Team Beagle: Artificial Evolution and Computational Biology
Coordinator : Guillaume Beslon | Assistant coordinator : Hugues Berry | Team presentation document (PDF) Team dedicated web site |
The expanded name for the Beagle research group is "Artificial Evolution and Computational Biology". Our aim is to position our research at the interface between biology and computer science and to contribute new results in biology by modeling biological systems. In other words we are making artifacts - from the Latin artis factum (an entity made by human art rather than by Nature) - and we explore them in order to understand Nature. Our research is based on an interdisciplinary scientic strategy: We are developing computer science formalisms and software for complex system modeling in synergy with multidisciplinary cooperations in the area of living sciences. Thanks to computational approaches we study abstractions of biological systems and processes in order to unravel the organizational principles of cellular systems.
Beagle gathers the LIRIS members implicated in the Equipe Projet Commune INRIA Beagle: https://team.inria.fr/beagle/
Team members
Prénom | Nom | Statut | Employeur | Implantation |
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Guillaume | Beslon | Professor | Institut National des Sciences Appliquées de Lyon | CEI (INRIA) |
Christophe | Rigotti | Associate Professor | Institut National des Sciences Appliquées de Lyon | Blaise Pascal (INSA) |
Jonathan | Rouzaud-Cornabas | Associate Professor | Institut National des Sciences Appliquées de Lyon | CEI (INRIA) |
Anton | Crombach | Research scientist | Autre | CEI (INRIA) |
Romain | Gallé | PhD student | Autre | CEI (INRIA) |
Thibaut | Peyric | PhD student | Autre | CEI (INRIA) |
Lisa | Chabrier | PhD student | Autre | CEI (INRIA) |
Juliette | Luiselli | PhD student | Institut National des Sciences Appliquées de Lyon | CEI (INRIA) |
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FAID 2019, Houston
LIRIS at FAID 2019 conference "French American Innovation Day" in Houston.
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Best Paper Award at the ALife 2018 Conference
Vincent Liard, David Parsons, Jonathan Rouzaud-Cornabas and Guillaume Beslon (Beagle Team) received the Best Paper Award at the ALife 2018 conference in Tokyo in July 2018 for their results on the evolution of complexity.
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Publications LIRIS pour l'équipe Artificial Evolution and Computational Biology (Beagle) (269)
- 2024 (14)
- Journals (4)
- International journals with peer review (4)
- Juliette Luiselli, Isaac Overcast, Andrew Rominger, Megan Ruffley, Hélène Morlon & James Rosindell (2024). "Detecting the ecological footprint of selection". PLoS ONE, vol. 19, #6, e0302794. doi : 10.1371/journal.pone.0302794. HAL : hal-04753991. .
- Lisa Chabrier, Anton Crombach, Sergio Peignier & Christophe Rigotti (2024). "Effective pruning for top-k feature search on the basis of SHAP values". IEEE Access, vol. 12, pp. 163079-163092. doi : 10.1109/ACCESS.2024.3489958. HAL : hal-04549416. .
- Lisa Blum Moyse & Hugues Berry (2024). "A Coupled Neural Field Model for the Standard Consolidation Theory". Journal of Theoretical Biology, vol. 588, p. 111818. HAL : hal-04527872. .
- Paul Banse, Santiago Elena & Guillaume Beslon (2024). "Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?". Virus Evolution. doi : 10.1093/ve/veae078. HAL : hal-04801559. .
- Conferences (5)
- International conferences with peer review (4)
- Hugo Daudey, David Parsons, David P. Parsons, Eric Tannier, Vincent Daubin, Bastien Boussau, Vincent Liard, Romain Gallé, Jonathan Rouzaud-Cornabas & Guillaume Beslon (2024). "Aevol 4b: Bridging the gap between artificial life and bioinformatics". ALIFE 2024 - International Conference for Artificial Life, 26 juillet 2024, Copenhague (Denmark), pp. 41-49. doi : 10.1162/isal_a_00716. HAL : hal-04667220. .
- Lisa Chabrier, Anton Crombach, Sergio Peignier & Christophe Rigotti (2024). "Detecting gene regulatory network rewiring as changes in marker regulatory associations using only single-cell gene expression data". IEEE 12th Data Mining in Biomedical Informatics and Healthcare Workshop (DMBIH'24), Abu Dhabi (United Arab Emirates), p. 10. HAL : hal-04808464. .
- Ruggero Pensa, Anton Crombach, Sergio Peignier & Christophe Rigotti (2024). "Combining SHAP-driven Co-clustering and Shallow Decision Trees to Explain XGBoost". 27th International Conference Discovery Science (DS'24), Pise (Italy). HAL : hal-04809871. .
- Catherine Pothier, Neyrinck Estelle, Lasserre Cécile, Rousset Baptiste, Rigotti Christophe, Marie-Pierre Doin & Durand Philippe (2024). "EXPLORING AN UNSUPERVISED DATA MINING APPROACH TO EXTRACT ASEISMIC SLIP EVENTS ALONG THE IZMIT SECTION OF THE NORTH ANATOLIAN FAULT, BASED ON FLATSIM TIME SERIES". 6th Symposium on Measurement of Earth surface Deformations with Earth Observation (MDIS'24), Orléans (France), p. 2. HAL : hal-04808572. .
- Other conferences (1)
- Lisa Chabrier, Anton Crombach, Sergio Peignier & Christophe Rigotti (2024). "Unraveling regulatory associations using explainable AI". Journée GT Machine learning pour la génomique LEGO à JOBIM 2024, 25 juin 2024, Toulouse (France). HAL : hal-04783821.
- Reports (1)
- Research reports/tecnical reports (1)
- Nicolas Méger, Tuan Nguyen, Christophe Rigotti, Catherine Pothier & Emmanuel Trouvé (2024). "Information gain-based selection of sequential patterns extracted from partial unimodal probabilistic bases of sequences". Research report, #2024-1. p. 85. URL: https://sites.google.com/view/cisp-prototype. HAL : hal-04472843. .
- Others (4)
- Thibaut Peyric, Anton Crombach & Thomas Guyet (2024). "Single-cell multi-omics data integration powered by PCA-like autoencoders". JOBIM 2024, 28 juin 2024, Toulouse (France). Poster. HAL : hal-04750060. .
- Nathan Quiblier, Jan-Michael Rye, Pierre Leclerc, Henri Truong, Abdelkrim Hannou, Laurent Héliot & Hugues Berry (2024). "Enhancing Fluorescence Correlation Spectroscopy with Machine Learning for Advanced Analysis of Anomalous Diffusion". ArXiv : 2407.12382. HAL : hal-04650578. .
- Claire Alamichel, Juan Calvo, Erwan Hingant, Saoussen Latrach, Nathan Quiblier & Romain Yvinec (2024). "Modeling compartmentalization within intracellular signaling pathway". HAL : hal-04098543. .
- Théotime Grohens, Sam Meyer & Guillaume Beslon (2024). "Emergence of Supercoiling-Mediated Regulatory Networks through Bacterial Chromosome Organization". doi : 10.1101/2022.09.23.509185. HAL : hal-04398893. .
- 2023 (5)
- Journals (1)
- International journals with peer review (1)
- Paul Banse, Juliette Luiselli, David Parsons, Théotime Grohens, Marco Foley, Leonardo Trujillo, Jonathan Rouzaud‐Cornabas, Carole Knibbe & Guillaume Beslon (2023). "Forward‐in‐time simulation of chromosomal rearrangements: The invisible backbone that sustains long‐term adaptation". Molecular Ecology. doi : 10.1111/mec.17234. HAL : hal-04350147. .
- Conferences (1)
- International conferences with peer review (1)
- Reza Kalhor, Guillaume Beslon, Manuel Lafond & Celine Scornavacca (2023). "Classifying the Post-duplication Fate of Paralogous Genes". RECOMB-CG 2023 - 20th conference on Comparative Genomics, 15 avril 2023, Istanbul (Turkey), pp. 1-18. doi : 10.1007/978-3-031-36911-7_1. HAL : hal-04239853. .
- HDR, thesis (3)
- Thesis (3)
- Paul Banse (2023). "Evolution beyond substitutions : Computational modeling of the impact of chromosomal rearrangements on evolutionary dynamics". HAL : tel-04689412. .
- Marco Foley (2023). "Dynamique des génomes bactériens : Une étude expérimentale in silico avec la plateforme Aevol". HAL : tel-04689684. .
- Lisa Blum Moyse (2023). "Computational neuroscience models at different levels of abstraction for synaptic plasticity, astrocyte modulation of synchronization and systems memory consolidation". HAL : tel-04390158. .
- 2022 (10)
- Journals (5)
- International journals with peer review (5)
- Leonardo Trujillo, Paul Banse & Guillaume Beslon (2022). "Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes". PLoS Computational Biology, vol. 18, #10, e1010647. doi : 10.1371/journal.pcbi.1010647. ArXiv : arXiv:2210.06804. HAL : hal-03866346. .
- Miguel A. Fortuna, Guillaume Beslon & Charles Ofria (2022). "Digital evolution: Insights for biologists". Frontiers in Ecology and Evolution. doi : 10.3389/fevo.2022.1037040. HAL : hal-03912093. .
- Audrey Denizot, Misa Arizono, Valentin Nägerl, Hugues Berry & Erik De Schutter (2022). "Control of Ca2+ signals by astrocyte nanoscale morphology at tripartite synapses". Glia. doi : 10.1002/glia.24258. HAL : hal-03582629. .
- Lisa Blum Moyse & Hugues Berry (2022). "Modelling the modulation of cortical Up-Down state switching by astrocytes". PLoS Computational Biology, vol. 18, #7, e1010296. doi : 10.1371/journal.pcbi.1010296. HAL : hal-03737962. .
- Hana Valenta, Nathan Quiblier, Valerio Laghi, Clément Cabriel & Justine Riti (2022). "Latest trends in bioimaging and building a proactive network of early-career young scientists around bioimaging in Europe". Biology Open, vol. 11, #12, bio059630. doi : 10.1242/bio.059630. HAL : hal-04403665. .
- HDR, thesis (1)
- Thesis (1)
- Théotime Grohens (2022). "Ride the supercoiling : Evolution of supercoiling-mediated gene regulatory networks through genomic inversions". HAL : tel-04146510. .
- Book edition (books, chapters, seminars, congress, special numbers) (1)
- Lucas Foulon, Christophe Rigotti, Serge Fenet & Denis Jouvin (2022). "Anomaly Detection Based on Sequence Indexation and CFOF Score Approximation". Advances in Knowledge Discovery and Management, Springer International Publishing, pp. 47-61. doi : 10.1007/978-3-030-90287-2_3. HAL : hal-03881940.
- Others (3)
- Lisa Chabrier, Anton Crombach, Sergio Peignier & Christophe Rigotti (2022). "Semi-supervised learning for tree-based regressors to improve the prediction of the interactions between genes". Symposium MaDICS, 11 juillet 2022, Lyon (France). Poster. HAL : hal-03894314. .
- François Smekens, Nicolas Freud, Bruno Sixou, Guillaume Beslon & Jean Michel Létang (2022). "Towards the optimization of ballistics in proton therapy using genetic algorithms: implementation issues". ArXiv : 2205.08283. HAL : hal-03702837.
- François Smekens, Nicolas Freud, Bruno Sixou, Guillaume Beslon & Jean Michel Létang (2022). "Variable length genetic algorithm with continuous parameters optimization of beam layout in proton therapy". ArXiv : 2205.08398. HAL : hal-03702842.
- 2021 (14)
- Journals (2)
- International journals with peer review (2)
- Sara Zeppilli, Tobias Ackels, Robin Attey, Nell Klimpert, Kimberly Ritola, Stefan Boeing, Anton Crombach, Andreas Schaefer & Alexander Fleischmann (2021). "Molecular characterization of projection neuron subtypes in the mouse olfactory bulb". eLife. doi : 10.7554/eLife.65445. HAL : hal-03473445.
- Simon Pageaud, Catherine Pothier, Christophe Rigotti, Anne Eyraud-Loisel, Jean-Pierre Bertoglio, Alexis Bienvenüe, Nicolas Leboisne, Nicolas Ponthus, Romain Gauchon et al. (2021). "Expected Evolution of COVID-19 Epidemic in France for Several Combinations of Vaccination Strategies and Barrier Measures". Vaccines, vol. 9, #12, p. 1462. doi : 10.3390/vaccines9121462. HAL : hal-03482342. .
- Conferences (5)
- International conferences with peer review (3)
- Leonardo Trujillo, Paul Banse & Guillaume Beslon (2021). "Simulating short-and long-term evolutionary dynamics on rugged landscapes". ALIFE 2021 - Conference on Artificial Life, 23 juillet 2021, Prague (Czech Republic), pp. 1-9. ArXiv : 2105.05520. HAL : hal-03426019. .
- Laurent Turpin, Thierry Gautier & Jonathan Rouzaud-Cornabas (2021). "X-Aevol: GPU implementation of an evolutionary experimentation simulator". GECCO 2021 - Genetic and Evolutionary Computation Conference, 14 juillet 2021, Lille France (France), pp. 1-9. doi : 10.1145/3449726.3463195. HAL : hal-03290799. .
- Anaïs Badoual, Misa Arizono, Audrey Denizot, Mathieu Ducros, Hugues Berry, U Valentin Nägerl & Charles Kervrann (2021). "Simulation of Astrocytic Calcium Dynamics in Lattice Light Sheet Microscopy Images". ISBI 2021 - IEEE International Symposium on Biomedical Imaging, 16 avril 2021, Nice (France), pp. 1-5. doi : 10.1109/ISBI48211.2021.9433984. HAL : hal-03106797. .
- National conferences with peer review (2)
- Noëlie Debs, Sergio Peignier, Clément Douarre, Théo Jourdan, Christophe Rigotti & Carole Frindel (2021). "Apprendre l'apprentissage automatique : un retour d'expérience". CETSIS 2021 - Colloque de l'Enseignement des Technologies et des Sciences de l'Information et des Systèmes, 10 juin 2021, Valenciennes (France), pp. 1-5. HAL : hal-03341954. .
- Nadia Bennani, Sylvie Cazalens, Vincent Cheutet, Claire Leschi, Odyssée Merveille, Camille Moriot, Delphine Muller, Timothée Pecatte, Catherine Pothier et al. (2021). "Apprivoiser l'hétérogénéité en informatique 1ère année". COLLOQINSA 2021 - 7e Colloque pédagogie et formation, 21 mai 2021, Valenciennes (France), pp. 1-6. HAL : hal-03230531. .
- Book edition (books, chapters, seminars, congress, special numbers) (2)
- Guillaume Beslon, Vincent Liard, David P. Parsons & Jonathan Rouzaud-Cornabas (2021). "Of Evolution, Systems and Complexity". Evolutionary Systems Biology II. doi : 10.1007/978-3-030-71737-7_1. HAL : hal-03136122. .
- Anton Crombach (2021). "Evolutionary Systems Biology". Anton Crombach, Springer International Publishing. doi : 10.1007/978-3-030-71737-7. HAL : hal-03473679.
- Reports (2)
- Research reports/tecnical reports (2)
- Simon Pageaud, Nicolas Ponthus, Romain Gauchon, Catherine Pothier, Christophe Rigotti, Anne Eyraud-Loisel, Jean-Pierre Bertoglio, Alexis Bienvenüe, François Gueyffier et al. (2021). "Adapting French COVID-19 vaccination campaign duration to variant dissemination". Research report. p. 24. HAL : hal-03294952. .
- Romain Gauchon, Nicolas Ponthus, Catherine Pothier, Christophe Rigotti, Vitaly Volpert, Stéphane Derrode, Jean-Pierre Bertoglio, Alexis Bienvenüe, Pierre-Olivier Goffard et al. (2021). "Lessons learnt from the use of compartmental models over the COVID-19 induced lockdown in France". Research report. p. 39. HAL : hal-03341704. .
- Others (3)
- Leonardo Trujillo, Paul Banse & Guillaume Beslon (2021). "Evolutionary escape from local fitness peaks through inversion mutations". CCS 2021 - Conference on Complex Systems. HAL : hal-03426022. .
- Aquilina Al Khoury, Samuel Bernard & Jonathan Rouzaud-Cornabas (2021). "Accuracy of Mixed Precision Computation in Large Coupled Biological Systems". HAL : hal-03249828. .
- Anaïs Badoual, Misa Arizono, Audrey Denizot, Mathieu Ducros, Hugues Berry, U Valentin Nägerl & Charles Kervrann (2021). "Simulation of Astrocytic Calcium Dynamics in Lattice Light Sheet Microscopy Images". ISBI 2021 - IEEE International Symposium on Biomedical Imaging, 16 avril 2021, Nice (France). Poster. HAL : hal-03516709. .
- 2020 (9)
- Journals (6)
- International journals with peer review (6)
- Maxime Woringer, Ignacio Izeddin, Cyril Favard & Hugues Berry (2020). "Anomalous Subdiffusion in Living Cells: Bridging the Gap Between Experiments and Realistic Models Through Collaborative Challenges". Frontiers in Physics, vol. 8, p. 134. doi : 10.3389/fphy.2020.00134. HAL : hal-02871984. .
- Stéphane Gaubert, Marianne Akian, Xavier Allamigeon, Marin Boyet, Baptiste Colin, Théotime Grohens, Laurent Massoulié, David Parsons, Frederic Adnet et al. (2020). "Understanding and monitoring the evolution of the Covid-19 epidemic from medical emergency calls: the example of the Paris area". Comptes Rendus. Mathématique, vol. 358, #7, pp. 843-875. doi : 10.5802/crmath.99. ArXiv : 2005.14186. HAL : hal-02648075. .
- Sergio Peignier, Christophe Rigotti & Guillaume Beslon (2020). "Evolutionary Subspace Clustering Using Variable Genome Length". Computational Intelligence, vol. 36, #2, pp. 574-612. doi : 10.1111/coin.12254. HAL : hal-02405598. .
- Kerstin Lenk, Eero Satuvuori, Jules Lallouette, Antonio Ladrón-De-Guevara, Hugues Berry & Jari Hyttinen (2020). "A Computational Model of Interactions Between Neuronal and Astrocytic Networks: The Role of Astrocytes in the Stability of the Neuronal Firing Rate". Frontiers in Computational Neuroscience, vol. 13, pp. 1-19. doi : 10.3389/fncom.2019.00092. HAL : hal-02453587. .
- Joel Lehman, Jeff Clune, Dusan Misevic, Christoph Adami, Julie Beaulieu, Peter J. Bentley, Samuel Bernard, Guillaume Beslon, David M. Bryson et al. (2020). "The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities". Artificial Life, vol. 26, #2, pp. 274-306. doi : 10.1162/artl_a_00319. ArXiv : 1803.03453. HAL : hal-01735473. .
- Vincent Liard, David Parsons, Jonathan Rouzaud-Cornabas & Guillaume Beslon (2020). "The complexity ratchet: Stronger than selection, stronger than evolvability, weaker than robustness". Artificial Life, vol. 26, #1, pp. 38-57. doi : 10.1162/artl_a_00312. HAL : hal-03136077. .
- Conferences (1)
- International conferences with peer review (1)
- Laurent Turpin, Jonathan Rouzaud-Cornabas, Thierry Gautier & Christian Pérez (2020). "P-Aevol: an OpenMP Parallelization of a Biological Evolution Simulator, Through Decomposition in Multiple Loops". 16th International Workshop on OpenMP, 24 septembre 2020, Austin (United States of America), pp. 52-66. doi : 10.1007/978-3-030-58144-2_4. HAL : hal-02962838. .
- HDR, thesis (1)
- Thesis (1)
- Vincent Liard (2020). "Origine évolutive de la complexité des systèmes biologiques : Une étude par évolution expérimentale in silico". HAL : tel-03177236. .
- Reports (1)
- Research reports/tecnical reports (1)
- Stéphane Derrode, Romain Gauchon, Nicolas Ponthus, Christophe Rigotti, Catherine Pothier, Vitaly Volpert, Stéphane Loisel, Jean-Pierre Bertoglio & Pascal Roy (2020). "Piecewise estimation of R0 by a simple SEIR model. Application to COVID-19 in French regions and departments until June 30, 2020". Research report. HAL : hal-02910202. .
- 2019 (17)
- Journals (6)
- International journals with peer review (6)
- Elise Parey & Anton Crombach (2019). "Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins". Genome Biology and Evolution, vol. 11, #3, pp. 660-677. doi : 10.1093/gbe/evz019. HAL : hal-02064719.
- Giuseppe Gangarossa, Sylvie Perez, Yulia Dembitskaya, Ilya Prokin, Hugues Berry & Laurent Venance (2019). "BDNF controls bidirectional endocannabinoid-plasticity at corticostriatal synapses". Cerebral Cortex, vol. bhz081, pp. 1-18. doi : 10.1093/cercor/bhz081. HAL : hal-02076121. .
- Audrey Denizot, Misa Arizono, Valentin Nägerl, Hédi Soula & Hugues Berry (2019). "Simulation of calcium signaling in fine astrocytic processes: effect of spatial properties on spontaneous activity". PLoS Computational Biology, vol. 15, 8, e1006795, pp. 1-33. doi : 10.1371/journal.pcbi.1006795. HAL : hal-02184344. .
- Nicolas Méger, Christophe Rigotti, Catherine Pothier, Tuan Nguyen, Felicity Lodge, Lionel Gueguen, Rémi Andréoli, Marie-Pierre Doin & Mihai Datcu (2019). "Ranking evolution maps for Satellite Image Time Series exploration: application to crustal deformation and environmental monitoring". Data Mining and Knowledge Discovery, vol. 33, #1, pp. 131-167. doi : 10.1007/s10618-018-0591-9. HAL : hal-01898015. .
- Carole Knibbe, Guillaume Beslon & Dusan Misevic (2019). "Introduction to the ECAL 2017 Special Issue". Artificial Life, vol. 25, #4, pp. 313-314. doi : 10.1162/artl_a_00298. HAL : hal-02428658. .
- Jacob Rutten, Paulien Hogeweg & Guillaume Beslon (2019). "Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure". BMC Evolutionary Biology, vol. 19, #1, pp. 1-17. doi : 10.1186/s12862-019-1507-z. HAL : hal-02350040. .
- Conferences (4)
- International conferences with peer review (3)
- Quentin Carde, Marco Foley, Carole Knibbe, David Parsons, Jonathan Rouzaud-Cornabas & Guillaume Beslon (2019). "How to reduce a genome? ALife as a tool to teach the scientific method to school pupils". ALIFE 2019 - Conference on Artificial Life, 2 août 2019, Newcastle (United Kingdom), pp. 497-504. doi : 10.1162/isal_a_00211. HAL : hal-02285718. .
- Tuan Nguyen, Nicolas Méger, Christophe Rigotti, Catherine Pothier, Noel Gourmelen & Emmanuel Trouvé (2019). "A pattern-based mining system for exploring Displacement Field Time Series". 19th IEEE International Conference on Data Mining (ICDM) Demo, 11 novembre 2019, Beijing (China), pp. 1110-1113. doi : 10.1109/ICDMW.2019.00165. HAL : hal-02361793. .
- Lucas Foulon, Serge Fenet, Christophe Rigotti & Denis Jouvin (2019). "Scoring Message Stream Anomalies in Railway Communication Systems". LMID 2019 - IEEE Workshop on Learning and Mining with Industrial Data, 11 novembre 2019, Beijing (China), pp. 1-8. doi : 10.1109/ICDMW.2019.00114. HAL : hal-02357924. .
- National conferences with peer review (1)
- Lucas Foulon, Christophe Rigotti, Serge Fenet & Denis Jouvin (2019). "Approximation du score CFOF de détection d’anomalie dans un arbre d’indexation iSAX : Application au contexte SI de la SNCF". EGC 2019 - 19ème Conférence francophone sur l'Extraction et la Gestion des Connaissances, 25 janvier 2019, Metz (France), pp. 1-12. HAL : hal-02019035. .
- HDR, thesis (1)
- Thesis (1)
- Audrey Denizot (2019). "Simulating calcium signaling in fine astrocytic processes". HAL : tel-02406699. .
- Book edition (books, chapters, seminars, congress, special numbers) (5)
- Jules Lallouette, Maurizio De Pittà & Hugues Berry (2019). "Astrocyte networks and intercellular calcium propagation". Computational Glioscience, Maurizio De Pittà, Hugues Berry, pp. 177-210. doi : 10.1007/978-3-030-00817-8_7. HAL : hal-01995852. .
- Maurizio De Pittà, Eshel Ben-Jacob & Hugues Berry (2019). "G protein-coupled receptor-mediated calcium signaling in astrocytes". Computational Glioscience, Maurizio De Pittà, Hugues Berry, Springer, pp. 115-150. doi : 10.1007/978-3-030-00817-8_5. HAL : hal-01995850. .
- Maurizio De Pittà & Hugues Berry (2019). "A Neuron-Glial Perspective for Computational Neuroscience". Computational Glioscience, Maurizio de Pittà, Hugues Berry, Spinger, pp. 3-35. doi : 10.1007/978-3-030-00817-8_1. HAL : hal-01995849. .
- Maurizio De Pittà & Hugues Berry (2019). "Computational Glioscience". Springer. doi : 10.1007/978-3-030-00817-8. HAL : hal-01995842.
- Audrey Denizot, Hugues Berry & Sharmila Venugopal (2019). "Intracellular Ca 2+ Dynamics in Astrocytes: Modeling the Underlying Spatiotemporal Diversity". Encyclopedia of Computational Neuroscience, pp. 1-19. HAL : hal-02419317. .
- Others (1)
- Lucas Foulon, Serge Fenet, Christophe Rigotti & Denis Jouvin (2019). "Detecting Anomalies over Message Streams in Railway Communication Systems". AALTD@ECML/PKDD 2019 - 4th Workshop on Advanced Analytics and Learning on Temporal Data. Poster, 20 septembre 2019, Wurzburg (Germany). Poster. HAL : hal-02357927. .
- 2018 (17)
- Journals (9)
- International journals with peer review (9)
- Yihui Cui, Ilya Prokin, Alexandre Mendes, Hugues Berry & Laurent Venance (2018). "Robustness of STDP to spike timing jitter". Scientific Reports, vol. 8, #1, 8139:1-15. doi : 10.1038/s41598-018-26436-y. HAL : hal-01788826. .
- Alexandre Foncelle, Alexandre Mendes, Joanna Jedrzejewska-Szmek, Silvana Valtcheva, Hugues Berry, Kim Blackwell & Laurent Venance (2018). "Modulation of spike-timing dependent plasticity: towards the inclusion of a third factor in computational models". Frontiers in Computational Neuroscience, vol. 12, p. 49. doi : 10.3389/fncom.2018.00049. HAL : hal-01809075. .
- Hao Xu, Sylvie Perez, Amandine Cornil, Bérangère Detraux, Ilya Prokin, Yihui Cui, Bertrand Degos, Hugues Berry, Alban De Kerchove D'exaerde & Laurent Venance (2018). "Dopamine-endocannabinoid interactions mediate spike-timing dependent potentiation in the striatum". Nature Communications, vol. 9, p. 4118. doi : 10.1038/s41467-018-06409-5. HAL : hal-01865929. .
- Jos Käfer, Andrea Betancourt, Avelyne Villain, Marie Fernandez, Clémentine Vignal, Gabriel Marais & Maud Tenaillon (2018). "Progress and Prospects in Gender Visibility at SMBE Annual Meetings". Genome Biology and Evolution, vol. 10, #3, pp. 901-908. doi : 10.1093/gbe/evy056. HAL : hal-02310560. .
- Franziska Oschmann, Hugues Berry, Klaus Obermayer & Kerstin Lenk (2018). "From in silico astrocyte cell models to neuron-astrocyte network models: A review". Brain Research Bulletin, vol. 136, pp. 76-84. doi : 10.1016/j.brainresbull.2017.01.027. HAL : hal-01461928. .
- Yihui Cui, Yan Yang, Zheyi Ni, Yiyan Dong, Guohong Cai, Alexandre Foncelle, Shuangshuang Ma, Kangning Sang, Siyang Tang et al. (2018). "Astroglial-Kir4.1 in Lateral Habenula Drives Neuronal Bursts to Mediate Depression". Nature, vol. 554, pp. 323-327. doi : 10.1038/nature25752. HAL : hal-01683191. .
- Chenju Yi, Jérémy Theillon, Annette Koulakoff, Hugues Berry & Christian Giaume (2018). "Monitoring gap junctional communication in astrocytes from acute adult mouse brain slices using the gap-FRAP technique". Journal of Neuroscience Methods, vol. 303, pp. 103-113. doi : 10.1016/j.jneumeth.2018.03.005. HAL : hal-01734652. .
- Berta Verd, Erik Clark, Karl Wotton, Hilde Janssens, Eva Jiménez-Guri, Anton Crombach & Johannes Jaeger (2018). "A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila". PLoS Biology, vol. 16, #2, p. 24. doi : 10.1371/journal.pbio.2003174. HAL : hal-01934923.
- Tuan Nguyen, Nicolas Méger, Christophe Rigotti, Catherine Pothier, Emmanuel Trouvé, Noel Gourmelen & Jean-Louis Mugnier (2018). "A pattern-based method for handling confidence measures while mining satellite displacement field time series. Application to Greenland ice sheet and Alpine glaciers". IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, vol. 11, #11, pp. 4390-4402. doi : 10.1109/JSTARS.2018.2874499. HAL : hal-01912708. .
- Conferences (4)
- International conferences with peer review (4)
- Tuan Nguyen, Nicolas Méger, Christophe Rigotti, Catherine Pothier, Emmanuel Trouvé & Jean-Louis Mugnier (2018). "Finding Complementary and Reliable Patterns in Displacement Field Time Series of Alpine Glaciers". IGARSS 2018 - IEEE International Geoscience and Remote Sensing Symposium, 27 juillet 2018, Valencia (Spain), pp. 4213-4216. HAL : hal-01868749. .
- Sergio Peignier, Christophe Rigotti, Anthony Rossi & Guillaume Beslon (2018). "Weight-based search to find clusters around medians in subspaces". SAC 2018 - ACM Symposium On Applied Computing, 13 avril 2018, Pau (France), pp. 1-10. HAL : hal-01869974. .
- Vincent Liard, David Parsons, Jonathan Rouzaud-Cornabas & Guillaume Beslon (2018). "The Complexity Ratchet: Stronger than selection, weaker than robustness". ALIFE 2018 - the 2018 conference on artificial Life, 27 juillet 2018, Tokyo (Japan), pp. 1-8. doi : 10.1162/isal_a_00051. HAL : hal-01882628. .
- Guillaume Beslon, Santiago Elena, Paulien Hogeweg, Dominique Schneider & Susan Stepney (2018). "Evolving Living Technologies-Insights from the EvoEvo project". SSBSE 2018 - 10th Symposium on Search-Based Software Engineering, 9 septembre 2018, Montpellier (France), pp. 46-62. doi : 10.1007/978-3-319-99241-9_2. HAL : hal-01882636. .
- HDR, thesis (1)
- Thesis (1)
- Alexandre Foncelle (2018). "Data-driven computational modelling for some of the implications of dopamine in the brain : From subcellular signalling to area networks". HAL : tel-02090797. .
- Others (3)
- Guillaume Beslon, Vincent Liard & Santiago Elena (2018). "Jump then Climb: can rearrangements predict the occurrence of mutational bursts?". Evolution 2018 - Congress on Evolutionary Biology, 22 août 2018, Montpellier (France). Poster. HAL : hal-01938800. .
- Vincent Liard, Jonathan Rouzaud-Cornabas, David Parsons & Guillaume Beslon (2018). "The complexity ratchet: stronger than selection". Beacon congress 2018, 11 août 2018, east-lansing (United States of America). Poster. HAL : hal-01938802. .
- Guillaume Beslon, Vincent Liard, David P. Parsons & Jonathan Rouzaud-Cornabas (2018). "In silico experimental evolution shows that complexity can rise even in simple environments". ICSB 2018 - 19th International Conference on Systems Biology, 1 novembre 2018, Lyon (France). Poster. HAL : hal-01939365. .
- 2017 (13)
- Journals (4)
- International journals with peer review (4)
- Guillaume Beslon & Dominique Schneider (2017). "Isee-resistance : using in silico experimental evolution to sensitize providers on antibiotic resistance". Antimicrobial Resistance and Infection Control, vol. 6Suppl 3, #52, p. 2. HAL : hal-01569262.
- Marie Fernandez, Clémentine Vignal & Hédi Soula (2017). "Impact of group size and social composition on group vocal activity and acoustic network in a social songbird". Animal Behaviour, vol. 127, pp. 163-178. doi : 10.1016/j.anbehav.2017.03.013. HAL : hal-01537565. .
- Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider & Guillaume Beslon (2017). "Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification". PLoS Computational Biology, vol. 13, #3, e1005459 (32 pages. doi : 10.1371/journal.pcbi.1005459.s006. HAL : hal-01508751. .
- Jonas Abernot, Guillaume Beslon, Simon Hickinbotham, Sergio Peignier & Christophe Rigotti (2017). "Evolving Instrument Based on Symbiont-Host Metaphor: a Commensal Computation". Journal of Creative Music Systems, vol. 2, #1, pp. 1-10. doi : 10.5920/JCMS.2017.11. HAL : hal-01596573. .
- Conferences (6)
- International conferences with peer review (4)
- Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider & Guillaume Beslon (2017). "Environmental seasonality drives digital populations towards stable cross-feeding". European Conference on Artificial Life (ECAL), 8 septembre 2017, Villeurbanne (France). HAL : hal-01569093. .
- Vincent Liard, Jonathan Rouzaud-Cornabas, Nicolas Comte & Guillaume Beslon (2017). "A 4-base model for the Aevol in-silico experimental evolution platform". European Conference on Artificial Life, 8 septembre 2017, Villeurbanne (France). HAL : hal-01569097. .
- Sergio Peignier, Jonas Abernot, Christophe Rigotti & Guillaume Beslon (2017). "EvoMove: Evolutionary-based living musical companion". European Conference on Artificial Life (ECAL), 8 septembre 2017, Villeurbanne (France), pp. 1-8. HAL : hal-01569091. .
- Tuan Nguyen, Nicolas Méger, Christophe Rigotti, Catherine Pothier, Emmanuel Trouvé & Noel Gourmelen (2017). "Handling coherence measures of displacement field time series: Application to Greenland ice sheet glaciers". 9th International Workshop on the Analysis of Multitemporal Remote Sensing Images (MultiTemp), 29 septembre 2017, Brugge (Belgium), pp. 1-4. doi : 10.1109/Multi-Temp.2017.8035228. HAL : hal-01591461.
- National conferences with peer review (2)
- Elodie Scholastique, Catherine Pothier, Louis Vinet, Christophe Rigotti & Nicole Bouillod (2017). "3D Geomodelling Contribution to the Mapping of Gravitational Hazards on the Hill of Croix-Rousse". Journées Aléas Gravitaires (JAG), 25 octobre 2017, Besançon (France), pp. 1-4. HAL : hal-01596585. .
- Nicolas Comte, Vincent Liard, Carole Knibbe & Guillaume Beslon (2017). "Aevol-4b: Toward a new simulation platform to benchmark phylogenetic tools". ALPHY (ALignments and PHYlogeny), 2 février 2017, Villeurbanne (France). HAL : hal-01569078. .
- HDR, thesis (1)
- Thesis (1)
- Charles Rocabert (2017). "Studying the evolution of bacterial micro-organisms by modeling and numerical simulation approaches". HAL : tel-01973793. .
- Book edition (books, chapters, seminars, congress, special numbers) (1)
- Nicolas Méger, Edoardo Pasolli, Christophe Rigotti, Emmanuel Trouvé & Farid Melgani (2017). "Satellite Image Time Series: mathematical models for data mining and missing data restoration". Mathematical Models for Remote Sensing Image Processing, Gabriele Moser, Josiane Zerubia, Springer International Publishing, pp. 357-398. doi : 10.1007/978-3-319-66330-2. HAL : hal-01567675.
- Others (1)
- Guillaume Beslon, Vincent Liard & Santiago F Elena (2017). "Testing evolution predictability using the aevol software". 16th international meeting of the European Society of Evolutionary Biology (ESEB 2017), 25 août 2017, Groningen (Netherlands). Poster. HAL : hal-01577115. .
- 2016 (36)
- Journals (7)
- International journals with peer review (7)
- Yihui Cui, Ilya Prokin, Hao Xu, Bruno Delord, Stéphane Genet, Laurent Venance & Hugues Berry (2016). "Endocannabinoid dynamics gate spike-timing dependent depression and potentiation". eLife, vol. 5, e13185 (32 pages. doi : 10.7554/eLife.13185. HAL : hal-01279901. .
- Wolfgang Banzhaf, Bert Baumgaertner, Guillaume Beslon, René Doursat, James A Foster, Barry Mcmullin, Vinicius Veloso De Melo, Thomas Miconi, Lee Spector et al. (2016). "Defining and simulating open-ended novelty: requirements, guidelines, and challenges.". Theorie in den Biowissenschaften / Theory in Biosciences. doi : 10.1007/s12064-016-0229-7. HAL : hal-01323108.
- Tim Taylor, Mark Bedau, Alastair Channon, David Ackley, Wolfgang Banzhaf, Guillaume Beslon, Emily Dolson, Tom Froese, Simon Hickinbotham et al. (2016). "Open-Ended Evolution: Perspectives from the OEE Workshop in York". Artificial Life, vol. 22, #3, pp. 408-423. doi : 10.1162/ARTL_a_00210. HAL : hal-01371116. .
- Priscila Biller, Laurent Guéguen, Carole Knibbe & Eric Tannier (2016). "Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation". Genome Biology and Evolution, vol. 8, #5, pp. 1427-1439. doi : 10.1093/gbe/evw083. HAL : hal-01334923. .
- Marie S. A. Fernandez, Hedi Soula, Mylène M. Mariette & Clémentine Vignal (2016). "A New Semi-automated Method for Assessing Avian Acoustic Networks Reveals that Juvenile and Adult Zebra Finches Have Separate Calling Networks.". Frontiers in Psychology. doi : 10.3389/fpsyg.2016.01816. HAL : hal-01435346. .
- Avelyne Villain, Marie S. A. Fernandez, Colette Bouchut, Hédi Soula & Clémentine Vignal (2016). "Songbird mates change their call structure and intra-pair communication at the nest in response to environmental noise". Animal Behaviour, vol. 116, pp. 113-129. doi : 10.1016/j.anbehav.2016.03.009. HAL : hal-01404754. .
- Hugues Berry, Thomas Lepoutre & Álvaro Mateos González (2016). "Quantitative convergence towards a self similar profile in an age-structured renewal equation for subdiffusion". Acta Applicandae Mathematicae, #145, pp. 15-45. ArXiv : 1503.08552. HAL : hal-01136667. .
- Conferences (13)
- International conferences with peer review (10)
- Yoram Vadée-Le-Brun, Jonathan Rouzaud-Cornabas & Guillaume Beslon (2016). "In Silico Experimental Evolution suggests a complex intertwining of selection, robustness and drift in the evolution of genetic networks complexity". Artificial Life, 8 juillet 2016, Cancun (Mexico). HAL : hal-01375645. .
- Youen Pericault, Catherine Pothier, Nicolas Méger, Emmanuel Trouvé, Flavien Vernier, Christophe Rigotti & Jean-Philippe Malet (2016). "Grouped frequent sequential patterns derived from terrestrial image time series tomonitor landslide behaviour – Application to the dynamics of the Sanières/Roche Plombée rockslide.". Geophysical Research Abstracts - EGU General Assembly 2016, 22 avril 2016, Vienna (Austria), pp. 1-1. HAL : hal-01306556.
- Jonas Abernot, Guillaume Beslon, Simon Hickinbotham, Sergio Peignier & Christophe Rigotti (2016). "A Commensal Architecture for Evolving Living Instruments". Conference on Computer Simulation of Musical Creativity, 19 juin 2016, Huddersfield (United Kingdom), pp. 1-8. HAL : hal-01368034.
- Jacob Rutten, Paulien Hogeweg & Guillaume Beslon (2016). "Evolution of mutator populations in constant environments". 2nd EvoEvo Workshop, satellite workshop of CCS2016, 20 septembre 2016, Amsterdam (Netherlands). HAL : hal-01375669. .
- Susan Stepney & Guillaume Beslon (2016). "Open-Endedness: Definitions and Shortcuts". 2nd EvoEvo Workshop, satellite workshop of CCS2016, 20 septembre 2016, Amsterdam (Netherlands). HAL : hal-01375671. .
- Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider & Guillaume Beslon (2016). "In Silico Experimental Evolution Highlights the Influence of Environmental Seasonality on Bacterial Diversification". 2nd EvoEvo Workshop, satellite workshop of CCS2016, 20 septembre 2016, Amsterdam (Netherlands). HAL : hal-01375677. .
- Guillaume Beslon, Vincent Liard & Santiago Elena (2016). "Evolvability drives innovation in viral genomes". 2nd EvoEvo Workshop, satellite workshop of CCS2016, 20 septembre 2016, Amsterdam (France). HAL : hal-01375665. .
- Tuan Nguyen, Nicolas Méger, Christophe Rigotti, Catherine Pothier & Rémi Andréoli (2016). "SITS-P2miner: Pattern-Based Mining of Satellite Image Time Series". European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD) Demo, 23 septembre 2016, Riva del Garda (Italy), pp. 63-66. doi : 10.1007/978-3-319-46131-1_14. HAL : hal-01367996.
- Priscila Biller, Carole Knibbe, Guillaume Beslon & Eric Tannier (2016). "Comparative Genomics on Artificial Life". Computability in Europe, 27 juin 2016, Paris (France), pp. 35-44. HAL : hal-01334930.
- Jérôme Gippet, Serge Fenet, Adeline Dumet, Bernard Kaufmann & Charles Rocabert (2016). "MoRIS: Model of Routes of Invasive Spread. Human-mediated dispersal, road network and invasion parameters". 5th International Conference on Ecology and Transportation: Integrating Transport Infrastructures with Living Landscapes, 2 septembre 2016, Lyon (France). HAL : hal-01412280.
- National conferences with peer review (3)
- Priscila Biller, Eric Tannier, Guillaume Beslon & Carole Knibbe (2016). "In silico experimental evolution provides independent and challenging benchmarks for comparative genomics". Journées ouvertes Biologie Informatique Mathématiques, 30 juin 2016, Lyon (France), pp. 79-82. HAL : hal-01375657. .
- Catherine Pothier, Rémi Andréoli, Nicolas Méger & Christophe Rigotti (2016). "Suivi de l'érosion par imagerie satellite et fouille de données spatio-temporelles". Journées Nationales de Géotechnique et de Géologie de l'Ingénieur, 8 juillet 2016, Nancy (France), pp. 1-8. HAL : hal-01367992.
- Vincent Henry, Arnaud Ferré, Christine Froidevaux, Anne Goelzer, Vincent Fromion, Sarah Cohen-Boulakia, Sandra Derozier, Marc Dinh, Ghislain Fiévet et al. (2016). "Représentation systémique multi-échelle des processus biologiques de la bactérie". IC2016 - Ingénierie des Connaissances, 6 juin 2016, Montpellier (France). HAL : hal-01442727. .
- HDR, thesis (1)
- Thesis (1)
- Ilya Prokin (2016). "Synaptic plasticity emerging from chemical reactions". HAL : hal-01514357.
- Reports (14)
- Research reports/tecnical reports (14)
- Guillaume Beslon, Jonas Abernot, Sergio Peignier & Christophe Rigotti (2016). "EvoEvo Deliverable 5.2". Research report. HAL : hal-01577180. .
- Guillaume Beslon & Paulien Hogeweg (2016). "EvoEvo Deliverable 6.6". Research report. HAL : hal-01577185. .
- Guillaume Beslon, Jonas Abernot, Santiago F. Elena, Dominique Schneider, Paulien Hogeweg, Susan Stepney & Christophe Rigotti (2016). "EvoEvo Deliverable 6.8". Research report. HAL : hal-01577187. .
- Guillaume Beslon, Jonas Abernot, Sergio Peignier & Christophe Rigotti (2016). "EvoEvo Deliverable 5.1". Research report. HAL : hal-01577177. .
- Susan Stepney, Guillaume Beslon & Tim Hoverd (2016). "EvoEvo Deliverable 4.3". Research report. HAL : hal-01577166. .
- Dominique Schneider, Guillaume Beslon, Santiago F. Elena & Otmane Lamrabet (2016). "EvoEvo Deliverable 1.6". Research report. HAL : hal-01577131. .
- Paulien Hogeweg & Guillaume Beslon (2016). "EvoEvo Deliverable 3.1". Research report. HAL : hal-01577153. .
- Paulien Hogeweg & Guillaume Beslon (2016). "EvoEvo Deliverable 3.2". Research report. HAL : hal-01577155. .
- Dominique Schneider, Guillaume Beslon, José-Luis Carrasco, Santiago F. Elena, Otmane Lamrabet & A. Willemsen (2016). "EvoEvo Deliverable 1.5". Research report. HAL : hal-01577130. .
- Santiago F. Elena, Guillaume Beslon, Otmane Lamrabet & Dominique Schneider (2016). "EvoEvo Deliverable 1.4". Research report. HAL : hal-01577128. .
- Santiago F. Elena, Dominique Schneider, Guillaume Beslon & Otmane Lamrabet (2016). "EvoEvo Deliverable 1.2". Research report. HAL : hal-01577126. .
- Santiago F. Elena, Guillaume Beslon, Otmane Lamrabet & Dominique Schneider (2016). "EvoEvo Deliverable 1.3". Research report. HAL : hal-01577127. .
- Paulien Hogeweg, Guillaume Beslon & Susan Stepney (2016). "EvoEvo Deliverable 3.4". Research report. HAL : hal-01577160. .
- Paulien Hogeweg & Guillaume Beslon (2016). "EvoEvo Deliverable 3.3". Research report. HAL : hal-01577156. .
- Others (1)
- Bérénice Batut, Guillaume Beslon & Carole Knibbe (2016). "Unexpected genome inflation and streamlining in variable environments". Journées ouvertes de Biologie Informatique & Mathématiques 2016, 30 juin 2016, Lyon (France). Poster. HAL : hal-01375653.
- 2015 (23)
- Journals (6)
- International journals with peer review (6)
- Emilie C. Perez, Marie Fernandez, Simon C. Griffith, Clémentine Vignal & Hedi Soula (2015). "Impact of visual contact on vocal interaction dynamics of pair bonded birds". Animal Behaviour, vol. 107, pp. 125-137. doi : 10.1016/j.anbehav.2015.05.019. HAL : hal-01253146. .
- Peggy Cellier, Thierry Charnois, Marc Plantevit, Christophe Rigotti, Bruno Crémilleux, Olivier Gandrillon, Jiri Klema & Jean-Luc Manguin (2015). "Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts". Journal of Biomedical Semantics, vol. 6, pp. 1-27. doi : 10.1186/s13326-015-0023-3. HAL : hal-01192959.
- Zayna Chaker, Saba Aïd, Hugues Berry & Martin Holzenberger (2015). "Suppression of IGF-I signals in neural stem cells enhances neurogenesis and olfactory function during aging". Aging Cell, pp. 847-856. doi : 10.1111/acel.12365. HAL : hal-01163564. .
- Yihui Cui, Vincent Paille, Hao Xu, Stéphane Genet, Bruno Delord, Elodie Fino, Hugues Berry & Laurent Venance (2015). "Endocannabinoids mediate bidirectional striatal spike-timing dependent plasticity". The Journal of Physiology, vol. 593, #13, pp. 2833-2849. doi : 10.1113/JP270324. HAL : hal-01141205. .
- Cyril Langlois, Thierry Douillard, Hui Yuan, Nicholas Blanchard, Armel Descamps-Mandine, Bertrand Van De Moortèle, Christophe Rigotti & Thierry Epicier (2015). "Crystal orientation mapping via ion channeling: An alternative to EBSD". Ultramicroscopy, vol. 157, pp. 65-72. doi : 10.1016/j.ultramic.2015.05.023. HAL : hal-01226846. .
- Ophélie Arnaud, Sam Meyer, Elodie Vallin, Guillaume Beslon & Olivier Gandrillon (2015). "Temperature-induced variation in gene expression burst size in metazoan cells". BMC Molecular Biology. doi : 10.1186/s12867-015-0048-2. HAL : hal-01248384.
- Conferences (11)
- International conferences with peer review (11)
- Charles Rocabert, Carole Knibbe & Guillaume Beslon (2015). "Towards a Integrated Evolutionary Model to Study Evolution of Evolution". EvoEvo Workshop (Satellite workshop of ECAL 2015), 24 juillet 2015, York (United Kingdom). HAL : hal-01252796. .
- Yoram Vadée-Le-Brun, Jonathan Rouzaud-Cornabas & Guillaume Beslon (2015). "Epigenetic inheritance speeds up evolution of artificial organisms". European Conference on Artificial Life, York (United Kingdom). doi : 10.7551/978-0-262-33027-5-ch078. HAL : hal-01248383. .
- Sergio Peignier, Christophe Rigotti & Guillaume Beslon (2015). "Subspace Clustering Using Evolvable Genome Structure". Genetic and Evolutionary Computation Conference (GECCO), 11 juillet 2015, Madrid (Spain), pp. 575-582. HAL : hal-01199136.
- Nicolas Méger, Christophe Rigotti & Catherine Pothier (2015). "Swap Randomization of Bases of Sequences for Mining Satellite Image Time Series". European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD), 11 septembre 2015, Porto (Portugal), pp. 190-205. HAL : hal-01200674.
- Youen Pericault, Catherine Pothier, Nicolas Meger, Christophe Rigotti, Flavien Vernier, Ha-Tai Pham & Emmanuel Trouvé (2015). "A swap randomization approach for mining motion field time series over the Argentiere glacier". 2015 8th International Workshop on the Analysis of Multitemporal Remote Sensing Images (Multi-Temp), 24 juillet 2015, Annecy (France), pp. 1-4. doi : 10.1109/Multi-Temp.2015.7245757. HAL : hal-01237206.
- Jérôme Gippet, Charles Rocabert, Serge Fenet, Adeline Dumet & Bernard Kaufmann (2015). "Modeling and evaluating human-mediated dispersal mechanisms at landscape scale: a study of road network and invasion parameters for Lasius neglectus ants invasive species". World Conference on Natural Resource Modeling, 1 juillet 2015, Bordeaux (France). HAL : hal-01242828. .
- Arnaud Lefray, Eddy Caron, Jonathan Rouzaud-Cornabas & Christian Toinard (2015). "Microarchitecture-Aware Virtual Machine Placement under Information Leakage Constraints". 8th IEEE International Conference on Cloud Computing (IEEE Cloud 2015), 2 juillet 2015, New-York (United States of America), pp. 588-595. doi : 10.1109/CLOUD.2015.84. HAL : hal-01240573. .
- Aline Bousquet, Jérémy Briffaut, Eddy Caron, Eva María Dominguez, Javier Franco, Arnaud Lefray, Oscar López, Saioa Ros, Jonathan Rouzaud-Cornabas et al. (2015). "Enforcing Security and Assurance Properties in Cloud Environment". 8th IEEE/ACM International Conference on Utility and Cloud Computing (UCC 2015), 10 décembre 2015, Limassol (Cyprus). HAL : hal-01240557. .
- Cyril Langlois, Thierry Douillard, Hui Yuan, Nicholas Blanchard, Armel Descamps-Mandine, Bertrand Van De Moortèle, Christophe Rigotti & Thierry Epicier (2015). "Crystal orientation mapping via ion channeling: an alternative to EBSD". Microscience Microscopy Congress 2015, 25 juin 2015, Manchester (United Kingdom). HAL : hal-02066168.
- Sergio Peignier, Christophe Rigotti & Guillaume Beslon (2015). "Subspace Clustering for all Seasons". EvoEvo Workshop (satellite workshop of ECAL 2015), 24 juillet 2015, york (United Kingdom), pp. 1-3. HAL : hal-01252793. .
- Cyril Langlois, Thierry Douillard, Hui Yuan, Nicholas Blanchard, Armel Descamps-Mandine, Bertrand Van De Moortèle, Christophe Rigotti, Thierry Epicier & Sébastien Dubail (2015). "Crystal Orientation Mapping using ion image series: iCHORD". EUROMAT, 20 septembre 2015, Warsaw (Poland). HAL : hal-02066188.
- Reports (6)
- Research reports/tecnical reports (6)
- Guillaume Beslon & Charles Rocabert (2015). "EvoEvo Deliverable 2.4". Research report. HAL : hal-01577140. .
- Guillaume Beslon & Charles Rocabert (2015). "EvoEvo Deliverable 2.2". Research report. HAL : hal-01577135. .
- Guillaume Beslon & Charles Rocabert (2015). "EvoEvo Deliverable 2.7". Research report. HAL : hal-01577147. .
- Guillaume Beslon & Charles Rocabert (2015). "EvoEvo Deliverable 2.6". Research report. HAL : hal-01577144. .
- Guillaume Beslon, Santiago F. Elena, Paulien Hogeweg, Dominique Schneider & Susan Stepney (2015). "EvoEvo Deliverable 6.5". Research report. HAL : hal-01577184. .
- Guillaume Beslon & Charles Rocabert (2015). "EvoEvo Deliverable 2.8". Research report. HAL : hal-01577149. .
- 2014 (24)
- Journals (13)
- International journals with peer review (13)
- Pierre-Nicolas Mougel, Christophe Rigotti, Marc Plantevit & Olivier Gandrillon (2014). "Finding maximal homogeneous clique sets". Knowledge and Information Systems (KAIS), vol. 39, #3, pp. 579-608. doi : 10.1007/s10115-013-0625-y. HAL : hal-00827164.
- Bérénice Batut, Carole Knibbe, Gabriel Marais & Vincent Daubin (2014). "Reductive genome evolution at both ends of bacterial population size spectrum". Nature Reviews Microbiology, vol. 12, #12, pp. 841-850. doi : 10.1038/nrmicro3331. HAL : hal-01092392.
- Guillaume Corre, Daniel Stockholm, Ophélie Arnaud, Gaël Kaneko, José Viñuelas, Yoshiaki Yamagata, Thi My Anh Neildez-Nguyen, Jean-Jacques Kupiec, Guillaume Beslon et al. (2014). "Stochastic Fluctuations and Distributed Control of Gene Expression Impact Cellular Memory". PLoS ONE, vol. 9, #12, e115574. doi : 10.1371/journal.pone.0115574. HAL : hal-01370311. .
- Jules Lallouette, Maurizio De Pittà, Eshel Ben-Jacob & Hugues Berry (2014). "The topology of astrocyte networks controls the propagation of intercellular calcium waves". BMC Neuroscience, vol. 15, Suppl 1, 205 (2 pages. HAL : hal-01026523. .
- Jules Lallouette, Maurizio De Pittà, Eshel Ben Jacob & Hugues Berry (2014). "Sparse short-distance connections enhance calcium wave propagation in a 3D model of astrocyte networks". Frontiers in Computational Neuroscience, vol. 8, 45 (18 pages. doi : 10.3389/fncom.2014.00045. HAL : hal-00967106. .
- Hédi Soula, Bertrand Caré, Guillaume Beslon & Hugues Berry (2014). "Comments to the Editor. Reply to the Comment by V.P. Shkilev on "Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium"". Biophysical Journal, vol. 106, #11, pp. 2544-2546. doi : 10.1016/j.bpj.2014.03.052. HAL : hal-00956603. .
- Maurizio De Pittà, Eshel Ben-Jacob & Hugues Berry (2014). "Astrocytic theory of working memory". BMC Neuroscience, vol. 15, Suppl 1, 206 (2 pages. HAL : hal-01026524. .
- Amanda Lo Van, Hédi Soula & Hugues Berry (2014). "Space-induced bifurcation in repression-based transcriptional circuits". BMC Systems Biology, vol. 8, 125 (14 pages. HAL : hal-01068558. .
- Sam Meyer & Guillaume Beslon (2014). "Torsion-Mediated Interaction between Adjacent Genes". PLoS Computational Biology, vol. 10, #9, e1003785. doi : 10.1371/journal.pcbi.1003785. HAL : hal-01090990. .
- Stephan Fischer, Samuel Bernard, Guillaume Beslon & Carole Knibbe (2014). "A Model for Genome Size Evolution". Bulletin of Mathematical Biology, vol. 76, #9, pp. 2249-2291. doi : 10.1007/s11538-014-9997-8. HAL : hal-01090984. .
- Gilad Wallach, Jules Lallouette, Nitzan Herzog, Maurizio De Pittà, Eshel Ben Jacob, Hugues Berry & Yael Hanein (2014). "Glutamate Mediated Astrocytic Filtering of Neuronal Activity". PLoS Computational Biology, vol. 12, #10, e1003964 (19 pages. doi : 10.1371/journal.pcbi.1003964. HAL : hal-01077738. .
- Hugues Berry & Hédi Soula (2014). "Spatial distributions at equilibrium under heterogeneous transient subdiffusion". Frontiers in Physiology, vol. 5, 437 (8 pages. doi : 10.3389/fphys.2014.00437. HAL : hal-01077735. .
- Hugues Berry & Hugues Chaté (2014). "Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes". Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, vol. 89, #2, 022708 (9 pages. doi : 10.1103/PhysRevE.89.022708. ArXiv : 1103.2206. HAL : inria-00575651. .
- Conferences (5)
- International conferences with peer review (4)
- Jeremie Naudé, Bruno Cessac, Hugues Berry & Bruno Delord (2014). "Effects of Cellular Homeostatic Intrinsic Plasticity on Dynamical and Computational Properties of Biological Recurrent Neural Networks". LACONEU 2014, 31 janvier 2014, Valparaiso (Chile), 1 page. HAL : hal-01095601.
- Carole Knibbe & David Parsons (2014). "What happened to my genes? Insights on gene family dynamics from digital genetics experiments". ALIFE 14 (14th Intl. Conf. on the Synthesis and Simulation of Living Systems), 30 juillet 2014, New York, NY (United States of America), pp. 33-40. doi : 10.7551/978-0-262-32621-6-ch006. HAL : hal-01093110.
- Felicity Lodge, Nicolas Meger, Christophe Rigotti, Catherine Pothier & Marie-Pierre Doin (2014). "Iterative Summarization of Satellite Image Time Series". IEEE International Geoscience and Remote Sensing Symposium (IGARSS 2014), Québec (Canada), pp. 1-4. HAL : hal-01091940.
- Eddy Caron & Jonathan Rouzaud-Cornabas (2014). "Improving Users' Isolation in IaaS: Virtual Machine Placement with Security Constraints". 7th IEEE International Conference on Cloud Computing (IEEE Cloud 2014), 2 juin 2014, Anchorage (United States of America), p. 8. doi : 10.1109/CLOUD.2014.19. HAL : hal-01240592. .
- National conferences with peer review (1)
- Christophe Rigotti, Felicity Lodge, Nicolas Méger, Catherine Pothier, Romain Jolivet & Cécile Lasserre (2014). "Monitoring of Tectonic Deformation by Mining Satellite Image Time Series". Reconnaissance de Formes et Intelligence Artificielle (RFIA) 2014, 4 juillet 2014, Rouen (France), pp. 1-6. HAL : hal-00988907. .
- Reports (6)
- Research reports/tecnical reports (6)
- Guillaume Beslon, Paul Andrews, Carole Knibbe & Charles Rocabert (2014). "EvoEvo Deliverable 2.1". Research report. HAL : hal-01577134. .
- Dominique Schneider, Guillaume Beslon, Santiago F. Elena & Otmane Lamrabet (2014). "EvoEvo Deliverable 1.1". Research report. HAL : hal-01577124. .
- Guillaume Beslon (2014). "EvoEvo Deliverable 6.1". Research report. HAL : hal-01577182. .
- Guillaume Beslon, Carole Knibbe & Charles Rocabert (2014). "EvoEvo Deliverable 2.5". Research report. HAL : hal-01577142. .
- Guillaume Beslon, Paulien Hogeweg, Carole Knibbe, Charles Rocabert & Susan Stepney (2014). "EvoEvo Deliverable 2.3". Research report. HAL : hal-01577138. .
- Guillaume Beslon, Santiago F. Elena & Dominique Schneider (2014). "EvoEvo Deliverable 6.2". Research report. HAL : hal-01577183. .
- 2013 (16)
- Journals (6)
- International journals with peer review (6)
- Hédi Soula, Bertrand Caré, Guillaume Beslon & Hugues Berry (2013). "Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium". Biophysical Journal, vol. 105, #9, pp. 2064-2073. doi : 10.1016/j.bpj.2013.07.023. ArXiv : 1207.5725. HAL : hal-00720515. .
- Bérénice Batut, David P. Parsons, Stephan Fischer, Guillaume Beslon & Carole Knibbe (2013). "In silico experimental evolution: a tool to test evolutionary scenarios". BMC Bioinformatics, vol. 14, Suppl 15, S11. HAL : hal-00873232. .
- Anne-Sophie Coquel, Jean-Pascal Jacob, Maël Primet, Alice Demarez, Mariella Dimiccoli, Thomas Julou, Lionel Moisan, Ariel Lindner & Hugues Berry (2013). "Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect". PLoS Computational Biology, vol. 9, #4, e1003038 (14 pages. doi : 10.1371/journal.pcbi.100303. ArXiv : 1303.1904. HAL : hal-00798053. .
- Jérémie Naudé, Bruno Cessac, Hugues Berry & Bruno Delord (2013). "Effects of Cellular Homeostatic Intrinsic Plasticity on Dynamical and Computational Properties of Biological Recurrent Neural Networks.". Journal of Neuroscience, vol. 33, #38, pp. 15032-15043. doi : 10.1523/JNEUROSCI.0870-13.2013. HAL : hal-00844218. .
- Bertrand R Caré & Hédi A Soula (2013). "Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime.". Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, vol. 87, #1, p. 012720. doi : 10.1103/PhysRevE.87.012720. HAL : hal-00858439. .
- José Viñuelas, Gaël Kaneko, Antoine Coulon, Elodie Vallin, Valérie Morin, Camila Mejia-Pous, Jean-Jacques Kupiec, Guillaume Beslon & Olivier Gandrillon (2013). "Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.". BMC Biology, vol. 11, #1, p. 15. doi : 10.1186/1741-7007-11-15. HAL : inserm-00817963. .
- Conferences (5)
- International conferences with peer review (3)
- Yihui Cui, Vincent Paille, Bruno Delord, Stéphane Genet, Elodie Fino, Laurent Venance & Hugues Berry (2013). "Endocannabinoids mediate spike-timing dependent potentiation and depression: a model-based experimental approach". the Twenty Second Annual Computational Neuroscience Meeting: CNS*2013, 13 juillet 2013, Paris (France), O1 (2 pages. doi : 10.1186/1471-2202-14-S1-O1. HAL : inserm-00842298. .
- Guillaume Beslon, Bérénice Batut, David P. Parsons, Dominique Schneider & Carole Knibbe (2013). "An alife game to teach evolution of antibiotic resistance". ECAL - 12th European Conference on Artificial Life - 2013, 6 septembre 2013, Taormina (Italy), pp. 43-50. HAL : hal-00849345.
- Bérénice Batut, David P. Parsons, Stephan Fischer, Guillaume Beslon & Carole Knibbe (2013). "In silico experimental evolution: a tool to test evolutionary scenarios". 11th RECOMB - Comparative Genomics 2013, 19 octobre 2013, Villeurbane (France). HAL : hal-04764366.
- National conferences with peer review (2)
- Felicity Lodge, Nicolas Meger, Christophe Rigotti, Lionel Gueguen, Catherine Pothier, Remi Andreoli, Marie-Pierre Doin & Mihai Datcu (2013). "GFS-pattern extraction in satellite image time series: application to the monitoring of Mount Etna". Atelier Mesure de Déformations par Imagerie Spatiale, 17 octobre 2013, Autrans (France), pp. 1-1. HAL : hal-01339287.
- Christophe Rigotti, Nicolas Meger, Felicity Lodge & Catherine Pothier (2013). "Fouille de données spatio-temporelles appliquée aux séries d'images satellite". Cité des Sciences et de l'Industrie - Rencontres du Numérique de l'ANR, 17 avril 2013, Paris (France). HAL : hal-01339286.
- HDR, thesis (1)
- Thesis (1)
- Gaël Kaneko (2013). "Analyse et modélisation de la stochasticité de l'expression génique dans des cellules eucaryotes". HAL : tel-00926607. .
- Book edition (books, chapters, seminars, congress, special numbers) (3)
- Hugues Berry & Guillaume Beslon (2013). "De la modélisation comme poésie. La modélisation de systèmes biologiques complexes vue par deux modélisateurs". Modéliser & simuler. Epistémologies et pratiques de la modélisation et de la simulation, Franck Varenne and Marc Silberstein, Editions Matériologiques, Paris. HAL : hal-00815550.
- Hugues Berry (2013). "Modélisation de la diffusion-réaction dans les milieux intracellulaires encombrés". Le vivant discret et continu, Glade, Nicolas and Stéphanou, Angélique, Editions Matériologiques, pp. 241-266. HAL : hal-00858738.
- Carole Knibbe (2013). "L'évolution expérimentale in silico". Modéliser et simuler - Epistémologies et pratiques de la modélisation et de la simulation - Tome 1, Franck Varenne and Marc Silberstein, Editions Matériologiques, pp. 581-610. HAL : hal-00850175.
- Others (1)
- Yihui Cui, Vincent Paille, Bruno Delord, Stéphane Genet, Elodie Fino, Laurent Venance & Hugues Berry (2013). "Endocannabinoids mediate spike-timing dependent potentiation and depression: a model-based experimental approach". Twenty Second Annual Computational Neuroscience Meeting : CNS 2013, 18 juillet 2013, Paris (France). Poster. HAL : hal-00842299. .
- 2012 (21)
- Journals (7)
- International journals with peer review (7)
- Olivier Gandrillon, Delphine Kolesnik-Antoine, Jean-Jacques Kupiec & Guillaume Beslon (2012). "Chance at the heart of the cell". Progress in Biophysics and Molecular Biology, vol. 110, #1, pp. 1-4. doi : 10.1016/j.pbiomolbio.2012.05.006. HAL : hal-00720052.
- José Viñuelas, Gaël Kaneko, Antoine Coulon, Guillaume Beslon & Olivier Gandrillon (2012). "Towards experimental manipulation of stochasticity in gene expression.". Progress in Biophysics and Molecular Biology, vol. 100, #1, epub ahead of print. doi : 10.1016/j.pbiomolbio.2012.04.010. HAL : hal-00720054.
- Sebastian Grauwin, Guillaume Beslon, Eric Fleury, Sara Franceschelli, Céline Robardet, Jean-Baptiste Rouquier & Pablo Jensen (2012). "Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity". Journal of the American Society for Information Science and Technology, vol. 63, #7, 10.1002/asi.22644. doi : 10.1002/asi.22644. ArXiv : 1206.2216. HAL : hal-00706567. .
- Andreea Julea, Nicolas Méger, Christophe Rigotti, Emmanuel Trouvé, Romain Jolivet & Philippe Bolon (2012). "Efficient Spatiotemporal Mining of Satellite Image Time Series for Agricultural Monitoring". Transactions on Machine Learning and Data Mining, vol. 5, #1, pp. 23-44. HAL : hal-00702433.
- Thomas Hindré, Carole Knibbe, Guillaume Beslon & Dominique Schneider (2012). "New insights into bacterial adaptation through in vivo and in silico experimental evolution". Nature Reviews Microbiology, vol. 10, #5, pp. 352-365. doi : 10.1038/nrmicro2750. HAL : hal-00696231.
- Hédi Soula, Antoine Coulon & Guillaume Beslon (2012). "Membrane microdomains emergence through non-homogeneous diffusion.". BMC Biophysics, vol. 5, #1, p. 6. doi : 10.1186/2046-1682-5-6. HAL : inserm-00768564. .
- Maurizio De Pittà, Vladislav Volman, Hugues Berry, Vladimir Parpura, Andrea Volterra & Eshel Ben-Jacob (2012). "Computational quest for understanding the role of astrocyte signaling in synaptic transmission and plasticity". Frontiers in Computational Neuroscience, vol. 6, #98, 98 (25 pages. doi : 10.3389/fncom.2012.00098. HAL : hal-00762313. .
- Conferences (9)
- International conferences with peer review (9)
- Bertrand Caré & Hedi Soula (2012). "The Effect of Membrane Receptor Clustering on Spatio- temporal Cell Signalling Dynamics". Proceedings of the 9th International Conference on Information Processing in Cells and Tissues 2012, Cambridge (United Kingdom), pp. 50-61. doi : 10.1007/978-3-642-28792-3_8. HAL : hal-00759519.
- David Parsons, Carole Knibbe & Guillaume Beslon (2012). "The Paradoxical Effects of Allelic Recombination on Fitness". Proceedings of Artificial Life XIII, 22 juillet 2012, East Lansing (France), pp. 536-537. HAL : hal-00759142.
- Jules Lallouette & Hugues Berry (2012). "Topology drives calcium wave propagation in 3d astrocyte network". Proceedings of the European Conference on Complex Systems 2012, 3 septembre 2012, Bruxelles (Belgium), pp. 453-463. doi : 10.1007/978-3-319-00395-5_56. HAL : hal-01339151.
- Pierre-Nicolas Mougel, Christophe Rigotti & Olivier Gandrillon (2012). "Finding Collections of Protein Modules in Protein-Protein Interaction Networks". Bioinformatics and Computational Biology (BICoB), Las Vegas (United States of America), pp. 216-222. HAL : hal-00758858.
- Jules Lallouette & Hugues Berry (2012). "Topology drives calcium wave propagation in 3D astrocyte networks". European Conference on Complex Systems 2012, Bruxelles (Belgium), pp. 453-463. HAL : hal-00758998. .
- Dusan Misevic, Antoine Frenoy, David Parsons & Francois Taddei (2012). "Effects of public good properties on the evolution of cooperation". Proceedings of Artificial Life XIII, 22 juillet 2012, East Lansing (United States of America), pp. 218-225. HAL : hal-00759140.
- Pierre-Nicolas Mougel, Christophe Rigotti & Olivier Gandrillon (2012). "Finding Collections of k-Clique Percolated Components in Attributed Graphs". Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Kuala Lumpur (Malaysia), pp. 181-192. HAL : hal-00758843.
- Nicolas Meger, Christophe Rigotti, Lionel Gueguen, Felicity Lodge, Catherine Pothier, Remi Andreoli & Mihai Datcu (2012). "Normalized Mutual Information-Based Ranking of Spatio-Temporal Localization Maps". 8th European Spatial Agency (ESA) - EUSC - JRC Conference on Image Information Mining, 24 octobre 2012, Oberpfaffenhofen (Germany), pp. 11-14. HAL : hal-01353105.
- Bertrand Caré & Hedi Soula (2012). "Impact of Receptor clustering on the membrane-based stage of a signalling pathway". BICOB, Las Vegas (United States of America). HAL : hal-00759520.
- HDR, thesis (3)
- Thesis (3)
- Pierre-Nicolas Mougel (2012). "Finding homogeneous collections of dense subgraphs using constraint-based data mining approaches". HAL : tel-00858751. .
- Bertrand Caré (2012). "Individual-based models for the functional impact of signalling proteins spatial distribution and diffusion heterogeneity". HAL : tel-00858499. .
- Anne-Sophie Coquel (2012). "Dynamique de l'agrégation protéique chez la bactérie Escherichia coli". HAL : tel-00778887. .
- Others (2)
- Jules Lallouette, Mati Goldberg, Maurizio De Pittà, Eshel Ben-Jacob & Hugues Berry (2012). "The remarkable effect of network topology on calcium wave propagation in astrocyte networks". Multidisciplinary approaches to quantify astrocyte neuron signaling, 14 juillet 2012, Barcelona (Spain). Poster. HAL : hal-00759232. .
- Bérénice Batut, Mathilde Dumond, Gabriel Marais, Guillaume Beslon & Carole Knibbe (2012). "Simulating evolutionary scenarios to test whether they can induce reductive evolution". SMBE 2012 : Society for Molecular Biology and Evolution, 26 juin 2012, Dublin (Ireland). Poster. HAL : hal-00762597.
- 2011 (15)
- Journals (6)
- International journals with peer review (5)
- Vic Norris, Abdallah Zemirline, Patrick Amar, Jean Nicolas Audinot, Pascal Ballet, Eshel Ben-Jacob, Gilles Bernot, Guillaume Beslon, Armelle Cabin et al. (2011). "Computing with bacterial constituents, cells and populations: from bioputing to bactoputing". Theorie in den Biowissenschaften / Theory in Biosciences, vol. 130, #3, pp. 211-228. doi : 10.1007/s12064-010-0118-4. HAL : hal-00643738.
- Bertrand Caré & Hédi Soula (2011). "Impact of receptor clustering on ligand binding.". BMC Systems Biology, vol. 5, #1, p. 48. doi : 10.1186/1752-0509-5-48. HAL : inserm-00663665. .
- Andreea Julea, Nicolas Méger, Philippe Bolon, Christophe Rigotti, Marie-Pierre Doin, Cécile Lasserre, Emmanuel Trouvé & Vasile N. Lazarescu (2011). "Unsupervised Spatiotemporal Mining of Satellite Image Time Series Using Grouped Frequent Sequential Patterns". IEEE Transactions on Geoscience and Remote Sensing, vol. 49, #4, pp. 1417-1430. doi : 10.1109/TGRS.2010.2081372. HAL : hal-00596806.
- Antoine Coulon, Guillaume Beslon & Hédi Soula (2011). "Enhanced Stimulus Encoding Capabilities with Spectral Selectivity in Inhibitory Circuits by STDP". Neural Computation, vol. 23, #4, pp. 882-908. HAL : inria-00593704.
- Hugues Berry & Nazim Fatès (2011). "Robustness of the Critical Behaviour in the Stochastic Greenberg-Hastings Cellular Automaton Model". International Journal of Unconventional Computing, vol. 7, 1-2, pp. 65-85. HAL : inria-00598379.
- National journals with peer review (1)
- Eric Bertin, Guillaume Beslon, Olivier Gandrillon, Sebastian Grauwin, Pablo Jensen & Nicolas Schabanel (2011). "Les complexités : point de vue d'un institut des systèmes complexes". Hermès, La Revue - Cognition, communication, politique, vol. 2, #60, pp. 145-150. doi : 10.4267/2042/45459. HAL : hal-00744520.
- Conferences (6)
- International conferences with peer review (5)
- Carole Knibbe, David P. Parsons & Guillaume Beslon (2011). "Parsimonious modeling of scaling laws in genomes and transcriptomes". Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems (ECAL 11), 8 août 2011, Paris (France), pp. 414-415. HAL : hal-00696870.
- Nicolas Méger, Romain Jolivet, Cécile Lasserre, Emmanuel Trouvé, Christophe Rigotti, Felicity Lodge, M. P. Doin, Stéphane Guillaso, Andreea Julea & Philippe Bolon (2011). "Spatio-Temporal Mining of ENVISAT SAR Interferogram Time Series over the Haiyuan Fault in China". 2011 6th International Workshop on the Analysis of Multi-temporal Remote Sensing Images (Multi-Temp), 14 juillet 2011, Trento (Italy), 10.1109/Multi-Temp.2011.6005067. doi : 10.1109/Multi-Temp.2011.6005067. HAL : hal-00621236.
- Andreea Julea, Nicolas Méger, Christophe Rigotti, Emmanuel Trouvé, Philippe Bolon & Vasile Lazarescu (2011). "Mining Pixel Evolutions in Satellite Image Time Series for Agricultural Monitoring". 11th Industrial Conference on Data Mining ICDM 2011, 3 septembre 2011, New-York (United States of America), pp. 189-203. doi : 10.1007/978-3-642-23184-1_15. HAL : hal-00620882.
- Andreea Julea, Fernanda Ledo, Nicolas Méger, Emmanuel Trouvé, Philippe Bolon, Christophe Rigotti, Renaud Fallourd, Jean-Marie Nicolas, Gabriel Vasile et al. (2011). "Polsar Radarsat-2 Satellite Image Time Series Mining Over the Chamonix Mont-Blanc Test Site". IGARSS 2011 - IEEE International Geoscience and Remote Sensing Symposium, 29 juillet 2011, Vancouver (Canada), pp 1191-1194. HAL : hal-00620881.
- David Parsons, Carole Knibbe & Guillaume Beslon (2011). "Homologous and Nonhomologous Rearrangements: Interactions and Effects on Evolvability.". Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems (ECAL 11), 8 août 2011, Paris (France), pp. 622-629. HAL : hal-00696902.
- National conferences with peer review (1)
- Pierre-Nicolas Mougel, Marc Plantevit, Christophe Rigotti, Olivier Gandrillon & Jean-François Boulicaut (2011). "Extraction sous Contraintes d'Ensembles de Cliques Homogènes". 11eme Conference Francophone sur l'Extraction et la Gestion des Connaissances (EGC'11), Brest (France), pp. 1-12. HAL : hal-00744808.
- HDR, thesis (1)
- Thesis (1)
- David Parsons (2011). "Sélection indirecte en évolution Darwinienne : Mécanismes et implications". HAL : tel-00715781. .
- Others (2)
- José Viñuelas, Gaël Kaneko, Valérie Morin, Elodie Vallin, Antoine Coulon, Camila Meijia-Pous, Guillaume Beslon & Olivier Gandrillon (2011). "Chromatin is a major player in regulating gene expression stochasticity in higher eukaryotic cells". Stochastic Systems Biology conference, 19 juillet 2011, Ascona (Switzerland). Poster. HAL : hal-01354566.
- François Smekens, Jean-Michel Létang, Nicolas Freud, Bruno Sixou & Guillaume Beslon (2011). "Optimization of proton therapy ballistics using a genetic algorithm". Particle Therapy Co-Operative Group, PTCOG, 8 mai 2011, Philadelphia (US) (United States of America). Poster. HAL : hal-01354428.
- 2010 (8)
- Journals (3)
- International journals with peer review (3)
- Antoine Coulon, Olivier Gandrillon & Guillaume Beslon (2010). "On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter.". BMC Systems Biology, vol. 4, p. 2. doi : 10.1186/1752-0509-4-2. HAL : hal-00542455. .
- Guillaume Beslon, David Parsons, Yolanda Sanchez-Dehesa, Jose-Maria Peña & Carole Knibbe (2010). "Scaling Laws in Bacterial Genomes: A Side-Effect of Selection of Mutational Robustness". BioSystems, vol. 102, #1, pp. 32-40. doi : 10.1016/j.biosystems.2010.07.009. HAL : inria-00593709.
- Guillaume Beslon, David P. Parsons, Jose-Maria Pena, Christophe Rigotti & Yolanda Sanchez-Dehesa (2010). "From Digital Genetics to Knowledge Discovery: Perspectives in Genetic Network Understanding". Intelligent Data Analysis, vol. 14, #2, pp. 173-191. doi : 10.3233/IDA-2010-0415. HAL : hal-00697024.
- Conferences (5)
- International conferences with peer review (2)
- Andreea Julea, Nicolas Méger, Christophe Rigotti, M. -P. Doin, Cécile Lasserre, Emmanuel Trouvé, Philippe Bolon & Vasile Lazarescu (2010). "Extraction of Frequent Grouped Sequential Patterns from Satellite Image Time Series". IEEE International Geoscience and Remote Sensing Symposium, IGARSS 2010., 30 juillet 2010, Honolulu (United States of America), p. 4. HAL : hal-00520601.
- David P. Parsons, Carole Knibbe & Guillaume Beslon (2010). "Importance of the rearrangement rates on the organization of transcription.". Proceedings of Artificial Life XII, 19 août 2010, Odense (Denmark), pp. 479-486. HAL : hal-00697043.
- National conferences with peer review (3)
- David P. Parsons, Carole Knibbe & Guillaume Beslon (2010). "Aevol : un modèle individu-centré pour l’étude de la structuration des génomes". MajecSTIC, 13 octobre 2010, Bordeaux (France), inconnue. HAL : hal-01381560.
- David P. Parsons, Carole Knibbe & Guillaume Beslon (2010). "Influence of the rearrangement rates on the organization of genome transcription". JOBIM, 7 juin 2010, Montpellier (France), inconnue. HAL : hal-01381518.
- David P. Parsons, Carole Knibbe & Guillaume Beslon (2010). "Influence of the rearrangement rates on the organization of genome transcription". Integrative Post-Genomics, 25 novembre 2010, Lyon (France), inconnue. HAL : hal-01381618.
- 2009 (4)
- Journals (1)
- International journals with peer review (1)
- Thierry Charnois, Marc Plantevit, Christophe Rigotti & Bruno Crémilleux (2009). "Fouille de données séquentielles pour l'extraction d'information dans les textes". Revue TAL : traitement automatique des langues, pp. 59-87. HAL : hal-01011618. .
- Conferences (2)
- International conferences with peer review (1)
- Guillaume Beslon, Yolanda Sanchez-Dehesa, David P. Parsons, Jose Maria Pena & Carole Knibbe (2009). "Scaling Laws in Digital Organisms". Proc. Information Processing in Cells and Tissues IPCAT'09, 5 avril 2009, Ascona (Switzerland), pp. 111-114. HAL : hal-01437632.
- National conferences with peer review (1)
- David P. Parsons, Guillaume Beslon, Carole Knibbe, Yolanda Sanchez-Dehesa & Jose Maria Pena (2009). "Evolution of scaling laws in artificial regulation networks". Integrative Post-Genomics, 18 novembre 2009, Lyon (France), pp. 22-22. HAL : hal-01437814.
- Others (1)
- José Viñuelas, Gaël Kaneko, Antoine Coulon, Guillaume Beslon & Olivier Gandrillon (2009). "Relationship between chromosomal features and gene expression stochasticity in higher eukaryotic cells". Integrative Post-Genomics, 18 novembre 2009, Lyon (France). Poster. HAL : hal-01437813.
- 2008 (11)
- Journals (2)
- National journals with peer review (2)
- C. Knibbe, J. M. Fayard & Guillaume Beslon (2008). "The topology of the protein network influences the dynamics of gene order: from systems biology to a systemic understanding of evolution". Artificial Life, vol. 14, #1, pp. 149-156. doi : 10.1162/artl.2008.14.1.149. HAL : hal-00391448.
- Antoine Coulon, Guillaume Beslon & Olivier Gandrillon (2008). "Large multiprotein structures modeling and simulation: the need for mesoscopic models.". Methods in Molecular Biology, vol. 484, pp. 537-58. doi : 10.1007/978-1-59745-398-1_32. HAL : hal-00294029.
- Conferences (8)
- National conferences with peer review (8)
- Guillaume Beslon (2008). "Evolution of genome structure : a computational approach". Workshop “Evolutionary Dynamics”, Utrecht (Netherlands). HAL : hal-01615228.
- Virginie Lefort & Guillaume Beslon (2008). "Optimisation incrémentale de réseaux de neurones RBF pour la régression via un algorithme évolutionnaire : RBF-Gene". Actes 8° Journées Francophones Extraction et Gestion des Connaissances EGC'08, 1 février 2008, Sophia-Antipolis (France), pp. 331-336. HAL : hal-01614293.
- Antoine Coulon (2008). "Dynamique de la régulation transcriptionnelle et stochasticité de l'expression génique". Séminaires de l'institut du thorax, Nantes (France). HAL : hal-01585257.
- Guillaume Beslon, Yolanda Sanchez-Dehesa & Jose Maria Pena (2008). "Modeling evolution of genetic regulation in artificial bacteria". European Conference on Complex Systems, 19 septembre 2008, Jérusalem (Israel), p. 4. HAL : hal-01614302.
- Antoine Coulon (2008). "Stochasticité de l'expression génique et dynamique des complexes de régulation". Biomaths seminar, Lyon (France). HAL : hal-01585208.
- Guillaume Beslon, Sara Franceschelli & Carole Knibbe (2008). "Petits bricolages en évolution". "Génies de la Bricole et du Bricolage", colloque en hommage à Claude Levy-Strauss, 28 novembre 2008, Lyon (France). HAL : hal-01614309.
- Antoine Coulon (2008). "Stochasticité de l'expression génique et dynamique des complexes de régulation". Seminar of the Symbiose project, Rennes (France). HAL : hal-01585198.
- Antoine Coulon (2008). "Mécanismes moléculaires de la stochasticité de l'expression des gènes". Le hasard au coeur de la cellule, 22 janvier 2008, Paris (France). HAL : hal-01585195.
- Others (1)
- Hédi Soula & Guillaume Beslon (2008). "Modeling membrane micro-domain formation through inhomogeneous diffusion". Integrative Post-Genomics, IPG'08, 21 novembre 2008, Lyon (France). Poster. HAL : hal-01614515.
- 2007 (9)
- Journals (1)
- National journals with peer review (1)
- Antoine Coulon, Hédi Soula, Olivier Mazet, Olivier Gandrillon & Guillaume Beslon (2007). "Modélisation cellulaire pour l'émergence de structures multiprotéiques auto-organisées". Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, vol. 26, pp. 123-148. doi : 10.3166/tsi.26.123-148. HAL : hal-01613745.
- Conferences (7)
- International conferences with peer review (2)
- Yolanda Sanchez-Dehesa, Jose Maria Pena & Guillaume Beslon (2007). "Generating Data form the Evolution of Artificial Regulatory Networks". Workshop Data Mining in Functional Genomics and Proteomics. Current Trends and Future Directions co-located with ECML/PKDD 07, 21 septembre 2007, Varsovie (Poland), pp. 91-103. HAL : hal-01613779.
- Gaël Kaneko, Carole Knibbe & Guillaume Beslon (2007). "Effect of bottlenecks on genome size: investigations by digital genetics". Integrative Post-Genomics, 28 novembre 2007, Lyon (France). HAL : hal-01596355.
- National conferences with peer review (5)
- Yolanda Sanchez-Dehesa, Jose Maria Pena & Guillaume Beslon (2007). "RAevol, un modèle de génétique digitale des réseaux de régulation". Réseaux d'Interactions : Analyse, Modélisation, Simulation, RIAMS 2007, 28 novembre 2007, Lyon (France). HAL : hal-01613852.
- Guillaume Beslon (2007). "Digital Genetics: Modéliser la dynamique évolutive des génomes". Journées communes des clusters environnement et informatique à l'INRIA Montbonnot, Grenoble (France). HAL : hal-01615201.
- Antoine Coulon (2007). "Vers des modèles multi-agents à l'échelle moléculaire". Session publique de l'Atelier Épigénèse, Programme d'épigenomique, Evry (France). HAL : hal-01585098.
- Guillaume Beslon (2007). "Systems Biology, where is the network ?". Santa-Fe Institute, Santa-Fe (United States of America). HAL : hal-01615180.
- Guillaume Beslon (2007). "Evolution de Second Ordre : le hasard sélectionné.". Spring school on interdisciplinarity in biology "Hasard et Fluctuations en Biologie", Berder (France). HAL : hal-01615166.
- Others (1)
- Antoine Coulon, Guillaume Beslon & Olivier Gandrillon (2007). "Binding cooperation and competition among transcription factors can cause complex stochastic properties in gene expression". Integrative Post-Genomics, IPG'07, 29 novembre 2007, Lyon (France). Poster. HAL : hal-01613869.
- 2006 (3)
- Journals (1)
- International journals with peer review (1)
- Wolfgang Banzhaf, Guillaume Beslon, Stephen Christensen, A. James, François Képès, Virginie Lefort, F. Julian, Miroslav Radman & Jeremy J. Ramsden (2006). "Guidelines: From artificial evolution to computational evolution: a research agenda". Nature Reviews Genetics, vol. 7, #9, pp. 729-735. doi : 10.1038/nrg1921. HAL : hal-00793902.
- Conferences (2)
- National conferences with peer review (2)
- Guillaume Beslon (2006). "Evolution et Robustesse : un équilibre complexe aux conséquences inattendues.". Journées de Gerland "Systèmes complexes et biologie", 12 décembre 2006, Lyon (France). HAL : hal-01615165.
- Guillaume Beslon (2006). "Multi-Agent Modeling of Nuclear Structures.". Spring workshop on biological systems modeling, Bombannes (France). HAL : hal-01615151.
Title | Type de projet | Dates contrat | Partenaire(s) |
---|---|---|---|
Covid Dynamics | Institutions | 2020 - 2021 | Hospices Civils de Lyon, Laboratoire de Biométrie et Biologie Evolutive, Laboratoire de Mécanique des Fluides et d’Acoustique, Institut Camille Jordan, Laboratoire de Tribologie et Dynamique des Systèmes, Laboratoire de Sciences Actuarielle et Financière |