Bibliography

Major publications by the team in recent years

• 1P. Biller, L. Guéguen, C. Knibbe, E. Tannier.
  Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation, in: Genome Biology and Evolution, 2016, vol. 8, n^o 5, pp. 1427-1439. [ DOI : 10.1093/gbe/evw083 ]
  https://hal.archives-ouvertes.fr/hal-01334923
• 2A.-S. Coquel, J.-P. Jacob, M. Primet, A. Demarez, M. Dimiccoli, T. Julou, L. Moisan, A. B. Lindner, H. Berry.
  Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect, in: PLoS Computational Biology, 2013, vol. 9, n^o 4. [ DOI : 10.1371/journal.pcbi.100303 ]
  http://hal.inria.fr/hal-00798053
• 3Y. Cui, I. Prokin, H. Xu, B. Delord, S. Genet, L. Venance, H. Berry.
  Endocannabinoid dynamics gate spike-timing dependent depression and potentiation, in: eLife, February 2016, vol. 5, 32 p, e13185. [ DOI : 10.7554/eLife.13185 ]
  https://hal.inria.fr/hal-01279901
• 4W. Duchemin, V. Daubin, E. Tannier.
  Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence, in: BMC Genomics, 2015, vol. 16, n^o Suppl 10, S9 p. [ DOI : 10.1007/978-3-319-19048-8_16 ]
  https://hal.inria.fr/hal-01179197
• 5S. Fischer, S. Bernard, G. Beslon, C. Knibbe.
  A model for genome size evolution, in: Bulletin of Mathematical Biology, September 2014, vol. 76, n^o 9, pp. 2249-2291. [ DOI : 10.1007/s11538-014-9997-8 ]
  https://hal.archives-ouvertes.fr/hal-01090964
• 6T. Hindré, C. Knibbe, G. Beslon, D. Schneider.
  New insights into bacterial adaptation through in vivo and in silico experimental evolution, in: Nature Reviews Microbiology, 2012, vol. 10, pp. 352-365.
  http://hal.inria.fr/hal-00696231
• 7P.-N. Mougel, C. Rigotti, M. Plantevit, O. Gandrillon.
  Finding maximal homogeneous clique sets, in: Knowledge and Information Systems, March 2013, vol. 35, n^o 1, pp. 1-30. [ DOI : 10.1007/s10115-013-0625-y ]
  http://hal.inria.fr/hal-00827164
• 8C. Rocabert, C. Knibbe, G. Beslon.
  Towards a Integrated Evolutionary Model to Study Evolution of Evolution, in: EvoEvo Workshop (Satellite workshop of ECAL 2015), York, United Kingdom, July 2015.
  https://hal.inria.fr/hal-01252796
• 9H. Soula, B. Caré, G. Beslon, H. Berry.
  Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium, in: Biophysical Journal, 2013, vol. 105, n^o 9, pp. 2064-2073. [ DOI : 10.1016/j.bpj.2013.07.023 ]
  http://hal.inria.fr/hal-00720515
• 10G. J. Szöllosi, B. Boussau, S. S. Abby, E. Tannier, V. Daubin.
  Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, in: Proceedings- National Academy of Sciences Usa, October 2012, vol. 109, n^o 43, pp. 17513-17518. [ DOI : 10.1073/pnas.1202997109 ]
  http://hal.inria.fr/hal-00740292
• 11J. Viñuelas, G. Kaneko, A. Coulon, E. Vallin, V. Morin, C. Mejia-Pous, J.-J. Kupiec, G. Beslon, O. Gandrillon.
  Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts, in: BMC Biology, February 2013, vol. 11, n^o 1, 15 p. [ DOI : 10.1186/1741-7007-11-15 ]
  http://hal.inria.fr/inserm-00817963

Publications of the year

Articles in International Peer-Reviewed Journals

• 12J. Abernot, G. Beslon, S. Hickinbotham, S. Peignier, C. Rigotti.
  Evolving Instrument Based on Symbiont-Host Metaphor: a Commensal Computation, in: Journal of Creative Music Systems, September 2017, vol. 2, n^o 1, pp. 1-10. [ DOI : 10.5920/JCMS.2017.11 ]
  https://hal.archives-ouvertes.fr/hal-01596573
• 13G. Beslon, D. Schneider.
  Isee-resistance : using in silico experimental evolution to sensitize providers on antibiotic resistance, in: Antimicrobial Resistance and Infection Control, June 2017, vol. 6(Suppl 3), n^o 52, 2 p.
  https://hal.archives-ouvertes.fr/hal-01569262
• 14L. Chabrolles, I. Ben Ammar, M. S. A. Fernandez, N. BOYER, J. Attia, P. J. Fonseca, M. C. P. Amorim, M. Beauchaud.
  Appraisal of unimodal cues during agonistic interactions in Maylandia zebra, in: PeerJ, August 2017, vol. 5, n^o e3643. [ DOI : 10.7717/peerj.3643 ]
  https://hal.archives-ouvertes.fr/hal-01663176
• 15Y. Cui, Y. Yang, Z. Ni, Y. Dong, G. Cai, A. Foncelle, S. Ma, K. Sang, S. Tang, Y. Li, Y. Shen, H. Berry, S. Wu, H. Hu.
  Astroglial-Kir4.1 in Lateral Habenula Drives Neuronal Bursts to Mediate Depression, in: Nature, 2018, n^o 1-48.
  https://hal.archives-ouvertes.fr/hal-01683191
• 16W. Duchemin, Y. Anselmetti, M. Patterson, Y. Ponty, S. Bérard, C. Chauve, C. Scornavacca, V. Daubin, E. Tannier.
  DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies, in: Genome Biology and Evolution, 2017, vol. 9, n^o 5, pp. 1312-1319.
  https://hal.inria.fr/hal-01503766
• 17M. S. Fernandez, C. Vignal, H. Soula.
  Impact of group size and social composition on group vocal activity and acoustic network in a social songbird, in: Animal Behaviour, February 2017, vol. 127, pp. 163-178. [ DOI : 10.1016/j.anbehav.2017.03.013 ]
  https://hal.archives-ouvertes.fr/hal-01537565
• 18G. Fertin, G. Jean, E. Tannier.
  Algorithms for computing the double cut and join distance on both gene order and intergenic sizes, in: Algorithms for Molecular Biology, 2017, vol. 12, 11 p. [ DOI : 10.1186/s13015-017-0107-y ]
  https://hal.archives-ouvertes.fr/hal-01533200
• 19E. Jacox, W. Mathias, E. Tannier, C. Scornavacca.
  Resolution and reconciliation of non-binarygene trees with transfers, duplicationsand losses, in: Bioinformatics, 2017, vol. 33, n^o 7, pp. 980-987. [ DOI : 10.1093/bioinformatics/btw778 ]
  https://hal.archives-ouvertes.fr/hal-01526643
• 20F. Oschmann, H. Berry, K. Obermayer, K. Lenk.
  From in silico astrocyte cell models to neuron-astrocyte network models: A review, in: Brain Research Bulletin, 2018, vol. 136, pp. 76-84. [ DOI : 10.1016/j.brainresbull.2017.01.027 ]
  https://hal.archives-ouvertes.fr/hal-01461928
• 21C. Rocabert, C. Knibbe, J. Consuegra, D. Schneider, G. Beslon.
  Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification, in: PLoS Computational Biology, March 2017, vol. 13, n^o 3, 32 p, e1005459. [ DOI : 10.1371/journal.pcbi.1005459.s006 ]
  https://hal.archives-ouvertes.fr/hal-01508751

International Conferences with Proceedings

• 22V. Liard, J. Rouzaud-Cornabas, N. Comte, G. Beslon.
  A 4-base model for the Aevol in-silico experimental evolution platform, in: European Conference on Artificial Life, Villeurbanne, France, Proceedings of the 14th European Conference on Artificial Life, September 2017.
  https://hal.archives-ouvertes.fr/hal-01569097
• 23T. Nguyen, N. Méger, C. Rigotti, C. Pothier, E. Trouvé, N. Gourmelen.
  Handling coherence measures of displacement field time series: Application to Greenland ice sheet glaciers, in: 9th International Workshop on the Analysis of Multitemporal Remote Sensing Images (MultiTemp), Brugge, Belgium, IEEE (editor), Proc. of the 9th International Workshop on the Analysis of Multitemporal Remote Sensing Images, June 2017, pp. 1-4. [ DOI : 10.1109/Multi-Temp.2017.8035228 ]
  https://hal.archives-ouvertes.fr/hal-01591461
• 24S. Peignier, J. Abernot, C. Rigotti, G. Beslon.
  EvoMove: Evolutionary-based living musical companion, in: European Conference on Artificial Life (ECAL), Villeurbanne, France, Proceedings of the 14th European Conference on Artificial Life, September 2017, pp. 1-8.
  https://hal.archives-ouvertes.fr/hal-01569091
• 25C. Rocabert, C. Knibbe, J. Consuegra, D. Schneider, G. Beslon.
  Environmental seasonality drives digital populations towards stable cross-feeding, in: European Conference on Artificial Life (ECAL), Villeurbanne, France, Proceedings of the 14th European Conference on Artificial Life, September 2017.
  https://hal.archives-ouvertes.fr/hal-01569093

National Conferences with Proceedings

• 26E. Scholastique, C. Pothier, L. Vinet, C. Rigotti, N. Bouillod.
  3D Geomodelling Contribution to the Mapping of Gravitational Hazards on the Hill of Croix-RousseE, in: Journées Aléas Gravitaires (JAG), Besançon, France, Actes des 5ièmes Journées Aléas Gravitaires, October 2017, pp. 1-4.
  https://hal.archives-ouvertes.fr/hal-01596585

Conferences without Proceedings

• 27N. Comte, V. Liard, C. Knibbe, G. Beslon.
  Aevol-4b: Toward a new simulation platform to benchmark phylogenetic tools, in: ALPHY (ALignments and PHYlogeny), Villeurbanne, France, February 2017.
  https://hal.archives-ouvertes.fr/hal-01569078

Scientific Books (or Scientific Book chapters)

• 28N. Méger, E. Pasolli, C. Rigotti, E. Trouvé, F. MELGANI.
  Satellite Image Time Series: mathematical models for data mining and missing data restoration, in: Mathematical Models for Remote Sensing Image Processing, G. Moser, J. Zerubia (editors), Springer International Publishing, November 2017, pp. 1-42. [ DOI : 10.1007/978-3-319-66330-2 ]
  https://hal.archives-ouvertes.fr/hal-01567675

Other Publications

• 29G. Beslon, V. F. Liard, S. F. Elena.
  Testing evolution predictability using the aevol software, August 2017, 16th international meeting of the European Society of Evolutionary Biology (ESEB 2017) , Poster.
  https://hal.archives-ouvertes.fr/hal-01577115
• 30C. Chauve, A. A. Rafiey, A. A. Davin, C. Scornavacca, P. Veber, B. Boussau, G. J. Szollosi, V. Daubin, E. A. Tannier.
  MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers, 2017, Recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100037). [ DOI : 10.1101/127548 ]
  https://hal.archives-ouvertes.fr/hal-01532738
• 31D. Garg, M. Patterson, W. Hager, A. Rao, D. R. Benson, G. T. Huntington.
  An overview of three pseudospectral methods for the numerical solution of optimal control problems, October 2017, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01615132
• 32D. Hasic, E. Tannier.
  Gene tree species tree reconciliation with gene conversion, September 2017, https://arxiv.org/abs/1703.08950 - working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01495707

References in notes

• 33O. Arnaud, S. Meyer, E. Vallin, G. Beslon, O. Gandrillon.
  Temperature-induced variation in gene expression burst size in metazoan cells, in: BMC Molecular Biology, November 2015, vol. 16, n^o 20. [ DOI : 10.1186/s12867-015-0048-2 ]
  https://hal.inria.fr/hal-01248384
• 34W. Banzhaf, B. Baumgaertner, G. Beslon, R. Doursat, J. A. Foster, B. McMullin, V. V. de Melo, T. Miconi, L. Spector, S. Stepney, R. White.
  Defining and simulating open-ended novelty: requirements, guidelines, and challenges, in: Theorie in den Biowissenschaften / Theory in Biosciences, May 2016. [ DOI : 10.1007/s12064-016-0229-7 ]
  https://hal.archives-ouvertes.fr/hal-01323108
• 35B. Batut, C. Knibbe, G. Marais, V. Daubin.
  Reductive genome evolution at both ends of bacterial population size spectrum, in: Nature Reviews Microbiology, December 2014, vol. 12, n^o 12, pp. 841-850. [ DOI : 10.1038/nrmicro3331 ]
  https://hal.archives-ouvertes.fr/hal-01092392
• 36B. Batut, D. P. Parsons, S. Fischer, G. Beslon, C. Knibbe.
  In silico experimental evolution: a tool to test evolutionary scenarios, in: BMC Bioinformatics, 2013, vol. 14, n^o Suppl 15, S11 p.
  https://hal.inria.fr/hal-00873232
• 37H. Berry, H. Chaté.
  Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes, in: Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, February 2014, vol. 89, n^o 2, 022708 (9 pages) p. [ DOI : 10.1103/PhysRevE.89.022708 ]
  https://hal.inria.fr/inria-00575651
• 38H. Berry, T. Lepoutre, Á. Mateos González.
  Quantitative convergence towards a self similar profile in an age-structured renewal equation for subdiffusion, in: Acta Applicandae Mathematicae, 2016, n^o 145, pp. 15-45, in press.
  https://hal.inria.fr/hal-01136667
• 39H. Berry, H. A. Soula.
  Spatial distributions at equilibrium under heterogeneous transient subdiffusion, in: Frontiers in Physiology, November 2014, vol. 5, 437 (8 pages) p. [ DOI : 10.3389/fphys.2014.00437 ]
  https://hal.inria.fr/hal-01077735
• 40G. Beslon, V. F. Liard, S. F. Elena.
  Evolvability drives innovation in viral genomes, in: 2nd EvoEvo Workshop, satellite workshop of CCS2016, Amsterdam, France, September 2016.
  https://hal.archives-ouvertes.fr/hal-01375665
• 41P. Biller, L. Guéguen, C. Knibbe, E. Tannier.
  Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation, in: Genome Biology and Evolution, 2016, vol. 8, n^o 5, pp. 1427-1439. [ DOI : 10.1093/gbe/evw083 ]
  https://hal.archives-ouvertes.fr/hal-01334923
• 42P. Biller, C. Knibbe, G. Beslon, E. Tannier.
  Comparative Genomics on Artificial Life, in: Computability in Europe, Paris, France, Pursuit of the Universal, Lecture Notes in Computer Science, 2016, vol. 9709, pp. 35-44.
  https://hal.archives-ouvertes.fr/hal-01334930
• 43V. Calvez, P. Gabriel, Á. Mateos González.
  Limiting Hamilton-Jacobi equation for the large scale asymptotics of a subdiffusion jump-renewal equation, September 2016, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01372949
• 44B. Caré, H. A. Soula.
  Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime, in: Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, January 2013, vol. 87, n^o 1, 012720 p. [ DOI : 10.1103/PhysRevE.87.012720 ]
  https://hal.archives-ouvertes.fr/hal-00858439
• 45C. Chauve, A. A. Rafiey, A. A. Davin, C. Scornavacca, P. Veber, B. Boussau, G. J. Szollosi, V. Daubin, E. Tannier.
  MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene Transfers, June 2017, working paper or preprint. [ DOI : 10.1101/127548 ]
  https://hal.archives-ouvertes.fr/hal-01532738
• 46N. Comte, V. Liard, C. Knibbe, G. Beslon.
  Aevol-4b: Toward a new simulation platform to benchmark phylogenetic tools, in: ALPHY (ALignments and PHYlogeny), Villeurbanne, France, February 2017.
  https://hal.archives-ouvertes.fr/hal-01569078
• 47A.-S. Coquel, J.-P. Jacob, M. Primet, A. Demarez, M. Dimiccoli, T. Julou, L. Moisan, A. B. Lindner, H. Berry.
  Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect, in: PLoS Computational Biology, 2013, vol. 9, n^o 4, e1003038 (14 pages) p. [ DOI : 10.1371/journal.pcbi.100303 ]
  https://hal.inria.fr/hal-00798053
• 48G. Corre, D. Stockholm, O. Arnaud, G. Kaneko, J. Viñuelas, Y. Yamagata, T. M. A. Neildez-Nguyen, J.-J. Kupiec, G. Beslon, O. Gandrillon, A. Paldi.
  Stochastic Fluctuations and Distributed Control of Gene Expression Impact Cellular Memory, in: PLoS ONE, December 2014, vol. 9, n^o 12, e115574 p. [ DOI : 10.1371/journal.pone.0115574 ]
  https://hal.archives-ouvertes.fr/hal-01370311
• 49Y. Cui, V. Paille, H. Xu, S. Genet, B. Delord, E. Fino, H. Berry, L. Venance.
  Endocannabinoids mediate bidirectional striatal spike-timing dependent plasticity, in: Journal of Physiology, 2015, vol. 593, n^o 13, pp. 2833-2849. [ DOI : 10.1113/JP270324 ]
  https://hal.inria.fr/hal-01141205
• 50Y. Cui, I. Prokin, H. Xu, B. Delord, S. Genet, L. Venance, H. Berry.
  Endocannabinoid dynamics gate spike-timing dependent depression and potentiation, in: eLife, February 2016, vol. 5, e13185 (32 pages) p. [ DOI : 10.7554/eLife.13185 ]
  https://hal.inria.fr/hal-01279901
• 51M. De Pittà, N. Brunel.
  Modulation of Synaptic Plasticity by Glutamatergic Gliotransmission: A Modeling Study, in: Neural plasticity, 2016. [ DOI : 10.1155/2016/7607924 ]
  https://hal.archives-ouvertes.fr/hal-01353306
• 52M. De Pittà, N. Brunel, A. Volterra.
  Astrocytes: Orchestrating Synaptic Plasticity?, in: Neuroscience, 2016, vol. 323, pp. 43-61. [ DOI : 10.1016/j.neuroscience.2015.04.001 ]
  https://hal.archives-ouvertes.fr/hal-01353308
• 53M. S. Fernandez, H. A. Soula, M. M. Mariette, C. Vignal.
  A New Semi-automated Method for Assessing Avian Acoustic Networks Reveals that Juvenile and Adult Zebra Finches Have Separate Calling Networks, in: Frontiers in Psychology, November 2016, vol. 7, n^o 1816. [ DOI : 10.3389/fpsyg.2016.01816 ]
  https://hal.archives-ouvertes.fr/hal-01435346
• 54M. S. Fernandez, C. Vignal, H. Soula.
  Impact of group size and social composition on group vocal activity and acoustic network in a social songbird, in: Animal Behaviour, February 2017, vol. 127, pp. 163-178. [ DOI : 10.1016/j.anbehav.2017.03.013 ]
  https://hal.archives-ouvertes.fr/hal-01537565
• 55S. Fischer, S. Bernard, G. Beslon, C. Knibbe.
  A Model for Genome Size Evolution, in: Bulletin of Mathematical Biology, 2014, vol. 76, n^o 9, pp. 2249 - 2291. [ DOI : 10.1007/s11538-014-9997-8 ]
  https://hal.archives-ouvertes.fr/hal-01090984
• 56P. Galison.
  Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
• 57A. Geloen, H. Soula, L. Hadji, E. Berger.
  Hysteresis of White Adipose Tissue, in: Open Journal of Endocrine and Metabolic Diseases, 2015, vol. 5, n^o 10, 138 p.
  https://hal.archives-ouvertes.fr/hal-01253148
• 58L. Hadji, E. Berger, H. A. Soula, H. Vidal, A. Géloën.
  White Adipose Tissue Resilience to Insulin Deprivation and Replacement, in: PLoS ONE, August 2014, vol. 9, n^o 8, 10 p. [ DOI : 10.1371/journal.pone.0106214 ]
  https://hal.inria.fr/hal-01092531
• 59T. Hindré, C. Knibbe, G. Beslon, D. Schneider.
  New insights into bacterial adaptation through in vivo and in silico experimental evolution, in: Nature Reviews Microbiology, 2012, vol. 10, pp. 352-365.
  http://hal.inria.fr/hal-00696231
• 60P. Hogeweg, G. Beslon.
  EvoEvo Deliverable 3.2, Inria Grenoble - Rhône-Alpes, October 2016.
  https://hal.archives-ouvertes.fr/hal-01577155
• 61C. Knibbe, D. P. Parsons.
  What happened to my genes? Insights on gene family dynamics from digital genetics experiments, in: ALIFE 14 (14th Intl. Conf. on the Synthesis and Simulation of Living Systems), New York, NY, United States, H. Sayama (editor), MIT Press, July 2014, pp. 33-40. [ DOI : 10.7551/978-0-262-32621-6-ch006 ]
  https://hal.archives-ouvertes.fr/hal-01093110
• 62J. Lallouette, M. De Pittà, E. Ben Jacob, H. Berry.
  Sparse short-distance connections enhance calcium wave propagation in a 3D model of astrocyte networks, in: Frontiers in Computational Neuroscience, 2014, vol. 8, 45 (18 pages) p. [ DOI : 10.3389/fncom.2014.00045 ]
  https://hal.inria.fr/hal-00967106
• 63V. Liard, J. Rouzaud-Cornabas, N. Comte, G. Beslon.
  A 4-base model for the Aevol in-silico experimental evolution platform, in: European Conference on Artificial Life, Villeurbanne, France, Proceedings of the 14th European Conference on Artificial Life, September 2017.
  https://hal.archives-ouvertes.fr/hal-01569097
• 64A. Lo Van, H. Soula, H. Berry.
  Space-induced bifurcation in repression-based transcriptional circuits, in: BMC Systems Biology, 2014, vol. 8, 125 (14 pages) p.
  https://hal.inria.fr/hal-01068558
• 65S. Meyer, G. Beslon.
  Torsion-Mediated Interaction between Adjacent Genes, in: PLoS Computational Biology, September 2014, vol. 10, n^o 9, e1003785 p. [ DOI : 10.1371/journal.pcbi.1003785 ]
  https://hal.archives-ouvertes.fr/hal-01090990
• 66J. Naudé, B. Cessac, H. Berry, B. Delord.
  Effects of Cellular Homeostatic Intrinsic Plasticity on Dynamical and Computational Properties of Biological Recurrent Neural Networks, in: Journal of Neuroscience, 2013, vol. 33, n^o 38, pp. 15032-15043. [ DOI : 10.1523/JNEUROSCI.0870-13.2013 ]
  https://hal.inria.fr/hal-00844218
• 67F. Oschmann, H. Berry, K. Obermayer, K. Lenk.
  From in silico astrocyte cell models to neuron-astrocyte network models: A review, in: Brain Research Bulletin, 2017, 9 pages p. [ DOI : 10.1016/j.brainresbull.2017.01.027 ]
  https://hal.archives-ouvertes.fr/hal-01461928
• 68S. Peignier, C. Rigotti, G. Beslon.
  Subspace Clustering for all Seasons, in: EvoEvo Workshop (satellite workshop of ECAL 2015), york, United Kingdom, July 2015, pp. 1-3.
  https://hal.inria.fr/hal-01252793
• 69S. Peignier, C. Rigotti, G. Beslon.
  Subspace Clustering Using Evolvable Genome Structure, in: Genetic and Evolutionary Computation Conference (GECCO), Madrid, Spain, July 2015, pp. 575-582.
  https://hal.archives-ouvertes.fr/hal-01199136
• 70E. C. Perez, J. E. Elie, I. C. A. Boucaud, T. Crouchet, C. Soulage, F. E. Theunissen, C. Vignal, H. A. Soula.
  Physiological resonance between mates through calls as possible evidence of empathic processes in songbirds, in: Hormones and Behavior, 2015, vol. 75, pp. 130–141. [ DOI : 10.1016/j.yhbeh.2015.09.002 ]
  https://hal.archives-ouvertes.fr/hal-01253147
• 71E. C. Perez, M. S. Fernandez, S. C. Griffith, C. Vignal, H. A. Soula.
  Impact of visual contact on vocal interaction dynamics of pair bonded birds, in: Animal Behaviour, April 2015, vol. 107, pp. 125-137. [ DOI : 10.1016/j.anbehav.2015.05.019 ]
  https://hal.archives-ouvertes.fr/hal-01538313
• 72C. Rocabert, C. Knibbe, G. Beslon.
  Towards a Integrated Evolutionary Model to Study Evolution of Evolution, in: EvoEvo Workshop (Satellite workshop of ECAL 2015), York, United Kingdom, July 2015.
  https://hal.inria.fr/hal-01252796
• 73C. Rocabert, C. Knibbe, J. Consuegra, D. Schneider, G. Beslon.
  In Silico Experimental Evolution Highlights the Influence of Environmental Seasonality on Bacterial Diversification, in: 2nd EvoEvo Workshop, satellite workshop of CCS2016, Amsterdam, Netherlands, September 2016.
  https://hal.archives-ouvertes.fr/hal-01375677
• 74C. Rocabert, C. Knibbe, J. Consuegra, D. Schneider, G. Beslon.
  Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification, in: PLoS Computational Biology, March 2017, vol. 13, n^o 3, e1005459 (32 pages) p. [ DOI : 10.1371/journal.pcbi.1005459.s006 ]
  https://hal.archives-ouvertes.fr/hal-01508751
• 75C. Rocabert, C. Knibbe, J. Consuegra, D. Schneider, G. Beslon.
  Environmental seasonality drives digital populations towards stable cross-feeding, in: European Conference on Artificial Life (ECAL), Villeurbanne, France, Proceedings of the 14th European Conference on Artificial Life, September 2017.
  https://hal.archives-ouvertes.fr/hal-01569093
• 76J. P. Rutten, P. Hogeweg, G. Beslon.
  Evolution of mutator populations in constant environments, in: 2nd EvoEvo Workshop, satellite workshop of CCS2016, Amsterdam, Netherlands, September 2016.
  https://hal.archives-ouvertes.fr/hal-01375669
• 77H. A. Soula, B. Caré, G. Beslon, H. Berry.
  Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium, in: Biophysical Journal, 2013, vol. 105, n^o 9, pp. 2064-2073. [ DOI : 10.1016/j.bpj.2013.07.023 ]
  https://hal.inria.fr/hal-00720515
• 78H. A. Soula, B. Caré, G. Beslon, H. Berry.
  Comments to the Editor. Reply to the Comment by V.P. Shkilev on ”Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium”, in: Biophysical Journal, 2014, vol. 106, n^o 11, pp. 2544-2546. [ DOI : 10.1016/j.bpj.2014.03.052 ]
  https://hal.inria.fr/hal-00956603
• 79H. A. Soula, A. Géloën, C. Soulage.
  Model of adipose tissue cellularity dynamics during food restriction, in: Journal of Theoretical Biology, January 2015, vol. 364, 10 p. [ DOI : 10.1016/j.jtbi.2014.08.046 ]
  https://hal.inria.fr/hal-01092535
• 80H. A. Soula, H. Julienne, C. Soulage, A. Géloën.
  Modelling adipocytes size distribution, in: Journal of Theoretical Biology, September 2013, vol. 332, pp. 89-95. [ DOI : 10.1016/j.jtbi.2013.04.025 ]
  https://hal.inria.fr/hal-00850474
• 81G. Szollosi, A. A. Davin, E. Tannier, V. Daubin, B. Boussau.
  Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, in: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990), 2015, vol. 370, 20140335 (11 pages) p. [ DOI : 10.1098/rstb.2014.0335 ]
  https://hal.archives-ouvertes.fr/hal-01218565
• 82G. J. Szollosi, W. Rosikiewicz, B. Boussau, E. Tannier, V. Daubin.
  Efficient Exploration of the Space of Reconciled Gene Trees, in: Systematic Biology, August 2013, vol. 62, n^o 6, pp. 901-912. [ DOI : 10.1093/sysbio/syt054 ]
  https://hal.archives-ouvertes.fr/hal-00856826
• 83G. J. Szollosi, E. Tannier, N. Lartillot, V. Daubin.
  Lateral Gene Transfer from the Dead, in: Systematic Biology, January 2013, vol. 62, n^o 3, pp. 386-397. [ DOI : 10.1093/sysbio/syt003 ]
  https://hal.archives-ouvertes.fr/hal-00784662
• 84G. Szöllösi, E. Tannier, V. Daubin, B. Boussau.
  The inference of gene trees with species trees, in: Systematic biology, 2015, vol. 64, n^o 1, pp. e42-e62. [ DOI : 10.1093/sysbio/syu048 ]
  https://hal.archives-ouvertes.fr/hal-00915301
• 85T. Taylor, M. Bedau, A. Channon, D. Ackley, W. Banzhaf, G. Beslon, E. Dolson, T. Froese, S. Hickinbotham, T. Ikegami, B. McMullin, N. Packard, S. Rasmussen, V. Nathaniel, E. Agmon, C. Edward, S. Mcgregor, C. Ofria, G. Ropella, L. Spector, K. O. Stanley, A. Stanton, C. Timperley, A. Vostinar, M. Wiser.
  Open-Ended Evolution: Perspectives from the OEE Workshop in York, in: Artificial Life, 2016, vol. 22, n^o 3, pp. 408-423. [ DOI : 10.1162/ARTL_a_00210 ]
  https://hal.archives-ouvertes.fr/hal-01371116
• 86Y. Vadée-Le-Brun, J. Rouzaud-Cornabas, G. Beslon.
  Epigenetic inheritance speeds up evolution of artificial organisms, in: European Conference on Artificial Life, York, United Kingdom, Proceedings of the European Conference on Artificial Life, July 2015. [ DOI : 10.7551/978-0-262-33027-5-ch078 ]
  https://hal.inria.fr/hal-01248383
• 87Y. Vadée-Le-Brun, J. Rouzaud-Cornabas, G. Beslon.
  In Silico Experimental Evolution suggests a complex intertwining of selection, robustness and drift in the evolution of genetic networks complexity, in: Artificial Life, Cancun, Mexico, Proceedings of the Artificial Life Conference 2016, MIT Press, July 2016.
  https://hal.archives-ouvertes.fr/hal-01375645
• 88A. S. Villain, M. S. Fernandez, C. Bouchut, H. Soula, C. Vignal.
  Songbird mates change their call structure and intra-pair communication at the nest in response to environmental noise, in: Animal Behaviour, June 2016, vol. 116, pp. 113-129. [ DOI : 10.1016/j.anbehav.2016.03.009 ]
  https://hal.archives-ouvertes.fr/hal-01404754
• 89J. Viñuelas, G. Kaneko, A. Coulon, E. Vallin, V. Morin, C. Mejia-Pous, J.-J. Kupiec, G. Beslon, O. Gandrillon.
  Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts, in: BMC Biology, February 2013, vol. 11, n^o 1, 15 p. [ DOI : 10.1186/1741-7007-11-15 ]
  http://www.hal.inserm.fr/inserm-00817963
• 90G. Wallach, J. Lallouette, N. Herzog, M. De Pittà, E. Ben Jacob, H. Berry, Y. Hanein.
  Glutamate Mediated Astrocytic Filtering of Neuronal Activity, in: PLoS Computational Biology, 2014, vol. 12, n^o 10, e1003964 (19 pages) p. [ DOI : 10.1371/journal.pcbi.1003964 ]
  https://hal.inria.fr/hal-01077738