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Bibliography

Major publications by the team in recent years
  • 1A.-S. Coquel, J.-P. Jacob, M. Primet, A. Demarez, M. Dimiccoli, T. Julou, L. Moisan, A. 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
  • 2M. 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, no 12.
  • 3S. 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
  • 4T. 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
  • 5A. Lo Van, H. Soula, H. Berry.

    Space-induced bifurcation in repression-based transcriptional circuits, in: BMC Systems Biology, 2014, vol. 8, 125 p.

    https://hal.inria.fr/hal-01068558
  • 6P.-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
  • 7H. 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
  • 8G. 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
  • 9J. 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

Doctoral Dissertations and Habilitation Theses

  • 10B. Batut.

    Study of reductive genome evolution in bacterial genomes with in silico evolution experiments and bioinformatics analyses, INSA de Lyon, November 2014.

    https://hal.inria.fr/tel-01092571

Articles in International Peer-Reviewed Journals

  • 11B. 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, no 12, pp. 841-850. [ DOI : 10.1038/nrmicro3331 ]

    https://hal.archives-ouvertes.fr/hal-01092392
  • 12H. Berry, H. Chaté.

    Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes, in: Physical Review E, February 2014, vol. 89, no 2, 022708. [ DOI : 10.1103/PhysRevE.89.022708 ]

    https://hal.inria.fr/inria-00575651
  • 13H. Berry, H. A. Soula.

    Spatial distributions at equilibrium under heterogeneous transient subdiffusion, in: Frontiers in Physiology, November 2014, vol. 5, 8 p. [ DOI : 10.3389/fphys.2014.00437 ]

    https://hal.inria.fr/hal-01077735
  • 14M. De Pittà, E. Ben-Jacob, H. Berry.

    Astrocytic theory of working memory, in: BMC Neuroscience, 2014, vol. 15, no Suppl 1, P206.

    https://hal.inria.fr/hal-01026524
  • 15S. Fischer, S. Bernard, G. Beslon, C. Knibbe.

    A Model for Genome Size Evolution, in: Bulletin of Mathematical Biology, 2014, vol. 76, no 9, pp. 2249 - 2291. [ DOI : 10.1007/s11538-014-9997-8 ]

    https://hal.archives-ouvertes.fr/hal-01090984
  • 16L. Hadji, E. Berger, H. Soula, H. Vidal, A. Géloën.

    White Adipose Tissue Resilience to Insulin Deprivation and Replacement, in: PLoS ONE, August 2014, vol. 9, no 8, 10 p. [ DOI : 10.1371/journal.pone.0106214 ]

    https://hal.inria.fr/hal-01092531
  • 17M. Jacquier, F. Crauste, C. O. Soulage, H. A. Soula.

    A predictive model of the dynamics of body weight and food intake in rats submitted to caloric restrictions, in: PLoS ONE, 2014, vol. 9, no 6, e100073. [ DOI : 10.1371/journal.pone.0100073 ]

    https://hal.inria.fr/hal-01017357
  • 18J. 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, 18 p. [ DOI : 10.3389/fncom.2014.00045 ]

    https://hal.inria.fr/hal-00967106
  • 19J. Lallouette, M. De Pittà, E. Ben-Jacob, H. Berry.

    The topology of astrocyte networks controls the propagation of intercellular calcium waves, in: BMC Neuroscience, 2014, vol. 15, no Suppl 1, P205.

    https://hal.inria.fr/hal-01026523
  • 20A. Lo Van, H. Soula, H. Berry.

    Space-induced bifurcation in repression-based transcriptional circuits, in: BMC Systems Biology, 2014, vol. 8, 14 p.

    https://hal.inria.fr/hal-01068558
  • 21S. Meyer, G. Beslon.

    Torsion-Mediated Interaction between Adjacent Genes, in: PLoS Computational Biology, September 2014, vol. 10, no 9, e1003785. [ DOI : 10.1371/journal.pcbi.1003785 ]

    https://hal.archives-ouvertes.fr/hal-01090990
  • 22I. Miklós, S. Z. Kiss, E. Tannier.

    Counting and sampling SCJ small parsimony solutions, in: Journal of Theoretical Computer Science (TCS), October 2014, vol. 552, pp. 83-98. [ DOI : 10.1016/j.tcs.2014.07.027 ]

    https://hal.archives-ouvertes.fr/hal-01077270
  • 23H. 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, no 11, pp. 2544-2546. [ DOI : 10.1016/j.bpj.2014.03.052 ]

    https://hal.inria.fr/hal-00956603
  • 24H. 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
  • 25G. Szöllősi, E. Tannier, V. Daubin, B. Boussau.

    The inference of gene trees with species trees, in: Systematic biology, 2015, vol. 64, no 1, pp. 42-62. [ DOI : 10.1093/sysbio/syu048 ]

    https://hal.archives-ouvertes.fr/hal-00915301
  • 26G. 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, no 10, e1003964. [ DOI : 10.1371/journal.pcbi.1003964 ]

    https://hal.inria.fr/hal-01077738

Invited Conferences

  • 27J. Naudé, B. Cessac, H. Berry, B. Delord.

    Effects of Cellular Homeostatic Intrinsic Plasticity on Dynamical and Computational Properties of Biological Recurrent Neural Networks, in: LACONEU 2014, Valparaiso, Chile, January 2014, vol. 33. [ DOI : 10.1523/JNEUROSCI.0870-13.2013 ]

    https://hal.inria.fr/hal-01095601

International Conferences with Proceedings

  • 28C. Knibbe, D. 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
  • 29F. Lodge, N. Meger, C. Rigotti, C. Pothier, M.-P. Doin.

    Iterative Summarization of Satellite Image Time Series, in: IEEE International Geoscience and Remote Sensing Symposium (IGARSS 2014), Québec, Canada, July 2014.

    https://hal.archives-ouvertes.fr/hal-01091940

National Conferences with Proceedings

  • 30C. Rigotti, F. Lodge, N. Méger, C. Pothier, R. Jolivet, C. Lasserre.

    Monitoring of Tectonic Deformation by Mining Satellite Image Time Series, in: Reconnaissance de Formes et Intelligence Artificielle (RFIA) 2014, Rouen, France, June 2014, 6 p.

    https://hal.archives-ouvertes.fr/hal-00988907

Scientific Books (or Scientific Book chapters)

References in notes
  • 32S. 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
  • 33J. 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
  • 34B. Batut, D. Parsons, S. Fischer, G. Beslon, C. Knibbe.

    In silico experimental evolution: a tool to test evolutionary scenarios, in: BMC Bioinformatics, October 2013, vol. 14, no Suppl 15, S11 p.

    http://hal.inria.fr/hal-00856813
  • 35H. 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.
  • 36G. 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.
  • 37G. 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.
  • 38G. 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.
  • 39B. 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
  • 40C. 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
  • 41A. 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.
  • 42A. 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
  • 43L. 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 ]
  • 44M. Eigen.

    Selforganization of matter and the evolution of biological macromolecules, in: Naturwissenschaften, 1971, vol. 58, no 10, pp. 465-523.
  • 45M. Elowitz, A. Levine, E. Siggia, P. Swain.

    Stochastic gene expression in a single cell, in: Science, 2002, vol. 297, no 5584, pp. 1183–1186.
  • 46J. Felsenstein.

    Inferring phylogenies, Sinauer Associates, 2004.
  • 47P. Galison.

    Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
  • 48T. 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
  • 49International 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
  • 50C. 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.
  • 51C. 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.
  • 52C. 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.
  • 53C. 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.
  • 54R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami.

    The evolutionary origin of complex features, in: Nature, 2003, vol. 423, pp. 139–144.
  • 55D. A. Liberles.

    Ancestral Sequence Reconstruction, Oxford University Press, 2007.
  • 56G. 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
  • 57I. 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
  • 58F. 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 ]
  • 59A. 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
  • 60D. 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.
  • 61D. 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.
  • 62M. 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
  • 63A. 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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