Project-Team Beagle
Members
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
Dissemination
Bibliography
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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, no 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, no 4. [ DOI : 10.1371/journal.pcbi.100303 ]
    http://hal.inria.fr/hal-00798053
  • 3Y. 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, no 13, pp. 2833-2849. [ DOI : 10.1113/JP270324 ]
    https://hal.inria.fr/hal-01141205
  • 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, no 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, no 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, no 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, no 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, no 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, no 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

  • 12W. 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: Theory in biosciences = Theorie in den Biowissenschaften, May 2016. [ DOI : 10.1007/s12064-016-0229-7 ]
    https://hal.archives-ouvertes.fr/hal-01323108
  • 13H. 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, no 145, pp. 15-45, in press.
    https://hal.inria.fr/hal-01136667
  • 14P. 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, no 5, pp. 1427-1439. [ DOI : 10.1093/gbe/evw083 ]
    https://hal.archives-ouvertes.fr/hal-01334923
  • 15L. Bulteau, G. Fertin, E. Tannier.
    Genome rearrangements with indels in intergenes restrict the scenario space, in: BMC Bioinformatics, 2016, vol. 17, no Suppl 14, 426 p. [ DOI : 10.1186/s12859-016-1264-6 ]
    https://hal.archives-ouvertes.fr/hal-01396842
  • 16Y. 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 p. [ DOI : 10.7554/eLife.13185 ]
    https://hal.inria.fr/hal-01279901
  • 17M. 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
  • 18M. 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
  • 19C. Lays, E. Tannier, T. Henry.
    Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?, in: Microbial Cell , 2016. [ DOI : 10.15698/mic2016.11.543 ]
    https://hal.archives-ouvertes.fr/hal-01394403
  • 20E. Noutahi, M. Semeria, M. Lafond, J. Seguin, B. Boussau, L. Guéguen, N. El-Mabrouk, E. Tannier.
    Efficient gene tree correction guided by genome evolution, in: PLoS ONE, 2016, vol. 11, no 8, e0159559 p. [ DOI : 10.1371/journal.pone.0159559 ]
    https://hal.archives-ouvertes.fr/hal-01162963
  • 21T. 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, no 3, pp. 408-423. [ DOI : 10.1162/ARTL_a_00210 ]
    https://hal.archives-ouvertes.fr/hal-01371116
  • 22A. Villain, M. S. Fernandez, C. Bouchut, H. Soula, C. Vignal.
    Songbird mates change their call structure and intrapair 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

Invited Conferences

International Conferences with Proceedings

  • 24J. Abernot, G. Beslon, S. Hickinbotham, S. Peignier, C. Rigotti.
    A Commensal Architecture for Evolving Living Instruments, in: Conference on Computer Simulation of Musical Creativity, Huddersfield, United Kingdom, June 2016.
    https://hal.archives-ouvertes.fr/hal-01368034
  • 25P. Biller, E. Tannier, G. Beslon, C. Knibbe.
    In silico experimental evolution provides independent and challenging benchmarks for comparative genomics, in: Journées ouvertes Biologie Informatique Mathématiques, Lyon, France, June 2016, pp. 79-82.
    https://hal.archives-ouvertes.fr/hal-01375657
  • 26G. Fertin, G. Jean, E. Tannier.
    Genome Rearrangements on both Gene Order and Intergenic Regions, in: WABI 2016, Aarhus, Denmark, Algorithms for Bioinformatics, 2016.
    https://hal.archives-ouvertes.fr/hal-01334942
  • 27J. Gippet, S. Fenet, A. Dumet, B. Kaufmann, C. Rocabert.
    MoRIS: Model of Routes of Invasive Spread. Human-mediated dispersal, road network and invasion parameters, in: 5th International Conference on Ecology and Transportation: Integrating Transport Infrastructures with Living Landscapes, Lyon, France, Proceedings of the IENE 2016 conference, August 2016.
    https://hal.inria.fr/hal-01412280
  • 28T. Nguyen, N. Méger, C. Rigotti, C. Pothier, R. Andréoli.
    SITS-P2miner: Pattern-Based Mining of Satellite Image Time Series, in: European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD) Demo, Riva del Garda, Italy, September 2016, pp. 63-66. [ DOI : 10.1007/978-3-319-46131-1_14 ]
    https://hal.archives-ouvertes.fr/hal-01367996
  • 29Y. 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

National Conferences with Proceedings

  • 30Y. Anselmetti, V. Berry, C. Chauve, A. Château, E. Tannier, S. Bérard.
    Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels, in: Journées Ouvertes Biologie Informatique Mathématiques, Lyon, France, 2016.
    https://hal.archives-ouvertes.fr/hal-01394409
  • 31A. Davín, G. J. Szöllosi, E. Tannier, B. Boussau, V. Daubin.
    Dating with transfers, in: Journées Ouvertes Biologie Informatique Mathématiques, Lyon, France, 2016.
    https://hal.archives-ouvertes.fr/hal-01394410
  • 32W. Duchemin, V. Daubin, E. Tannier.
    Nucleotide, gene and genome evolution : a score to bind them all, in: Journées Ouvertes Biologie Informatique Mathématiques, Lyon, France, 2016.
    https://hal.archives-ouvertes.fr/hal-01394417
  • 33C. Pothier, R. Andréoli, N. Méger, C. Rigotti.
    Erosion monitoring by satellite image analysis and spatiotemporal data mining, in: Journées Nationales de Géotechnique et de Géologie de l'Ingénieur, Nancy, France, July 2016.
    https://hal.archives-ouvertes.fr/hal-01367992

Conferences without Proceedings

  • 34G. 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
  • 35Y. Pericault, C. Pothier, N. Méger, E. Trouvé, F. Vernier, C. Rigotti, J.-P. Malet.
    Grouped frequent sequential patterns derived from terrestrial image time series tomonitor landslide behaviour – Application to the dynamics of the Sanières/Roche Plombée rockslide., in: Geophysical Research Abstracts - EGU General Assembly 2016, Vienna, Austria, April 2016.
    https://hal.archives-ouvertes.fr/hal-01306556
  • 36C. 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
  • 37J. 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
  • 38S. Stepney, G. Beslon.
    Open-Endedness: Definitions and Shortcuts, in: 2nd EvoEvo Workshop, satellite workshop of CCS2016, Amsterdam, Netherlands, September 2016.
    https://hal.archives-ouvertes.fr/hal-01375671

Scientific Books (or Scientific Book chapters)

Other Publications

  • 41B. Batut, G. Beslon, C. Knibbe.
    Unexpected genome inflation and streamlining in variable environments, June 2016, pp. 320-322, Journées ouvertes de Biologie Informatique & Mathématiques 2016, Poster.
    https://hal.archives-ouvertes.fr/hal-01375653
  • 42V. 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
References in notes
  • 43S. S. Abby, E. Tannier, M. Gouy, V. Daubin.
    Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, in: BMC Bioinformatics, 2010, vol. 11, 13 p.
    http://dx.doi.org/10.1186/1471-2105-11-324
  • 44J. A. Bailey, R. Baertsch, W. J. Kent, D. Haussler, E. E. Eichler.
    Hotspots of mammalian chromosomal evolution, in: Genome Biol, 2004, vol. 5, no 4, 7 p.
    http://dx.doi.org/10.1186/gb-2004-5-4-r23
  • 45H. Berry.
    Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation, in: Biophys J, 2002, vol. 83, no 4, pp. 1891–1901.
  • 46G. 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, no 1, pp. 32-40.
  • 47G. 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, pp. 111-114.
  • 48G. 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, no 2, pp. 173-191.
  • 49B. Caré, H. A. Soula.
    Impact of receptor clustering on ligand binding, in: BMC Systems Biology, March 2011, vol. 5, no 1, 48 p, PMID: 21453460. [ DOI : 10.1186/1752-0509-5-48 ]
    http://www.ncbi.nlm.nih.gov/pubmed/21453460
  • 50C. Chauve, H. Gavranovic, A. Ouangraoua, E. Tannier.
    Yeast ancestral genome reconstructions: the possibilities of computational methods II, in: J Comput Biol, Sep 2010, vol. 17, no 9, pp. 1097–1112.
    http://dx.doi.org/10.1089/cmb.2010.0092
  • 51A. 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, no 1, 2 p.
  • 52A. E. Darling, I. Miklós, M. A. Ragan.
    Dynamics of genome rearrangement in bacterial populations, in: PLoS Genet, 2008, vol. 4, no 7, e1000128.
    http://dx.doi.org/10.1371/journal.pgen.1000128
  • 53L. A. David, E. J. Alm.
    Rapid evolutionary innovation during an Archaean genetic expansion, in: Nature, Jan 2011, vol. 469, no 7328, pp. 93–96. [ DOI : 10.1038/nature09649 ]
  • 54M. Eigen.
    Selforganization of matter and the evolution of biological macromolecules, in: Naturwissenschaften, 1971, vol. 58, no 10, pp. 465-523.
  • 55M. Elowitz, A. Levine, E. Siggia, P. Swain.
    Stochastic gene expression in a single cell, in: Science, 2002, vol. 297, no 5584, pp. 1183–1186.
  • 56J. Felsenstein.
    Inferring phylogenies, Sinauer Associates, 2004.
  • 57P. Galison.
    Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
  • 58T. 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
  • 59M. Imbert, L. Pouilloux, J. Rouzaud-Cornabas, A. Lèbre, T. Hirofuchi.
    Using the EXECO toolbox to perform automatic and reproducible cloud experiments, in: 1st International Workshop on UsiNg and building ClOud Testbeds (UNICO, collocated with IEEE CloudCom 2013, Bristol, United Kingdom, December 2013.
    https://hal.inria.fr/hal-00861886
  • 60International Aphid Genomics Consortium.
    Genome sequence of the pea aphid Acyrthosiphon pisum, in: PLoS Biol, Feb 2010, vol. 8, no 2, e1000313.
    http://dx.doi.org/10.1371/journal.pbio.1000313
  • 61C. 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, no 10, pp. 2344-2353.
  • 62C. 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, no 1, pp. 149-156.
  • 63C. 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, 174 p.
  • 64C. 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, no 4, pp. 621–630.
  • 65R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami.
    The evolutionary origin of complex features, in: Nature, 2003, vol. 423, pp. 139–144.
  • 66D. A. Liberles.
    Ancestral Sequence Reconstruction, Oxford University Press, 2007.
  • 67G. A. B. Marais, A. Forrest, E. Kamau, J. Käfer, V. Daubin, D. Charlesworth.
    Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene, in: PLoS One, 2011, vol. 6, no 8, e21915.
    http://dx.doi.org/10.1371/journal.pone.0021915
  • 68I. Miklós, E. Tannier.
    Bayesian sampling of genomic rearrangement scenarios via double cut and join, in: Bioinformatics, Dec 2010, vol. 26, no 24, pp. 3012–3019.
    http://dx.doi.org/10.1093/bioinformatics/btq574
  • 69F. Murat, J.-H. Xu, E. Tannier, M. Abrouk, N. Guilhot, C. Pont, J. Messing, J. Salse.
    Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution, in: Genome Res, Nov 2010, vol. 20, no 11, pp. 1545–1557. [ DOI : 10.1101/gr.109744.110 ]
  • 70A. Ouangraoua, E. Tannier, C. Chauve.
    Reconstructing the architecture of the ancestral amniote genome, in: Bioinformatics, Oct 2011, vol. 27, no 19, pp. 2664–2671.
    http://dx.doi.org/10.1093/bioinformatics/btr461
  • 71D. P. Parsons, C. Knibbe, G. Beslon.
    Importance of the rearrangement rates on the organization of transcription, in: Proceedings of Artificial Life 12, MIT Press, 2010, pp. 479-486.
  • 72D. 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, pp. 622–629.
  • 73M. Sémon, K. H. Wolfe.
    Consequences of genome duplication, in: Curr Opin Genet Dev, Dec 2007, vol. 17, no 6, pp. 505–512.
    http://dx.doi.org/10.1016/j.gde.2007.09.007
  • 74A. Tofigh, M. Hallett, J. Lagergren.
    Simultaneous identification of duplications and lateral gene transfers, in: IEEE/ACM Trans Comput Biol Bioinform, 2011, vol. 8, no 2, pp. 517–535.
    http://dx.doi.org/10.1109/TCBB.2010.14

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