Project-Team Beagle
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Research Program
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Bibliography

Major publications by the team in recent years
  • 1B. 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
  • 2G. Beslon, B. Batut, D. P. Parsons, D. Schneider, C. Knibbe.
    An alife game to teach evolution of antibiotic resistance, in: ECAL - 12th European Conference on Artificial Life - 2013, Taormina, Italy, MIT Press, 2013.
    http://hal.inria.fr/hal-00849345
  • 3A.-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
  • 4M. 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.
  • 5T. 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
  • 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
  • 7J. Naudé, J. T. Paz, H. Berry, B. Delord.
    A theory of rate coding control by intrinsic plasticity effects, in: PLoS Computational Biology, 2012, vol. 8, no 1. [ DOI : 10.1371/ journal.pcbi.1002349 ]
    http://hal.inria.fr/hal-00645336
  • 8M. Patterson, G. Szöllősi, V. Daubin, E. Tannier.
    Lateral gene transfer, rearrangement, reconciliation, in: BMC Bioinformatics, 2013, vol. 14, no Suppl 15, S4 p.
    http://hal.inria.fr/hal-00873233
  • 9A. Rajaraman, E. Tannier, C. Chauve.
    FPSAC: Fast Phylogenetic Scaffolding of Ancient Contigs, in: Bioinformatics, December 2013, vol. 29, no 23, pp. 2987-2994.
    http://hal.inria.fr/hal-00859185
  • 10H. 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
  • 11G. 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
  • 12J. 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

  • 13S. Fischer.
    Modélisation de l'évolution de la taille des génomes et de leur densité en gènes par mutations locales et grands réarrangements chromosomiques, INSA de Lyon, December 2013.
    http://hal.inria.fr/tel-00924831
  • 14G. Kaneko.
    Analyse et modélisation de la stochasticité de l'expression génique dans des cellules eucaryotes, INSA de Lyon, September 2013.
    http://hal.inria.fr/tel-00926607

Articles in International Peer-Reviewed Journals

  • 15B. 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
  • 16H. Berry, H. Chaté.
    Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes, in: Physical Review E, 2014.
    http://hal.inria.fr/inria-00575651
  • 17B. Boussau, G. J. Szöllosi, L. Duret, M. Gouy, E. Tannier, V. Daubin.
    Genome-scale coestimation of species and gene trees, in: Genome Research, February 2013, vol. 23, pp. 323-330. [ DOI : 10.1101/gr.141978.112 ]
    http://hal.inria.fr/hal-00750148
  • 18B. R. Caré, H. A. Soula.
    Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime, in: Physical Review E, January 2013, vol. 87, no 1. [ DOI : 10.1103/PhysRevE.87.012720 ]
    http://hal.inria.fr/hal-00858439
  • 19A.-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
  • 20M. L. Croze, R. E. Vella, N. J. Pillon, H. A. Soula, L. Hadji, M. Guichardant, C. O. Soulage.
    Chronic treatment with myo-inositol reduces white adipose tissue accretion and improves insulin sensitivity in female mice, in: The Journal of Nutritional Biochemistry, February 2013, vol. 24, no 2, pp. 457-66. [ DOI : 10.1016/j.jnutbio.2012.01.008 ]
    http://hal.inria.fr/hal-00759518
  • 21L. Koppe, N. J. Pillon, R. E. Vella, M. L. Croze, C. C. Pelletier, S. Chambert, Z. Massy, G. Glorieux, R. Vanholder, Y. Dugenet, H. A. Soula, D. Fouque, C. O. Soulage.
    p-Cresyl sulfate promotes insulin resistance associated with CKD, in: Journal of the American Society of Nephrology, January 2013, vol. 24, no 1, pp. 88-99. [ DOI : 10.1681/ASN.2012050503 ]
    http://hal.inria.fr/hal-00850482
  • 22M. Lafond, M. Semeria, K. Swenson, E. Tannier, N. El-Mabrouk.
    Gene tree correction guided by orthology, in: BMC Bioinformatics, 2013, vol. 14, no Suppl 15, S5 p.
    http://hal.inria.fr/hal-00873235
  • 23P.-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
  • 24J. 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, no 38, pp. 15032-15043. [ DOI : 10.1523/JNEUROSCI.0870-13.2013 ]
    http://hal.inria.fr/hal-00844218
  • 25M. Patterson, G. Szöllősi, V. Daubin, E. Tannier.
    Lateral gene transfer, rearrangement, reconciliation, in: BMC Bioinformatics, 2013, vol. 14, no Suppl 15, S4 p.
    http://hal.inria.fr/hal-00873233
  • 26A. Rajaraman, E. Tannier, C. Chauve.
    FPSAC: Fast Phylogenetic Scaffolding of Ancient Contigs, in: Bioinformatics, September 2013, vol. 29, no 23, pp. 2987-2994. [ DOI : 10.1093/bioinformatics/btt527 ]
    http://hal.inria.fr/hal-00859185
  • 27H. 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
  • 28H. A. Soula, H. Julienne, C. O. Soulage, A. Géloën.
    Modelling adipocytes size distribution, in: J Theor Biol, Journal-Full = Journal of theoretical biology, September 2013, vol. 332, pp. 89-95. [ DOI : 10.1016/j.jtbi.2013.04.025 ]
    http://hal.inria.fr/hal-00850474
  • 29G. J. Szöllosi, W. Rosikiewicz, B. Boussau, E. Tannier, V. Daubin.
    Efficient Exploration of the Space of Reconciled Gene Trees, in: Systematic Biology, August 2013, epub ahead of print. [ DOI : 10.1093/sysbio/syt054 ]
    http://hal.inria.fr/hal-00856826
  • 30G. J. Szöllosi, E. Tannier, N. Lartillot, V. Daubin.
    Lateral Gene Transfer from the Dead, in: Systematic Biology, January 2013, epub ahead of print. [ DOI : 10.1093/sysbio/syt003 ]
    http://hal.inria.fr/hal-00784662
  • 31J. 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

Articles in Non Peer-Reviewed Journals

International Conferences with Proceedings

  • 33G. Beslon, B. Batut, D. P. Parsons, D. Schneider, C. Knibbe.
    An alife game to teach evolution of antibiotic resistance, in: ECAL - 12th European Conference on Artificial Life - 2013, Taormina, Italy, MIT Press, 2013.
    http://hal.inria.fr/hal-00849345
  • 34Y. Cui, V. Paille, B. Delord, S. Genet, E. Fino, L. Venance, H. Berry.
    Endocannabinoids mediate spike-timing dependent potentiation and depression: a model-based experimental approach, in: the Twenty Second Annual Computational Neuroscience Meeting: CNS*2013, Paris, France, G. S. Cymbalyuk, A. A. Prinz (editors), Biomed Central, 2013, vol. 14, O1 p. [ DOI : 10.1186/1471-2202-14-S1-O1 ]
    http://hal.inria.fr/inserm-00842298

Scientific Books (or Scientific Book chapters)

  • 35H. Berry.
    Modélisation de la diffusion-réaction dans les milieux intracellulaires encombrés, in: Le vivant discret et continu, N. Glade, A. Stéphanou (editors), Editions Matériologiques, September 2013, pp. 241-266.
    http://hal.inria.fr/hal-00858738
  • 36H. Berry, G. Beslon.
    De la modélisation comme poésie. La modélisation de systèmes biologiques complexes vue par deux modélisateurs, in: Modéliser & simuler. Epistémologies et pratiques de la modélisation et de la simulation, F. Varenne, M. Silberstein (editors), Editions Matériologiques, Paris, April 2013, vol. 1.
    http://hal.inria.fr/hal-00815550
  • 37C. Chauve, N. El-Mabrouk, E. Tannier.
    Models and Algorithms for Genome Evolution, Springer, 2013, 318 p.
    http://hal.inria.fr/hal-00847154
  • 38C. Chauve, N. El-Mabrouk, L. Gueguen, M. Semeria, E. Tannier.
    Duplication, Rearrangement and Reconciliation, in: Models and Algorithms for Genome Evolution, Springer, 2013.
    http://hal.inria.fr/hal-00847155
  • 39J.-G. Dumas, J.-L. Roch, E. Tannier, S. Varette.
    Foundations of Coding: Compression, Encryption, Error-Correction, –, 2014, A paraître.
    http://hal.inria.fr/hal-00765802
  • 40J.-G. Dumas, J.-L. Roch, E. Tannier, S. Varrette.
    Théorie des Codes : compression, cryptage, correction, 2e edition, Sciences Sup, Dunod, August 2013, 384 p.
    http://hal.inria.fr/hal-00932851
  • 41C. Knibbe.
    L'évolution expérimentale in silico, in: Modéliser et simuler - Epistémologies et pratiques de la modélisation et de la simulation - Tome 1, F. Varenne, M. Silberstein (editors), Editions Matériologiques, April 2013, pp. 581-610.
    http://hal.inria.fr/hal-00850175

Other Publications

  • 42C. Chauve, M. Patterson, A. Rajaraman.
    Hypergraph covering problems motivated by genome assembly questions, 2013, 13 pages+3 page appendix A short version will appear in the proceedings of IWOCA 2013.
    http://hal.inria.fr/hal-00849753
  • 43Y. Cui, V. Paille, B. Delord, S. Genet, E. Fino, L. Venance, H. Berry.
    Endocannabinoids mediate spike-timing dependent potentiation and depression: a model-based experimental approach, in: Twenty Second Annual Computational Neuroscience Meeting : CNS 2013, Paris, France, July 2013, 01 p. [ DOI : 10.1186/1471-2202-14-S1-O1 ]
    http://hal.inria.fr/hal-00842299
  • 44A. Rajaraman, E. Tannier, C. Chauve.
    The genome of the medieval Black Death agent (extended abstract), 2013, Extended abstract of a talk presented at the conference JOBIM 2013. Full paper submitted.
    https://colloque.inra.fr/jobim2013_eng/, http://hal.inria.fr/hal-00849754
  • 45G. Szöllősi, E. Tannier, V. Daubin, B. Boussau.
    The inference of gene trees with species trees, 2013, arXiv:1311.0651.
    http://hal.inria.fr/hal-00915301
References in notes
  • 46S. S. Abby, E. Tannier, M. Gouy, V. Daubin.
    Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, in: BMC Bioinformatics, 2010, vol. 11, 324 p.
    http://dx.doi.org/10.1186/1471-2105-11-324
  • 47J.-M. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin, B. M. Porcel, B. Ségurens, V. Daubin, V. Anthouard, N. Aiach, O. Arnaiz, A. Billaut, J. Beisson, I. Blanc, K. Bouhouche, F. Câmara, S. Duharcourt, R. Guigó, D. Gogendeau, M. Katinka, A.-M. Keller, R. Kissmehl, C. Klotz, F. Koll, A. Le Mouël, G. Lepère, S. Malinsky, M. Nowacki, J. K. Nowak, H. Plattner, J. Poulain, F. Ruiz, V. Serrano, M. Zagulski, P. Dessen, M. Bétermier, J. Weissenbach, C. Scarpelli, V. Schächter, L. Sperling, E. Meyer, J. Cohen, P. Wincker.
    Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, in: Nature, Nov 2006, vol. 444, no 7116, pp. 171–178.
    http://dx.doi.org/10.1038/nature05230
  • 48J. 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, R23 p.
    http://dx.doi.org/10.1186/gb-2004-5-4-r23
  • 49H. 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.
  • 50G. 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.
  • 51G. 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.
  • 52G. 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.
  • 53B. R. 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
  • 54C. 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
  • 55A. 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.
  • 56A. 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
  • 57V. Daubin, N. A. Moran, H. Ochman.
    Phylogenetics and the cohesion of bacterial genomes, in: Science, Aug 2003, vol. 301, no 5634, pp. 829–832.
    http://dx.doi.org/10.1126/science.1086568
  • 58L. 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 ]
  • 59M. Eigen.
    Selforganization of matter and the evolution of biological macromolecules, in: Naturwissenschaften, 1971, vol. 58, no 10, pp. 465-523.
  • 60M. Elowitz, A. Levine, E. Siggia, P. Swain.
    Stochastic gene expression in a single cell, in: Science, 2002, vol. 297, no 5584, pp. 1183–1186.
  • 61J. Felsenstein.
    Inferring phylogenies, Sinauer Associates, 2004.
  • 62P. Galison.
    Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
  • 63T. 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
  • 64International 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
  • 65O. Jaillon, J.-M. Aury, F. Brunet, J.-L. Petit, N. Stange-Thomann, E. Mauceli, L. Bouneau, C. Fischer, C. Ozouf-Costaz, A. Bernot, S. Nicaud, D. Jaffe, S. Fisher, G. Lutfalla, C. Dossat, B. Ségurens, C. Dasilva, M. Salanoubat, M. Levy, N. Boudet, S. Castellano, V. Anthouard, C. Jubin, V. Castelli, M. Katinka, B. Vacherie, C. Biémont, Z. Skalli, L. Cattolico, J. Poulain, V. De Berardinis, C. Cruaud, S. Duprat, P. Brottier, J.-P. Coutanceau, J. Gouzy, G. Parra, G. Lardier, C. Chapple, K. J. McKernan, P. McEwan, S. Bosak, M. Kellis, J.-N. Volff, R. Guigó, M. C. Zody, J. Mesirov, K. Lindblad-Toh, B. Birren, C. Nusbaum, D. Kahn, M. Robinson-Rechavi, V. Laudet, V. Schächter, F. Quétier, W. Saurin, C. Scarpelli, P. Wincker, E. S. Lander, J. Weissenbach, H. R. Crollius.
    Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype., in: Nature, Oct 2004, vol. 431, no 7011, pp. 946–957.
    http://dx.doi.org/10.1038/nature03025
  • 66C. 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.
  • 67C. 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. 149-156c.
  • 68C. 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.
  • 69C. 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.
  • 70R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami.
    The evolutionary origin of complex features, in: Nature, 2003, vol. 423, pp. 139–144.
  • 71D. A. Liberles.
    Ancestral Sequence Reconstruction, Oxford University Press, 2007.
  • 72J. Ma, L. Zhang, B. B. Suh, B. J. Raney, R. C. Burhans, W. J. Kent, M. Blanchette, D. Haussler, W. Miller.
    Reconstructing contiguous regions of an ancestral genome, in: Genome Res, Dec 2006, vol. 16, no 12, pp. 1557–1565.
    http://dx.doi.org/10.1101/gr.5383506
  • 73G. 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
  • 74I. 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
  • 75M. Muffato, A. Louis, C.-E. Poisnel, H. R. Crollius.
    Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes., in: Bioinformatics, Apr 2010, vol. 26, no 8, pp. 1119–1121.
    http://dx.doi.org/10.1093/bioinformatics/btq079
  • 76F. 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 ]
  • 77A. 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
  • 78D. 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.
  • 79D. 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.
  • 80M. 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
  • 81A. 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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