BioInfo

Publications

2017

Journal articles

  • 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.
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  • 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, 2017. doi:10.1016/j.future.2017.01.012.
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  • 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.
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  • Loïc Paulevé. Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, September 2017. In press. doi:10.1109/TCBB.2017.2749225.
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  • 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.
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  • Sabine Pérès, Mario Jolicœur, Cécile Moulin, Philippe Dague, and Stefan Schuster. How important is thermodynamics for computing elementary flux modes?. PLoS ONE, 2017.
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Conference papers

  • 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.
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  • 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.
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  • 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.
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  • 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.
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2016

Journal articles

  • 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.
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  • 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.
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  • 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, October 2016. doi:10.3390/metabo6040033.
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  • 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.
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  • Lirong Huang, Loïc Paulevé, Christoph Zechner, Michael Unger, Anders S. Hansen, and Heinz Koeppl. Reconstructing dynamic molecular states from single-cell time series. Interface, September 2016. doi:10.1098/rsif.2016.0533.
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  • 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.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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  • 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.
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  • Juraj Kolčák, David Šafránek, Stefan Haar, and Loïc Paulevé. Unfolding of Parametric Boolean Networks. In The Seventh International Workshop on Static Analysis and Systems Biology (SASB 2016), volume accepted of Electronic Notes in Theoretical Computer Science. Edimbourg, United Kingdom, September 2016. Elsevier.
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  • 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.
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  • 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.
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  • Loïc Paulevé. Goal-Oriented Reduction of Automata Networks. In Nicola Paoletti Ezio Bartocci, Pietro Lio, editor, 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.
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  • 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.
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  • 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.
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Edited proceedings

  • 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.
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Thesis

  • Melanie Boudard. Prediction of three-dimensional structure of RNA molecules by regret minimization. Theses, Université Paris-Saclay, April 2016.
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  • Marc Bouffard. Design, modeling and simulation in silico of an artificial biological nanosystem for medical diagnosis. Theses, Université Paris-Saclay, September 2016.
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  • Adrien Rougny. Qualitative methods for the construction and the analysis of SBGN molecular networks. Theses, Université Paris-Saclay, October 2016.
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Posters

  • 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.
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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.
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  • Sarah Cohen-Boulakia and Patrick Valduriez. Bioinformatics big data processing. Research Report RR-8915, Inria Sophia Antipolis ; LRI - CNRS, University Paris-Sud, May 2016.
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2015

Journal articles

  • 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.
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  • 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, pages 5:10760, June 2015. doi:10.1038/srep10760.
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  • 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), pages 2051, August 2015.
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  • Sarah Cohen-Boulakia and Patrick Valduriez. Querying and Managing bioinformatic data for molecular biology. Techniques de l'Ingenieur, pages BIO7055, June 2015.
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  • Alexis Courbet, Franck Molina, and Patrick Amar. Computing with Synthetic Protocells. Acta Biotheoretica, pages 15, May 2015. doi:10.1007/s10441-015-9258-8.
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  • 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.
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  • Maxime Folschette, Loïc Paulevé, Morgan Magnin, and Olivier Roux. Sufficient Conditions for Reachability in Automata Networks with Priorities. Journal of Theoretical Computer Science (TCS), 2015. doi:10.1016/j.tcs.2015.08.040.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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  • 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.
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  • 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.
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  • Christophe Pradal, Christian Fournier, Patrick Valduriez, and Sarah Cohen-Boulakia. OpenAlea: Scientific Workflows Combining Data Analysis and Simulation. In SSDBM 2015: 27th International Conference on Scientific and Statistical Database Management. San Diego, United States, June 2015. doi:10.1145/2791347.2791365.
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  • 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.
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Edited proceedings

  • Vic Norris Patrick Amar, François Képès, editor. advances in Systems and Synthetic Biology, EDP Sciences, March 2015.
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  • Alain Denise, Olivier Lespinet, and Mireille Régnier, editors. Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics, Orsay, France, November 2015.
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  • 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.
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Thesis

  • Bryan Brancotte. Rank aggregation with ties : algorithms, user guidance et applications to biologicals data. Theses, Université Paris Sud - Paris XI, September 2015.
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  • Sarah Cohen-Boulakia. Data Integration in the Life Sciences: Scientific Workflows, Provenance, and Ranking. Habilitation à diriger des recherches, Université Paris-Sud, June 2015.
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Posters

  • Bryan Brancotte, Bastien Rance, Alain Denise, and Sarah Cohen-Boulakia. Interrogation de bases de données biologiques publiques par reformulation de requêtes et classement des résultats avec ConQuR-Bio. JOBIM (Journées Ouvertes Biologie Informatique Mathématiques), July 2015. Poster.
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  • 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.
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  • Adrien Rougny, Christine Froidevaux, and Loïc Paulevé. Two Qualitative Dynamics Semantics for SBGN Process Description Maps. CMSB'15, September 2015. Poster.
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2014

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.
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  • 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.
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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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • Adrien Guilhot-Gaudeffroy, Jérôme Azé, Julie Bernauer, and Christine Froidevaux. Apprentissage de fonctions de tri pour la prédiction d'interactions protéine-ARN. In Extraction et Gestion des Connaissances. Rennes, France, January 2014.
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  • 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 Medical Informatics Europe, 1070–1074. Istanbul, Turkey, August 2014.
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  • 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. Evry, France, March 2014. edp science.
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  • 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.
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  • Johannes Starlinger, Sarah Cohen-Boulakia, Sanjeev Khanna, Susan Davidson, and Ulf Leser. Layer Decomposition: An Effective Structure-based Approach for Scientific Workflow Similarity. In IEEE e-Science conference. Guarujá, Brazil, October 2014.
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  • 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.
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Edited proceedings

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

  • Adrien Guilhot-Gaudeffroy. Modelling and scoring of protein-RNA complexes. Theses, Université Paris Sud - Paris XI, September 2014.
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  • Bo Yang. Bioinformatics analysis and consensus ranking for biological high throughput data. Theses, Université Paris Sud - Paris XI, September 2014.
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Posters

  • 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.
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2013

Journal articles

  • 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.
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  • Vic Norris, Patrick Amar, Guillaume Legent, Camille Ripoll, Michel Thellier, and Judit Ovadi. Sensor potency of the moonlighting enzyme-decorated cytoskeleton. BMC Biochemistry, February 2013. doi:10.1186/1471-2091-14-3.
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  • 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.
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  • Sabine Pérès, Liza Felicori, and Franck Molina. Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation.. PLoS ONE, 8(10):e76143, 2013. doi:10.1371/journal.pone.0076143.
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  • Sabine Pérès, Liza Felicori, and Franck Molina. Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation. PLoS ONE, 2013.
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  • 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.
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Conference papers

  • 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.
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  • 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, à paraître. Toulouse, France, 2013.
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  • 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.
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  • 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.
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  • 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.
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Edited proceedings

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

  • Patrick Amar. Contributions to the study of the dynamics of biological systems and to computing systems in synthetic biology. Habilitation à diriger des recherches, Université Paris Sud - Paris XI, December 2013.
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  • Jiuqiang Chen. Designing scientific workflow following a structure and provenance-aware strategy. Theses, Université Paris Sud - Paris XI, October 2013.
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2012

Books

  • Jérôme Azé, Nicolas Béchet, Laure Berti-Équille, Sylvie Guillaume, Mathieu Roche, and Fatiha Sais. Mesurer et évaluer la qualité des données et des connaissances. Éditions Hermann, 2012.
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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(893048):5 pages, 2012. doi:10.1155/2012.
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  • Damien M. De Vienne and Jérôme Azé. Efficient Prediction of Co-Complexed Proteins Based on Coevolution. PLoS ONE, November 2012.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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Edited proceedings

  • V. Norris P. Amar, F. Kepes, editor. Proceedings of The 2012 Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics, EDP Sciences, May 2012.
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Thesis

  • Jérôme Azé. Protein-Protein prediction and protein-protein docking by ensemble learning. Habilitation à diriger des recherches, Université Paris Sud - Paris XI, November 2012.
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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.
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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.
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  • 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.
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  • Sarah Cohen-Boulakia and Ulf Leser. Search, adapt, and reuse: the future of scientific workflows. SIGMOD record, 2011. doi:10.1145/2034863.2034865.
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  • 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.
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  • 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 J.J 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.
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  • 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.
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  • 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.
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  • 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.
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Conference papers

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

  • Proceedings of the Sophia-Antipolis Spring School on Modelling Complex Biological Systems in the context of genomics, France, May 2011. None, EDP Sciences.
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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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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  • 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.
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  • Cédric Saule, Mireille Regnier, Jean-Marc Steyaert, and Alain Denise. Counting RNA pseudoknotted structures (extended abstract). In Sara Billey and Victor Reiner, 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.
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  • 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.
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Edited proceedings

  • Proceedings of the Evry Spring School on Modelling Complex Biological Systems in the context of genomics, France, March 2010. None, EDP Sciences.
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2009

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.
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  • 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.
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  • 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.
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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. PVLDB, Proc. of the 35th Int. Conf. on Very Large Data Bases, 2(2):1638–1641, 2009.
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  • 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.
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Conference papers

  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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Edited proceedings

  • Proceedings of the Nice 2009 spring school on Modelling Complex Biological Systems in the context of genomics, France, May 2009. None, EDP Sciences.
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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.
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  • 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.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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  • 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.
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Edited proceedings

  • Proceedings of the Lille 2008 spring school on Modelling Complex Biological Systems in the context of genomics, France, April 2008. None, EDP Sciences.
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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.
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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.
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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.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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Edited proceedings

  • Proceedings of the Evry 2007 spring school on Modelling Complex Biological Systems in the context of genomics, France, May 2007. None, EDP Sciences.
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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.
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  • 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.
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  • 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.
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Conference papers

  • 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.
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  • Dominique Barth, Alain Denise, and Romain Rivière. Motifs Enumeration Algorithms in Biological Networks. In , aaa. aaa, 2006.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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Edited proceedings

  • Proceedings of the Bordeaux spring school on Modelling Complex Biological Systems in the context of genomics, France, April 2006. None, EDP Sciences.
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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.
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Conference papers

  • Jérôme Azé, Mathieu Roche, Yves Kodratoff, and Michèle Sebag. Preference Learning in Terminology Extraction: A ROC-based approach. In Jacques Janssen and Philippe Lenca, editors, , 209–219. 2005.
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  • 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.
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  • Thomas Moncion, Guillaume Hutzler, and Patrick Amar. Validation d'une simulation à base d'agents par l'utilisation d'un réseau de Petri. In Systèmes multi-agents vers la conception de systèmes artificiels socio-mimétiques (JFSMA 2005), 187–190. France, 2005.
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  • 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.
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Edited proceedings

  • Proceedings of the Montpellier spring school on Modelling Complex Biological Systems in the context of genomics, France, April 2005. None, EDP Sciences.
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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.
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  • Mireille Régnier and Alain Denise. Rare Events and Conditional Events on Random Strings. Discrete Mathematics and Theoretical Computer Science, 6(2):191–214, 2004.
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Conference papers

  • 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.
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Edited proceedings

  • Proceedings of the EVRY spring school on Modelling and simulation of biological processes in the context of genomics, France, June 2004. None, Platypus Press.
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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.
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Edited proceedings

  • Proceedings of the DIEPPE spring school on Modelling and simulation of biological processes in the context of genomics, France, May 2003. None, Platypus Press.
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Thesis

  • Jérôme Azé. Knowledge extraction from numerical and textual data. Theses, Université Paris Sud - Paris XI, December 2003.
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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.
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  • 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.
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Conference papers

  • 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 Patrick Amar, François Képès, Victor Norris, and Philippe Tracqui, editors, Actes du Colloque Modélisation et simulation de processus biologiques dans le contexte de la génomique, 257–280. Autrans, France, 2002.
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Edited proceedings

  • Proceedings of the AUTRANS spring school on Modelling and simulation of biological processes in the context of genomics, France, September 2002. None.
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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.
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