Bibliography

• 1H. Berry, N. Fatès.
  
  Robustness of the critical behavior in the stochastic Greenberg-Hastings cellular automaton model, in: Int. J. Unconv. Comput., 2011, vol. 7, n^o 1–2, p. 65-85.
• 2E. Bertin, G. Beslon, O. Gandrillon, S. Grauwin, P. Jensen, N. Schabanel.
  
  Les complexités : point de vue d'un institut des systèmes complexes, in: Hermès, June 2011, n^o 60, p. 145–150.
  
  http://liris.cnrs.fr/publis/?id=5283
• 3B. Care, H. A. Soula.
  
  Impact of receptor clustering on ligand binding, in: BMC Systems Biology, March 2011, vol. 5, n^o 48, 13 p. p, PMID: 21453460. [ DOI : 10.1186/1752-0509-5-48 ]
  
  http://www.ncbi.nlm.nih.gov/pubmed/21453460
• 4A. Coulon, G. Beslon, H. A. Soula.
  
  Enhanced Stimulus Encoding Capabilities with Spectral Selectivity in Inhibitory Circuits by STDP, in: Neural Computation, April 2011, vol. 23, n^o 4, p. 882–908.
  
  http://liris.cnrs.fr/publis/?id=4836
• 5M. De Pittà, V. Volman, H. Berry, E. Ben-Jacob.
  
  A tale of two stories: astrocyte regulation of synaptic depression and facilitation, in: PLoS Computational Biology, 2011, vol. 7, n^o 12, e1002293 p.
• 6T. Hindre, C. Knibbe, G. Beslon, D. Schneider.
  
  New insights into bacterial adaptive abilities by in vivo and in silico experimental evolution, in: Nature Reviews Microbiology, 2011, to appear.
• 7A. Julea, N. Meger, C. Rigotti, E. Trouve, R. Jolivet, P. Bolon.
  
  Efficient Spatiotemporal Mining of Satellite Image Time Series for Agricultural Monitoring, in: Transactions on Machine Learning and Data Mining, 2011, vol. 4, n^o 2, p. 75–97.
• 8C. Knibbe, D. P. Parsons, G. Beslon.
  
  Parsimonious modeling of scaling laws in genomes and transcriptomes, in: European Conference on Artificial Life (ECAL), MIT Press, 2011, p. 414–415.
• 9J. Naudé, J. Paz, H. Berry, B. Delord.
  
  A theory of rate coding control by intrinsic plasticity effects, in: PloS Computational Biology, 2011, to appear.
• 10D. P. Parsons, C. Knibbe, G. Beslon.
  
  Homologous and nonhomologous rearrangements: Interactions and effects on evolvability, in: European Conference on Artificial Life (ECAL), MIT Press, 2011, p. 622–629.

Doctoral Dissertations and Habilitation Theses

• 11D. P. Parsons.
  
  Selection indirecte en Évolution Darwinienne : Mécanismes et Implications, PhD Thesis, Institut National des Sciences Appliquées de Lyon, 2011.

Articles in International Peer-Reviewed Journal

• 12H. Berry, N. Fatès.
  
  Robustness of the critical behavior in the stochastic Greenberg-Hastings cellular automaton model, in: Int. J. Unconv. Comput., 2011, vol. 7, n^o 1–2, p. 65-85.
• 13N. Bessonov, F. Crauste, S. Fisher, P. Kurbatova, V. Volpert.
  
  Application of Hybrid Models to Blood Cell Production in the Bone Marrow, in: Math. Model. Nat. Phenom., 2011, vol. 6, n^o 7, p. 2-12.
  
  http://hal.inria.fr/hal-00649217/en
• 14B. Care, H. A. Soula.
  
  Impact of receptor clustering on ligand binding, in: BMC Systems Biology, March 2011, vol. 5, n^o 48, 13 p. p, PMID: 21453460. [ DOI : 10.1186/1752-0509-5-48 ]
  
  http://www.ncbi.nlm.nih.gov/pubmed/21453460
• 15A. Coulon, G. Beslon, H. A. Soula.
  
  Enhanced Stimulus Encoding Capabilities with Spectral Selectivity in Inhibitory Circuits by STDP, in: Neural Computation, April 2011, vol. 23, n^o 4, p. 882–908.
  
  http://liris.cnrs.fr/publis/?id=4836
• 16M. De Pittà, V. Volman, H. Berry, E. Ben-Jacob.
  
  A tale of two stories: astrocyte regulation of synaptic depression and facilitation, in: PLoS Computational Biology, 2011, vol. 7, n^o 12, e1002293 p.
• 17T. Hindre, C. Knibbe, G. Beslon, D. Schneider.
  
  New insights into bacterial adaptive abilities by in vivo and in silico experimental evolution, in: Nature Reviews Microbiology, 2011, to appear.
• 18A. Julea, N. Meger, P. Bolon, C. Rigotti, M.-P. Doin, C. Lasserre, E. Trouve, V. Lazarescu.
  
  Unsupervised Spatiotemporal Mining of Satellite Image Time Series using Grouped Frequent Sequential Patterns, in: IEEE Transactions on Geoscience and Remote Sensing, 2011, vol. 49, n^o 4, p. 1417–1430.
• 19A. Julea, N. Meger, C. Rigotti, E. Trouve, R. Jolivet, P. Bolon.
  
  Efficient Spatiotemporal Mining of Satellite Image Time Series for Agricultural Monitoring, in: Transactions on Machine Learning and Data Mining, 2011, vol. 4, n^o 2, p. 75–97.
• 20J. Naudé, J. Paz, H. Berry, B. Delord.
  
  A theory of rate coding control by intrinsic plasticity effects, in: PloS Computational Biology, 2011, to appear.

Articles in National Peer-Reviewed Journal

• 21E. Bertin, G. Beslon, O. Gandrillon, S. Grauwin, P. Jensen, N. Schabanel.
  
  Les complexités : point de vue d'un institut des systèmes complexes, in: Hermès, June 2011, n^o 60, p. 145–150.
  
  http://liris.cnrs.fr/publis/?id=5283

International Conferences with Proceedings

• 22A. Hashmi, H. Berry, O. Temam, M. Lipasti.
  
  Automatic Abstraction and Fault Tolerance in Cortical Microachitectures, in: 38th ACM/IEEE International Symposium on Computer Architecture, ISCA 2011, San Jose, CA, USA, June 2011, 10 p. p.
• 23A. Julea, L. Fernanda, N. Meger, E. Trouve, P. Bolon, C. Rigotti, R. Fallourd, J.-M. Nicolas, G. Vasile, O. Harant, L. Ferro-Famil.
  
  Polsar Radarsat-2 Satellite Image Time Series Mining Over the Chamonix Mont-Blanc Test Site, in: Proceedings of the IEEE International Geoscience and Remote Sensing Symposium (IGARSS 2011), Vancouver, Canada, July 2011, p. pp 1191-1194.
  
  http://hal.archives-ouvertes.fr/hal-00620881/en/
• 24A. Julea, N. Meger, C. Rigotti, E. Trouve, P. Bolon, V. Lazarescu.
  
  Mining pixel evolutions in satellite image time series for agricultural monitoring, in: Proceedings of the 11th international conference on Advances in data mining: applications and theoretical aspects, Berlin, Heidelberg, ICDM'11, Springer-Verlag, 2011, p. 189–203.
  
  http://dl.acm.org/citation.cfm?id=2033796.2033815
• 25C. Knibbe, D. P. Parsons, G. Beslon.
  
  Parsimonious modeling of scaling laws in genomes and transcriptomes, in: European Conference on Artificial Life (ECAL), MIT Press, 2011, p. 414–415.
• 26N. Meger, R. Jolivet, C. Lasserre, E. Trouve, C. Rigotti, F. Lodge, M.-P. Doin, S. Guillaso, A. Julea, P. Bolon.
  
  Spatio-Temporal Mining of ENVISAT SAR Interferogram Time Series over the Haiyuan Fault in China, in: 2011 6th International Workshop on the Analysis of Multi-temporal Remote Sensing Images (Multi-Temp), Trento, Italie, August 2011, p. 10.1109/Multi-Temp.2011.6005067. [ DOI : 10.1109/Multi-Temp.2011.6005067 ]
  
  http://hal.archives-ouvertes.fr/hal-00621236/en/
• 27D. P. Parsons, C. Knibbe, G. Beslon.
  
  Homologous and nonhomologous rearrangements: Interactions and effects on evolvability, in: European Conference on Artificial Life (ECAL), MIT Press, 2011, p. 622–629.

National Conferences with Proceeding

• 28P.-N. Mougel, M. Plantevit, C. Rigotti, O. Gandrillon, J.-F. Boulicaut.
  
  Extraction sous Contraintes d'Ensembles de Cliques Homogènes, in: 11eme Conférence Francophone sur l'Extraction et la Gestion des Connaissances (EGC), January 2011, p. 443–454.
  
  http://liris.cnrs.fr/publis/?id=4915

Other Publications

• 29H. Berry, H. Chaté.
  
  Anomalous subdiffusion due to obstacles : A critical survey, 2011, arxiv.
  
  http://www.arxiv.org/abs/1103.2206v1

• 30H. Berry.
  
  Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation., in: Biophys J, 2002, vol. 83, n^o 4, p. 1891–1901.
• 31G. Beslon, D. P. Parsons, Y. Sanchez-Dehesa, J.-M. Peña, C. Knibbe.
  
  Scaling Laws in Bacterial Genomes: A Side-Effect of Selection of Mutational Robustness, in: BioSystems, 2010, vol. 102, n^o 1, p. 32-40.
• 32G. Beslon, Y. Sanchez-Dehesa, D. P. Parsons, J.-M. Peña, C. Knibbe.
  
  Scaling Laws in Digital Organisms, in: Proceedings of Information Processing in Cells and Tissues (IPCAT'09), 2009, p. 111-114.
• 33G. Beslon, Y. Sanchez-Dehesa, D. P. Parsons, C. Rigotti, J.-M. Peña.
  
  From Digital Genetics to Knowledge Discovery: Perspectives in Genetic Network Understanding, in: Intelligent Data Analysis journal (IDAj), 2010, vol. 14, n^o 2, p. 173-191.
• 34A. Coulon, O. Gandrillon, G. Beslon.
  
  On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter, in: BMC Systems Biology, 2010, vol. 4, n^o 1, 2 p.
• 35M. Eigen.
  
  Selforganization of matter and the evolution of biological macromolecules, in: Naturwissenschaften, 1971, vol. 58, n^o 10, p. 465-523.
• 36M. Elowitz, A. Levine, E. Siggia, P. Swain.
  
  Stochastic gene expression in a single cell, in: Science, 2002, vol. 297, n^o 5584, p. 1183–1186.
• 37P. Galison.
  
  Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
• 38C. Knibbe, A. Coulon, J.-M. Fayard, G. Beslon.
  
  A long term evolutionary pressure on the amount of noncoding DNA, in: Molecular Biology and Evolution, 2007, vol. 24, n^o 10, p. 2344-2353.
• 39C. Knibbe, J.-M. Fayard, G. Beslon.
  
  The topology of the protein network influences the dynamics of gene order : From systems biology to a systemic understanding of evolution, in: Artificial Life, 2008, vol. 14, n^o 1, p. 149-156c.
• 40C. Knibbe.
  
  Structuration de génomes par sélection indirecte de la variabilité mutationnelle, une approche par modélisation et simulation, PhD Thesis, Institut National des Sciences Appliquées de Lyon, 2006.
• 41C. Knibbe, O. Mazet, F. Chaudier, J.-M. Fayard, G. Beslon.
  
  Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences, in: Journal of Theoretical Biology, 2007, vol. 244, n^o 4, p. 621–630.
• 42D. P. Parsons, C. Knibbe, G. Beslon.
  
  Importance of the rearrangement rates on the organization of transcription, in: Proceedings of Artificial Life 12, MIT Press ed., 2010, p. 479-486.