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. 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
• 2Y. 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
• 3W. 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
• 4S. 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
• 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, n^o 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, n^o 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, n^o 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, 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

• 10Y. Anselmetti, V. Berry, C. Chauve, A. Chateau, E. Tannier, S. Bérard.
  Ancestral gene synteny reconstruction improves extant species scaffolding, in: BMC Genomics, 2015, vol. 16, n^o Suppl 10, S11. [ DOI : 10.1101/023085 ]
  https://hal.archives-ouvertes.fr/hal-01180303
• 11O. 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
• 12P. Biller, L. Guéguen, E. Tannier.
  Moments of genome evolution by Double Cut-and-Join, in: BMC Bioinformatics, 2015, vol. 16, n^o Suppl 14, S7. [ DOI : 10.1186/1471-2105-16-S14-S7 ]
  https://hal.inria.fr/hal-01179597
• 13P. Cellier, T. Charnois, M. Plantevit, C. Rigotti, B. Crémilleux, O. Gandrillon, J. Klema, J.-L. Manguin.
  Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts, in: Journal of Biomedical Semantics, 2015, vol. 6, 27 p. [ DOI : 10.1186/s13326-015-0023-3 ]
  https://hal.archives-ouvertes.fr/hal-01192959
• 14Z. Chaker, S. Aïd, H. Berry, M. Holzenberger.
  Suppression of IGF-I signals in neural stem cells enhances neurogenesis and olfactory function during aging, in: Aging Cell, July 2015, 10 p. [ DOI : 10.1111/acel.12365 ]
  https://hal.inria.fr/hal-01163564
• 15F. Crauste, E. Terry, I. L. Mercier, J. Mafille, S. Djebali, T. Andrieu, B. Mercier, G. Kaneko, C. Arpin, J. Marvel, O. Gandrillon.
  Predicting pathogen-specific CD8 T cell immune responses from a modeling approach, in: Journal of Theoretical Biology, June 2015, vol. 374, pp. 66-82. [ DOI : 10.1016/j.jtbi.2015.03.033 ]
  https://hal.archives-ouvertes.fr/hal-01242319
• 16Y. 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
• 17W. 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. [ DOI : 10.1007/978-3-319-19048-8_16 ]
  https://hal.inria.fr/hal-01179197
• 18A. 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
• 19M. Jacquier, H. A. Soula, F. Crauste.
  A mathematical model of leptin resistance, in: Mathematical Biosciences, September 2015, vol. 267. [ DOI : 10.1016/j.mbs.2015.06.008 ]
  https://hal.inria.fr/hal-01233483
• 20C. Langlois, T. Douillard, H. Yuan, N. P. Blanchard, A. Descamps-Mandine, B. Van De Moortèle, C. Rigotti, T. Epicier.
  Crystal orientation mapping via ion channeling: An alternative to EBSD, in: Ultramicroscopy, October 2015, vol. 157, pp. 65-72. [ DOI : 10.1016/j.ultramic.2015.05.023 ]
  https://hal.archives-ouvertes.fr/hal-01226846
• 21F. Murat, R. R. Zhang, S. Guizard, H. Gavranovic, R. Flores, D. Steinbach, H. Quesneville, E. Tannier, J. Salse.
  Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops, in: Genome Biology and Evolution, 2015, vol. 7, n^o 3, pp. 735-749. [ DOI : 10.1093/gbe/evv014 ]
  https://hal.archives-ouvertes.fr/hal-01133906
• 22E. C. Perez, J. E. Elie, I. C. Boucaud, T. Crouchet, C. O. Soulage, H. A. Soula, F. E. Theunissen, C. Vignal.
  Physiological resonance between mates through calls as possible evidence of empathic processes in songbirds, in: Hormones and Behavior, 2015, vol. 75, pp. 130–141.
  https://hal.archives-ouvertes.fr/hal-01253147
• 23E. Perez, M. Fernandez, S. Griffith, C. Vignal, H. A. Soula.
  Impact of visual contact on vocal interaction dynamics of pair-bonded birds, in: Animal Behaviour, 2015, vol. 107, pp. 125–137.
  https://hal.archives-ouvertes.fr/hal-01253146
• 24M. Semeria, E. Tannier, L. Guéguen.
  Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies, in: BMC Bioinformatics, 2015, vol. 16, n^o Suppl 14, S5. [ DOI : 10.1186/1471-2105-16-S14-S5 ]
  https://hal.inria.fr/hal-01179596
• 25H. 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
• 26G. 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, 2015. [ DOI : 10.1098/rstb.2014.0335 ]
  https://hal.archives-ouvertes.fr/hal-01218565
• 27G. Szöllősi, 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

International Conferences with Proceedings

• 28A. Bousquet, J. Briffaut, E. Caron, E. María Dominguez, J. Franco, A. Lefray, O. López, S. Ros, J. Rouzaud-Cornabas, C. Toinard, M. Uriarte.
  Enforcing Security and Assurance Properties in Cloud Environment, in: 8th IEEE/ACM International Conference on Utility and Cloud Computing (UCC 2015), Limassol, Cyprus, 8th IEEE/ACM International Conference on Utility and Cloud Computing, University of Cyprus, December 2015.
  https://hal.inria.fr/hal-01240557
• 29A. Lefray, E. Caron, J. Rouzaud-Cornabas, C. Toinard.
  Microarchitecture-Aware Virtual Machine Placement under Information Leakage Constraints, in: 8th IEEE International Conference on Cloud Computing (IEEE Cloud 2015), New-York, United States, June 2015, n^o Print ISBN: 978-1-4673-7286-2, pp. 588 - 595, http://www.thecloudcomputing.org/2015/. [ DOI : 10.1109/CLOUD.2015.84 ]
  https://hal.inria.fr/hal-01240573
• 30N. Méger, C. Rigotti, C. Pothier.
  Swap Randomization of Bases of Sequences for Mining Satellite Image Time Series, in: European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD), Porto, Portugal, Lecture Notes in Computer Science volume 9285, September 2015.
  https://hal.archives-ouvertes.fr/hal-01200674
• 32Y. Pericault, C. Pothier, N. Meger, C. Rigotti, F. Vernier, H.-T. Pham, E. Trouve.
  A swap randomization approach for mining motion field time series over the Argentiere glacier, in: 2015 8th International Workshop on the Analysis of Multitemporal Remote Sensing Images (Multi-Temp), Annecy, France, July 2015. [ DOI : 10.1109/Multi-Temp.2015.7245757 ]
  https://hal.archives-ouvertes.fr/hal-01237206
• 33Y. 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

Conferences without Proceedings

• 34J. Gippet, C. Rocabert, S. Fenet, A. Dumet, B. Kaufmann.
  Modeling and evaluating human-mediated dispersal mechanisms at landscape scale: a study of road network and invation parameters for Lasius neglectus ants invasive species, in: World Conference on Natural Resource Modeling, Bordeaux, France, June 2015.
  https://hal.archives-ouvertes.fr/hal-01242828
• 35S. Peignier, C. Rigotti, G. Beslon.
  Subspace Clustering for all Seasons, in: EvoEvo Workshop (satellite workshop of ECAL 2015), york, United Kingdom, July 2015.
  https://hal.inria.fr/hal-01252793
• 36C. 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

Scientific Books (or Scientific Book chapters)

• 37J.-G. Dumas, J.-L. Roch, E. Tannier, S. Varrette.
  Foundations of Coding: Compression, Encryption, Error-Correction, Wiley, 2015, 376 p.
  https://hal.archives-ouvertes.fr/hal-00765802

Other Publications

• 38H. Berry, T. Lepoutre, Á. Mateos González.
  Quantitative convergence towards a self similar profile in an age-structured renewal equation for subdiffusion, March 2015, working paper or preprint.
  https://hal.inria.fr/hal-01136667
• 39E. Noutahi, M. Semeria, M. Lafond, J. Seguin, B. Boussau, L. Guéguen, N. El-Mabrouk, E. Tannier.
  Efficient gene tree correction guided by species and synteny evolution, August 2015, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01162963

References in notes

• 40S. 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.
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• 41J. A. Bailey, R. Baertsch, W. J. Kent, D. Haussler, E. E. Eichler.
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  Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation, in: Biophys J, 2002, vol. 83, n^o 4, pp. 1891–1901.
• 43G. 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, n^o 1, pp. 32-40.
• 44G. 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.
• 45G. Beslon, Y. Sanchez-Dehesa, D. P. Parsons, C. Rigotti, J.-M. Peña.
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• 46B. Caré, H. A. Soula.
  Impact of receptor clustering on ligand binding, in: BMC Systems Biology, March 2011, vol. 5, n^o 1, 48 p, PMID: 21453460. [ DOI : 10.1186/1752-0509-5-48 ]
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• 47C. Chauve, H. Gavranovic, A. Ouangraoua, E. Tannier.
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• 48A. 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, n^o 1, 2 p.
• 49A. E. Darling, I. Miklós, M. A. Ragan.
  Dynamics of genome rearrangement in bacterial populations, in: PLoS Genet, 2008, vol. 4, n^o 7, e1000128.
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• 50L. A. David, E. J. Alm.
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• 51M. Eigen.
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• 52M. Elowitz, A. Levine, E. Siggia, P. Swain.
  Stochastic gene expression in a single cell, in: Science, 2002, vol. 297, n^o 5584, pp. 1183–1186.
• 53J. Felsenstein.
  Inferring phylogenies, Sinauer Associates, 2004.
• 54P. Galison.
  Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
• 55T. 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
• 56International Aphid Genomics Consortium.
  Genome sequence of the pea aphid Acyrthosiphon pisum, in: PLoS Biol, Feb 2010, vol. 8, n^o 2, e1000313.
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• 57C. 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, n^o 10, pp. 2344-2353.
• 58C. 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, n^o 1, pp. 149-156.
• 59C. 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.
• 60C. 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, n^o 4, pp. 621–630.
• 61R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami.
  The evolutionary origin of complex features, in: Nature, 2003, vol. 423, pp. 139–144.
• 62D. A. Liberles.
  Ancestral Sequence Reconstruction, Oxford University Press, 2007.
• 63G. 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, n^o 8, e21915.
  http://dx.doi.org/10.1371/journal.pone.0021915
• 64I. Miklós, E. Tannier.
  Bayesian sampling of genomic rearrangement scenarios via double cut and join, in: Bioinformatics, Dec 2010, vol. 26, n^o 24, pp. 3012–3019.
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• 65F. 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, n^o 11, pp. 1545–1557. [ DOI : 10.1101/gr.109744.110 ]
• 66A. Ouangraoua, E. Tannier, C. Chauve.
  Reconstructing the architecture of the ancestral amniote genome, in: Bioinformatics, Oct 2011, vol. 27, n^o 19, pp. 2664–2671.
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• 67D. 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.
• 68D. 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.
• 69M. Sémon, K. H. Wolfe.
  Consequences of genome duplication, in: Curr Opin Genet Dev, Dec 2007, vol. 17, n^o 6, pp. 505–512.
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• 70A. Tofigh, M. Hallett, J. Lagergren.
  Simultaneous identification of duplications and lateral gene transfers, in: IEEE/ACM Trans Comput Biol Bioinform, 2011, vol. 8, n^o 2, pp. 517–535.
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