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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journal

  • 1S. Blanquart, O. Gascuel.

    Mitochondrial genes support a common origin of Plasmodium falciparum and relatives with rodent malaria parasites., in: BMC Evolutionary Biology, March 2011.

    http://hal.inria.fr/inria-00636084/en
  • 2M.-J. Cros, A. de Monte, J. Mariette, P. Bardou, B. Grenier-Boley, D. Gautheret, H. Touzet, C. Gaspin.

    RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA, in: RNA, September 2011, vol. 17, p. 1947-1956.

    http://rnajournal.cshlp.org/content/17/11/1947.long
  • 3M. Giraud, J.-S. Varré.

    Parallel Position Weight Matrices Algorithms, in: Parallel Computing, 2011, vol. 37, p. 466-478. [ DOI : 10.1016/j.parco.2010.10.001 ]

    http://hal.inria.fr/hal-00623404/en
  • 4M. Léonard, L. Mouchard, M. Salson.

    On the number of elements to reorder when updating a suffix array, in: Journal of Discrete Algorithms, January 2011. [ DOI : 10.1016/j.jda.2011.01.002 ]

    http://hal.inria.fr/inria-00636066/en
  • 5A. Ouangraoua, A. Bergeron, K. Swenson.

    Theory and practice of ultra-perfection, in: Journal of Computational Biology, 2011, vol. 18, no 9, p. 1219-1230.

    http://hal.inria.fr/inria-00635033/en
  • 6A. Ouangraoua, V. Guignon, S. Hamel, C. Chauve.

    A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes, in: Theoretical Computer Science, 2011, vol. 412, no 8-10, p. 753-764.

    http://hal.inria.fr/inria-00635043/en
  • 7A. Ouangraoua, K. Swenson, C. Chauve.

    A 2-Approximation for the Minimum Duplication Speciation Problem, in: Journal of Computational Biology, 2011, vol. 18, no 9, p. 1041-1053.

    http://hal.inria.fr/inria-00635025/en
  • 8A. Ouangraoua, E. Tannier, C. Chauve.

    Reconstructing the architecture of the ancestral amniote genome, in: Bioinformatics, 2011, no 19, p. 2664-2671.

    http://hal.inria.fr/inria-00635016/en
  • 9N. Philippe, M. Salson, T. Lecroq, M. Léonard, T. Commes, E. Rivals.

    Querying Large Read Collections in Main Memory: A Versatile data Structure, in: BMC Bioinformatics, Jun 2011, vol. 12, 242+ p. [ DOI : 10.1186/1471-2105-12-242 ]

    http://hal.inria.fr/lirmm-00632958/en
  • 10A. Thomas, J.-S. Varré, A. Ouangraoua.

    Genome Dedoubling by DCJ and Reversal, in: BMC Bioinformatics, 2011, vol. 12, no Suppl 9, S20 p, Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics.

    http://hal.inria.fr/inria-00635003/en

International Conferences with Proceedings

  • 11A. Gambin, S. Lasota, M. Startek, M. Sykulski, L. Noé, G. Kucherov.

    Subset seed extension to Protein BLAST, in: Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2011), SciTePress, 2011, p. 149-158. [ DOI : 10.5220/0003147601490158 ]

    http://hal.inria.fr/inria-00609791/en
  • 12F. Levé, R. Groult, G. Arnaud, C. Séguin, R. Gaymay, M. Giraud.

    Rhythm extraction from polyphonic symbolic music, in: 12th International Society for Music Information Retrieval Conference (ISMIR 2011), United States, 2011, p. 375-380.

    http://hal.inria.fr/hal-00636058/en
  • 13T. T. Tran, M. Giraud, J.-S. Varré.

    Bit-Parallel Multiple Pattern Matching, in: Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11), Torun, Poland, 2011.

    http://hal.inria.fr/inria-00637227/en

Conferences without Proceedings

  • 14J.-F. Berthelot, C. Deltel, M. Giraud, S. Janot, L. Jourdan, D. Lavenier, H. Touzet, J.-S. Varré.

    biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics, in: JOBIM 2011, Paris, France, July 2011.

    http://hal.inria.fr/hal-00637847/en
  • 15M. 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

Scientific Books (or Scientific Book chapters)

  • 16J.-S. Varré, B. Schmidt, S. Janot, M. Giraud.

    Manycore high-performance computing in bioinformatics, in: Advances in Genomic Sequence Analysis and Pattern Discovery, L. Elnitski, H. Piontkivska, L. R. Welch (editors), World Scientific, 2011, chapter 8 p.

    http://hal.inria.fr/hal-00563408/en
References in notes
  • 17G. Blin, A. Denise, S. Dulucq, C. Herrbach, H. Touzet.

    Alignment of RNA structures, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008.

    http://dx.doi.org/10.1109/TCBB.2008.28
  • 18G. Blin, H. Touzet.

    How to Compare Arc-Annotated Sequences: The Alignment Hierarchy, in: 13th International Symposium on String Processing and Information Retrieval (SPIRE), Lecture Notes in Computer Science, Springer Verlag, 2006, vol. 4209, p. 291–303. [ DOI : 10.1007/11880561_24 ]

    http://www.springerlink.com/content/4k37q116j2720832/
  • 19S. Caboche, M. Pupin, V. Leclère, P. Jacques, G. Kucherov.

    Structural pattern matching of nonribosomal peptides, in: BMC Structural Biology, March 18 2009, vol. 9:15. [ DOI : 10.1186/1472-6807-9-15 ]

    http://www.biomedcentral.com/1472-6807/9/15
  • 20S. Dulucq, H. Touzet.

    Decomposition algorithms for the tree edit distance problem, in: Journal of Discrete Algorithms, 2005, p. 448-471.

    http://dx.doi.org/10.1016/j.jda.2004.08.018
  • 21P. Gardner, R. Giegerich.

    A comprehensive comparison of comparative RNA structure prediction approaches, in: BMC Bioinformatics, 2004, vol. 5(140).
  • 22G. Kucherov, L. Noé, M. Roytberg.

    Multi-seed lossless filtration, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, January-March 2005, vol. 2, no 1, p. 51–61.
  • 23G. Kucherov, L. Noé, M. Roytberg.

    A unifying framework for seed sensitivity and its application to subset seeds, in: Journal of Bioinformatics and Computational Biology, 2006, vol. 4, no 2, p. 553–569. [ DOI : doi:10.1142/S0219720006001977 ]

    http://www.worldscinet.com/jbcb/04/0402/S0219720006001977.html
  • 24G. Kucherov, L. Noé, M. Roytberg.

    Subset Seed Automaton, in: 12th International Conference on Implementation and Application of Automata (CIAA 07), Lecture Notes in Computer Science, Springer Verlag, 2007, vol. 4783, p. 180–191. [ DOI : 10.1007/978-3-540-76336-9_18 ]

    http://www.springerlink.com/content/y824l20554002756/
  • 25F. Lipmann, W. Gevers, H. Kleinkauf, R. J. Roskoski.

    Polypeptide synthesis on protein templates: the enzymatic synthesis of gramicidin S and tyrocidine., in: Adv Enzymol Relat Areas Mol Biol, 1971, vol. 35, p. 1–34.
  • 26L. Noé, M. Gîrdea, G. Kucherov.

    Designing efficient spaced seeds for SOLiD read mapping, in: Advances in Bioinformatics, July 2010, vol. 2010. [ DOI : 10.1155/2010/708501 ]

    http://www.hindawi.com/journals/abi/2010/708501/
  • 27L. Noé, M. Gîrdea, G. Kucherov.

    Seed design framework for mapping SOLiD reads, in: Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), April 25-28, 2010, Lisbon (Portugal), B. Berger (editor), Lecture Notes in Computer Science, Springer, April 2010, vol. 6044, p. 384–396. [ DOI : 10.1007/978-3-642-12683-3_25 ]

    http://www.springerlink.com/content/41535x341gu34131/
  • 28L. Noé, G. Kucherov.

    YASS: enhancing the sensitivity of DNA similarity search, in: Nucleic Acid Research, 2005, vol. 33, p. W540-W543.
  • 29A. Ouangraoua, P. Ferraro.

    A constrained edit distance algorithm between semi-ordered trees, in: Theor. Comput. Sci., 2009, vol. 410, no 8-10, p. 837-846.
  • 30A. Ouangraoua, P. Ferraro.

    A new constrained edit distance between quotiented ordered trees, in: J. Discrete Algorithms, 2009, vol. 7, no 1, p. 78-89.
  • 31A. Ouangraoua, P. Ferraro, L. Tichit, S. Dulucq.

    Local similarity between quotiented ordered trees, in: J. Discrete Algorithms, 2007, vol. 5, no 1, p. 23-35.
  • 32A. Ouangraoua, K. Swenson, C. Chauve.

    An approximation algorithm for computing a parsimonious first speciation in the gene duplication model, in: Proceedings of RECOMB-Comparative Genomics, LNBI 6398, 2010, vol. 6398, p. 290-302.
  • 33P. Peterlongo, L. Noé, D. Lavenier, G. les Georges, J. Jacques, G. Kucherov, M. Giraud.

    Protein similarity search with subset seeds on a dedicated reconfigur able hardware, in: Parallel Processing and Applied Mathematics / Parallel Biocomputi ng Conference (PPAM / PBC 07), R. Wyrzykowski, J. Dongarra, K. Karczewski, J. Wasniewski (editors), Lecture Notes in Computer Science (LNCS), 2008, vol. 4967, p. 1240-1248. [ DOI : 10.1007/978-3-540-68111-3 ]

    http://www.lifl.fr/~giraud/publis/peterlongo-pbc-07.pdf
  • 34P. Peterlongo, L. Noé, D. Lavenier, V. H. Nguyen, G. Kucherov, M. Giraud.

    Optimal neighborhood indexing for protein similarity search, in: BMC Bioinformatics, 2008, vol. 9, no 534. [ DOI : 10.1186/1471-2105-9-534 ]

    http://www.biomedcentral.com/1471-2105/9/534
  • 35M. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, G. Kucherov.

    On subset seeds for protein alignment, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, vol. 6, no 3, p. 483–494.

    http://www.lifl.fr/~noe/files/pp_TCBB09_preprint.pdf
  • 36M. Salson, T. Lecroq, M. Léonard, L. Mouchard.

    A Four-Stage Algorithm for Updating a Burrows-Wheeler Transform, in: Theoretical Computer Science, 2009, vol. 410, no 43, p. 4350–4359.
  • 37M. Salson, T. Lecroq, M. Léonard, L. Mouchard.

    Dynamic Extended Suffix Array, in: Journal of Discrete Algorithms, 2010, vol. 8, p. 241–257.
  • 38H. Touzet.

    Comparing similar ordered trees in linear-time, in: Journal of Discrete Algorithms, 2007, vol. 5, no 4, p. 696-705. [ DOI : 10.1016/j.jda.2006.07.002 ]

    http://linkinghub.elsevier.com/retrieve/pii/S1570866706000700
  • 39S. Wu, U. Manber.

    Fast Text Searching Allowing Errors, in: Communications of the ACM, october 1992, vol. 35, no 10, p. 83–91.