Team Symbiose

Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Other Grants and Activities
Dissemination
Bibliography

Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

[1]
J. Gruel.
From biological data to molecular modelisation; application to TGF-beta signaling and hepatic fibrosis, Université de Rennes1, 2009, Ph. D. Thesis.
[2]
V. H. Nguyen.
Traitement parallèle des comparaisons intensives de séquences génomiques, Université de Rennes 1, 2009
http://tel.archives-ouvertes.fr/tel-00435792/fr/, Ph. D. Thesis.

Articles in International Peer-Reviewed Journal

[3]
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
http://hal.archives-ouvertes.fr/hal-00423353/en/.
[4]
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
http://hal.inria.fr/inria-00426749/en/.
[5]
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
http://hal.inria.fr/inria-00359115/en/.
[6]
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
http://dx.doi.org/10.1371/journal.pone.0006397.
[7]
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
http://hal.inria.fr/inria-00429806/en/.
[8]
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.
[9]
R. Chikhi, D. Lavenier.
Paired-end read length lower bounds for genome re-sequencing, in: Bmc Bioinformatics, 10 2009
http://hal.inria.fr/inria-00426856/en/.
[10]
A. Crudu, A. Debussche, O. Radulescu.
Hybrid stochastic simplifications for multiscale gene networks, in: Bmc Systems Biology, 2009, vol. 3, 89 p
http://hal.inria.fr/inria-00431227/en/.
[11]
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.
[12]
M. Galle, P. Peterlongo, F. Coste.
In-place update of suffix array while recoding words, in: International Journal of Foundations of Computer Science, 2009
http://hal.inria.fr/inria-00430406/en/.
[13]
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
http://www.biomedcentral.com/1471-2105/10/151.
[14]
A. Gorban, O. Radulescu, A. Zinovyev.
Asymptotology of Chemical Reaction Networks, in: Chemical Engineering Science, 2009
http://hal.inria.fr/inria-00431225/en/.
[15]
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
http://dx.doi.org/10.1186/1756-0500-2-193.
[16]
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
http://hal.inria.fr/inria-00429804/en/.
[17]
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
http://hal.inria.fr/inria-00426746/en/.
[18]
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.
[19]
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
http://hal.inria.fr/inria-00323840/en/.
[20]
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
http://hal.inria.fr/inria-00431228/en/.
[21]
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
http://hal.inria.fr/inria-00431229/en/.
[22]
V. H. Nguyen, D. Lavenier.
PLAST: parallel local alignment search tool for database comparison, in: Bmc Bioinformatics, 10 2009, vol. 10, 329 p
http://hal.inria.fr/inria-00425301/en/.
[23]
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.
[24]
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
http://hal.inria.fr/inria-00425377/en/.
[25]
V. Poirriez, N. Yanev, R. Andonov.
A Hybrid Algorithm for the Unbounded Knapsack Problem, in: Discrete Optimization, 2009, vol. 6, p. 110-124
http://hal.inria.fr/inria-00335065/en/.
[26]
C. Rousseau, M. Gonnet, M. Leromancer, J. Nicolas.
CRISPI: a CRISPR Interactive database, in: Bioinformatics, 2009, vol. 24, no 25, p. 3317-3318
http://dx.doi.org/10.1093/bioinformatics/btp586.
[27]
A. Siegel, J. Thuswaldner.
Topological properties of Rauzy fractals, in: Mémoires de la SMF, 2010.
[28]
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
http://hal.inria.fr/inria-00431224/en/.

Articles in Non Peer-Reviewed Journal

[29]
J. Nicolas.
Décoder le vivant, in: Doc Sciences, 2009, p. 26-33
http://hal.inria.fr/inria-00438517/en/.
[30]
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
http://hal.inria.fr/inria-00429811/en/.

International Peer-Reviewed Conference/Proceedings

[31]
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
http://hal.inria.fr/inria-00429801/en/.
[32]
J. Bourdon, I. Rusu.
Statistical Properties of Factor Oracles, in: COMBINATORIAL PATTERN MATCHING, France, Springer Verlag, 2009, vol. LNBI 5577, p. 326-338
http://hal.archives-ouvertes.fr/hal-00415952/en/.
[33]
S. Carat, R. Houlgatte, J. Bourdon.
A statistical method for PWM clustering, in: Moscow Conference on Computational Molecular Biology, Russie, 2009
http://hal.archives-ouvertes.fr/hal-00415980/en/.
[34]
R. Chikhi, D. Lavenier.
Paired-end reaf legth lower bounds for genome resequensing, in: ISMB / ECCB, Stockholm, 2009.
[35]
G. Collet, R. Andonov, N. Yanev, J.-F. Gibrat.
Protein Threading, in: 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, France, 06 2009
http://hal.inria.fr/inria-00412642/en/.
[36]
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
http://hal.inria.fr/inria-00429809/en/.
[37]
P. KUNTZ, I.-C. LERMAN.
Graph and Hierarchical-based approaches for structuring association rule sets, in: 11th IFCS International Conference 2009, H. Bock (editor), Dresden University, 2009.
[38]
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
http://hal.archives-ouvertes.fr/hal-00435766/en/.
[39]
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
http://hal.archives-ouvertes.fr/hal-00416396/en/.
[40]
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
http://dx.doi.org/10.1109/ICWS.2009.143.
[41]
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
http://doi.ieeecomputersociety.org/10.1109/IPDPS.2009.5161206.
[42]
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
http://hal.inria.fr/inria-00425373/en/.
[43]
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
http://hal.archives-ouvertes.fr/hal-00425543/en/.

Workshops without Proceedings

[44]
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
http://hal.archives-ouvertes.fr/hal-00435771/en/.
[45]
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
http://hal.inria.fr/inria-00435735/en/.
[46]
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
http://hal.archives-ouvertes.fr/hal-00435777/en/.
[47]
A. Siegel.
From pure discrete spectrum conditions to topological properties of self-affine tiles, in: Aperiodic Order, Royaume-Uni, 2009
http://hal.inria.fr/inria-00429814/en/.
[48]
A. Siegel.
Rational numbers with purely periodic beta-expansions, in: Fractals and Tilings, Autriche, 2009
http://hal.inria.fr/inria-00429815/en/.

Scientific Books (or Scientific Book chapters)

[49]
I.-C. LERMAN.
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.
[50]
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
http://hal.inria.fr/inria-00425370/en/.

Internal Reports

[51]
T. Bitard Feildel.
Création d'une bibliothèque de coeurs structuraux pour le protein threading. Utilisation des familles structurales., Université de Rennes 1, 2009
http://hal.inria.fr/inria-00435113/en/, Stage.
[52]
G. Collet, R. Andonov, N. Yanev, J.-F. Gibrat.
Flexible Alignments for Protein Threading, INRIA, 2009
http://hal.inria.fr/inria-00355546/en/, Research Report.
[53]
F. Colombel.
Identification in silico d'un nouveau gène de la famille des TNF (tumor necrosis factor), INSA, 2009
http://hal.inria.fr/inria-00431114/en/, Stage.
[54]
M. Le Borgne.
Solving loosely coupled constraints, IRISA / INRIA, 2009
http://hal.inria.fr/inria-00397098/en/, Research Report.
[55]
I.-C. Lerman, P. Kuntz.
Directed binary hierarchies and directed ultrametrics, IRISA / INRIA, 2009
http://hal.inria.fr/inria-00357532/en/, Research Report.
[56]
I.-C. Lerman, P. Kuntz.
Directed binary hierarchies and directed ultrametrics, IRISA / INRIA, 2009
http://hal.inria.fr/inria-00361727/en/, Research Report.
[57]
I.-C. LERMAN, P. KUNTZ.
Directed binary hierarchies and directed ultrametrics, IRISA-INRIA, February 2009, no 6815, Rapport de recherche.
[58]
N. Malod-Dognin, R. Andonov, N. Yanev.
Maximum Cliques in Protein Structure Comparison, IRISA / INRIA, 2009
http://hal.inria.fr/inria-00422198/en/, Research Report.
[59]
N. Malod-Dognin, R. Andonov, N. Yanev.
Solving Maximum Clique Problem for Protein Structure Similarity, IRISA / INRIA, 2009
http://hal.inria.fr/inria-00356816/en/, Research Report.
[60]
V. Picard.
Pondération d'automates modélisant des familles de protéines et significativité des scores, ENS Cachan antenne Bretagne, 2009
http://hal.inria.fr/inria-00431111/en/, Stage.

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