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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1M. Gallé.

    Searching for Compact Hierarchical Structures in DNA by means of the Smallest Grammar Problem, Université Rennes 1, February 2011.

    http://hal.inria.fr/tel-00595494/en
  • 2G. Rizk.

    Parallélisation sur matériel graphique : contributions au repliement d'ARN et à l'alignement de séquences, Université Rennes 1, January 2011.

    http://hal.inria.fr/tel-00634901/en

Articles in International Peer-Reviewed Journal

  • 3R. Andonov, N. Malod-Dognin, N. Yanev.

    Maximum Contact Map Overlap Revisited, in: Journal of Computational Biology, January 2011, vol. 18, no 1, p. 1-15. [ DOI : 10.1089/cmb.2009.0196 ]

    http://hal.inria.fr/inria-00536624/en
  • 4V. Berthé, A. Siegel, W. Steiner, P. Surer, J. Thuswaldner.

    Fractal tiles associated with shift radix systems, in: Advances in Mathematics, January 2011, vol. 226, no 1, p. 139-175. [ DOI : 10.1016/j.aim.2010.06.010 ]

    http://hal.inria.fr/hal-00407999/en
  • 5J. Bourdon, D. Eveillard, A. Siegel.

    Integrating quantitative knowledge into a qualitative gene regulatory network., in: PLoS Computational Biology, September 2011, vol. 7, no 9. [ DOI : 10.1371/journal.pcbi.1002157 ]

    http://hal.inria.fr/hal-00626708/en
  • 6R. Carrascosa, F. Coste, M. Gallé, G. Infante-Lopez.

    Searching for Smallest Grammars on Large Sequences and Application to DNA, in: Journal of Discrete Algorithms, 2011. [ DOI : 10.1016/j.jda.2011.04.006 ]

    http://hal.inria.fr/inria-00536633/en
  • 7R. Carrascosa, F. Coste, M. Gallé, G. Infante-Lopez.

    The Smallest Grammar Problem as Constituents Choice and Minimal Grammar Parsing, in: Algorithms, October 2011, no 4, p. 262-284. [ DOI : 10.3390/a4040262 ]

    http://hal.inria.fr/inria-00638445/en
  • 8G. Collet, R. Andonov, J.-F. Gibrat, N. Yanev.

    Local protein threading by Mixed Integer Programming, in: Discrete Applied Mathematics, 2011, vol. 159, no 16, p. 1707-1716. [ DOI : 10.1016/j.dam.2010.05.024 ]

    http://hal.inria.fr/inria-00536537/en
  • 9D. Earl, K. Bradnam, R. Chikhi, D. Lavenier, G. Chapuis, D. Naquin, N. Maillet, I. Korf, B. Paten.

    Assemblathon 1: A competitive assessment of de novo short read assembly methods, in: Genome Research, September 2011, International competition of de novo genome assembly. The Symbiose team (IRISA/CNRS/ENS Cachan Brittany) participated to this competition.. [ DOI : 10.1101/gr.126599.111 ]

    http://hal.inria.fr/inria-00637571/en
  • 10J. Gruel, M. Le Borgne, N. Lemeur, N. Théret.

    Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns, in: BMC Bioinformatics, September 2011, 12:365 p.

    http://hal.inria.fr/hal-00641785/en
  • 11J. M. Guberman, J. Ai, F. Moreews, J. Zhang, A. Kasprzyk.

    BioMart Central Portal: an open database network for the biological community, in: Database: The Journal of Biological Databases and Curation, September 2011. [ DOI : 10.1093/database/bar041 ]

    http://hal.inria.fr/inria-00638749/en
  • 12C. Guziolowski, S. Blachon, T. Baumuratova, G. Stoll, O. Radulescu, A. Siegel.

    Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling., in: IEEE/ACM Trans Comput Biol Bioinform, 2011, vol. 8, no 5, p. 1223-1234. [ DOI : 10.1109/TCBB.2010.71 ]

    http://hal.inria.fr/inria-00538134/en
  • 13J. Jaquiéry, S. Stoeckel, C. Rispe, L. Mieuzet, F. Legeai, J.-C. Simon.

    Accelerated evolution of sex chromosomes in aphids, an X0 system., in: Molecular Biology and Evolution, October 2011, to appear. [ DOI : 10.1093/molbev/msr252 ]

    http://hal.inria.fr/hal-00639983/en
  • 14F. Lecerc, A. Bretaudeau, O. Sallou, C. Désert, Y. Blum, S. Lagarrigue, O. Demeure.

    AnnotQTL: a new tool to gather functional and comparative information on a genomic region, in: Nucleic Acids Research, May 2011, to appear. [ DOI : 10.1093/nar/gkr361 ]

    http://hal.inria.fr/hal-00597398/en
  • 15F. Legeai, S. Malpel, N. Montagné, C. Monsempes, F. Cousserans, C. Merlin, M.-C. François, M. Maïbèche-Coisné, F. Gavory, J. Poulain, E. Jacquin-Joly.

    An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research., in: BMC Genomics, 2011, vol. 12, 86 p. [ DOI : 10.1186/1471-2164-12-86 ]

    http://hal.inria.fr/hal-00639985/en
  • 16C. Lemaitre, A. Barré, C. Citti, F. Tardy, F. Thiaucourt, P. Sirand-Pugnet, P. Thebault.

    A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships, in: BMC Bioinformatics, 2011, to appear.

    http://hal.inria.fr/hal-00643361/en
  • 17F. Moreews, G. Rauffet, P. Dehais, C. Klopp.

    SigReannot-mart: a query environment for expression microarray probe re-annotations., in: Database (Oxford), 2011, vol. 2011. [ DOI : 10.1093/database/bar025 ]

    http://hal.inria.fr/inria-00638684/en
  • 18O. Radulescu, A. Siegel, E. Pecou, C. Chatelain, S. Lagarrigue.

    Genetically regulated metabolic networks: Gale-Nikaido modules and differential inequalities, in: Transactions on Computational Systems Biology, 2011, no Lecture Notes in Computer Science 6575, p. 110-130. [ DOI : 10.1007/978-3-642-19748-2_6 ]

    http://hal.inria.fr/inria-00538136/en
  • 19T. Tonon, D. Eveillard, S. Prigent, J. Bourdon, P. Potin, C. Boyen, A. Siegel.

    Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment, in: OMICS, 2011.

    http://hal.inria.fr/inria-00636965/en
  • 20A. C. M. Vialette-Guiraud, M. Alaux, F. Legeai, C. Finet, P. Chambrier, S. C. Brown, A. Chauvet, C. Magdalena, P. J. Rudall, C. P. Scutt.

    Cabomba as a model for studies of early angiosperm evolution., in: Annals of Botany, September 2011, vol. 108, no 4, p. 589-98. [ DOI : 10.1093/aob/mcr088 ]

    http://hal.inria.fr/hal-00639984/en
  • 21A. Véron, C. Lemaitre, C. Gautier, V. Lacroix, M.-F. Sagot.

    Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, in: BMC Genomics, 2011, vol. 12, no 1, 303 p. [ DOI : 10.1186/1471-2164-12-303 ]

    http://hal.inria.fr/inserm-00617206/en
  • 22I. Wohlers, R. Andonov, G. W. Klau.

    Algorithm engineering for optimal alignment of protein structure distance matrices, in: Optimization Letters, April 2011. [ DOI : 10.1007/s11590-011-0313-3 ]

    http://hal.inria.fr/inria-00586067/en

International Conferences with Proceedings

  • 23R. Chikhi, G. Chapuis, D. Lavenier.

    Parallel and memory-efficient reads indexing for genome assembly, in: Parallel Bio-Computing 2011, torun, Poland, October 2011.

    http://hal.inria.fr/inria-00637536/en
  • 24R. Chikhi, D. Lavenier.

    Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph, in: 11th Workshop on Algorithms in Bioinformatics (WABI 2011), T. Przytycka, M.-F. Sagot (editors), Lecture Notes in Computer Science, Springer Berlin / Heidelberg, 2011, vol. 6833, p. 39-48. [ DOI : 10.1007/978-3-642-23038-7_4 ]

    http://hal.inria.fr/inria-00637535/en
  • 25A. Cornu, S. Derrien, D. Lavenier.

    HLS Tools for FPGA : faster development with better performances, in: Proceeding of the 7th International Symposium on Applied Reconfigurable Computing, Belfast, United Kingdom, March 2011, vol. 6578, p. 67-78.

    http://hal.inria.fr/hal-00637830/en
  • 26M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot.

    Finding Long and Multiple Repeats with Edit Distance, in: The Prague Stringology Conference 2011, Prague, Czech Republic, August 2011.

    http://hal.inria.fr/inria-00608208/en
  • 27M. Giraud, S. Janot, J.-F. Berthelot, C. Deltel, L. Jourdan, D. Lavenier, H. Touzet, J.-S. Varré.

    Biomanycores, open-source parallel code for many-core bioinformatics, in: Bioinformatics Open Source Conference (BOSC 2011), Vienne, Austria, 2011.

    http://hal.inria.fr/inria-00623390/en
  • 28N. Malod-Dognin, M. Le Boudic-Jamin, P. Kamath, R. Andonov.

    Using Dominances for Solving the Protein Family Identification Problem, in: 11th Workshop on Algorithms in Bioinformatics (WABI 2011), T. Przytycka, M.-F. Sagot (editors), Lecture Notes in Computer Science, Springer Berlin / Heidelberg, 2011, vol. 6833, p. 201-212. [ DOI : 10.1007/978-3-642-23038-7_18 ]

    http://hal.inria.fr/inria-00609432/en
  • 29F. Moreews, J. Piat, O. Sallou.

    OBIWEE : an open source bioinformatics cloud environment, in: BOSC 2011 - 12th Annual Bioinformatics Open Source Conference, Vienne, Austria, July 2011.

    http://hal.inria.fr/inria-00638715/en
  • 30A. Mucherino, C. Lavor, L. Liberti.

    A symmetry-driven BP algorithm for the Discretizable Molecular Distance Geometry Problem, in: IEEE International Conference on Bioinformatics and Biomedicine, Atlanta, United States, IEEE, 2011.

    http://hal.inria.fr/inria-00637771/en
  • 31A. Mucherino, I. Wohlers, G. W. Klau, R. Andonov.

    Sparsifying Distance Matrices for Protein-Protein Structure Alignments, in: CTW2011, Rome, Italy, June 2011.

    http://hal.inria.fr/hal-00642794/en
  • 32J. Piat, F. Moreews, O. Collin, D. Lavenier, A. Cornu.

    SLICEE: A Service oriented middleware for intensive scientific computation, in: SERVICES 2011, WASHINGTON DC, United States, IEEE (editor), July 2011.

    http://hal.inria.fr/inria-00638694/en

National Conferences with Proceeding

  • 33M. Le Boudic-Jamin, N. Malod-Dognin, A. Cornu, J. Nicolas, R. Andonov.

    Identification rapide de familles protéiques par dominance, in: 12th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF), Saint-Étienne, France, École Nationale Supérieure des Mines de Saint-Étienne, March 2011, vol. 2, p. 791-792, Publié dans le douzième congrès de la Société Française de Recherche Opérationnelle et d'Aide à la Décision (ROADEF 2011)..

    http://hal.inria.fr/inria-00611457/en

Conferences without Proceedings

  • 34P. Blavy, F. Gondret, T. Sven, C. Guziolowski, S. Lagarrigue, J. Van Milgen, A. Siegel.

    A new method for modeling reactions and regulations to analyze high-throughout data, in: 4th International Symposium on Animal Functional Genomics, Dublin, Ireland, Sorcha De Gras, October 2011.

    http://hal.inria.fr/hal-00640720/en
  • 35G. Chapuis, O. Filangi, P. Leroy, J.-M. Elsen, D. Lavenier.

    GPU Accelerted QTLMap, in: The 15th QTL-MAS workshop, France, May 2011.

    http://hal.inria.fr/hal-00637840/en

Scientific Books (or Scientific Book chapters)

  • 36J. Bourdon, D. Eveillard.

    Probabilistic Approaches for Investigating Biological Networks, in: Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, M. Elloumi, A. Y. Zomaya (editors), Wiley, January 2011, 1066 p.

    http://hal.inria.fr/hal-00531568/en
  • 37D. Lavenier, G. Rizk, S. Rajopadhye.

    GPU accelerated RNA folding algorithm, in: GPU Computing Gems, Wen-mei W. Hwu (editor), ELSEVIER, February 2011, 560 p, pages 199-210. [ DOI : 10.0123849888 ]

    http://hal.inria.fr/hal-00637827/en

Internal Reports

Scientific Popularization

Other Publications