Team Symbiose

Overall Objectives
Scientific Foundations
Application Domains
New Results
Other Grants and Activities


Publications of the year

Doctoral Dissertations and Habilitation Theses

J. Gruel.
From biological data to molecular modelisation; application to TGF-beta signaling and hepatic fibrosis, Université de Rennes1, 2009, Ph. D. Thesis.
V. H. Nguyen.
Traitement parallèle des comparaisons intensives de séquences génomiques, Université de Rennes 1, 2009, Ph. D. Thesis.

Articles in International Peer-Reviewed Journal

J. Ahmad, J. Bourdon, D. Eveillard, J. Fromentin, O. Roux, C. Sinoquet.
Temporal constraints of a gene regulatory network: refining a qualitative simulation, in: BioSystems, Special Issue on Gene Regulatory Networks, 2009, 10.1016/j.biosystems.2009.05.002 p
A. Bankhead, I. Sach, C. Ni, N. Le Meur, M. Kruger, M. Ferrer, R. Gentleman, C. Rohl.
Knowledge based identification of essential signaling from genome-scale siRNA experiments., in: BMC Syst Biol, 2009, vol. 3, 80 p
M. Barret, P. Frey-Klett, M. Boutin, A.-Y. Guillerm-Erckelboudt, F. Martin, L. Guillot, A. Sarniguet.
The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29Arp, in: New Phytologist, 2009, vol. 181, p. 435-447
Y. Bigot, S. Renault, J. Nicolas, C. Moundras, M.-V. Demattei, S. Samain, D. K. Bideshi, B. A. Federici.
Symbiotic Virus at the Evolutionary Intersection of Three Types of Large DNA Viruses; Iridoviruses, Ascoviruses, and Ichnoviruses, in: PLoS ONE, 07 2009, vol. 4, no 7, e6397 p
P. Blavy, F. Gondret, H. Guillou, S. Lagarrigue, P. Martin, J. Van Milgen, O. Radulescu, A. Siegel.
A minimal model for hepatic fatty acid balance during fasting: Application to PPAR alpha-deficient mice, in: Journal of Theoretical Biology, 2009, vol. 261, p. 266-278
P. Casel, F. Moreews, S. Lagarrigue, C. Klopp.
sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters, in: BMC Proc, 2009, vol. 3 Suppl 4, S3 p.
R. Chikhi, D. Lavenier.
Paired-end read length lower bounds for genome re-sequencing, in: Bmc Bioinformatics, 10 2009
A. Crudu, A. Debussche, O. Radulescu.
Hybrid stochastic simplifications for multiscale gene networks, in: Bmc Systems Biology, 2009, vol. 3, 89 p
E. Fleury, A. Huvet, C. Lelong, J. De Lorgeril, V. Boulo, Y. Gueguen, E. Bachere, A. Tanguy, D. Moraga, C. Fabioux, P. Lindeque, J. Shaw, R. Reinhardt, P. Prunet, G. Davey, S. Lapegue, C. Sauvage, C. Corporeau, J. Moal, F. Gavory, P. Wincker, F. Moreews, C. Klopp, M. Mathieu, P. Boudry, P. Favrel.
Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase, in: BMC Genomics, Jul 2009, vol. 10, 341 p.
M. Galle, P. Peterlongo, F. Coste.
In-place update of suffix array while recoding words, in: International Journal of Foundations of Computer Science, 2009
A. Gattiker, L. Hermida, R. Liechti, I. Xenarios, O. Collin, J. Rougemont, M. Primig.
MIMAS 3.0 is a Multiomics Information Management and Annotation System, in: BMC Bioinformatics, 2009, vol. 10, no 1, 151 p
A. Gorban, O. Radulescu, A. Zinovyev.
Asymptotology of Chemical Reaction Networks, in: Chemical Engineering Science, 2009
J. Gruel, M. Le Borgne, N. Le Meur, N. Théret.
In silico investigation of ADAM12 effect on TGF-beta receptors trafficking., in: BMC Res Notes, 2009, vol. 2, 193 p
C. Guziolowski, A. Bourdé, F. Moreews, A. Siegel.
BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks, in: Bmc Genomics, 2009, vol. 26, 244 p
F. Hahne, N. Le Meur, R. R. Brinkman, B. Ellis, P. Haaland, D. Sarkar, J. Spidlen, E. Strain, R. Gentleman.
flowCore: a Bioconductor package for high throughput flow cytometry., in: Bmc Bioinformatics, 2009, vol. 10, 106 p
F. Legeai, S. Shigenobu, J.-P. Gauthier, J. Colbourne, C. Rispe, O. Collin, S. Richards, A. Wilson, D. Tagu.
AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome, in: Insect Molecular Biology, 2010, sous presse.
I.-C. Lerman.
Analyse logique, combinatoire et statistique de la construction d'une hiérarchie implicative ; niveaux et noeuds significatifs, in: Revue Mathématiques et sciences Humaines Mathematics and Social Sciences, 2009
M. Manu, S. Surkova, A. V. Spirov, V. Gursky, H. Janssens, A.-R. Kim, O. Radulescu, C. E. Vanario-Alonso, D. Sharp, M. Samsonova, J. Reinitz.
Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors, in: PLoS Computational Biology, 2009, vol. 5, 3 p
M. Manu, S. Surkova, A. V. Spirov, V. Gursky, H. Janssens, A.-R. Kim, C. E. Vanario-Alonso, O. Radulescu, D. H. Sharp, M. Samsonova, J. Reinitz.
Canalization of gene expression in the Drosophila blastoderm by gap genes cross regulation, in: Plos Biology, 2009, vol. 7, 3 p
V. H. Nguyen, D. Lavenier.
PLAST: parallel local alignment search tool for database comparison, in: Bmc Bioinformatics, 10 2009, vol. 10, 329 p
P. Peterlongo, F. Coste, M. Galle.
In-place update of suffix array while recoding words, in: International Journal of Foundations of Computer Science (IJFCS), 2010.
P. Peterlongo, G. A. T. Sacomoto, A. P. Do Lago, N. Pisanti, M.-F. Sagot.
Lossless filter for multiple repeats with bounded edit distance., in: Algorithms for Molecular Biology :: Amb, 2009, vol. 4, 3 p
V. Poirriez, N. Yanev, R. Andonov.
A Hybrid Algorithm for the Unbounded Knapsack Problem, in: Discrete Optimization, 2009, vol. 6, p. 110-124
C. Rousseau, M. Gonnet, M. Leromancer, J. Nicolas.
CRISPI: a CRISPR Interactive database, in: Bioinformatics, 2009, vol. 24, no 25, p. 3317-3318
A. Siegel, J. Thuswaldner.
Topological properties of Rauzy fractals, in: Mémoires de la SMF, 2010.
S. Vakulenko, M. Manu, J. Reinitz, O. Radulescu.
Size Regulation in the Segmentation of Drosophila: Interacting Interfaces between Localized Domains of Gene Expression Ensure Robust Spatial Patterning, in: Phys.Rev.Lett., 2009, vol. 103, 168102 p

Articles in Non Peer-Reviewed Journal

J. Nicolas.
Décoder le vivant, in: Doc Sciences, 2009, p. 26-33
A. Siegel, B. Adamczewski, W. Steiner.
Présentation de "Numeration: Mathematics and Computer Science" (CIRM, 2009), in: Actes des rencontres du CIRM, 2009, vol. 1, p. 1-2

International Peer-Reviewed Conference/Proceedings

S. Blachon, G. Stoll, C. Guziolowski, A. Zinovyev, E. Barillot, A. Siegel, O. Radulescu.
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks, in: AIAI 2009 Workshop – Workshop on Biomedical Informatics and Intelligent Approaches in the Support of Genomic Medicine (BMIINT), Grèce, 04 2009, vol. 475, p. 72-87
J. Bourdon, I. Rusu.
Statistical Properties of Factor Oracles, in: COMBINATORIAL PATTERN MATCHING, France, Springer Verlag, 2009, vol. LNBI 5577, p. 326-338
S. Carat, R. Houlgatte, J. Bourdon.
A statistical method for PWM clustering, in: Moscow Conference on Computational Molecular Biology, Russie, 2009
R. Chikhi, D. Lavenier.
Paired-end reaf legth lower bounds for genome resequensing, in: ISMB / ECCB, Stockholm, 2009.
G. Collet, R. Andonov, N. Yanev, J.-F. Gibrat.
Protein Threading, in: 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, France, 06 2009
C. Guziolowski, J. Gruel, O. Radulescu, A. Siegel.
Curating a large-scale regulatory network by evaluating its consistency with expression datasets, in: CIBB 2008: Computational Intelligence Methods for Bioinformatics and Biostatistics CIBB 2008: Computational Intelligence Methods for Bioinformatics and Biostatistics - Selected revised papers, Italie, 2009, vol. 5488, p. 144-155
Graph and Hierarchical-based approaches for structuring association rule sets, in: 11th IFCS International Conference 2009, H. Bock (editor), Dresden University, 2009.
N. Le Meur, J. Gruel, M. Le Borgne, N. Théret.
Modeling the influence of EGF and TGF-b pathways in tumor progression of hepatocellular carcinoma., in: Asian Pacific Association for Study of the Liver, Hong-Kong, 2009, vol. 3, 64, FP107 p
S. Lemosquet, J. Bourdon, J. Guinard-Flament, A. Siegel, J. Van Milgen.
A Generic Stochiometric Model to Analyse the Metabolic Flexibility of the Mammary Gland in Lactating Dairy Cows, in: 7th Workshop Modelling Nutrient Digestion and Utilization in Farm Animals, France, 2009
F. Moreews.
A Framework for Building Reliable Distributed Bioinformatics Service Repositories, in: ICWS 2009. IEEE International Conference on Web Services, July 2009, p. 1018–1019
V. H. Nguyen, A. Cornu, D. Lavenier.
Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform, in: International Parallel and Distributed Processing Symposium - Reconfigurable Architectures Workshop - IPDPS, Italie, 2009, p. 1-7
P. Peterlongo, J. Nicolas, D. Lavenier, R. Vorc'H, J. Querellou.
c-GAMMA: Comparative Genome Analysis of Molecular Markers, in: Pattern Recognition in Bioinformatics, Royaume-Uni, 08 2009
G. Rizk, D. Lavenier.
GPU accelerated Rna folding algorithm, in: 9th International Conference on Computational Science, États-Unis d'Amérique, J. Allen, al (editors), 05 2009, vol. 5544, 1031 p

Workshops without Proceedings

N. Le Meur, J. Gruel, M. Le Borgne, N. Théret.
Multiclock discrete models of the eukaryotic cell cycle., in: Journées Ouvertes en Biologie, Informatique et Mathématiques. Journée Satellite, France, 2009
N. Le Meur, F. Hahne, D. Sarkar, B. Ellis, J. Spidlen, R. R. Brinkman, R. Gentleman.
High throughput flow cytometry analysis with Bioconductor, in: Advanced Flow Cytometry Analysis 2009, France, 2009
N. Le Meur, F. Hahne, D. Sarkar, B. Ellis, J. Spidlen, R. R. Brinkman, R. Gentleman.
High throughput flow cytometry analysis with Bioconductor., in: useR! 2009, France, 2009
A. Siegel.
From pure discrete spectrum conditions to topological properties of self-affine tiles, in: Aperiodic Order, Royaume-Uni, 2009
A. Siegel.
Rational numbers with purely periodic beta-expansions, in: Fractals and Tilings, Autriche, 2009

Scientific Books (or Scientific Book chapters)

Analyse de la vraisemblance des liens relationnels: une méthodologie d'analyse classificatoire des données, in: Apprentissage artificiel et fouille de données, RNTI A3, Y. Bennani, E. Viennet (editors), Cépaduès, 2009, p. 93-126.
N. Pisanti, M. Giraud, P. Peterlongo.
Filters and seeds approaches for fast homology searches in large datasets, in: Algorithms in computational molecular biology, M. Elloumi, A. Y. Zomaya (editors), John Wiley & sons, 2009

Internal Reports

T. Bitard Feildel.
Création d'une bibliothèque de coeurs structuraux pour le protein threading. Utilisation des familles structurales., Université de Rennes 1, 2009, Stage.
G. Collet, R. Andonov, N. Yanev, J.-F. Gibrat.
Flexible Alignments for Protein Threading, INRIA, 2009, Research Report.
F. Colombel.
Identification in silico d'un nouveau gène de la famille des TNF (tumor necrosis factor), INSA, 2009, Stage.
M. Le Borgne.
Solving loosely coupled constraints, IRISA / INRIA, 2009, Research Report.
I.-C. Lerman, P. Kuntz.
Directed binary hierarchies and directed ultrametrics, IRISA / INRIA, 2009, Research Report.
I.-C. Lerman, P. Kuntz.
Directed binary hierarchies and directed ultrametrics, IRISA / INRIA, 2009, Research Report.
Directed binary hierarchies and directed ultrametrics, IRISA-INRIA, February 2009, no 6815, Rapport de recherche.
N. Malod-Dognin, R. Andonov, N. Yanev.
Maximum Cliques in Protein Structure Comparison, IRISA / INRIA, 2009, Research Report.
N. Malod-Dognin, R. Andonov, N. Yanev.
Solving Maximum Clique Problem for Protein Structure Similarity, IRISA / INRIA, 2009, Research Report.
V. Picard.
Pondération d'automates modélisant des familles de protéines et significativité des scores, ENS Cachan antenne Bretagne, 2009, Stage.

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