Bibliography

Major publications by the team in recent years

1S. S. Abby, E. Tannier, M. Gouy, V. Daubin.

Lateral gene transfer as a support for the tree of life., in: Proceedings of the National Academy of Sciences, March 2012, vol. 109, n^o 13, p. 4962-4967. [ DOI : 10.1073/pnas.1116871109 ]

http://hal.inria.fr/hal-00681090
2E. Bertin, G. Beslon, O. Gandrillon, S. Grauwin, P. Jensen, N. Schabanel.

Les complexités : point de vue d'un institut des systèmes complexes, in: Hermès, June 2011, n^o 60, p. 145–150.

http://liris.cnrs.fr/publis/?id=5283
3B. Caré, H. A. Soula.

Impact of receptor clustering on ligand binding, in: BMC Systems Biology, March 2011, vol. 5, n^o 48, 13 p, PMID: 21453460. [ DOI : 10.1186/1752-0509-5-48 ]

http://www.ncbi.nlm.nih.gov/pubmed/21453460
4A. Coulon, G. Beslon, H. A. Soula.

Enhanced Stimulus Encoding Capabilities with Spectral Selectivity in Inhibitory Circuits by STDP, in: Neural Computation, April 2011, vol. 23, n^o 4, p. 882–908.

http://liris.cnrs.fr/publis/?id=4836
5M. 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, n^o 12, e1002293 p.
6A. Hashmi, H. Berry, O. Temam, M. Lipasti.

Automatic Abstraction and Fault Tolerance in Cortical Microachitectures, in: 38th ACM/IEEE International Symposium on Computer Architecture, ISCA 2011, San Jose, CA, USA, June 2011.
7T. 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, p. 352-365.

http://hal.inria.fr/hal-00696231
8A. Julea, N. Méger, C. Rigotti, E. Trouvé, R. Jolivet, P. Bolon.

Efficient Spatiotemporal Mining of Satellite Image Time Series for Agricultural Monitoring, in: Transactions on Machine Learning and Data Mining, July 2012, vol. 5, n^o 1, p. 23-44.

http://hal.inria.fr/hal-00702433
9C. Knibbe, D. P. Parsons, G. Beslon.

Parsimonious modeling of scaling laws in genomes and transcriptomes, in: European Conference on Artificial Life (ECAL), MIT Press, 2011, p. 414–415.
10J. 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, n^o 1, e1002349 p. [ DOI : 10.1371/ journal.pcbi.1002349 ]

http://hal.inria.fr/hal-00645336
11D. 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, p. 622–629.
12G. 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, p. 17513-17518. [ DOI : 10.1073/pnas.1202997109 ]

http://hal.inria.fr/hal-00740292

Publications of the year

Doctoral Dissertations and Habilitation Theses

13B. Caré.

Modèles individu-centrés de l'impact fonctionnel des hétérogénéités de diffusion et de distribution spatiale des protéines de signalisation cellulaire, INSA Lyon, 2012.
14A.-S. Coquel.

Dynamique de l'agrégation protéique chez la bactérie Escherichia coli, INSA Lyon, ED 512 Informatique Mathématiques, Lyon, France, November 2012.
15P.-N. Mougel.

Finding homogenous collections of dense subgraphs using constraint-based data mining approaches. Application to the analysis of scientific collaboration networks and protein interaction graphs, INSA Lyon, 2012.

Articles in International Peer-Reviewed Journals

16S. S. Abby, E. Tannier, M. Gouy, V. Daubin.

Lateral gene transfer as a support for the tree of life., in: Proceedings of the National Academy of Sciences, March 2012, vol. 109, n^o 13, p. 4962-4967. [ DOI : 10.1073/pnas.1116871109 ]

http://hal.inria.fr/hal-00681090
17B. Boussau, G. J. Szöllosi, L. Duret, M. Gouy, E. Tannier, V. Daubin.

Genome-scale coestimation of species and gene trees., in: Genome Res, 2013.

http://dx.doi.org/10.1101/gr.141978.112
18S. Bérard, C. Gallien, B. Boussau, G. J. Szöllosi, V. Daubin, E. Tannier.

Evolution of gene neighborhoods within reconciled phylogenies., in: Bioinformatics, September 2012, vol. 28, n^o 18, p. i382-i388. [ DOI : 10.1093/bioinformatics/bts374 ]

http://hal.inria.fr/hal-00733178
19M. 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: J Nutr Biochem, May 2012.

http://dx.doi.org/10.1016/j.jnutbio.2012.01.008
20S. Fischer, P. Kurbatova, N. Bessonov, O. Gandrillon, V. Volpert, F. Crauste.

Modeling erythroblastic islands: Using a hybrid model to assess the function of central macrophage, in: Journal of Theoretical Biology, 2012, vol. 298, p. 92–106.
21O. Gandrillon, D. Kolesnik-Antoine, J.-J. Kupiec, G. Beslon.

Chance at the heart of the cell., in: Prog Biophys Mol Biol, Sep 2012, vol. 110, n^o 1, p. 1–4.

http://dx.doi.org/10.1016/j.pbiomolbio.2012.05.006
22S. Grauwin, G. Beslon, E. Fleury, S. Franceschelli, C. Robardet, J.-B. Rouquier, P. Jensen.

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity, in: Journal of the American Society for Information Science and Technology, 2012, 10.1002/asi.22644. [ DOI : 10.1002/asi.22644 ]

http://hal.inria.fr/hal-00706567
23T. 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, p. 352-365.

http://hal.inria.fr/hal-00696231
24B. R. Jones, A. Rajaraman, E. Tannier, C. Chauve.

ANGES: reconstructing ANcestral GEnomeS maps., in: Bioinformatics, September 2012, vol. 28, n^o 18, p. 2388-90. [ DOI : 10.1093/bioinformatics/bts457 ]

http://hal.inria.fr/hal-00733180
25A. Julea, N. Méger, C. Rigotti, E. Trouvé, R. Jolivet, P. Bolon.

Efficient Spatiotemporal Mining of Satellite Image Time Series for Agricultural Monitoring, in: Transactions on Machine Learning and Data Mining, July 2012, vol. 5, n^o 1, p. 23-44.

http://hal.inria.fr/hal-00702433
26J. Maňuch, M. Patterson, R. Wittler, C. Chauve, E. Tannier.

Linearization of ancestral multichromosomal genomes, in: BMC Bioinformatics, 2012, vol. 13(Suppl 19), S11 p.
27I. Miklos, E. Tannier.

Approximating the number of Double Cut-and-Join scenarios, in: Theoretical Computer Science, June 2012, vol. 439, p. 30-40.

http://hal.inria.fr/hal-00699567
28J. 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, n^o 1, e1002349. [ DOI : 10.1371/ journal.pcbi.1002349 ]

http://hal.inria.fr/hal-00645336
29E. C. Perez, J. E. Elie, C. O. Soulage, H. A. Soula, N. Mathevon, C. Vignal.

The acoustic expression of stress in a songbird: does corticosterone drive isolation-induced modifications of zebra finch calls?, in: Horm Behav, Apr 2012, vol. 61, n^o 4, p. 573-81.

http://dx.doi.org/10.1016/j.yhbeh.2012.02.004
30H. A. Soula, A. Coulon, G. Beslon.

Membrane microdomains emergence through non-homogeneous diffusion, in: BMC Biophysics, 2012, vol. 5, n^o 1, 6 p. [ DOI : 10.1186/2046-1682-5-6 ]

http://hal.inria.fr/hal-00696274
31G. 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, p. 17513-17518. [ DOI : 10.1073/pnas.1202997109 ]

http://hal.inria.fr/hal-00740292
32G. J. Szöllosi, E. Tannier, N. Lartillot, V. Daubin.

Lateral gene transfer from the dead, in: Systematic Biology, 2013.
33J. Viñuelas, G. Kaneko, A. Coulon, G. Beslon, O. Gandrillon.

Towards experimental manipulation of stochasticity in gene expression., in: Prog Biophys Mol Biol, Sep 2012, vol. 110, n^o 1, p. 44–53.

http://dx.doi.org/10.1016/j.pbiomolbio.2012.04.010
34N. Vlassopoulos, N. Fatès, H. Berry, B. Girau.

Large-scale Simulations on FPGAs: Finding the Asymptotic Critical Threshold of the Greenberg-Hastings Cellular Automata, in: Journal of Cellular Automata, 2012, vol. 7, n^o 1, p. 5-29.

http://hal.inria.fr/hal-00644660

International Conferences with Proceedings

35M. Bernt, K.-M. Chao, J.-W. Kao, M. Middendorf, E. Tannier.

Preserving Inversion Phylogeny Reconstruction, in: WABI, Slovenia, 2012, p. 1-13.

http://hal.inria.fr/hal-00733188
36B. Caré, H. A. Soula.

Impact of receptor clustering on the membrane-based stage of a signalling pathway, in: 4nd International Conference on Bioinformatics and Computational Biology, 2012, p. 1-6.
37B. Caré, H. A. Soula.

The Effect of Membrane Receptor Clustering on Spatio- temporal Cell Signalling Dynamics, in: Proceedings of the 9th International Conference on Information Processing in Cells and Tissues 2012, Cambridge, United Kingdom, 2012, vol. 7723, p. 50-61.

http://hal.inria.fr/hal-00759519
38J. Lallouette, H. Berry.

Topology drives calcium wave propagation in 3D astrocyte networks, in: European Conference on Complex Systems 2012, Bruxelles, Belgique, 2012, This work was supported by the Israel-France High Council for Science and Technology Research..

http://hal.inria.fr/hal-00758998
40P.-N. Mougel, C. Rigotti, O. Gandrillon.

Finding Collections of k-Clique Percolated Components in Attributed Graphs, in: Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Kuala Lumpur, Malaisie, LNCS, 2012, vol. 7302, p. 181–192.

http://hal.inria.fr/hal-00758843
41P.-N. Mougel, C. Rigotti, O. Gandrillon.

Finding Collections of Protein Modules in Protein-Protein Interaction Networks, in: Bioinformatics and Computational Biology (BICoB), Las Vegas, États-Unis, 2012, p. 216-222.

http://hal.inria.fr/hal-00758858
42D. P. Parsons, C. Knibbe, G. Beslon.

The Paradoxical Effects of Allelic Recombination on Fitness, in: Artificial Life XIII, 2012.

Other Publications

43H. A. Soula, B. Caré, G. Beslon, H. Berry.

Anomalous versus non-homogeneous diffusion in the ligand-binding equilibrium: when size matters, This research was supported by Inria grant ”AE ColAge” and a fellowship from Rhone-Alpes Region to B.C..

http://hal.inria.fr/hal-00720515

References in notes

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Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests., in: BMC Bioinformatics, 2010, vol. 11, 324 p.

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45J.-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, n^o 7116, p. 171–178.

http://dx.doi.org/10.1038/nature05230
46J. A. Bailey, R. Baertsch, W. J. Kent, D. Haussler, E. E. Eichler.

Hotspots of mammalian chromosomal evolution., in: Genome Biol, 2004, vol. 5, n^o 4, R23 p.

http://dx.doi.org/10.1186/gb-2004-5-4-r23
47H. Berry.

Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation., in: Biophys J, 2002, vol. 83, n^o 4, p. 1891–1901.
48G. 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, p. 32-40.
49G. 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, p. 111-114.
50G. 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, n^o 2, p. 173-191.
51C. 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, n^o 9, p. 1097–1112.

http://dx.doi.org/10.1089/cmb.2010.0092
52A. E. Darling, I. Miklós, M. A. Ragan.

Dynamics of genome rearrangement in bacterial populations., in: PLoS Genet, 2008, vol. 4, n^o 7, e1000128.

http://dx.doi.org/10.1371/journal.pgen.1000128
53V. Daubin, N. A. Moran, H. Ochman.

Phylogenetics and the cohesion of bacterial genomes., in: Science, Aug 2003, vol. 301, n^o 5634, p. 829–832.

http://dx.doi.org/10.1126/science.1086568
54L. A. David, E. J. Alm.

Rapid evolutionary innovation during an Archaean genetic expansion., in: Nature, Jan 2011, vol. 469, n^o 7328, p. 93–96.

http://dx.doi.org/10.1038/nature09649
55M. Eigen.

Selforganization of matter and the evolution of biological macromolecules, in: Naturwissenschaften, 1971, vol. 58, n^o 10, p. 465-523.
56M. Elowitz, A. Levine, E. Siggia, P. Swain.

Stochastic gene expression in a single cell, in: Science, 2002, vol. 297, n^o 5584, p. 1183–1186.
57J. Felsenstein.

Inferring phylogenies, Sinauer Associates, 2004.
58P. Galison.

Image and Logic: A Material Culture of Microphysics, University Of Chicago Press, 1997.
59T. 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, p. 352-365.

http://hal.inria.fr/hal-00696231
60 International Aphid Genomics Consortium.

Genome sequence of the pea aphid Acyrthosiphon pisum., in: PLoS Biol, Feb 2010, vol. 8, n^o 2, e1000313.

http://dx.doi.org/10.1371/journal.pbio.1000313
61O. 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, n^o 7011, p. 946–957.

http://dx.doi.org/10.1038/nature03025
62C. 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, p. 2344-2353.
63C. 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, p. 149-156c.
64C. 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.
65C. 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, p. 621–630.
66R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami.

The evolutionary origin of complex features, in: Nature, 2003, vol. 423, p. 139–144.
67D. A. Liberles.

Ancestral Sequence Reconstruction, Oxford University Press, 2007.
68J. 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, n^o 12, p. 1557–1565.

http://dx.doi.org/10.1101/gr.5383506
69G. 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
70I. Miklós, E. Tannier.

Bayesian sampling of genomic rearrangement scenarios via double cut and join., in: Bioinformatics, Dec 2010, vol. 26, n^o 24, p. 3012–3019.

http://dx.doi.org/10.1093/bioinformatics/btq574
71M. 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, n^o 8, p. 1119–1121.

http://dx.doi.org/10.1093/bioinformatics/btq079
72F. 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, p. 1545–1557.

http://dx.doi.org/10.1101/gr.109744.110
73A. Ouangraoua, E. Tannier, C. Chauve.

Reconstructing the architecture of the ancestral amniote genome., in: Bioinformatics, Oct 2011, vol. 27, n^o 19, p. 2664–2671.

http://dx.doi.org/10.1093/bioinformatics/btr461
74D. P. Parsons, C. Knibbe, G. Beslon.

Importance of the rearrangement rates on the organization of transcription, in: Proceedings of Artificial Life 12, MIT Press ed., 2010, p. 479-486.
75D. 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, p. 622–629.
76M. Sémon, K. H. Wolfe.

Consequences of genome duplication., in: Curr Opin Genet Dev, Dec 2007, vol. 17, n^o 6, p. 505–512.

http://dx.doi.org/10.1016/j.gde.2007.09.007
77A. 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, p. 517–535.

http://dx.doi.org/10.1109/TCBB.2010.14

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