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A BDI agent architecture for the GAMA modeling and simulation platform

Patrick Taillandier , Mathieu Bourgais , Philippe Caillou , Carole Adam , Benoit Gaudou
MABS 2016 - 17th International Workshop on Multi-Agent-Based Simulation, May 2016, Singapour, Singapore. 155 p., ⟨10.1007/978-3-319-67477-3_1⟩
Conference papers hal-02744133v1
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Validation of a morphogenesis model of Drosophila early development by a multi-objective evolutionary optimization algorithm

Rui Dilão , Daniele Muraro , Miguel Nicolau , Marc Schoenauer
European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Apr 2009, Tübingen, Germany. pp.176-190
Conference papers inria-00378037v1

A new protein-protein docking scoring function based on interface residue properties.

Julie Bernauer , Jérôme Azé , Joël Janin , Anne Poupon
Bioinformatics, 2007, 23 (5), pp.555-62. ⟨10.1093/bioinformatics/btl654⟩
Journal articles inria-00431697v1
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A formalization of the computational impact of intrinsic plasticity

Jérémie Naudé , Stéphane Genet , Hugues Berry , Séverine Mahon , Jeanne Paz , et al.
Deuxième conférence française de Neurosciences Computationnelles, "Neurocomp08", Oct 2008, Marseille, France
Conference papers hal-00331558v1
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Pattern Matching in Protein-Protein Interaction Graphs

Gaëlle Brevier-Giberti , Roméo Rizzi , Stéphane Vialette
FCT 2007, Aug 2007, Budapest, Hungary. pp.137-148, ⟨10.1007/978-3-540-74240-1_13⟩
Conference papers hal-00199009v1
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A Pseudo-Boolean programming approach for computing the breakpoint distance between two genomes with duplicate genes

Sébastien Angibaud , Guillaume Fertin , Irena Rusu , Annelyse Thevenin , Stéphane Vialette
5th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2007), 2007, San Diego, United States. pp.16-29
Conference papers hal-00417902v1
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How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation

Sébastien Angibaud , Guillaume Fertin , Irena Rusu , Stéphane Vialette
4th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2006), 2007, Montréal, Canada. pp.75-86
Conference papers hal-00418258v1
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A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms

Yann Ponty , Cédric Saule
WABI - 11th Workshop on Algorithms in Bioinformatics - 2011, 2011, Saarbrucken, Germany
Conference papers inria-00601060v1

Asymptotics of RNA shapes

William Andrew Lorenz , Peter Clote , Yann Ponty
Journal of Computational Biology, 2008, 15 (1), pp.31--63. ⟨10.1089/cmb.2006.0153⟩
Journal articles inria-00548861v1
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Fast Inference of Individual Admixture Coefficients Using Geographic Data

Kevin Caye , Flora Jay , Olivier J.J. Michel , Olivier François
Annals of Applied Statistics, 2018, 12 (1), pp.586-608. ⟨10.1214/17-AOAS1106⟩
Journal articles hal-01676712v1

Artificial Evolution, 13th International Conference, Evolution Artificielle, EA 2017, Paris, France, October 25-27, 2017, Revised Selected Papers

Evelyne Lutton , Pierrick Legrand , Pierre Parrend , Nicolas Monmarché , Marc Schoenauer
Springer, LNCS - Lecture Notes in Computer Science (10764), 2018, Artificial Evolution, 978-3-319-78132-7. ⟨10.1007/978-3-319-78133-4⟩
Books hal-01910443v1
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Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

Vladimir Reinharz , Antoine Soulé , Eric Westhof , Jérôme Waldispühl , Alain Denise
Nucleic Acids Research, 2018
Journal articles hal-01745345v1
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Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic Pathways

Alexandra Zaharia , Bernard Labedan , Christine Froidevaux , Alain Denise
SeqBio 2016, Nov 2016, Nantes, France
Conference papers hal-01745390v1
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Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data

Misbah Razzaq , Loïc Paulevé , Anne Siegel , Julio Saez-Rodriguez , Jérémie Bourdon , et al.
PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩
Journal articles hal-01897020v1
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Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities.

Adrien Guilhot-Gaudeffroy , Christine Froidevaux , Jérôme Azé , Julie Bernauer
PLoS ONE, 2014, 9 (9), pp.e108928. ⟨10.1371/journal.pone.0108928⟩
Journal articles hal-01071876v1
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Search, adapt, and reuse: the future of scientific workflows

Sarah Cohen-Boulakia , Ulf Leser
SIGMOD record, 2011, ⟨10.1145/2034863.2034865⟩
Journal articles inria-00638043v1

SPI-DNA: End-to-end Deep Learning Approach for Demographic History Inference

Théophile Sanchez , Guillaume Charpiat , Flora Jay
Paris-Saclay Junior Conference on Data Science and Engineering, Sep 2017, Orsay, France
Conference papers hal-01679385v1

Hypothesis: Local variations in the speed of individual DNA replication forks determine the phenotype of daughter cells

Vic Norris , François Képès , Patrick Amar , Ina Koch , Laurent Janniere
Medical Research Archives, 2017, 5 (12), ⟨10.18103/mra.v5i12.1598⟩
Journal articles hal-01672912v1

Automated prediction of three-way junction topological families in RNA secondary structures

Alexis Lamiable , Dominique Barth , Alain Denise , Franck Quessette , Sandrine Vial , et al.
Computational Biology and Chemistry, 2012, 37, pp.1-5
Journal articles hal-00641738v1

Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis

Assel Issabekova , Olga Berillo , Mireille Regnier , Anatoly Ivashchenko
Bioinformation, 2012, 8 (11), pp.513-518. ⟨10.6026/97320630008513⟩
Journal articles hal-00736694v1

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.

Julie Bernauer , Xuhui Huang , Adelene y L Sim , Michael Levitt
RNA, 2011, 17 (6), pp.1066-75. ⟨10.1261/rna.2543711⟩
Journal articles inria-00624999v1
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Expected distance between terminal nucleotides of RNA secondary structures.

Peter Clote , Yann Ponty , Jean-Marc Steyaert
Journal of Mathematical Biology, 2012, 65 (3), pp.581-99. ⟨10.1007/s00285-011-0467-8⟩
Journal articles inria-00619921v1
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Concretizing the Process Hitting into Biological Regulatory Networks

Maxime Folschette , Loïc Paulevé , Katsumi Inoue , Morgan Magnin , Olivier Roux
Computational Methods in Systems Biology, Oct 2012, London, United Kingdom. p. 166-186, ⟨10.1007/978-3-642-33636-2_11⟩
Conference papers hal-00704569v2
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A Rigorous Runtime Analysis for Quasi-Random Restarts and Decreasing Stepsize

Marc Schoenauer , Fabien Teytaud , Olivier Teytaud
Artificial Evolution, Oct 2011, Angers, France
Conference papers inria-00625855v1

Interrogation et gestion de données bio-informatiques pour la biologie moléculaire

Sarah Cohen-Boulakia , Patrick Valduriez
Techniques de l'Ingenieur, 2015, Interrogation et gestion de données bio-informatiques pour la biologie moléculaire, TIP140WEB, pp.BIO7055. ⟨10.51257/a-v1-bio7055⟩
Journal articles hal-01160897v1

Maximum expected accurate structural neighbors of an RNA secondary structure

Feng Lou , Peter Clote
Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011, Orlando, United States
Conference papers hal-00783862v1

An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure.

Alexis Lamiable , Franck Quessette , Sandrine Vial , Dominique Barth , Alain Denise
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, 10 (1), pp.193-199. ⟨10.1109/TCBB.2012.148⟩
Journal articles hal-00832110v1

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.

Jérôme Waldispühl , Yann Ponty
Journal of Computational Biology, 2011, 18 (11), pp.1465-79. ⟨10.1089/cmb.2011.0181⟩
Journal articles hal-00681928v1
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Exploitation des algorithmes génétiques pour la prédiction de structure de complexe protéine-protéine

Thomas Bourquard
Intelligence artificielle [cs.AI]. Université Paris Sud - Paris XI, 2009. Français. ⟨NNT : ⟩
Theses tel-00782396v1

Maximum expected accuracy structural neighbors of an RNA secondary structure.

Peter Clote , Feng Lou , William A Lorenz
BMC Bioinformatics, 2012, 13 Suppl 5, pp.S6. ⟨10.1186/1471-2105-13-S5-S6⟩
Journal articles hal-00783859v1