Publications

2021

Journal articles

• Frédérique Bassino, Mathilde Bouvel, Valentin Féray, Lucas Gerin, Mickaël Maazoun, and Adeline Pierrot. Random cographs: Brownian graphon limit and asymptotic degree distribution. Random Structures \\& Algorithms, July 2021. 36 pages, 6 figures. doi:10.1002/rsa.21033.
  [ HAL ] [ Bibtex ]

• Jean Cury, Benjamin C Haller, Guillaume Achaz, and Flora Jay. Simulation of bacterial populations with SLiM. Peer Community in Evolutionary Biology, March 2021. doi:10.1101/2020.09.28.316869.
  [ HAL ] [ Bibtex ]

• Jean-Baptiste Lamy. A data science approach to drug safety: Semantic and visual mining of adverse drug events from clinical trials of pain treatments. Artificial Intelligence in Medicine, pages 102074, May 2021. doi:10.1016/j.artmed.2021.102074.
  [ HAL ] [ Bibtex ]

• Van Thu Nguyen, Philippe Riviere, Pierre Ripoll, Julien Barnier, Romain Vuillemot, Philippe Ravaud, Isabelle Boutron, COVID NMA Consortium, Solaf Alawadhi, Sihem Amer-Yahia, Camila Ávila, Aïda Bafeta, Julia Baudry, Claudia Bollig, Hillary Bonnet, Marinette Bouet, Guillaume Cabanac, Anna Chaimani, David Chavalarias, Yaolong Chen, Astrid Chevance, Sarah Cohen-Boulakia, Emmanuel Coquery, Françoise Conil, Mauricia Davidson, Laura De Nale, Declan Devane, Elise Diard, Bastien Doreau, Theodoros Evrenoglou, Alice Fabri, Gilles Feron, Gabriel Ferrand, Leopold Fezeu, Mathilde Fouet, Lina Ghosn El Chall, Carolina Graña, Giacomo Grasselli, François Grolleau, Mohand-Said Hacid, Loubna Haddy, Camilla Hansen, Ameer Hohlfeld, Asbjørn Hróbjartsson, Chantal JULIA, Dimitris Mavridis, Joerg Meerpohl, Brice Meyer, Nivantha Naidoo, Theodora Oikonomidi, Elizabeth Pienaar, Fiona Quirke, Gabriel Rada, Carolina Riveros, Marie Sauvant, Christine Schmucker, Farouk Toumani, David Tovey, Jun Xia, Xuan Yu, Emina Zoletic, and Pierre Zweigenbaum. Research response to coronavirus disease 2019 needed better coordination and collaboration: a living mapping of registered trials. Journal of Clinical Epidemiology, 130:107–116, 2021. doi:10.1016/j.jclinepi.2020.10.010.
  [ HAL ] [ Bibtex ]

• Burak Yelmen, Aurélien Decelle, Linda Ongaro, Davide Marnetto, Corentin Tallec, Francesco Montinaro, Cyril Furtlehner, Luca Pagani, and Flora Jay. Creating artificial human genomes using generative neural networks. PLoS Genetics, February 2021. doi:10.1371/journal.pgen.1009303.
  [ HAL ] [ Bibtex ]

Conferences and workshops

• Coline Gianfrotta, Vladimir Reinharz, Dominique Barth, and Alain Denise. A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures. In 19th Symposium on Experimental Algorithms. Nice (virtuel), France, June 2021. doi:10.4230/LIPIcs.SEA.2021.19.
  [ HAL ] [ Bibtex ]

Thesis

• Pierre Andrieu. Passage à l'échelle, propriétés et qualité des algorithmes de classements consensuels pour les données biologiques massives. Theses, Université Paris-Saclay, June 2021.
  [ HAL ] [ Bibtex ]

Reports and working papers

• Pierre Andrieu, Sarah Cohen-Boulakia, and Alain Denise. Classements consensuels de données biologiques massives. Research Report, Université Paris-Saclay/Université Paris-Sud ; Laboratoire Interdisciplinaire des Sciences du Numérique, May 2021.
  [ HAL ] [ Bibtex ]

• Théophile Sanchez, Erik Madison Bray, Pierre Jobic, Jérémy Guez, Guillaume Charpiat, Jean Cury, and Flora Jay. dnadna: DEEP NEURAL ARCHITECTURES FOR DNA - A DEEP LEARNING FRAMEWORK FOR POPULATION GENETIC INFERENCE. working paper or preprint, September 2021.
  [ HAL ] [ Bibtex ]

2020

Journal articles

• Patrick Amar. Pandæsim: An Epidemic Spreading Stochastic Simulator. Biology, 9(9):299, September 2020. doi:10.3390/biology9090299.
  [ HAL ] [ Bibtex ]

• 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, 22(11):3565–3639, 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 ]

• Olivier François and Flora Jay. Factor analysis of ancient population genomic samples. Nature Communications, 2020. doi:10.1038/s41467-020-18335-6.
  [ HAL ] [ Bibtex ]

• Maxime Mahout, Ross Carlson, and Sabine Peres. Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism. Processes, 8(12):1649, December 2020. doi:10.3390/pr8121649.
  [ HAL ] [ Bibtex ]

• Vasili Pankratov, Francesco Montinaro, Alena Kushniarevich, Georgi Hudjashov, Flora Jay, Lauri Saag, Rodrigo Flores, Davide Marnetto, Marten Seppel, Mart Kals, Urmo Vosa, Cristian Taccioli, Märt Möls, Lili Milani, Anto Aasa, Daniel John Lawson, Tonu Esko, Reedik Mägi, Luca Pagani, Andres Metspalu, and Mait Metspalu. Differences in local population history at the finest level: the case of the Estonian population. European Journal of Human Genetics, 2020. doi:10.1038/s41431-020-0699-4.
  [ HAL ] [ Bibtex ]

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

• Théophile Sanchez, Jean Cury, Guillaume Charpiat, and Flora Jay. Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation. Molecular Ecology Resources, 2020. doi:10.1111/1755-0998.13224.
  [ HAL ] [ Bibtex ]

• Francisco Santos Schneider, Amar Patrick, Asma Bahri, Julien Espeut, Mellis Alali, François Fages, and Franck Molina. Biomachines For Medical Diagnosis. Advanced Materials Letters, 11(4):1–5, April 2020. doi:10.5185/amlett.2020.041499.
  [ HAL ] [ Bibtex ]

• Laurent Schwartz, Sabine Peres, Mario Jolicoeur, and Jorgelindo Da veiga moreira. Cancer and Alzheimer's disease: intracellular pH scales the metabolic disorders. Biogerontology, 21(6):683–694, December 2020. doi:10.1007/s10522-020-09888-6.
  [ HAL ] [ Bibtex ]

• Laurent Schwartz, Sabine S. Peres, Mario Jolicoeur, and Jorgelindo Da veiga moreira. Cancer and Alzheimer's disease: intracellular pH scales the metabolic disorders. Biogerontology, 21(6):683–694, December 2020. doi:10.1007/s10522-020-09888-6.
  [ HAL ] [ Bibtex ]

Conferences and workshops

• Véronique Benzaken, Sarah Cohen-Boulakia, Évelyne Contejean, Chantal Keller, and Rébecca Zucchini. Vers une formalisation en Coq de la provenance de données. In Zaynah Dargaye and Yann Regis-Gianas, editors, 31ème Journées Francophones des Langages Applicatifs, 31ème Journées Francophones des Langages Applicatifs, 72–87. Gruissan, France, January 2020.
  [ HAL ] [ Bibtex ]

• 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), volume 12314 of Lecture Notes in Computer Science, 193–209. Online, Germany, 2020. Springer. doi:10.1007/978-3-030-60327-4_11.
  [ HAL ] [ Bibtex ]

• Jean-Baptiste Lamy. Comparison of four visual analytics techniques for the visualization of adverse drug event rates in clinical trials. In International Conference Information Visualisation. Vienna, Austria, September 2020.
  [ HAL ] [ Bibtex ]

• Jean-Baptiste Lamy. Visualization of potential drug synergies. In International Conference on Informatics, Management and Technology in Healthcare. Athen, Greece, July 2020.
  [ HAL ] [ Bibtex ]

• Jean-Baptiste Lamy and Flora Jay. Combiner arbres phylogénétiques et visualisation d'ensembles. In Atelier Visualisation d'informations, interaction et fouille de données. Bruxelles, Belgium, January 2020.
  [ HAL ] [ Bibtex ]

• Abdelmalek Mouazer, Karima Sedki, Rosy Tsopra, and Jean-Baptiste Lamy. Visualization of drug interactions for supporting medication review. In International Conference on Informatics, Management and Technology in Healthcare. Athen, Greece, July 2020.
  [ HAL ] [ Bibtex ]

Book sections

• Sabine S. Peres and Vincent Fromion. Thermodynamic Approaches in Flux Analysis. In Metabolic Flux Analysis in Eukaryotic Cells, pages 359–367. January 2020. doi:10.1007/978-1-0716-0159-4_17.
  [ 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 ]

• Jean-Baptiste Lamy. A data science approach to drug safety: Semantic and visual mining of adverse drug events from clinical trials of pain treatments. working paper or preprint, October 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 and Engineering, 21(5):87–93, September 2019. doi:10.1109/MCSE.2019.2921898.
  [ HAL ] [ Bibtex ]

• Xiaojie Ren, Jean-Sébastien Deschênes, Réjean Tremblay, Sabine Peres, and Mario Jolicoeur. 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 ]

• 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 ]

• Jorgelindo Da Veiga Moreira, Laurent Schwartz, and Sabine S. Peres. Modulating mitochondria horsepower for biotechnological applications. In Metabolic Pathway Analysis 2019. Riga, Latvia, August 2019.
  [ 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. 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 ]

• Sabine S. Peres, Stefan Schuster, and Philippe Dague. Thermodynamic constraints for identifying elementary flux modes. Biochemical Society Transactions, 46(3):641–647, June 2018. doi:10.1042/BST20170260.
  [ HAL ] [ Bibtex ]

• Christophe Pradal, Sarah Cohen-Boulakia, Gaëtan 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(3):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. Bio-calculateur booléen à base de réseaux métaboliques intégré dans une vésicule artificielle: temporisation par oscillateur enzymatique. 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 ]

• Vincent J. Henry, Anne Goelzer, Arnaud Ferré, Stéphan Fischer, Marc Dinh, Valentin LOUX, Christine Froidevaux, and Vincent Fromion. The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. Journal of Biomedical Semantics, 8(53):16 pages, 2017. doi:10.1186/s13326-017-0165-6.
  [ 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, Jérôme 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 ]

• Jorgelindo Moreira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Sabine S. Peres, Loïc Paulevé, Marcel Nogueira, Jean-Marc Steyaert, and Laurent Schwartz. The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect. Metabolites, 6(4):33, December 2016. doi:10.3390/metabo6040033.
  [ 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 Rodríguez, 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 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. 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. Prédiction de structure tridimensionnelle de molécules d'ARN par minimisation de regret. Theses, Université Paris Saclay (COmUE), April 2016.
  [ HAL ] [ Bibtex ]

• Marc Bouffard. Conception, modélisation et simulation in silico d'un nanosystème biologique artificiel pour le diagnostic médical. 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. Méthodes qualitatives pour la construction et l'analyse des réseaux moléculaires SBGN. 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

• Sarah Cohen-Boulakia and Patrick Valduriez. Traitement de données bioinformatiques massives (Big Data). 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 Crepieux, 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. Interrogation et gestion de données bio-informatiques pour la biologie moléculaire. 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. Agrégation de classements avec égalités : algorithmes, guides à l'utilisateur et applications aux données biologiques. 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 25th European Medical Informatics Conference (MIE), volume 20 of Studies in Health Technology and Informatics, 1070–1074. Istanbul, Turkey, August 2014. doi:10.3233/978-1-61499-432-9-1070.
  [ 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. Modélisation et score de complexes protéine-ARN. 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. International Journal on Software Tools for Technology Transfer, 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.
  [ 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, Francois Vallee, Marie M. 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 ]

• 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 ]

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. Paris, 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 ]

• Michel Thellier, Guillaume Legent, Patrick Amar, Vic Norris, and Camille Ripoll. Steady-state kinetic behaviour of functioning-dependent structures. FEBS Journal, 273(18):4287–4299, September 2006. doi:10.1111/j.1742-4658.2006.05425.x.
  [ 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 ]

• Guillaume Mercier, Nathalie Berthault, Jérémie Mary, Julie Peyre, Anestis Antoniadis, Jean-Paul Comet, Antoine Cornuéjols, Christine Froidevaux, and Marie Dutreix. Biological detection of low radiation doses by combining results of two microarray analysis methods. Nucleic Acids Research, 32(1):e12, January 2004. doi:10.1093/nar/gnh002.
  [ 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, 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, Abdallah Zemirline, and Olivier Michel. 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 ]