAUDIN, Bruno MASSENAVETTE, Etienne Javouhey, Christophe Milési, Sandrine Essouri, Jean-Michel Liet, Mickael Afanetti, Sabine Durand, Philippe Durand, Jean Christophe Rozé, Didier Dupont, Gilles Cambonie, Marco Rusca, Anne-Claire Lukaszewicz, Isabelle Crassard, Jean-Pierre Guichard, Damien Bresson, Didier Payen de la Garanderie, Marie Cantier, Candice Sabben, Liliane Louedec, Sandrine Delbosc, Clement Journe, Phalla Ou, Isabelle Klein, Françoise Chau, Agnès Lefort, Jean-Philippe Desilles, Jean-Baptiste Michel, Mikael Mazighi, Omar Ben Hadj Salem, Sophie Demeret, Francis Bolgert, Tarek Sharshar, David Grabli, Safa Arib, Ilaria Alice Crippa, Alexis Soummer, Nicolas Engrand, Pierre Guedin, Sorin ALDEA, Charles Cerf, Victoire Desailly, Pierre Pasquier, Patrick Brun, Damien Roux, Gwendoline Latournerie, Laetitia Kasprzyk, Vincent Grosjean, Amine Latreche, Pierre Habert, Stéphane Huot, Timon Jobin, Antoine Tesniere, Didier Dreyfuss, Jean-Damien Ricard, Alexandre Mignon, François-Xavier Laithier, Tahar Chouihed, Stéphane Albizzati, Edoardo Camenzind, Fabrice Vanhuyse, Bruno Lévy, Martin Cour, Fabienne Venet, Romain Hernu, Julie Demaret, Guillaume Monneret, Florence Dumas, Lionel Lamhaut, Julien Rosencher, Frédéric Pène, Olivier Varenne, Xavier Jouven, Christian Spaulding, Alain Cariou, Franck Bonnetain, Eloi Marijon, Jean Philippe Empana, Adrien Mirouse, Matthieu Resche-Rigon, Julien Mayaux, Antoine Rabbat, Anne Pascale Meert, Dominique Benoit, Fabrice Bruneel, Elie Azoulay, Claire Dupuis, Carole Schwebel, Dany Goldgran-Toledano, Guillaume Marcotte, Antoine Lafarge, Claire Pichereau, Igor Théodose, Marion Scotto, Delphine Kemlin, Etienne Ghrenassia, Benoît Schlemmer, Damien Vimpere, Lionel Galicier, Damien Contou, Emmanuel Guérot, David Grimaldi, Sylvie Ricome, Eric Maury, Gaetan Plantefeve, Armand Mekontso Dessap, Christian Brun-Buisson, Nicolas De Prost, Bruno-Pierre Dubé, Julie Delemazure, Ludivine Rousseau, Xavier Drouot, Véronique Diaz, Yohann Rebollar, Jean-Pierre Frat, Arnaud Thille, Dalinda Ait Aissa, Pierre Coquet, Jean Ruiz, Fabrice Ferré, Lucille Hoarau, Béatrice Riu-Poulenc, Benoît Bataille, Jean-Luc Baudel, Naïke Bige, Jalel Tahiri, Vincent Dubée, Bertrand Guidet, Liu Jinglun, Feng Shen, Xavier Monnet, Olivier Leroy, Philippe Montravers, Jean-Michel Constantin, Hervé Dupont, Didier Guillemot, Olivier Lortholary, Pierre-François Perrigault, Jean-Pierre Gangneux, Armand Mekontso-Dessap, Chloe Jansen, Marie Lecronier, Valade Sandrine, Jean-Paul Mira, Sophie Blein, Nathalie Marin, Christophe Rousseau, Julien Charpentier, Alexandre Pachot, Sami Hraiech, Julien Bordes, Lamballerie Xavier De, Jean-Louis Mege, Jean-Marie Forel, Christophe Guervilly, Melanie Adda, Didier Raoult, Laurent Papazian, Zoé Cohen-Solal, Nancy Kentish-Barnes, Virginie Souppart, Lionel Kerhuel, Carole Haubertin, Isabelle Exbrayat, Elodie Rozières, Audrey Argain, Agnès Suc, Michel Vignes, Pierre Cougot, Olivier Fourcade, Elodie Brunel, Florence Tubach, Emeline Dubief, Blandine Pasquet, Sylvie Guillo, Charlotte Pierron, Marion Grimaud, Caroline Farnoux, Amélie Maillard, Hélène Prodanovic, Ahmed Idbaih, Agusti Alentorn, Jean-Yves Delattre, Etienne de Montmollin, Noëlle Brule, Marie Conrad, Frédéric Dailler, Jean-Christophe Navellou, Mikael Alves, Jean-Marie Tonnelier, Stephane Ruckly, Géraldine Picard, Véronique Rogemond, Jérôme Honnorat, Chiara Marzorati, Christine Lebert, Pierre Perez, Giuseppe Citerio, Stephane Legriel, Simona Tripon, Maxime Mallet, Marika Rudler, Francoise Imbert-Bismut, Dominique Thabut, Emmanuel Canet, Stanislas Faguer, Anne-Sophie Moreau, François Barbier, Sybille Merceron, Christophe Guitton, Francois Labadie, Etienne Faucher, Kada Klouche, Sylvie Chevret, Stéphanie Ragot, Thierry Boulain, Angéline Jamet, Alain Mercat, Laurent Brochard, Antoine Roux, Virginie Lemiale, Guillaume Franchineau, Guillaume Lebreton, Ania Nieszkowska, Pascal Leprince, Jean Louis Trouillet, Alain Combes, Matthieu Schmidt, Loïc Barrot, Gaël Piton, Michael Bailey, Rakshit Panwar, Nicolas Belin, François Belon, Cyrille Patry, Mathilde Grandperrin, Claire Chaignat, Guylaine Labro, Bérengère Vivet, Gilles Capellier, Estelle Guérin, Elsa Tavernier, Emmanuelle Mercier, Valérie Gissot, Christine Vallejo, Bruno Francois, Céline Ravry, Nicolas Pichon, Catherine Chapellas, Anne-Laure Fedou, Antoine Galy, Marie-Cécile Ploy, Olivier Barraud, Aurelie Thooft, Raphael Conotte, Jean-Marie Colet, Matthieu Le Dorze, Virginie Tarazona, Caren Brumpt, Hélène Moins-Teisserenc, Fabrice Uhel, Imane Azzaoui, Murielle Grégoire, Céline Pangault, Joelle Dulong, Luc Cynober, Mikaël Roussel, Yves Le Tulzo, Karin Tarte, Julien Demiselle, Johann Auchabie, Pierre François Dequin, Nicolas Chudeau, François Fourrier, Steven Grange, Lise Piquilloud, Alexandre Lautrette, Sonia Boyer, Julien Letheulle, Anne Sophie Truche, Christophe Clec'h, Philippe Zaoui, Virginie Laurent, Dany Goldgran Toledano, Sophie Perinel Ragey, Antoine Gros, Anne Sylvie Dumenil, Samir Jamali, Mikhael Chouraqui, Antoine Dewitte, Brigitte Chastel, Pauline Carles, Catherine Fleureau, Olivier Joannes-Boyau, Alexandre Ouattara, Adrien Joseph, Adeline Max, Talia Lerin, Charles Gregoire, Martin Kloeckner, Cédric Bruel, Sandie Brochon, François Philippart, Emmanuelle Pichot, Clara Simons, Andrew Flint, Rinaldo Bellomo, David Pilcher, Allen Cheng, Colin Hegarty, Anthony Martinelli, Benjamin Howden, Michael Reade, Zoe Mcquilten, Cédric Bretonnière, Daniel Villers, M. Soares, Frédéric Gonzalez, François Vincent, Clémence Fauché, Samuel Gay, Olivier Skowron, Albrice Levrat, Didier Dorez, Arnaud Foucrier, Sebastian Pease, Tobias Gauss, Catherine Paugam, Julie Gorham, Lieveke Ameye, Marianne Paesmans, Thierry Berghmans, Jean-Paul Sculier, Anne-Pascale Meert, Pauline Deras, Orianne Martinez, Pascal Latry, Xavier Capdevila, Jonathan Charbit, J. Jaubert, Celia Etiennar, Lucie Ginoux, Jean-Luc Sebbah, Hakim Haouache, Gilles Dhonneur, I. Moussaid, O. Ghazaoui, Kamal Belkadi, S. El Youssoufi, S. Salmi, Laure Pajot, Benjamin Zuber, Jean Pierre Bedos, Benoit Dupont, Axelle Eugène, Françoise Galateau-Sallé, Baptiste Michard, Alexandra Boivin, Max Guillot, Marie-Line Harlay, Ralf Janssen-Langenstein, Maleka Schenck, Bernard Ellero, Marie-Lorraine Woehl-Jaegle, Camille Besch, Vincent Castelain, Philippe Bachellier, Francis Schneider, Christophe Camus, Fawzi Saliba, Bernard Goubaux, Agnès Bonadona, Laurence Lavayssiere, Alice Quinart, Olivier Barbot, Sébastien Dharancy, Bertrand Delafosse, Helene Barraud, Arnaud Galbois, Benoit Veber, Sophie Cayot, Bruno Souche, Clara Locher, Olivier Roux, Francesco Figorilli, Antonella Putignano, Pauline Houssel, Claire Francoz, Emmanuel Weiss, Banwari Agarwal, Rajiv Jalan, François Durand, Rebeh Daoudi, Moez Kaddour, Hatem Ghadhoune, E. Rachedi, J. Guissouma, A. Ben Slimene, W. Azzeza, H. Brahmi, H. Elghord, Ahmed Youssef Kada, Radia Chikh, Roza Slimani, Kheireddine. a Bouyoucef, Kais Regaieg, Chtara Kamilia, Najeh Baccouche, Olfa Turki, Anis Chaari, Hmida Chokri Ben, Mounir Bouaziz, Manel Zekri, Kais Rgieg, Chokri Bhimada, Bouaziz Mounir, Élodie Lang, Stephane Welschbillig, Mathilde Perrin, Jean-Michel Devys, Soumia Benbernou, Houria Mokhtari-Djebli, Sofiane Ilies, Khalida Bouyacoub, Abdelkader Azza, Elie Zogheib, Joseph Nader, Léonie Villeret, Mathieu Guilbart, Patricia Besserve, Thierry Caus, Ciro Mastroianni, Francesca Santi, Guillaume Hékimian, Leprince Pascal, Jean Chastre, Virginie Perrier, Benjamin Deniau, Fanny Klasen, Jean Pierre Ponthus, Polysie Ngasseu, Virginie Amilien, Elise Barsam, Pierre Lehericey, Martial Tchir, Jean Francois Georger, Bérénice Puech, David Vandroux, Arnaud Roussiaux, Dominique Belcour, Cyril Ferdynus, Olivier Martinet, Julien Jabot, Marion Fresco, Gaëlle Demeilliers-Pfister, Veronique Merle, Valéry Brunel, Bertrand Dureuil, Sébastien Leydier, Isabelle Clerc-Urmès, Jérémie Lemarié, Charles-Henri Maigrat, Aurélie Cravoisy-Popovic, Damien Barraud, Lionel Nace, Nelly Agrinier, Pierre-Edouard Bollaert, Jean-Louis Daban, Mathieu Boutonnet, Guillaume Dumas, Elisabeth Falzone, Patrick Jault, Bernard Lenoir, Joseph Nsiala Makunza, Nathalie Mejeni, Amélie Mazaud, Sébastien Béague, Anne-Flore Rousselle, Alain Durocher, pauline perez, Alexandra Grinea, Naoures Bedoui, Alina Stoian, Loredana Baboi, Florent Gobert, Hodane Yonis, Romain Tapponier, Arnaud Bruyneel, Thierry Bonus, Grégory Cuvelier, Sharam Machayeckhi, Sandra Olieuz, Alexandre Legrand, Fatma Feki, Amira Jamoussi, Takoua Merhebene, Emna Braham, Asma Ghariani, Faouzi El Mezni, Leila Slim, Jalila Ben Khelil, Mohamed Besbes, Antoine Marchalot, Gaëtan Beduneau, Dorothée Carpentier, Emmanuel Besnier, Gioia Gastaldi, Julien Abily, Marion Beuzelin, Mai-Anh Nay, Julie Mankikian, Virginie Herve, Marie Soulie, Pierrick Cronier, Elie Kantor, Laura Federici, Marion Gilbert, Ilham Mezhari, Gérald Choukroun, Sophie Marque, Jean-Pierre Fulgencio, Clarisse Blayau, Tài Pham, Michel Djibre, Matthieu Reffienna, Sébastien Lefort, Anne-Sophie Debue, Fabrice Daviaud, Sarah Cabon, Zakaria Addou, Ali Douah, Mohamed Moussati, Kamel Belhabiche, Nabil Aouffen, Sylvie Soulier, Philippe Mauriat, Nadir Tafer, Guillaume Mortamet, Alessandro Amaddeo, Sonia Khirani, Brigitte Fauroux, Gennadiy Khanes, Olga Liutko, Svitlana Bidnenko, Emilie Doye, Nicolas Voirin, Delphine Maucort-Boulch, Karine Kolev-Descamp, Imane El Aouane, Aben Essid, Wallid Hammami, Isabelle Haegy, Jacques Bataille, Jean Bergounioux, Luc Morin, Samiran Ray, Graeme Maclaren, Simon Nadel, Martin Kneyber, Mark Peters, Koos Jansen, Daniele De Luca, Clare Wilson, Luregn Schlapbach, Pierre Tissieres, Anne-Claire Girard, Elodie Savajols, Antoine Burguet, Denis Semama, Stephanie Litzler-Renault, Hana Fredj, Malek Hassouna, Youssef Zied El Hechmi, Mohamed Ali Cherif, Jerbi Zouheir, Ahmed Dernane, Fouad Bouakkaz, Lhoucine Ben Taleb, A. Zeddine Mouhsen, Aissam Lyazidi, Jean-Christophe Marie Richard, AHMED MOUHSEN, Mohammed Harmouchi, Mourad Rattal, Matthias Huck, Thomas Leclerc, Nicolas Donat, Audrey Cirodde, Jean-Vivien Schaal, Yannick Masson, Clement Hoffmann, Laura Cerland, Ruddy Valentino, C. Chabartier, Laurent Villain-Coquet, Jean-Louis Ferge, Y. Brouste, Hossein Mehdaoui, Maha Louriz, Naoufal Madani, Fatiha Amlaiky, Tarek Dendane, Khalid Abidi, Aicha Zekraoui, Amine Ali Zeggwagh, Redouane Abouqal, Affra Brahim, Fehmi Ferhi, Mohamed Amine Bouslama, Khaled Benjazia, Abid Zeineb, Dhaouadi Mahassen, julien Cadiet, Marine Ferron, Valentine Prat, Angélique Erraud, Virginie Aillerie, Mathieu Mével, Amandine Grabherr, John C Chatham, Chantal Gauthier, Benjamin Lauzier, Bertrand Rozec, Jérémie Joffre, Xavier Loyer, Jean-Rémi Lavillegrand, Lynda Zeboudj, Ludivine Laurans, Bruno Esposito, Alain Tedgui, Ziad Mallat, Chaojie Wei, Narimane Al Kattani, Huguette Louis, Sophie Orlowski, Pierre-Louis Tharaux, Mélanie Burban, Grégory Meyer, Anne Olland, Blandine Yver, Florence Toti, Valerie Schini-kerth, Alexandra Monnier, Pierrick Leborgne, Ferhat Meziani, Thomas Clavier, Mulder Paulus, Hélène Castel, Vincent Richard, Stéphanie Pons, David Skurnik, Sophie Six, Karim Jaffal, Clara Vigneron, Audrey Large, Julien Bador, Serge Aho, Sébastien Prin, Yosr Touil, Soufia Ayed, Habiba Sik Ali, Najla Tilouch, Houda Mateur, I. Talik, Rim Mrabet Gharbi, Mohamed Fekih Hassen, Souheil Elatrous, Isabelle Patry, Xavier Bertrand, Jean-Ralph Zahar, Wafa Essaied, Martin Wolkewitz, Mickaël Soued, Fabrice Cook, David Lobo, Roman Mounier, Aurélie Emirian, Jean Winoc Decousser, Mohamed Toufik Slaoui, Abdellatif Benslama, Dorothée Valance, Nicolas Allou, Jérôme Allyn, Elodie Jean-Bart, Floriane Bel., Fabienne Morey, Nicholas Sedillot, Lucie Biard, Richard Galliot, Romain Zunarelli, Bernard-Alex Gaüzere, Jean-Charles Cartier, Thomas Jouve, Marie-Noëlle Hilleret, Rebecca Hamidfar-Roy, Claire Ara-Somohano, Clémence Minet, Aline Pourcelet, Jean-Michel Hougardy, Pierre Defrance, Louis De Laforcade, Alexandre Boyer, Didier Gruson, Benjamin Clouzeau, Najah Hajjam, Houda Nasri, Hamdi Doghri, Nicolas Mongardon, Eric Levesque, Marie-Anaïs Bastide, Jack Richecoeur, Eric Frenoy, Christian Lemaire, Frederique Schortgen, Sebastien Preau, Franck Ehooman, Claire Montlahuc, Jean Bardon, Nicolas Postel-Vinay, Mehdi Lafi, Frédéric Jacobs, Dominique Prat, Matthieu Le Meur, Guy Moneger, Nadège Demars, Pierre Trouiller, noémie tencé, Inès Zaien, Martine Wolf, Jérôme Allardet-Servent, Melissa Lebsir, Christian Dubroca, Mireille Portugal, Matthias Castanier, Thomas Signouret, Rettinavelou Soundaravelou, Anne Lepidi, Philippe Halfon, Jean-Marie Seghboyan, Camille Gamblin, Nadia Benturquia, Olivier Roussel, Lucie Chevillard, Patricia Risède, Jacques Callebert, Messaouda Khelfa, Youssef Blel, H. Thabet, M. Amamou, A. Lillo- Le Louët, C. Le Beller, B. Vivien, Pierre Carli, H. Le Louët, Fatma Essafi, Nasreddine Foudhaili, Abdelaziz Ben Slimen, Rami Jabla, Hedia Hammed, Mahdi Marzouk, Nesrine Boujelbene, Fahmi Dachraoui, Asma Hachani, Saousen Ben Abdallah, Hend Ben Lakhal, Chaima Ghribi, Imen Ben Ali, Imen Abdellaoui, Lamia Ouanes-Besbes, Fekri Abroug, Suela Demiri, Christine Lorut, Daniel Luu Van Lang, Aurélie Lefebvre, Marco Alifano, Jean-Francois Reignard, Marc Samama, Daniel Dusser, Nicolas Roche, François Reminiac, Cassandre Landel, Samuel Gensburger, Thomas Bocar, Lydiane Mordier, Marion Philippe, Deborah Le Pennec, Laurent Vecellio, Stephan Ehrmann, Laurent Poiroux, David Thevoz, Julien Simons, Jean Roeseler, Anthéa Loiez, Stéphanie Gérard, Nicolas Dousse, Sylvie L'hotellier, Elodie Baumgarten, Stéphanie Borschneck, Fatima Kharcha, Cécile Ghander, Christophe Trésallet, Etienne Puymirat, Jean-Yves Fagon, Philippe Aegerter, Jean-Luc Diehl, Caroline Hauw-Berlemont, Gilles Chatellier, Nicolas Danchin, Nadia Aissaoui, Nadia Aissat, R. Bernard, Julien Amour, Adrien Bouglé, Charles Vidal, Djavidi Nima, Varnous Shaida, Amandine Dorget, Nicolas Bréchot, Rabi Toufiki, Youssef Mouaffak, Ahmed Rhassan El Adib, M. Amine, S. Moumine, Marie Jonard, Anne Sophie Ducloy-Bouthors, Pierre Bouju, Nicolas Barbarot, Arnaud Gacouin, Pierre Fillâtre, Guillaume Grillet, Angélique Goepp, Anne-Laure Clairet, Samuel Limat, Christian Cornette, Amira Fatnassi, Chiheb Romdhani, Walid Sammoud, Iheb Labbene, Mustapha Ferjani, Hind Taibi, Ijlal Elatiqi, A. Iraqui, Rachid Cherkab, Wafae Haddad, Chafik Elkettani, Lahoucine Barrou, Fabien Cave, Nicolas Lerolle, Pierre Louis Doutrellot, Benoit Vaysse, M. Inan, K. Khelfoun, M. Nasserallah, C. Legrand-Monteil, S. Tasseel-Ponche, Benjamin Kowalski, Anne Guaguere, Claire Boulle-Geronimi, Juliette Masse, Clément Vanbaelinghem, Patrick Herbecq, Syrine Draief, Lazhari Gharsallah, Imen Rahmani, Bahija Gasri, Sofiene Tlaili, Rym Hammouda, Amen Allah Messadi, Philippe Michel, Bruno Gelée, Fouad Fadel, Marie Thuong, Sandra Ait-Aoudia, Salima Laddi, Mohamed-Mohcen Sahraoui, Michel MULLER, Anna Faucher, Bertrand Hermann, Julie BUSSON, Julie Dhumeaux, Nicole Ericher, Pierre Lucas, Magalie Dumas, Céline Chapelle, Benedicte Philippon-Jouve, Jérôme Morel, Pascal Beuret, Tymothée Poitou, Philippe Petua, Albert Prades, Marion Basty, Clément Monet, Benjamin Mounet, Emmanuel Futier, Audrey Leroux, Xavier Oudinot, Marc Laurent, Sebastien Jochmans, Jean-Emmanuel Alphonsine, Ly Van Vong, Nathalie Rolin, Oumar Sy, Jean Serbource-Goguel, Olivier Ellrodt, Mehran Monchi, Turki Olfa, Benhamida Chokri, Hedi Chelly, Amélie Trichot, Gwenhael Colin, Isabelle Vinatier, Konstantinos Bachoumas, Jean-Claude Lacherade, Maud Fiancette, Aurélie Joret, Aihem Yehia, Matthieu Henry-Laguarrigue, Laurent Martin-Lefevre, Keyvan Razazi, Mathieu Surenaud, Alexandre Bedet, Aurélien Seemann, Sophie Hue, Raphaël Clere-Jehl, Anne-Laure Charles, Bernard Geny, Pascal Bilbault, Gabriel Lejour, Simon Bourcier, Pierre Yves Boêlle, Nemlaghi Safaa, Sylvie Paulus, Claire Flamens, Jean Neidecker, Cecile Allioux, Romain Guedj, Isabelle Guellec, Julia Guilbert, Pierre-Louis Leger, Maryne Demoulin, Amélie Durandy, Sandrine Jean, Ricardo Carbajal, Aurelie Morand, Laurent Zieleskiewicz, Olivier Brissaud, Stéphane Le Bel, Zoe Meresse, Michel Panuel, Laurent Thomachot, Marc Leone, Fabrice Michel, Anna Deho', Laïly Sadozai, Stéphane Dauger, Sonia Prot-Labarthe, Mathieu GENUINI, Moulin Florence, Jean-Marc Tréluyer, Sylvain Renolleau, Emmanuelle Chalavon, Rodrigue Dessein, Bruno Grandbastien, Sarah Pesin, Francois Dubos, Stephane LETEURTRE, Marie-Aude Puel, Marie Szulc, Anais Philippe, Francois Severac, Dominique Astruc, Pierre Kuhn, Philippe Desprez, Benoît Colomb, Anne Marie Petion, Laurent Queudet, Solenn Remy, Mouaffak Youssef, Nadia Roumeliotis, Christian Dong, Geraldine Pettersen, Louis Crevier, Guillaume Emeriaud, Jérôme Naudin, Laetitia Abdallah, Marion Ganier, Karine Frannais, Dylia Douglas, Cecile Flusin, David Brossier, Redha Eltaani, Michaël Sauthier, Bernard Guillois, Jérôme Rambaud, Michelle Larroquet, Alain Amblard, Noella Lode, Isabelle Casadevall, Katia Kessous, Hervé Walti, Huixiong Chen, Sahar Habacha, Bassem Chatbri, Cyril Masniere, Bruno Megarbane, Samar Souissi, Hatem El Ghord, N. Kouraichi, Nozha Brahmi, Takoua Marhbène, Islam Mejri, Douha Lakhdar, Takoua Merhabane, Hé la Maamouri, Oestreicher Charlotte, Helena Wegelius, Caroline Landelle, Jacques Schrenzel, Laurent Kaiser, Hind Belhadj, Paul Chanareille, Adélie Ladureau, Alice Sanna, Amélie Rolle, Bertrand Pons, Pascale Piednoir, Fanny Ardisson, Frédéric Martino, Thomas Bernos, Khalid Elkoun, Elie Elain, Roland Lawson, Matthieu Resh-Rigon, Sophie Belorgey, Guillaume Thiery, Caroline Hauw Berlemont, Cyprian Pricopi, Françoise Barthes, Thansya Doddie, Mj Nsiala, Nh Situakibanza, Be Amisi, Mj Kazadi, Ma Kilembe, Christophe Clément, François Lamontagne, Valérie Nocquet Boyer, Sébastien Naimo, Ronan Raulais, Emilie Genevois, Lucie Bouchoud, Filippo Boroli, Nour Abidi, Mohamed Abbas, Stefan Harbarth, Jerôme Pugin, Pierre-Emmanuel Charles, Caroline Dereux, Stanislas De Guillebon, Eloise Morisse, Julie France, Deborah Gasser, Philippe Badia, Walter Picard, P. Corne, I. De Boulastel, S. Seguin, A. BLASCO, V. Ledur, Olivier Jonquet, Paktoris-Papine Sophie, margaux artiguenave, Faten El Sayed, Florence Espinasse, Aurélien Dinh, Cyril Charron, Benjamin Lebas, Sophie Hatsch, Quentin Maestraggi, Anne-Florence Dureau, François Faitot, Dimitri Margetis, Odile Bouvet, Didier Chevret, Erick Denamur, Justine Simonet, Philippe Vest, Vincent Peigne, Séverine Couffin, M. Cheikh Bouhlel, Ahmed Khedher, Kaoula Meddeb, A. Azouzi, Y. Hamdaoui, Jihene Ayachi, W. Brahim, Rania Bouneb, Nans Florens, Julie Varéon, Arnaud Malatray, Laurent Argaud, Pierre Dupland, Romain Vergier, Pauline Issaurat, Philippe Estagnasie, Pierre Squara, Alain Brusset, Vincent Génin, Ali Jendoubi, Rifka Jlassi, Bassem Hamrouni, Yahia Marzougui, Jihen Kouka, Salma Ghedira, Mohamed Houissa, Kaouther Dhifaoui, Johanna Oziel, Alexy Tran Dinh, Caroline Neulier, Marlène Amara, Nicaise Nebot, Gilles Troché, Nelly Breton, Sébastien Cavelot, Béatrice Pangon, Jacques Merrer, Francois Labaste, Jean-Marie Conil, Julia Grossac, Stéphanie Ruiz, Marion Grare, Vincent Minville, Bernard Georges, Guillaume Van Der Meersch, Philippe Karoubi, Christophe Huang, Helene Carbonne, Rishma Amarsy, Joaquim Mateo, Sophie Leloup Von Edelsberg, Christelle Vercheval, Pierre Damas, Chaker Bouguerra, Noura Naas, Joris Muller, Mickaël Schaeffer, Pierre Tran Ba Loc, Stephanie Deboscker, Marie-Line Harley, Thierry Lavigne, Jennifer Brunet, Bertrand Canoville, François Lellouche, Erwan L'Her, Pierre Alexandre Bouchard, Tamer Elfaramawy, Benoit Gosselin, Sarah Guégan, Jean-Bernard Michotte, Enrico Staderini, Jonathan Dugernier, Rares Rusu, Giuseppe Liistro, Grégory Reychler, Mathieu Simon, Elmaati Essoukaki, Jean Bernard Michotte, Olivier Contal, Becem Trabelsi, Hedi Garsallah, Khaoula Harira, Cédric Rafat, Eric Mariotte, Caroline Le Jeune, Pascal Roy, Mauricette Michallet, Yoann Zerbib, François Baudin, François Blot, Caroline Bornstain, Stéphanie Gelinotte, Jean-Philippe Rigaud, Fabienne Tamion, Marie Bouteloup, Michael Darmon, H. Nouira, Su Degirmenci, Christine Kummerlen, Eugénie Delile, Pierre-Alain Thiébaut, Jean-Claude Do Rego, David Coquerel, Rémi Nevière, Laure Ichou, Nicolas Carbonell, Pierre-Emmanuel Rautou, Jean-Baptiste Nousbaum, Christophe RENOU, Rodolphe Anty, Luce Landraud, Hafid Ait-Oufella, Rémi Coudroy, Jean-Claude Lecron, Michael Helary, Jonathan Paillot, Sébastien Pili-Floury, Asma Ezzamouri, Mohamed Shaker Salem, Lamia Kerdjana, Mihaela Dumitrescu, Olivier Mimoz, Bertrand Debaene, Virginie Migeot, Claire Dahyot-Fizelier, Sana Khedher, Amira Maoui, Benoit Champigneulle, Lara Zafrani, Jean-Baptiste Lascarrou, Floriane Lissonde, Aurélie Le Thuaut, Jean Reignier, Laura Platon, Jérôme Lambert, David Lagier, Jeanpaul Brun, Antoine Sannini, Laurent Chow-Chine, Magali Bisbal, Marion Faucher, Djamel Mokart, Leï la Mourtada, Lemiale Virgnie, Alexandre Gaudet, Erika Parmentier-Decrucq, Nathalie De Freitas Caires, Sylvain Dubucquoi, Philippe Lassalle, Daniel Mathieu, Jean-Christophe Richard, Romain Tapponnier, Luc Quintin, C. Pichot, F. Petitjeans, Antoine Guillon, Youenn Jouan, Daborah Breah, Fabien Gueugnon, Emilie Dalloneau, Thomas Baranek, Clémence Henry, Eric E. Morello, Jc Renauld, M. Pichavant, Philippe Gosset, Y. Courty, Patrice Diot, Mustapha Si-Tahar, Constance Vuillard, Béatrice La Combe, Pauline Ponsin, Guillaume BODDAERT, Bertrand Grand, Yohan Baudoin, Stéphane Bonnet, Salah Snouda, Mohamed Fehmi Abbes, Imen Benchiekh, Ines Sedghiani, Jihane Belayachi, Leila Debono, Adrien Auvet, Lydie Nadal-Desbarats, Jacques Tankovic, Redouane Dahoumane, Hafid Ait Oufella, Georges Offenstadt, Amel Filali, Emmanuel Faure, Olivier Nigeon, H. Bazus, Jihad Mallat, Didier Thevenin, Sophie Lempereur-Legros, Didier Ledoux, Monique Nys, Zied Hajjej, Jonathan Messika, Olivier Clermont, Alexandra Aubry, Romain Fernandes, Cécile Garnaud, Muriel Cornet, Patricia Pavèse, Luc Foroni, Sandrine Boisset, Daniè le Maubon, Maha Abid, Hanane Ezzouine, Constant Aniolo Edith, Benjamin Sztrymf, Jean-Emmanuel Serre, L. Landreau, Vanessa Jean-Michel, Francis Couturaud, Elizabeth Moore, Pierre-Yves Egreteau, Jean-Michel Boles, Jean-Etienne Herbrecht, Charlotte Kaeuffer, Anne Meyer, Khaouther Ben Arfi, Fabrice Lesage, Sylvie Séguret, Laurent DUPIC, Laure De Saint Blanquat, Anne-Sophie Baptiste, Hugues Georges, Pierre-Yves Delannoy, Patrick Devos, Dolores Albarracín, A. Ducousso-Lacaze, Julien Dufour, Séverin Cabasson, Anne Veinstein, Delphine Chatellier, Vivien Hong Tuan Ha, Nicolas Lau, Lucie Mimoun, Xavier Forceville, Adel Maamar, Stéphanie Chevalier, Vlad Botoc, Stephane Rouleau, Arnaud Desachy, Sylvie Calvat, Charles Lafon, Christophe Cracco, Nicolas Van Grunderbeeck, J. Temime, Perrine Molmy, G. Gasan, Agathe Béranger, Hélène Chappuy, Pierre-Marie Bertrand, Alexandra Beurton, Laëtitia Bodet-Contentin, Pierre-Eric Danin, Elsa Dubois, Yasemin Karaca, Pierre Mora, Dominique Vodovar, Yohan Desbrosses, Adrien Chauchet, Etienne Daguindau, Eric Deconinck, Akli Chermak, Marinne Baron, Laure Calvet, Anne Françoise Sapin, Bruno Pereira, Lucie Vettoretti, Jacques Lacroix, Lucy Clayton, Elham Sabri, Laurent Bardiaux, Pierre Tiberghien, Paul Hebert, Etienne Lengline, Gérard Socié, Edith Borcoman, Katerina Rusinová, Aurélien Sutra Del Galy, Mélanie Mercier, Jean-François Hamel, Tommy Raveau, Marie-Pierre Moles, Aline Clavert, Mathilde Hunault-Berger, Norbert Ifrah, Aline Schmidt-Tanguy, Serge Carreira, Sophie Lavault, Olivier Pallanca, Elise Morawiec, Isabelle Arnulf, Thomas D'humières, Cédric Carrié, Chloé Gisbert-Mora, Éline Bonnardel, Matthieu Biais, Gilles Hilbert, Côme Bureau, Thomas Joannon, Aude Marincamp, Jean-Daniel Chiche, Alexis Ferré, Daniel Lichtenstein, Gilbert Meziere, Martin Dres, Céline Gonzalez, Olfa Hamzaoui, Thomas Geffriaud, François Leleu, Florence Boissier, Elise Cuquemelle, Pascal Lim, R. Amara, Mohamed Boussarsar, Julie Léger, Christophe Jacob, Koceila Bouferache, Philippe Vignon, Claire Ragot, Laure Corradi, Laure Maurice, S. Julliand, Anna DEHO, Fleur Le Bourgeois, Aurélien Jacquot, Frédéric Valla, Flavie Letois, Alexandre Salvadori, Gaia Ottonello, Stéphane Blanot, Juliette Montmayeur, Gilles Orliaguet, Flora Habas, Julien Baleine, Julia Lebouhellec, Clémentine Combes, Maryline CHOMTON, Philippe Jouvet, Bruno Ranchin, Marie Alice Macher, Theophile Gaillot, Mabrouk Bahloul, Murielle Moine, François Xavier Ageron, Claire Jannel, Thierry Debillon, Isabelle Wroblewski, Matthieu Duprey, Vincent Jarlier, Charles-Edouard Luyt, Sébastien Bailly, Thomas Longval, David Schnell, Christophe Padoin, Yves Cohen, Amel Mokline, Emna Gaies, Sameh Triki, Anis Klouz, Mouhamed Moussa, Flavie Desrumaux, Faten May, Marion Perrin, Jean-Claude Nguyen, Kelly Tiercelet, Julien Fournier, Mélanie Cherin, Marie Dominique Kitzis, Benoît Misset, Cyrille Mathien, Antoine Poidevin, Luis Donatti, Joy Mootien, Luís Pinto, Mathieu Egard, Gokhan Bodur, Guillaume Barberet, Carmen Ionescu, Frédérique Ganster, Philippe Guiot, Khaldoun Kuteifan, Alain Mpela, Jonathan Chelly, Laurent Guérin, Romain Persichini, Thomas Hullin, Nicolas Deye, Pierre Aubertein, Marine Paul, Claudio Sandroni, Olivier Passouant, Guillaume Geri, Camille Chenevier-Gobeaux, Frédéric Batteux, Jean-François Llitjos, Ludovic Drouet, Sébastian Voicu, Patrick Henry, Jean-Guillaume Dillinger, Wulfran Bougouin, Dabor Resiere, A. Dessoy, Valérie Faivre, Charles Damoisel, Benjamin Soyer, Anne-Cécile Galoisy, Laurent Mauvieux, Fatiha Zobairi, Eduardo Anglès-Cano, Laure Stiel, Caroline Piau, Jean-Marc Tadié, Thomas Daix, Robin Jeannet, Jean Feuillard, Lucie Jolly, Amir Boufenzer, Kevin Carrasco, Marc Derive, Sébastien Gibot, Hamid Merdji, Nadia Belaidouni, Julie Toubiana, Yann L'Hermitte, France Woimant, Catherine Oppenheim, Christophe Couvreur, François Dolveck, Magali Devriese, Sophie Dupeyrat, Patrick Ray, Guillaume Lefèvre, Nicolas Roothaer, Amélie Carpentier, Fabien Vaniet, Antoine Maisonneuve, Eric Wiel, Sébastien Canu, Emmanuelle Hammad, Francois Antonini, Marion Poirier, Coralie Vigne, Malik Haddam, Julie Alingrin, Laurence Dangers, Gilles Mangiapan, Isabelle Huet, Xavier DHALLUIN, Nathalie Bautin, Jean Jacques Quiot, Corinne Appere De Vecchi, Cecile Chenivesse, Khalil Tarmiz, Fatma Kaaniche Medhioub, Mariem Smaoui, Chaigar Mohammed Cheikh, E. El Alami, Fanny Mochel, Damien Galanaud, Louis Puybasset, Marion Lodey, Elsa Guiller, Nicolas Weiss, Stein Silva, Corine Vuillaume, Francesco De Pasquale, Jean François Démonet, Fabrice Sinnah, Marie Amelie Dalloz, Marie Pia d'Ortho, Anny Rouvel-Tallec, David Couret, Aurélie Catan, Brice Nativel, Cynthia Planesse, Nicolas Diotel, Olivier Meilhac, Fabian Roy-Gash, Christophe Lebard, Anne-Gaelle Si Larbi, Virginie Gaudin, France Bonnin, Oceane Sultan, Cecile Hoc, Emmanuel Mathieu, Bertrand Lapergue, Frédéric Bourdain, Margot Caron, Antoine Parrot, Vincent Labbé, El Mahdi Hafiani, Christophe Quesnel, Stéphanie Genay, Bertrand Decaudin, Sabine Ethgen, Pascal Odou, Gilles Lebuffe, Stéphane Gaudry, Cecile Aubron, Zoe Mcquilte, Maïté Garrouste-Orgeas, Lilia Soufir, Bernard Allaouchiche, Bruno Verdière, Martine Nyunga, Noémie Banaias, Delphine Colling, Marie Kauv, Erik Blondeau, Islem Ouanes, Édouard Auclin, Caroline Haw-Berlemont, Julien Taieb, Stéphane Oudard, Genevieve Morissette, Wassim Kechaou, Catherine Litalien, Aïcha Merouani, Véronique Phan, Josée Bouchard, Julie Starck, Nelly Briand, Philippe Sachs, François Angoulvant, Julie Sommet, L. Holvoet, M. Benkerrou, Lélia DREYFUS, Fabienne Bordet, Sandrine Touzet, Angélique Denis, Julien Le coz Le Coz, Gérard Chéron, Rima Nabbout, Geraldine Patteau, Claire Heilbronner, Philippe HUBERT, Mehdi Oualha, Nabil Tabet Aoul, Benjamin Crulli, Baruch Toledano, Nancy Poirier, Suzanne Vobecky, Hosni Khouadja, René Robert, M. Vinet, Camille Vinclair, Julie Boisramé-Helms, François Beloncle, Peter Radermacher, Pierre Asfar, Elisabeth Coupez, Julien Bohe, Cláudia Righy Shinotsuka, Pietro Caironi, Paola Villois, Vito Fontana, Jacques Creteur, Franck Pourcine, Ly Vong, Claire Marie Weyer, Benoit Akando, Razach Abdallah, Morgane Wetzstein, Julien Maizel, Nadiejda Antier, Yasmina Serroukh, Karim Zouaoui Boudjeltia, Anne Joosten, Alexandre Rousseau, Lélia Grunebaum, Xavier Delabranche, Yoganaden Mootien, Rostane Gaci, Jean-Romain Garric, Agathe Delbove, Cédric Darreau, Auguste Dargent, Agnès Soudry-Faure, Marc Pineton de Chambrun, Pierre Demondion, Jean-Christophe Blanchard, Sydney Chocron, Nicolas Meneveau, Filippo Corsi, Pierre-Emmanuel Meynieu, Benjamin Repusseau, Arnaud Germain, Guillaume Baudry, Lucie Hierle, Guillaume Besch, Guillemette Thomas, Nadim Cassir, Stéphanie Dizier, Antoine Roch, Grégoire Trebbia, Kiruba Govindaradjou, Jérôme Devaquet, Clement Picard, François Parquin, Morgan Leguen, Marie-Louise Felten, Edouard Sage, Alain Chapelier, Maxens Decavele, Michaël Duruisseaux, Jocelyne Fleury, Martine Antoine, Marie-France Carette, Marie Wislez, Claire Givel, Constance De Margerie-Mellon, Eric De Kerviler, Yacine Tandjaoui-Lambiotte, Olivia Freynet, Antoine Kimmoun, Elisabeth Baux, Vincent Das, Patrice Talec, Nadia Anguel, Guillaume Louis, Nicolas Girerd, Pauline Tallon, Alice Hadchouel-Duvergé, Nadège Salvi, Pascale Cairet, Christophe Delacourt, Blandine Lefebvre Blandine, Laurence Beraud, Zoé Coppere, Antonin Lamazière, François Lionnet, Muriel Fartoukh, Samuel Lehingue, Xavier D'Journo, Forel Jean-Marie, Ronan Thibault, Anne-Marie Makhlouf, Aurélien Mulliez, Cristina Gonzalez, Sylvain Dadet, Gintautas Kekstas, Jean-Charles Preiser, Kozjek Nada Rotovnik, Isabel Ceniceros Rozalen, Kinga Kupczyk, Zeljko Krznaric, Noël J. Cano, Claude Pichard, Bénédicte Gaillard- Le Roux, Corinne Jotterand, Shancy ROOZE, Clemence Moullet, Aurélia Henin, Florence Ettori, Christophe Zemmour, Jean Marie Boher, Michel Arnaout, Audrey Feltry, Salah Adel Ben, Juliette Audibert, Alexandre Conia, Olivier Gontier, Mouldi Hamrouni, Thierry Lherm, Abdelkader Ouchenir, Jérôme Rétif, Alain Proudhom, Chantal Lagardere, Stéphane Tissot, Pierre Kalfon, Lynn Sacre, Antoine Villa, Alaywa Khadija, Robert Garnier, Brigitte Vasset, Annette Heinzelman, Romain Jouffroy, Elsa Démarest Durand, Patricia Compagnon, Neila Maaroufi, A. M'rad, Alia Jebri, Hassen Ben Ghezala, Céline Legout, Frédéric J. Baud, Anne Castot-Villepelet, Sandrine Valade, Olivier Lesieur, Benjamin Delmas, Benoit Visseaux, Johana Cohen, Liem Binh Luong Nguyen, Caroline Morbieu, Charles Burdet, François-Xavier Lescure, Laurence Armand-Lefevre, Yazdan Yazdanpanah, Nadira Houhou-Fidouh, Marine Cazaux, Le Goff Jérôme, Véronique Meignin, David Boutboul, Philippe Rispail, Vincent Brunot, N. Besnard, Patrice Céballos, Annabelle Stoclin, Federico Rotolo, Muriel Wartelle, Yosr Hicheri, Sylvia Maillet, Elisabeth Chachaty, Jean-Pierre Pignon, Marion Venot, Mathieu Delorme, Emilie Bialais, Dupuis Julie, Laura Paoloni, Xavier Wittebolle, Cheryl Hickmann, Diego Castanares-Zapatero, Antoine Tordeur, Lise Colmant, Xavier Wittebole, Giuseppe Tirone, Pierre-Francois Laterre, Lorraine Ducroux, Claire Kemlin, Eric Moulton, Charlotte Rosso, Aymeric Le Neindre, Silvia Mongodi, Béaïd Bouhemad, Joana Rodrigues, Caroline Botteau, François Waroquier, Karel Christiaens, Frank Vantrimpont, Frédéric Duprez, Charbel Elkhawand, Christophe Poiré, and Frank Vermeesh. French Intensive Care Society, International congress – Réanimation 2016. Annals of Intensive Care, 6(S1):236, June 2016. doi:10.1186/s13613-016-0114-z.
    HAL ] [ Bibtex ]

  • Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, and Carito Guziolowski. Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming. BioSystems, 2016. doi:10.1016/j.biosystems.2016.07.009.
    HAL ] [ Bibtex ]

  • Adrien Rougny, Christine Froidevaux, Laurence Calzone, and Loïc Paulevé. Qualitative dynamics semantics for SBGN process description. BMC Systems Biology, 2016. doi:10.1186/s12918-016-0285-0.
    HAL ] [ Bibtex ]

  • Johannes Starlinger, Sarah Cohen-Boulakia, Sanjeev Khanna, Susan Davidson, and Ulf Leser. Effective and Efficient Similarity Search in Scientific Workflow Repositories. Future Generation Computer Systems, 56:584–594, 2016. doi:10.1016/j.future.2015.06.012.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Bertrand Beauvoit, Sophie Colombie, Razanne Issa, Jean-Pierre Mazat, Christine Nazaret, and Sabine Pérès. Human-Scale Metabolic Network of Central Carbon Metabolism: application to serine metabolism from glutamine in Cancer Cells. In advances in Systems and Synthetic Biology. Evry, France, March 2016.
    HAL ] [ Bibtex ]

  • Simon Boitard, Willy Rodriguez, Flora Jay, Stefano Mona, and Frederic Austerlitz. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. In conférence Jaques Monod ”Coalescence des approches théoriques et expérimentales en génomique évolutive et biologie des systèmes”, np. roscoff, France, 2016.
    HAL ] [ Bibtex ]

  • Simon Boitard, Willy Rodriguez, Flora Jay, Stefano Mona, and Frédéric Austerlitz. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. In GDR AIEM, np. Montpellier, France, November 2016.
    HAL ] [ Bibtex ]

  • Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, and Loïc Paulevé. Identification of Bifurcations in Biological Regulatory Networks using Answer-Set Programming. In Constraint-Based Methods for Bioinformatics Workshop. Toulouse, France, September 2016.
    HAL ] [ Bibtex ]

  • Vincent Henry, Arnaud Ferré, Christine Froidevaux, Anne A. Goelzer, Vincent Fromion, Sarah Cohen-Boulakia, Sandra Derozier, Marc Dinh, Ghislain Fievet, Stéphan Fischer, Jean-Francois Gibrat, Valentin LOUX, and Sabine Pérès. Représentation systémique multi-échelle des processus biologiques de la bactérie. In IC201: 27es Journées francophones d'Ingénierie des Connaissances. Montpellier, France, June 2016.
    HAL ] [ Bibtex ]

  • Vincent J. Henry, Arnaud Ferré, Christine Froidevaux, Anne A. Goelzer, Vincent V. Fromion, Sarah Cohen-Boulakia, Sandra S. Derozier, Marc Dinh, Ghislain Fiévet, Stephan Fischer, Jean-Francois J.-F. Gibrat, Valentin LOUX Loux, and Sabine Pérès. Représentation systémique multi-échelle des processus biologiques de la bactérie. In IC2016 - Ingénierie des Connaissances. Montpellier, France, June 2016.
    HAL ] [ Bibtex ]

  • Juraj Kolčák, David Šafránek, Stefan Haar, and Loïc Paulevé. Unfolding of Parametric Boolean Networks. In 7th International Workshop on Static Analysis and Systems Biology (SASB 2016), volume 335 of Electronic Notes in Theoretical Computer Science, 67–90. Edimbourg, United Kingdom, September 2016. Elsevier. doi:10.1016/j.entcs.2018.03.009.
    HAL ] [ Bibtex ]

  • Hugues Mandon, Stefan Haar, and Loïc Paulevé. Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph. In Eugenio Cinquemani and Alexandre Donzé, editors, Fifth International Workshop on Hybrid Systems Biology (HSB 2016), volume 9957 of Lecture Notes in Computer Science, 113–127. Grenoble, France, October 2016. Springer International Publishing. doi:10.1007/978-3-319-47151-8_8.
    HAL ] [ Bibtex ]

  • Morterol Martin, Philippe Dague, Sabine Pérès, and Laurent Simon. Minimality of Metabolic Flux Modes under Boolean Regulation Constraints. In 12th International Workshop on Constraint-Based Methods for Bioinformatics WCB'16. Toulouse, France, September 2016.
    HAL ] [ Bibtex ]

  • Loïc Paulevé. Goal-Oriented Reduction of Automata Networks. In Ezio Bartocci, Pietro Lio, and Nicola Paoletti, editors, 14th International Conference on Computational Methods in Systems Biology (CMSB 2016), volume 9859 of Lecture Notes in Computer Science, 252–272. Cambridge, United Kingdom, September 2016. Springer International Publishing. doi:10.1007/978-3-319-45177-0_16.
    HAL ] [ Bibtex ]

  • Lukas Studer, Loïc Paulevé, Christoph Zechner, Matthias Reumann, Maria Rodriguez Martinez, and Heinz Koeppl. Marginalized Continuous Time Bayesian Networks for Network Reconstruction from Incomplete Observations. In AAAI Conference on Artificial Intelligence. Phoenix, Arizona, United States, February 2016.
    HAL ] [ Bibtex ]

  • Wei Wang, Matthieu Barba, Philippe Rinaudo, Alain Denise, and Yann Ponty. Homology -modeling of complex structural RNAs. In JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016. Lyon, France, June 2016.
    HAL ] [ Bibtex ]

  • Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, and Alain Denise. Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic Pathways. In SeqBio 2016. Nantes, France, November 2016.
    HAL ] [ Bibtex ]

Edited proceedings

  • Patrick Amar, François Képès, and Vic Norris, editors. advances in Systems and Synthetic Biology, Evry, France, March 2016. EDP Sciences.
    HAL ] [ Bibtex ]

  • Loïc Paulevé and Nathalie Theret, editors. 6th International Workshop on Static Analysis and Systems Biology (SASB 2015), volume 326 of Electronic Notes in Theoretical Computer Science, Saint-Malo, France, October 2016. Elsevier.
    HAL ] [ Bibtex ]

Thesis

  • Melanie Boudard. Prediction of three-dimensional structure of RNA molecules by regret minimization. Theses, Université Paris Saclay (COmUE), April 2016.
    HAL ] [ Bibtex ]

  • Marc Bouffard. Design, modeling and simulation in silico of an artificial biological nanosystem for medical diagnosis. Theses, Université Paris Saclay (COmUE), September 2016.
    HAL ] [ Bibtex ]

  • Martin Morterol. Méthodes avancées de raisonnement en logique propositionnelle : application aux réseaux métaboliques. Theses, Université Paris-Saclay, December 2016.
    HAL ] [ Bibtex ]

  • Adrien Rougny. Qualitative methods for the construction and the analysis of SBGN molecular networks. Theses, Université Paris Saclay (COmUE), October 2016.
    HAL ] [ Bibtex ]

Other publications

  • Loïc Paulevé. Pint, a static analyzer for dynamics of Automata Networks. 14th International Conference on Computational Methods in Systems Biology (CMSB 2016), September 2016. Poster.
    HAL ] [ Bibtex ]

Reports and working papers

  • Frédérique Bassino, Mathilde Bouvel, Valentin Féray, Lucas Gerin, and Adeline Pierrot. The Brownian limit of separable permutations. working paper or preprint, February 2016.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia and Patrick Valduriez. Bioinformatics big data processing. Research Report RR-8915, Inria Sophia Antipolis ; LRI - CNRS, University Paris-Sud, May 2016.
    HAL ] [ Bibtex ]

2015

Journal articles

  • Frédérique Bassino, Mathilde Bouvel, Adeline Pierrot, and Dominique Rossin. An algorithm for deciding the finiteness of the number of simple permutations in permutation classes. Advances in Applied Mathematics, 64:124 – 200, March 2015. doi:10.1016/j.aam.2014.12.001.
    HAL ] [ Bibtex ]

  • Mélanie Boudard, Julie Bernauer, Dominique Barth, Johanne Cohen, and Alain Denise. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies. PLoS ONE, 10(8):e0136444, August 2015. doi:10.1371/journal.pone.0136444.
    HAL ] [ Bibtex ]

  • Thomas Bourquard, Flavie Landomiel, Eric Reiter, Pascale Crépieux, David W. Ritchie, Jérôme Azé, and Anne Poupon. Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex. Scientific Reports, 5:5:10760, June 2015. doi:10.1038/srep10760.
    HAL ] [ Bibtex ]

  • Bryan Brancotte, Bo Yang, Guillaume Blin, Sarah Cohen-Boulakia, Alain Denise, and Sylvie Hamel. Rank aggregation with ties: Experiments and Analysis. Proceedings of the VLDB Endowment (PVLDB), 8(11):1202–1213, July 2015. doi:10.14778/2809974.2809982.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia and Patrick Valduriez. Querying and Managing bioinformatic data for molecular biology. Techniques de l'Ingenieur, TIP140WEB:BIO7055, November 2015.
    HAL ] [ Bibtex ]

  • Alexis Courbet, Franck Molina, and Patrick Amar. Computing with Synthetic Protocells. Acta Biotheoretica, pages 15, May 2015. doi:10.1007/s10441-015-9258-8.
    HAL ] [ Bibtex ]

  • Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Identification of Biological Regulatory Networks from Process Hitting models. Theoretical Computer Science, 568:39, February 2015. doi:10.1016/j.tcs.2014.12.002.
    HAL ] [ Bibtex ]

  • Maxime Folschette, Loïc Paulevé, Morgan Magnin, and Olivier Roux. Sufficient Conditions for Reachability in Automata Networks with Priorities. Theoretical Computer Science, 2015. doi:10.1016/j.tcs.2015.08.040.
    HAL ] [ Bibtex ]

  • Jorgelindo da Veiga Moreira, Sabine Pérès, Jean-Marc Steyaert, Erwan Bigan, Loïc Paulevé, Marcel Levy Nogeira, and Laurent Schwartz. Cell cycle progression is regulated by intertwined redox oscillators. Theoretical Biology and Medical Modelling, 12(1):10, May 2015. doi:10.1186/s12976-015-0005-2.
    HAL ] [ Bibtex ]

  • Loïc Paulevé, Maxime Folschette, Morgan Magnin, and Olivier Roux. Analyses statiques de la dynamique des réseaux d'automates indéterministes. Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, 34(4):22, 2015. doi:10.3166/TSI.34.463-484.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Marc Bouffard, Franck Molina, and Patrick Amar. Extracting logic gates from a metabolic network. In advances in Systems and Synthetic Biology, 13. Strasbourg, France, March 2015.
    HAL ] [ Bibtex ]

  • Vincent Le Gallic, Alain Denise, and Yann Ponty. Résultats algorithmiques pour le design d'ARN avec contraintes de séquence. In SeqBio 2015, 26–31. Orsay, France, November 2015.
    HAL ] [ Bibtex ]

  • Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, and Carito Guziolowski. Boolean Network Identification from Multiplex Time Series Data. In Olivier Roux and Jérémie Bourdon, editors, CMSB 2015 - 13th conference on Computational Methods for Systems Biology, volume 9308 of Lecture Notes in Computer Science, 170–181. Nantes, France, September 2015. Springer International Publishing. doi:10.1007/978-3-319-23401-4_15.
    HAL ] [ Bibtex ]

  • Christophe Pradal, Christian Fournier, Patrick Valduriez, and Sarah Cohen-Boulakia. OpenAlea: Scientific Workflows Combining Data Analysis and Simulation. In SSDBM: Scientific and Statistical Database Management, Proceedings of the 27th International Conference on Scientific and Statistical Database Management. San Diego, United States, June 2015. ACM - Association for Computing Machinery. doi:10.1145/2791347.2791365.
    HAL ] [ Bibtex ]

  • Adrien Rougny, Yoshitaka Yamamoto, Hidetomo Nabeshima, Gauvain Bourgne, Anne Poupon, Katsumi Inoue, and Christine Froidevaux. Completing signaling networks by abductive reasoning with perturbation experiments. In 25th International Conference on Inductive Logic Programming. Kyoto, Japan, August 2015.
    HAL ] [ Bibtex ]

Edited proceedings

  • Vic Norris Patrick Amar, François Képès, editor. advances in Systems and Synthetic Biology, EDP Sciences, March 2015.
    HAL ] [ Bibtex ]

  • Alain Denise, Olivier Lespinet, and Mireille Régnier, editors. Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics, Orsay, France, November 2015.
    HAL ] [ Bibtex ]

  • Loïc Paulevé and Heinz Koeppl, editors. 5th International Workshop on Static Analysis and Systems Biology (SASB 2014), volume 316 of Electronic Notes in Theoretical Computer Science, Munich, Germany, September 2015. Elsevier.
    HAL ] [ Bibtex ]

Thesis

  • Bryan Brancotte. Rank aggregation with ties : algorithms, user guidance et applications to biologicals data. Theses, Université Paris Sud - Paris XI, September 2015.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia. Data Integration in the Life Sciences: Scientific Workflows, Provenance, and Ranking. Habilitation à diriger des recherches, Université Paris-Sud, June 2015.
    HAL ] [ Bibtex ]

  • Cong Zeng. Classification of RNA Pseudoknots and Comparison of Structure Prediction Methods. Theses, Université Paris Sud - Paris XI, July 2015.
    HAL ] [ Bibtex ]

Other publications

  • Christian Fournier, Simon Artzet, Jérôme Chopard, Michael Mielewczik, Nicolas Brichet, Llorenç Cabrera, Xavier Sirault, Sarah Cohen-Boulakia, and Christophe Pradal. Phenomenal: a software framework for model-assisted analysis of high throughput plant phenotyping data. IAMPS 2015 (International Workshop on Image Analysis Methods for the Plant Sciences), September 2015. Poster.
    HAL ] [ Bibtex ]

  • Adrien Rougny, Christine Froidevaux, and Loïc Paulevé. Two Qualitative Dynamics Semantics for SBGN Process Description Maps. CMSB'15, September 2015. Poster.
    HAL ] [ Bibtex ]

2014

Journal articles

  • Sarah Cohen-Boulakia, Jiuqiang Chen, Paolo Missier, Carole Goble, Alan Williams, and Christine Froidevaux. Distilling structure in Taverna scientific workflows: a refactoring approach. BMC Bioinformatics, 15(Suppl 1):S12, 2014.
    HAL ] [ Bibtex ]

  • Alain Denise and Philippe Rinaudo. Optimisation problems for pairwise RNA sequence and structure comparison: a brief survey. Transactions on Computational Collective Intelligence, 13:70–82, January 2014. doi:10.1007/978-3-642-54455-2_3.
    HAL ] [ Bibtex ]

  • Adrien Guilhot-Gaudeffroy, Christine Froidevaux, Jérôme Azé, and Julie Bernauer. Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities. PLoS ONE, 9(9):e108928, 2014. doi:10.1371/journal.pone.0108928.
    HAL ] [ Bibtex ]

  • Cécile Pereira, Alain Denise, and Olivier Lespinet. A meta-approach for improving the prediction and the functional annotation of ortholog groups. BMC Genomics, 2014. doi:10.1186/1471-2164-15-S6-S16.
    HAL ] [ Bibtex ]

  • Changwei Shao, Bo Yang, Tongbin Wu, Jie Huang, Peng Tang, Yu Zhou, Jie Zhou, Jinsong Qiu, Li Jiang, Hairi Li, Geng Chen, Hui Sun, Yi Zhang, Alain Denise, Dong-Er Zhang, and Xiang-Dong Fu. Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome. Nature Structural and Molecular Biology, 21:997–1005, 2014. doi:10.1038/nsmb.2906.
    HAL ] [ Bibtex ]

  • Johannes Starlinger, Bryan Brancotte, Sarah Cohen-Boulakia, and Ulf Leser. Similarity Search for Scientific Workflows. Proceedings of the VLDB Endowment (PVLDB), 7(12):1143–1154, September 2014. doi:10.14778/2732977.2732988.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Patrick Amar. Systèmes oscillants chaotiques en biologie. In Ecole de Printemps 2014 de la Société Francophone de Biologie Théorique. St Flour, France, May 2014. Société Francophone de Biologie Théorique.
    HAL ] [ Bibtex ]

  • Patrick Amar, Muriel Baillieul, Dominique Barth, Bertrand LeCun, Franck Quessette, and Sandrine Vial. Parallel biological in silico simulation. In 29th Intenational Symposium on Computer and Information Sciences, 387–394. Krakow, Poland, October 2014. doi:10.1007/978-3-319-09465-6_40.
    HAL ] [ Bibtex ]

  • Bryan Brancotte, Bastien Rance, Alain Denise, and Sarah Cohen-Boulakia. ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data. In 10th International Conference, Data Integration in the Life Sciences, 128 – 142. Lisbon, Portugal, July 2014. doi:10.1007/978-3-319-08590-6_13.
    HAL ] [ Bibtex ]

  • Thomas Chatain, Stefan Haar, Loïg Jezequel, Loïc Paulevé, and Stefan Schwoon. Characterization of Reachable Attractors Using Petri Net Unfoldings. In Pedro Mendes, Joseph Dada, and Kieran Smallbone, editors, CMSB 2014, volume 8859 of LNCS/LNBI, 14. Manchester, United Kingdom, November 2014. Springer International Publishing. doi:10.1007/978-3-319-12982-2_10.
    HAL ] [ Bibtex ]

  • Jiuqiang Chen, Sarah Cohen-Boulakia, Christine Froidevaux, Carole Goble, Paolo Missier, and Alan Williams. DistillFlow: removing redundancy in scientific workflows. In SSDBM '14 Proceedings of the 26th International Conference on Scientific and Statistical Database Management. Aalborg, Denmark, June 2014. doi:10.1145/2618243.2618287.
    HAL ] [ Bibtex ]

  • Adrien Guilhot-Gaudeffroy, Jérôme Azé, Julie Bernauer, and Christine Froidevaux. Apprentissage de fonctions de tri pour la prédiction d'interactions protéine-ARN. In EGC: Extraction et Gestion des Connaissances, volume RNTI-E-26 of Revue des Nouvelles Technologies de l'Information, 479–484. Rennes, France, January 2014. Cépaduès-éditions.
    HAL ] [ Bibtex ]

  • Thomas Opitz, Jérôme Azé, Sandra Bringay, Cyrille Joutard, Christian Lavergne, and Caroline Mollevi. Breast cancer and quality of life: medical information extraction from health forums. In MIE: Medical Informatics Europe, 1070–1074. Istanbul, Turkey, August 2014.
    HAL ] [ Bibtex ]

  • Bertrand P Beauvoit, Sophie Colombié, Jean-Pierre Mazat, Christine Nazaret, and Sabine Pérès. Systematic study of a metabolic network. In advances in Systems and Synthetic Biology, Proceedings of The Evry Spring School on advances in Systems and Synthetic Biology, 173 p. Evry, France, March 2014. edp science.
    HAL ] [ Bibtex ]

  • Sabine Pérès, Morterol Martin, and Laurent Simon. SAT-Based Metabolics Pathways Analysis without Compilation. In Pedro Mendes Joseph Dada Kieran Smallbone, editor, CMSB 2014, LNCS/LNBI. Manchester, United Kingdom, November 2014. Springer Berlin Heidelberg.
    HAL ] [ Bibtex ]

  • Johannes Starlinger, Sarah Cohen-Boulakia, Sanjeev Khanna, Susan Davidson, and Ulf Leser. Layer Decomposition: An Effective Structure-based Approach for Scientific Workflow Similarity. In International Conference on e-Science, 169–176. Guarujá, Brazil, October 2014. IEEE. doi:10.1109/eScience.2014.19.
    HAL ] [ Bibtex ]

  • Yoshitaka Yamamoto, Adrien Rougny, Hidetomo Nabeshima, Katsumi Inoue, Hisao Moriya, Christine Froidevaux, and Koji Iwanuma. Completing SBGN-AF Networks by Logic-Based Hypothesis Finding. In Formal Methods In Macro-Biology, volume 8738 of Formal Methods in Macro-Biology, 165–179. Nouméa, New Caledonia, September 2014. Springer. doi:10.1007/978-3-319-10398-3_14.
    HAL ] [ Bibtex ]

Book sections

  • Loïc Paulevé, Courtney Chancellor, Maxime Folschette, Morgan Magnin, and Olivier Roux. Analyzing Large Network Dynamics with Process Hitting. In Luis Fariñas del Cerro and Katsumi Inoue, editors, Logical Modeling of Biological Systems, pages 125 – 166. Wiley, July 2014.
    HAL ] [ Bibtex ]

  • Adrien Rougny, Christine Froidevaux, Yoshitaka Yamamoto, and Katsumi Inoue. Analyzing SBGN-AF Networks Using Normal Logic Programs. In Logical Modeling of Biological Systems. Wiley, July 2014. doi:10.1002/9781119005223.ch9.
    HAL ] [ Bibtex ]

Edited proceedings

  • Patrick Amar, François Képès, and Vic Norris, editors. avances in Systems and Synthetic Biology, EDP Sciences, March 2014.
    HAL ] [ Bibtex ]

Thesis

  • Adrien Guilhot-Gaudeffroy. Modelling and scoring of protein-RNA complexes. Theses, Université Paris Sud - Paris XI, September 2014.
    HAL ] [ Bibtex ]

  • Bo Yang. Bioinformatics analysis and consensus ranking for biological high throughput data. Theses, Université Paris Sud - Paris XI ; Université de Wuhan (Chine), September 2014.
    HAL ] [ Bibtex ]

Other publications

  • Simon S. Boitard, Flora Jay, and Frédéric Austerlitz. Inferring demographic history from whole genome using Approximate Bayesian Computation. Annual meeting of the American Society of Human Genetics (ASHG), October 2014. Poster.
    HAL ] [ Bibtex ]

  • Cécile Pereira, Alain Denise, and Olivier Lespinet. A new method for improving the prediction and the functional annotation of ortholog groups. Proc. ECCB'14, the 13th European Conference on Computational Biology, 2014. Poster.
    HAL ] [ Bibtex ]

2013

Journal articles

  • Matthieu Barba, Raphaël Dutoit, Christianne Legrain, and Bernard Labedan. Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism. BMC Systems Biology, 7:99, 2013. doi:10.1186/1752-0509-7-99.
    HAL ] [ Bibtex ]

  • Alexis Lamiable, Franck Quessette, Sandrine Vial, Dominique Barth, and Alain Denise. An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(1):193–199, 2013. doi:10.1109/TCBB.2012.148.
    HAL ] [ Bibtex ]

  • Vic Norris, Patrick Amar, Guillaume Legent, Camille Ripoll, Michel Thellier, and Judit Ovadi. Sensor potency of the moonlighting enzyme-decorated cytoskeleton. BMC Biochemistry, 14(3):1–10, February 2013. doi:10.1186/1471-2091-14-3.
    HAL ] [ Bibtex ]

  • Johan Oudinet, Alain Denise, and Marie-Claude Gaudel. A new dichotomic algorithm for the uniform random generation of words in regular languages (journal version). Theoretical Computer Science, 502:165–176, September 2013.
    HAL ] [ Bibtex ]

  • Sabine Pérès, Liza L. Felicori, and Franck Molina. Elementary Flux Modes Analysis of Functional Domain Networks Allows a Better Metabolic Pathway Interpretation. PLoS ONE, October 2013. doi:10.1371/journal.pone.0076143.
    HAL ] [ Bibtex ]

  • Nicolas Seghezzi, Marie-Joelle Virolle, and Patrick Amar. Novel insights regarding the sigmoidal pattern of resistance to neomycin conferred by the aphII gene, in Streptomyces lividans. AMB Express, 3(1):13, February 2013. doi:10.1186/2191-0855-3-13.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Thomas Bourquard, Damien Mathieu De Vienne, and Jérôme Azé. Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli. In Djamel A. Zighed and Gilles Venturini, editors, EGC 2013 - 13eme conférence Francophone sur l'Extraction et la Gestion des Connaissances, volume E.24 of RNTI, 419–430. Toulouse, France, January 2013. Florence Sèdes (IRIT Toulouse - Université Paul Sabatier) et André Péninou (IRIT Toulouse - Université Toulouse 2), Hermann.
    HAL ] [ Bibtex ]

  • Cécile Pereira, Jérôme Azé, Alain Denise, Christine Drevet, Christine Froidevaux, Philippe Silar, and Olivier Lespinet. Comparative analysis of phylogenetic profiles for the enzymatic characterization of fungal group. In JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, à paraître. Toulouse, France, July 2013.
    HAL ] [ Bibtex ]

  • Sabine Pérès. Analysis of metabolic networks using elementary flux modes. In edp science, editor, Advances in systems and synthetic biology, 165–170. La Colle-sur-Loup, France, March 2013.
    HAL ] [ Bibtex ]

  • Adrien Rougny, Christine Froidevaux, Yoshitaka Yamamoto, and Katsumi Inoue. Translating the SBGN-AF language into logic to analyze signalling networks. In Katsumi Inoue and Chiaki Sakama, editors, LNMR - 1st International Workshop on Learning and Non Monotonic Reasoning, volume arXiv:1311.4639, 44–55. La Coruña, Spain, September 2013. CORR.
    HAL ] [ Bibtex ]

  • Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, and Alain Denise. Flexible RNA design under structure and sequence constraints using formal languages. In ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013. Bethesda, Washigton DC, United States, September 2013.
    HAL ] [ Bibtex ]

Edited proceedings

  • Patrick Amar and François Képès andVic Norris, editors. avances in Systems and Synthetic Biology, EDP Sciences, March 2013.
    HAL ] [ Bibtex ]

Thesis

  • Patrick Amar. Contributions à l'étude de la dynamique des systèmes biologiques et aux systèmes de calcul en biologie synthétique. Habilitation à diriger des recherches, Université Paris Sud - Paris XI, December 2013.
    HAL ] [ Bibtex ]

  • Jiuqiang Chen. Designing scientific workflow following a structure and provenance-aware strategy. Theses, Université Paris Sud - Paris XI, October 2013.
    HAL ] [ Bibtex ]

  • Jiuqiang Chen. Designing scientific workflows following a structure and provenance-aware strategy. Theses, Université Paris Sud - Paris XI, October 2013.
    HAL ] [ Bibtex ]

2012

Books

  • Jérôme Azé, Nicolas Béchet, Laure Berti-Équille, Sylvie Guillaume, Mathieu Roche, and Fatiha Saïs. Mesurer et évaluer la qualité des données et des connaissances. Éditions Hermann, 2012.
    HAL ] [ Bibtex ]

Journal articles

  • Julien Allali, Cédric Saule, Cedric Chauve, Yves D'Aubenton-Carafa, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine De Monte, Aida Ouangraoua, Marie-France Sagot, Michel Termier, Claude Thermes, and Hélène Touzet. BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms. Advances in Bioinformatics, 2012:1–5, 2012. doi:10.1155/2012/893048.
    HAL ] [ Bibtex ]

  • Damien M. De Vienne and Jérôme Azé. Efficient Prediction of Co-Complexed Proteins Based on Coevolution. PLoS ONE, 7(11):1–13, November 2012. doi:10.1371/journal.pone.0048728.
    HAL ] [ Bibtex ]

  • Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lassaigne, Johan Oudinet, and Sylvain Peyronnet. Coverage-biased random exploration of large models and application to testing. Software Tools for Technology Transfer (STTT), 14(1):73–93, 2012.
    HAL ] [ Bibtex ]

  • Matthew R. Lakin, Loïc Paulevé, and Andrew Phillips. Stochastic simulation of multiple process calculi for biology. Theoretical Computer Science, 431:181–206, May 2012. doi:10.1016/j.tcs.2011.12.057.
    HAL ] [ Bibtex ]

  • Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, and Eric Westhof. Automated prediction of three-way junction topological families in RNA secondary structures. Computational Biology and Chemistry, 37:1–5, January 2012. doi:10.1016.
    HAL ] [ Bibtex ]

  • Vic Norris and Patrick Amar. Chromosome Replication in Escherichia coli: Life on the Scales. Life (Chicago, Ill. : 1978), 2(4):286–312, October 2012. doi:10.3390/life2040286.
    HAL ] [ Bibtex ]

  • Vic Norris, Alain R Thierry, Patrick Amar, Barry I Holland, and Franck Molina. The Mimic Chain Reaction. Journal of Molecular Microbiology and Biotechnology, 22(5):335–343, December 2012. doi:10.1159/000345328.
    HAL ] [ Bibtex ]

  • Loïc Paulevé, Morgan Magnin, and Olivier Roux. Static analysis of Biological Regulatory Networks dynamics using abstract interpretation. Mathematical Structures in Computer Science, 22(04):pp 651–685, May 2012. doi:10.1017/S0960129511000739.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Hugo Alatrista Salas, Jérôme Azé, Sandra Bringay, Flavie Cernesson, Frédéric Flouvat, Nazha Selmaoui-Folcher, and Maguelonne Teisseire. The Least Temporal Contradiction Measure: Application to Hydrological Data. In AGILE: International Conference on Geographic Information Science, 197–202. Avignon, France, 2012.
    HAL ] [ Bibtex ]

  • Patrick Amar. Comparative study of some methods for simulation of biochemical reactions. In Ecole de Printemps 2012 de la Société Francophone de Biologie Théorique. Saint Flour, France, June 2012.
    HAL ] [ Bibtex ]

  • Patrick Amar and Loïc Paulevé. HSIM: an hybrid stochastic simulation system for systems biology. In The Third International Workshop on Static Analysis and Systems Biology (SASB 2012), volume 313, 3 – 21. Deauville, France, September 2012. doi:10.1016/j.entcs.2015.04.016.
    HAL ] [ Bibtex ]

  • Zahira Aslaoui-Errafi, Sarah Cohen-Boulakia, Christine Froidevaux, Pauline Gloaguen, Anne Poupon, Adrien Rougny, and Meriem Yahiaoui. Towards a logic-based method to infer provenance-aware molecular networks. In Proc. of the 1st ECML/PKDD International workshop on Learning and Discovery in Symbolic Systems Biology (LDSSB), 103–110. Bristol, United Kingdom, September 2012.
    HAL ] [ Bibtex ]

  • Jiuqiang Chen, Christine Froidevaux, Carole Goble, Alan Williams, and Sarah Cohen-Boulakia. Distilling Structure in Scientific Workflows. In Proc. of the 12th International Workshop on Network Tools and Applications in Biology, Nettab 2012 (Poster), volume 18 of Supp B, 10–102. Como, Italy, November 2012. EMBnet.journal.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia, Christine Froidevaux, and Jiuqiang Chen. Réécriture de workflows scientifiques et provenance. In Proc. of the 28th Journées de Bases de Données Avancées. Clermont Ferrand, France, October 2012.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia, Christine Froidevaux, and Jiuqiang Chen. Scientific Workflow Rewriting while Preserving Provenance. In Proc. of the 8th IEEE International Conference in eScience. Chicago, United States, October 2012. IEEE.
    HAL ] [ Bibtex ]

  • Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Abducing Biological Regulatory Networks from Process Hitting models. In ECML-PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology. Bristol, United Kingdom, September 2012.
    HAL ] [ Bibtex ]

  • Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Concretizing the Process Hitting into Biological Regulatory Networks. In Computational Methods in Systems Biology, p. 166–186. London, United Kingdom, October 2012. Springer Berlin Heidelberg. Accepted at the conference CMSB 2012. http://sites.brunel.ac.uk/cmsb2012. doi:10.1007/978-3-642-33636-2_11.
    HAL ] [ Bibtex ]

  • Stefan Janssen, Loïc Paulevé, Yann Ponty, Balaji Raman, and Matthias Zytnicki. Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space? In IWBDA - 4th International Workshop on Bio-Design Automation - 2012. San Francisco, United States, June 2012.
    HAL ] [ Bibtex ]

  • Fabrice Jossinet, Alexis Lamiable, Philippe Rinaudo, Liza Al-Shikhley, Franck Quessette, Sandrine Vial, Dominique Barth, Eric Westhof, and Alain Denise. Graph Algorithms and Software Framework for Interactive RNA Structure Modelling. In Journees Ouvertes de Biologie Informatique et Mathematiques - JOBIM'12, 475–476. Rennes, France, July 2012.
    HAL ] [ Bibtex ]

  • Philippe Rinaudo, Yann Ponty, Dominique Barth, and Alain Denise. Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. In Ben Raphael and Jijun Tang, editors, WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, tba. Ljubljana, Slovenia, September 2012. University of Ljubljana.
    HAL ] [ Bibtex ]

  • Johannes Starlinger, Sarah Cohen-Boulakia, and Ulf Leser. (Re)Use in Public Scientific Workflow Repositories. In Anastasia Ailamaki, editor, Scientific and Statistical Database Management - 24th International Conference, SSDBM 2012, volume 7338 of LNCS, 361–378. Chania, Greece, June 2012. Springer.
    HAL ] [ Bibtex ]

Edited proceedings

  • P. Amar, F. Kepes, and V. Norris, editors. Proceedings of The 2012 Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics, EDP Sciences, May 2012.
    HAL ] [ Bibtex ]

Thesis

  • Jérôme Azé. Prédiction d'Interactions et Amarrage Protéine-Protéine par combinaison de classifieurs. Habilitation à diriger des recherches, Université Paris Sud - Paris XI, November 2012.
    HAL ] [ Bibtex ]

Reports and working papers

  • Araks Martirosyan, Loïc Paulevé, Clair Poignard, Mireille Régnier, Jean-Marc Steyaert, and Laurent Schwartz. A Dynamical Model for the Transmembrane Potential Regulation by pH. Research Report, LIX, Ecole polytechnique, September 2012.
    HAL ] [ Bibtex ]

2011

Journal articles

  • Thomas Bourquard, Julie Bernauer, Jérôme Azé, and Anne Poupon. A collaborative filtering approach for protein-protein docking scoring functions. PLoS ONE, 6(4):e18541, 2011. doi:10.1371/journal.pone.0018541.
    HAL ] [ Bibtex ]

  • Bryan Brancotte, Anne Biton, Isabelle Bernard-Pierrot, François Radvanyi, Fabien Reyal, and Sarah Cohen-Boulakia. Gene List significance at-a-glance with GeneValorization. Bioinformatics, 27(8):1187–9, April 2011. doi:10.1093/bioinformatics/btr073.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia and Ulf Leser. Search, adapt, and reuse: the future of scientific workflows. SIGMOD record, 2011. doi:10.1145/2034863.2034865.
    HAL ] [ Bibtex ]

  • Sarel J Fleishman, Timothy A Whitehead, Eva-Maria Strauch, Jacob E Corn, Sanbo Qin, Huan-Xiang Zhou, Julie C Mitchell, Omar N A Demerdash, Mayuko Takeda-Shitaka, Genki Terashi, Iain H Moal, Xiaofan Li, Paul A Bates, Martin Zacharias, Hahnbeom Park, Jun-Su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jérôme Azé, Seren Soner, Sefik Kerem Ovalı, Pemra Ozbek, Nir Ben Tal, Türkan Haliloglu, Howook Hwang, Thom Vreven, Brian G Pierce, Zhiping Weng, Laura Pérez-Cano, Carles Pons, Juan Fernández-Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Patapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M Standley, Haruki Nakamura, Kengo Kinoshita, Camden M Driggers, Robert G Hall, Jessica L Morgan, Victor L Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L Kastritis, Alexandre M J J Bonvin, Weiyi Zhang, Carlos J Camacho, Krishna P Kilambi, Aroop Sircar, Jeffrey J Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodríguez, Daisuke Kihara, P Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J Wodak, Joel Janin, and David Baker. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology. Journal of Molecular Biology, pages in press, September 2011. doi:10.1016/j.jmb.2011.09.031.
    HAL ] [ Bibtex ]

  • Vic Norris, Abdallah Zemirline, Patrick Amar, Jean Nicolas Audinot, Pascal Ballet, Eshel Ben-Jacob, Gilles Bernot, Guillaume Beslon, Armelle Cabin, Eric Fanchon, Jean-Louis Giavitto, Nicolas Glade, Patrick Greussay, Yohann Grondin, James A Foster, Guillaume Hutzler, Jürgen Jost, Francois Kepes, Olivier Michel, Franck Molina, Jacqueline Signorini, Pasquale Stano, and Alain R Thierry. Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. Theorie in den Biowissenschaften / Theory in Biosciences, 130(3):211–228, September 2011. doi:10.1007/s12064-010-0118-4.
    HAL ] [ Bibtex ]

  • Sabine Pérès, F. Vallée, Marie Beurton-Aimar, and Jean-Pierre Mazat. ACoM: A classification method for elementary flux modes based on motif finding. BioSystems, 103(3):410–419, 2011.
    HAL ] [ Bibtex ]

  • Cédric Saule, Mireille Regnier, Jean-Marc Steyaert, and Alain Denise. Counting RNA pseudoknotted structures. Journal of Computational Biology, 18(10):1339–1351, October 2011. doi:10.1089/cmb.2010.0086.
    HAL ] [ Bibtex ]

  • Nicolas Seghezzi, Patrick Amar, Brian Koebmann, Peter R Jensen, and Marie-Joëlle Virolle. The construction of a library of synthetic promoters revealed some specific features of strong Streptomyces promoters. Applied Microbiology and Biotechnology, 90(2):615–23, April 2011. doi:10.1007/s00253-010-3018-0.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Marie Agier, Christine Froidevaux, Jean-Marc Petit, Yoan Renaud, and Jef Wijsen. On Armstrong-compliant Logical Query Languages. In George H. L. Fletcher and Slawek Staworko, editors, 4th International Workshop on Logic in Databases, (EDBT/ICDT '10 joint conference), LID, 33–40. Uppsala, Sweden, 2011. George H. L. Fletcher and Slawek Staworko, ACM.
    HAL ] [ Bibtex ]

  • Jérôme Azé, Thomas Bourquard, Sylvie Hamel, Anne Poupon, and David Ritchie. Using Kendall-Tau Meta-Bagging to Improve Protein-Protein Docking Predictions. In M. Loog, editor, PRIB 2011, 284–295. DELFT, Netherlands, November 2011. Marcel Reinders and Dick de Ridder.
    HAL ] [ Bibtex ]

  • Thomas Bourquard, Jérôme Azé, Anne Poupon, and David Ritchie. Protein-protein docking based on shape complementarity and Voronoi fingerprint. In Eduardo PC ROCHA Emmanuel BARILLOT, Christine F ROIDEVAUX, editor, Journées Ouvertes Biologie Informatique Mathématiques, JOBIM 2011, 9–16. Paris, France, June 2011. Institut Pasteur.
    HAL ] [ Bibtex ]

  • Peter Clote, Lou Feng, and Alain Denise. A new approach to suboptimal pairwise sequence alignment. In CompBio 2011: IASTED International Conference on Computational Bioscience. Cambridge, United Kingdom, 2011.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia, Alain Denise, and Sylvie Hamel. Using medians to generate consensus rankings for biological data. In SSDBM 2011: Scientific and Statistical Database Management Conference. Portland, United States, 2011.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia and Ulf Leser. Next Generation Data Integration for the Life Sciences. In IEEE International Conference on Data Engineering (ICDE). Hannover, Germany, April 2011.
    HAL ] [ Bibtex ]

  • Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, and Sylvain Peyronnet. Uniform Monte-Carlo Model Checking. In FASE 2011. Saarbrücken, Germany, 2011.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the Sophia-Antipolis Spring School on Modelling Complex Biological Systems in the context of genomics, France, May 2011. EDP Sciences.
    HAL ] [ Bibtex ]

2010

Journal articles

  • Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, and Helene Touzet. Alignments of RNA structures. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(2):309–322, 2010. doi:10.1109/TCBB.2008.28.
    HAL ] [ Bibtex ]

  • Alain Denise, Yann Ponty, and Michel Termier. Controlled non uniform random generation of decomposable structures. Theoretical Computer Science, 411(40-42):3527–3552, 2010. doi:10.1016/j.tcs.2010.05.010.
    HAL ] [ Bibtex ]

  • Claire Herrbach, Alain Denise, and Serge Dulucq. Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm. Theoretical Computer Science, 411:2423–2432, 2010.
    HAL ] [ Bibtex ]

  • Wei Liu, Yu Zhou, Zexi Hu, Tao Sun, Alain Denise, Xiang-Dong Fu, and Yi Zhang. Regulation of splicing enhancer activities by RNA secondary structures. FEBS Letters, 584(21):4401–7, November 2010. doi:10.1016/j.febslet.2010.09.039.
    HAL ] [ Bibtex ]

  • Thomas Moncion, Patrick Amar, and Guillaume Hutzler. Automatic characterization of emergent phenomena in complex systems. Journal of Biological Physics and Chemistry, 10:16–23, 2010.
    HAL ] [ Bibtex ]

  • Sabine Pérès, Francois Vallee, Marie M. Beurton-Aimar, and Jean-Pierre Mazat. ACoM: A classification method for elementary flux modes based on motif finding. BioSystems, pages Volume 103, Issue 3, March 2011, Pages 410–419, December 2010.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Susan Davidson, Sanjeev Khanna, Sudeepa Roy, Sarah Cohen-Boulakia, Zhuowei Bao, and Anat Eyal. Privacy Issues in Scientific Workflow Provenance. In 1st Int. Workshop on Workflow Approaches to New Data-centric Science (SIGMOD Workshop). Indianapolis, United States, June 2010.
    HAL ] [ Bibtex ]

  • Johan Oudinet, Alain Denise, and Marie-Claude Gaudel. A new dichotomic algorithm for the uniform random generation of words in regular languages. In GASCom 2010. Montreal, Canada, 2010.
    HAL ] [ Bibtex ]

  • Cédric Saule, Mireille Regnier, Jean-Marc Steyaert, and Alain Denise. Counting RNA pseudoknotted structures (extended abstract). In Billey, Sara, Reiner, and Victor, editors, 22nd International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC 2010), volume DMTCS Proceedings vol. AN, 22nd International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC 2010) of DMTCS Proceedings, 1037–1048. San Francisco, United States, 2010. Discrete Mathematics and Theoretical Computer Science.
    HAL ] [ Bibtex ]

  • Cédric Saule, Claire Wallon, and Alain Denise. Uniform and non-uniform random generation of RNA secondary structures with pseudoknots. In GASCOM. Montreal, Canada, September 2010.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the Evry Spring School on Modelling Complex Biological Systems in the context of genomics, France, March 2010. EDP Sciences.
    HAL ] [ Bibtex ]

2009

Journal articles

  • Zhuowei Bao, Sarah Cohen-Boulakia, Susan Davidson, Pierrick Girard, Anat Eyal, Sanjeev Khanna, and Sudeepa Roy. PDiffView: Viewing the Difference in Provenance of Workflow Results. Proceedings of the VLDB Endowment (PVLDB), 2(2):1638–1641, 2009.
    HAL ] [ Bibtex ]

  • Kévin Darty, Alain Denise, and Yann Ponty. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25(15):1974–5, August 2009. doi:10.1093/bioinformatics/btp250.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Zhuowei Bao, Sarah Cohen-Boulakia, Susan Davidson, Anat Eyal, and Sanjeev Khanna. Differencing Provenance in Scientific Workflows. In Proc. of the 25th Int. Conf. on Data Engineering (ICDE), IEEE, 808–819. Shanghai, China, March 2009.
    HAL ] [ Bibtex ]

  • Rance Bastien, Jean-François Gibrat, and Christine Froidevaux. An Adaptive Combination of Matchers: Application to the Mapping of Biological Ontologies for Genome Annotation. In Norman W. Paton, Paolo Missier, and Cornelia Hedeler, editors, DILS 2009-6th International Workshop on Data Integration in the Life Sciences, volume 5647 of Lecture Notes in Computer Science, 113–126. Manchester, United Kingdom, July 2009. Springer. doi:10.1007/978-3-642-02879-3_10.
    HAL ] [ Bibtex ]

  • Thomas Bourquard, Julie Bernauer, Jérôme Azé, and Anne Poupon. Comparing Voronoi and Laguerre tessellations in the protein-protein docking context. In Sixth annual International Symposium on Voronoi Diagrams. Copenhagen, Denmark, June 2009. F. Anton and J. Andreas Bærentzen - Technical University of Denmark.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia and Kevin Masini. BioBrowsing: Making the Most of the Data Available in Entrez. In 21st Int. Conf. in Scientific and Statistical Database Management (SSDBM), LNCS 5566, Springer, 283–291. New Orlean, United States, June 2009.
    HAL ] [ Bibtex ]

  • Susan Davidson, Yi Chen, Peng Sun, and Sarah Cohen-Boulakia. On User Views in Scientific Workflow Systems (Invited Paper). In Proc. of the the First Int. Workshop on the role of Semantic Web in Provenance Management (ISWC 2009 Workshop). Washington DC, United States, October 2009.
    HAL ] [ Bibtex ]

  • Bao Zhuowei, Sarah Cohen-Boulakia, Susan B. Davidson, and Pierrick Girard. PDiffView: Viewing the Difference in Provenance of Workflow Results. In VLDB- Very Large DataBase systems-2009, volume 2, 1638–1641. Lyon, France, August 2009. Serge Abiteboul and Tova Milo and Jignesh Patel and Philippe Rigaux, VLDB Journal.
    HAL ] [ Bibtex ]

Book sections

  • Sarah Cohen-Boulakia and Wang Chiew Tan. Provenance in Scientific Databases. In M. Tamer Özsu Ling Liu, editor, Encyclopedia of Database Systems, pages 2202–2207. Springer US, 2009.
    HAL ] [ Bibtex ]

  • Zoé Lacroix, R. Cartik, Peter Mork, Rami Rifaieh, Mark Wilkinson, Juliana Freire, and Sarah Cohen-Boulakia. Biological Resource Discovery. In M. Tamer Özsu Ling Liu, editor, Encyclopedia of Database Systems, pages 220–223. Springer US, 2009.
    HAL ] [ Bibtex ]

  • Zoé Lacroix, R. Cartik, Peter Mork, Mark Wilkinson, and Sarah Cohen-Boulakia. Biological Metadata Management. In Ling Liu and M. Tamer Özsu, editors, Encyclopedia of Database Systems, pages 215–219. Springer US, 2009.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the Nice 2009 spring school on Modelling Complex Biological Systems in the context of genomics, France, May 2009. EDP Sciences.
    HAL ] [ Bibtex ]

Thesis

  • Annelyse Thévenin. Aspects algorithmiques des réarrangements génomiques : duplications et ordres partiels. Theses, Université Paris Sud - Paris XI, November 2009.
    HAL ] [ Bibtex ]

2008

Journal articles

  • Patrick Amar, Guillaume Legent, Michel Thellier, Camille Ripoll, Gilles Bernot, Thomas Nystrom, Milton H Saier, and Vic Norris. A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency. BMC Systems Biology, 2:27, 2008. doi:10.1186/1752-0509-2-27.
    HAL ] [ Bibtex ]

  • Amos Bairoch, Sarah Cohen-Boulakia, and Christine Froidevaux. Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008. BMC Bioinformatics, 9 Suppl 8:S1, 2008. doi:10.1186/1471-2105-9-S8-S1.
    HAL ] [ Bibtex ]

  • Mahassine Djelloul and Alain Denise. Automated motif extraction and classification in RNA tertiary structures. RNA, 14(12):2489–97, December 2008. doi:10.1261/rna.1061108.
    HAL ] [ Bibtex ]

  • Frédéric Lemoine, Bernard Labedan, and Christine Froidevaux. GenoQuery: a new querying module for functional annotation in a genomic warehouse. Bioinformatics, 24(13):i322–9, July 2008. doi:10.1093/bioinformatics/btn159.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Julien Allali, Yves D'Aubenton-Carafa, Cedric Chauve, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine De Monte, Aïda Ouangraoua, Marie-France Sagot, C. Saule, Michel Termier, Claude Thermes, and Helene Touzet. Benchmarking RNA secondary structure comparison algorithms. In JOBIM'08, 67–68. Lille, France, 2008.
    HAL ] [ Bibtex ]

  • Victor Norris, Abdallah Zemirline, Patrick Amar, Pascal Ballet, Eshel Ben Jacob, Gilles Bernot, Guillaume Beslon, Eric Fanchon, Jean-Louis Giavitto, Nicolas Glade, Patrick Greussay, Yohann Grondin, James A. Foster, Guillaume Hutzler, François Képès, Olivier Michel, Gradimir Misevic, Franck Molina, Jacqueline Signorini, Pasquale Stano, and Alain Thierry. From bioputing to bactoputing: computing with bacteria. In Proceedings of the Lille Spring School on Modelling Complex Biological Systems in the Context of Genomics. France, 2008.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the Lille 2008 spring school on Modelling Complex Biological Systems in the context of genomics, France, April 2008. EDP Sciences.
    HAL ] [ Bibtex ]

2007

Books

  • Violaine Prince, Yves Kodratoff, Jérôme Azé, and Mathieu Roche. Défi Fouille de Textes : reconnaissance automatique des auteurs de discours - Campagne DEFT'05 (TALN'05). volume E10 of Revue RNTI (Revue des Nouvelles Technologies de l'Information). Cépaduès, 2007.
    HAL ] [ Bibtex ]

Journal articles

  • Jérôme Azé, Mathieu Roche, Erick Alphonse, Ahmed Amrani, Thomas Heitz, and Amar-Djalil Mezaour. Bilan du premier défi francophone de Fouille de Textes. Revue des Nouvelles Technologies de l'Information, RNTI-E-10:15–38, 2007.
    HAL ] [ Bibtex ]

  • Dominique Barth, Johanne Cohen, Alain Denise, and Romain Rivière. Shuffling biological sequences with motif constraints. Journal of Discrete Algorithms, 2007. A paraître, accès en ligne depuis le 9 juin 2007. doi:10.1016/j.jda.2007.06.001.
    HAL ] [ Bibtex ]

  • Julie Bernauer, Jérôme Azé, Joël Janin, and Anne Poupon. A new protein-protein docking scoring function based on interface residue properties. Bioinformatics, 23(5):555–62, March 2007. doi:10.1093/bioinformatics/btl654.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Thomas Moncion, Guillaume Hutzler, and Patrick Amar. Detection of emergent phenomena in multi-agent systems. In Proceedings of the Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics. Evry, France, 2007.
    HAL ] [ Bibtex ]

Book sections

  • Israël-César Lerman and Jérôme Azé. A New Probabilistic Measure of Interestingness for Association Rules, Based on the Likelihood of the Link. In F. Guillet and H. Hamilton, editors, Quality Measures in Data Mining. Studies in Computational Intelligence, pages 207–236. Springer, 2007.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the Evry 2007 spring school on Modelling Complex Biological Systems in the context of genomics, France, May 2007. EDP Sciences.
    HAL ] [ Bibtex ]

2006

Journal articles

  • Yann Ponty, Michel Termier, and Alain Denise. GenRGenS: Software for Generating Random Genomic Sequences and Structures. Bioinformatics, 22(12):1534–1535, 2006. doi:10.1093/bioinformatics/btl113.
    HAL ] [ Bibtex ]

  • Alain Thierry, François Képès, Patrick Amar, Georgia Barlovatz-Meimon, Gilles Bernot, Marie Beurton-Aimar, Marie Dutreix, Jean-Louis Giavitto, Janine Guespin, Jean-Pierre Mazat, Vic Norris, Vincent Schafter, Philippe Tracqui, Christophe Godin, and Franck Molina. Modelling of complex biological systems in the context of genomics: an account of a multidisciplinary thematic seminar held in Montpellier (France) in April 2005. Journal of Biological Physics and Chemistry, 6:103–107, 2006.
    HAL ] [ Bibtex ]

  • Alain R Thierry, François Képès, Patrick Amar, Georgia Barlovatz-Meimon, Gilles Bernot, Marie Beurton-Aimar, Marie Dutreix, Jean-Louis Giavitto, Janine Guespin, Jean-Pierre Mazat, Victor Norris, Vincent Schächter, Philippe Tracqui, Christophe Godin, and Franck Molina. Modelling of biological complex systems in the context of genomics. An account of a multidisciplinary thematic seminar held in Montpellier (France) in April 2005. Journal of Biological Physics and Chemistry, 6:103–107, 2006.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Jérôme Azé, Thomas Heitz, Augusta Mela, Amar-Djalil Mezaour, Peter Peinl, and Mathieu Roche. Présentation de DEFT'06 (DEfi Fouille de Textes). In Atelier DEFT'06 : DEfi Fouille de Textes, 10. September 2006.
    HAL ] [ Bibtex ]

  • Dominique Barth, Alain Denise, and Romain Rivière. Motifs Enumeration Algorithms in Biological Networks. In aaa. aaa, 2006.
    HAL ] [ Bibtex ]

  • Sarah Cohen-Boulakia, Christine Froidevaux, and Emmanuel Pietriga. Selecting Biological Data Sources and Tools with XPR, a Path Language for RDF. In Pacific Symposium on Biocomputing, 116–127. Maui, USA, United States, January 2006.
    HAL ] [ Bibtex ]

  • Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lasseigne, and Sylvain Peyronnet. Uniform Random Sampling of Traces in Very Large Models. In Robert Merkel Johannes Mayer, editor, First International Workshop on Random Testing, 10–19. Portland, Maine, United States, 2006. ACM.
    HAL ] [ Bibtex ]

  • Thomas Heitz, Jérôme Azé, Mathieu Roche, Augusta Mela, Peter Peinl, and Mezaour Amar Djalil. Présentation de DEFT 06 (DÉfi Fouille de Textes). In Atelier DEFT'06 - SDN'06 (Semaine du Document Numérique), Actes de l'atelier DEFT'06, SDN'06 (Semaine du Document Numérique), 1–10. Fribourg, Switzerland, 2006.
    HAL ] [ Bibtex ]

  • Thomas Moncion, Guillaume Hutzler, and Patrick Amar. Verification of Biochemical Agent-Based Models Using Petri Nets. In International Symposium on Agent Based Modeling and Simulation (ABModSim 2006), 695–700. Vianna, Austria, 2006.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the Bordeaux spring school on Modelling Complex Biological Systems in the context of genomics, France, April 2006. EDP Sciences.
    HAL ] [ Bibtex ]

2005

Journal articles

  • Julie Bernauer, Anne Poupon, Jérôme Azé, and Joël Janin. A docking analysis of the statistical physics of protein-protein recognition. Physical Biology, 2(2):S17–23, June 2005. doi:10.1088/1478-3975/2/2/S02.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Julie Bernauer, Jérôme Azé, Joël Janin, and Anne Poupon. Une nouvelle fonction de score pour l'amarrage protéine-protéine fondée sur les diagrammes de Voronoï. In Journées Ouvertes de Biologie Informatique Mathématiques. Lyon, France, July 2005.
    HAL ] [ Bibtex ]

  • Thomas Moncion, Guillaume Hutzler, and Patrick Amar. Validation d&apos;une simulation à base d&apos;agents par l&apos;utilisation d&apos;un réseau de Petri. In Systèmes multi-agents vers la conception de systèmes artificiels socio-mimétiques (JFSMA 2005), 187–190. France, 2005.
    HAL ] [ Bibtex ]

  • Thomas Moncion, Guillaume Hutzler, and Patrick Amar. Validation of an Agent Based System Using Petri Nets. In Proceedings of the fourth international joint conference on Autonomous agents and multiagent systems, 1365–1366. Netherlands, 2005. doi:10.1145/1082473.1082775.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the Montpellier spring school on Modelling Complex Biological Systems in the context of genomics, France, April 2005. EDP Sciences.
    HAL ] [ Bibtex ]

2004

Journal articles

  • Patrick Amar, Gilles Bernot, and Victor Norris. HSIM: a simulation programme to study large assemblies of proteins. Journal of Biological Physics and Chemistry, 4:124–130, 2004.
    HAL ] [ Bibtex ]

  • Mireille Régnier and Alain Denise. Rare Events and Conditional Events on Random Strings. Discrete Mathematics and Theoretical Computer Science, 6(2):191–214, 2004.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Dominique Barth, Johanne Cohen, Alain Denise, and Romain Rivière. Shuffling biological sequencess with motifs constraints. In Algorithms and Computational Methods for Biochemical and Evolutionary Networks - CompBioNets'2004, 18 p. Recife, Brazil, December 2004. Colloque avec actes et comité de lecture. internationale.
    HAL ] [ Bibtex ]

  • Marie Dutreix, Jean-Paul Comet, Antoine Cornuéjols, and Christine Froidevaux. Determination of cellular drug targets: searching for functional information in the jungle of microarrays data. In Current trends in drug discovery research” (CTDDR-2004). Lucknow, India, February 2004.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the EVRY spring school on Modelling and simulation of biological processes in the context of genomics, France, June 2004. Platypus Press.
    HAL ] [ Bibtex ]

2003

Journal articles

  • Victor Norris, Patrick Amar, Gilles Bernot, Jean-Louis Giavitto, Christophe Godin, Janine Guespin, Hélène Pollard, Philippe Tracqui, and François Képès. Modelling and simulation of biological processes in the context of genomics. Journal of Biological Physics and Chemistry, 3:106–110, 2003.
    HAL ] [ Bibtex ]

Book sections

  • Jérémie Mary, Guillaume Mercier, Jean-Paul Comet, Antoine Cornuéjols, Christine Froidevaux, and Marie Dutreix. Using an attribute estimation technique for the analysis of microarray data. In P. Amar, F. Képès, V. Norris, and P. Tracqui, editors, Proc. of the Dieppe Spring school on Modelling and simulation of biological processes in the context of genomics, Proc. of the Dieppe Spring school on Modelling and simulation of biological processes in the context of genomics. Publisher Frontier group, 2003.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the DIEPPE spring school on Modelling and simulation of biological processes in the context of genomics, France, May 2003. Platypus Press.
    HAL ] [ Bibtex ]

Thesis

  • Jérôme Azé. Knowledge extraction from numerical and textual data. Theses, Université Paris Sud - Paris XI, December 2003.
    HAL ] [ Bibtex ]

2002

Journal articles

  • Patrick Amar, Pascal Ballet, Georgia Barlovatz-Meimon, Arndt Benecke, Gilles Bernot, Yves Bouligand, Paul Bourguine, Franck Delaplace, Jean-Marc Delosme, Maurice Demarty, Itzhak Fishov, Jean Fourmentin-Guilbert, Joe Fralick, Jean-Louis Giavitto, Bernard Gleyse, Christophe Godin, Roberto. Incitti, François Képès, Catherine Lange, Lois Le Sceller, Corinne Loutellier, Olivier Michel, Franck Molina, Chantal Monnier, René Natowicz, Vic Norris, Nicole Orange, Hélène Pollard, Derek Raine, Camille Ripoll, Josette Rouviere-Yaniv, Milton Saier, Paul Soler, Pierre Tambourin, Michel Thellier, Philippe Tracqui, Dave Ussery, Jean-Claude Vincent, Jean-Pierre Vannier, Philippa Wiggins, and Abdallah Zemirline. Hyperstructures, genome analysis and I-Cells. Acta Biotheoretica, 50(4):357–373, 2002. doi:10.1023/A:1022629004589.
    HAL ] [ Bibtex ]

  • Cyril Banderier, Philippe Flajolet, Danièle Gardy, Mireille Bousquet-Mélou, Alain Denise, and Dominique Gouyou-Beauchamps. Generating functions for generating trees. Discrete Mathematics, 246 (1-3):29–55, 2002. This article corresponds, up to minor typo corrections, to the article submitted to Discrete Mathematics (Elsevier) in Nov. 1999, and published in its vol. 246(1-3), March 2002, pp. 29-55.
    HAL ] [ Bibtex ]

Conferences and workshops

  • Abdallah Zemirline, Pascal Ballet, Lionel Marcé, Patrick Amar, Gilles Bernot, Franck Delaplace, Jean-Louis Giavitto, Olivier Michel, Jean-Marc Delosme, Roberto Incitti, Paul Bourgine, Christophe Godin, François Képès, Philippe Tracqui, Victor Norris, Janine Guespin, Maurice Demarty, and Camille Ripoll. Cellular automata, reaction-diffusion and multiagents systems for artificial cell modelling. In Amar, Patrick, Képès, François, Norris, Victor, Tracqui, and Philippe, editors, Actes du Colloque Modélisation et simulation de processus biologiques dans le contexte de la génomique, 257–280. Autrans, France, 2002.
    HAL ] [ Bibtex ]

Edited proceedings

  • Proceedings of the AUTRANS spring school on Modelling and simulation of biological processes in the context of genomics, France, September 2002.
    HAL ] [ Bibtex ]

1998

Journal articles

  • Alain Denise, Isabelle Dutour, and Paul Zimmermann. CS: a MuPAD package for counting and randomly generating combinatorial structures. MathPAD, 8:23–30, 1998.
    HAL ] [ Bibtex ]