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. Szöllősi, 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

• 12Y. Anselmetti, W. Duchemin, E. Tannier, C. Chauve, S. Bérard.
  
  Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes, in: BMC Genomics, May 2018, vol. 19, n^o S2, pp. 1-15. [ DOI : 10.1186/s12864-018-4466-7 ]
  
  https://hal.archives-ouvertes.fr/hal-01791884
• 13Y. Chen, M. Arnal-Levron, F. Hullin-Matsuda, C. Knibbe, P. Moulin, C. Luquain-Costaz, I. Delton.
  
  In vitro oxidized HDL and HDL from type 2 diabetes patients have reduced ability to efflux oxysterols from THP-1 macrophages, in: Biochimie, October 2018, vol. 153, pp. 232-237. [ DOI : 10.1016/j.biochi.2018.04.018 ]
  
  https://hal.inria.fr/hal-01952968
• 14Y. Cui, I. Prokin, A. Mendes, H. Berry, L. Venance.
  
  Robustness of STDP to spike timing jitter, in: Scientific Reports, May 2018, vol. 8, n^o 1, pp. 8139:1-15. [ DOI : 10.1038/s41598-018-26436-y ]
  
  https://hal.inria.fr/hal-01788826
• 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, February 2018, vol. 554, pp. 323-327. [ DOI : 10.1038/nature25752 ]
  
  https://hal.archives-ouvertes.fr/hal-01683191
• 16A. Davín, E. Tannier, T. Williams, B. Boussau, V. Daubin, G. Szöllősi.
  
  Gene transfers can date the tree of life, in: Nature Ecology & Evolution, May 2018, vol. 2, n^o 5, pp. 904 - 909. [ DOI : 10.1038/s41559-018-0525-3 ]
  
  https://hal.archives-ouvertes.fr/hal-01774884
• 17W. Duchemin, G. Gence, A.-M. Arigon Chifolleau, L. Arvestad, M. Bansal, V. Berry, B. Boussau, F. Chevenet, N. Comte, A. Davín, C. Dessimoz, D. Dylus, D. Hasic, D. Mallo, R. Planel, D. Posada, C. Scornavacca, G. Szöllősi, L. Zhang, E. Tannier, V. Daubin.
  
  RecPhyloXML - a format for reconciled gene trees, in: Bioinformatics, May 2018, pp. 1-8. [ DOI : 10.1093/bioinformatics/bty389 ]
  
  https://hal-lirmm.ccsd.cnrs.fr/lirmm-01800296
• 18A. Foncelle, A. Mendes, J. Jedrzejewska-Szmek, S. Valtcheva, H. Berry, K. T. Blackwell, L. Venance.
  
  Modulation of spike-timing dependent plasticity: towards the inclusion of a third factor in computational models, in: Frontiers in Computational Neuroscience, July 2018, vol. 12, 49 p. [ DOI : 10.3389/fncom.2018.00049 ]
  
  https://hal.inria.fr/hal-01809075
• 19C. Knibbe.
  
  Souvenirs from ECAL 2017: create, play, experiment, discover – revealing the experimental power of virtual worlds, in: Adaptive Behavior, February 2018, vol. 26, n^o 1, pp. 37-40.
  
  https://hal.inria.fr/hal-01952933
• 20N. Méger, C. Rigotti, C. Pothier, T. Nguyen, F. Lodge, L. Gueguen, R. Andréoli, M.-P. Doin, M. Datcu.
  
  Ranking evolution maps for Satellite Image Time Series exploration: application to crustal deformation and environmental monitoring, in: Data Mining and Knowledge Discovery, October 2018, pp. 1-37. [ DOI : 10.1007/s10618-018-0591-9 ]
  
  https://hal.archives-ouvertes.fr/hal-01898015
• 21T. Nguyen, N. Méger, C. Rigotti, C. Pothier, E. Trouvé, N. Gourmelen, J.-L. Mugnier.
  
  A pattern-based method for handling confidence measures while mining satellite displacement field time series. Application to Greenland ice sheet and Alpine glaciers, in: IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, October 2018, vol. 11, n^o 11, pp. 1 - 13. [ DOI : 10.1109/JSTARS.2018.2874499 ]
  
  https://hal.archives-ouvertes.fr/hal-01912708
• 22F. 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
• 23H. Xu, S. Pérez, A. Cornil, B. Detraux, I. Prokin, Y. Cui, B. Degos, H. Berry, A. De Kerchove D'Exaerde, L. Venance.
  
  Dopamine-endocannabinoid interactions mediate spike-timing dependent potentiation in the striatum, in: Nature Communications, October 2018, vol. 9, 4118 p. [ DOI : 10.1038/s41467-018-06409-5 ]
  
  https://hal.inria.fr/hal-01865929
• 24C. Yi, J. Theillon, A. Koulakoff, H. Berry, C. Giaume.
  
  Monitoring gap junctional communication in astrocytes from acute adult mouse brain slices using the gap-FRAP technique, in: Journal of Neuroscience Methods, 2018, vol. 303, pp. 103-113. [ DOI : 10.1016/j.jneumeth.2018.03.005 ]
  
  https://hal.archives-ouvertes.fr/hal-01734652

International Conferences with Proceedings

• 25T. Nguyen, N. Méger, C. Rigotti, C. Pothier, E. Trouvé, J.-L. Mugnier.
  
  Finding Complementary and Reliable Patterns in Displacement Field Time Series of Alpine Glaciers, in: IGARSS 2018 - IEEE International Geoscience and Remote Sensing Symposium, Valencia, Spain, Proceedings of the 38th IEEE International Geoscience and Remote Sensing Symposium, July 2018, pp. 4213-4216.
  
  https://hal.archives-ouvertes.fr/hal-01868749

Conferences without Proceedings

• 27G. Beslon, S. F. Elena, P. Hogeweg, D. Schneider, S. Stepney.
  
  Evolving Living Technologies-Insights from the EvoEvo project, in: SSBSE 2018 - 10th Symposium on Search-Based Software Engineering, Montpellier, France, LNCS, Springer, September 2018, vol. 11036, pp. 46-62. [ DOI : 10.1007/978-3-319-99241-9_2 ]
  
  https://hal.archives-ouvertes.fr/hal-01882636

Scientific Books (or Scientific Book chapters)

• 29Y. Anselmetti, N. Luhmann, S. Bérard, E. Tannier, C. Chauve.
  
  Comparative Methods for Reconstructing Ancient GenomeOrganization, in: Comparative Genomics: Methods and Protocols, 2018.
  
  https://hal.archives-ouvertes.fr/hal-01690366

Other Publications

• 30G. Beslon, V. F. Liard, S. F. Elena.
  
  Jump then Climb: can rearrangements predict the occurrence of mutational bursts?, August 2018, 1 p, Evolution 2018 - Congress on Evolutionary Biology, Poster.
  
  https://hal.archives-ouvertes.fr/hal-01938800
• 31G. Beslon, V. F. Liard, D. P. Parsons, J. Rouzaud-Cornabas.
  
  In silico experimental evolution shows that complexity can rise even in simple environments, October 2018, 1 p, ICSB 2018 - 19th International Conference on Systems Biology, Poster.
  
  https://hal.inria.fr/hal-01939365
• 32J. Lehman, J. Clune, D. Misevic, C. Adami, J. Beaulieu, P. J. Bentley, S. Bernard, G. Beslon, D. M. Bryson, N. Cheney, A. Cully, S. Donciuex, F. C. Dyer, K. O. Ellefsen, R. Feldt, S. Fischer, S. Forrest, A. Frenoy, C. Gagneé, L. Le Goff, L. M. Grabowski, B. Hodjat, L. Keller, C. Knibbe, P. Krcah, R. E. Lenski, H. Lipson, R. MacCurdy, C. Maestre, R. Miikkulainen, S. Mitri, D. E. Moriarty, J.-B. Mouret, A. D. Nguyen, C. Ofria, M. Parizeau, D. Parsons, R. T. Pennock, W. F. Punch, T. S. Ray, M. Schoenauer, E. Shulte, K. Sims, K. O. Stanley, F. Taddei, D. Tarapore, S. Thibault, W. Weimer, R. Watson, J. Yosinksi.
  
  The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities, March 2018, https://arxiv.org/abs/1803.03453 - working paper or preprint.
  
  https://hal.inria.fr/hal-01735473
• 33V. F. Liard, J. Rouzaud-Cornabas, D. P. Parsons, G. Beslon.
  
  The complexity ratchet: stronger than selection, August 2018, 1 p, Beacon congress 2018, Poster.
  
  https://hal.archives-ouvertes.fr/hal-01938802

References in notes

• 34P. Galison.
  
  Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
• 35B. Verd, E. Clark, K. Wotton, H. Janssens, E. Jiménez-Guri, A. Crombach, J. Jaeger.
  
  A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila, in: PLoS Biology, February 2018, vol. 16, n^o 2. [ DOI : 10.1371/journal.pbio.2003174 ]
  
  https://hal.inria.fr/hal-01934923
• 36C. Vors, G. Pineau, L. Gabert, al..
  
  Modulating absorption and postprandial handling of dietary fatty acids by structuring fat in the meal: a randomized crossover clinical trial, in: Am J Clin Nutr, 2013, vol. 97, pp. 23–36.