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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1E. Kopylova.

    Algorithmes bio-informatiques pour l'analyse de données de séquençage à haut débit, Université des Sciences et Technologie de Lille - Lille I, December 2013.

    http://hal.inria.fr/tel-00919185
  • 2M. Pupin.

    Modèles bio-informatiques pour les peptides non-ribosomiques et leurs synthétases, Université des Sciences et Technologie de Lille - Lille I, December 2013, Habilitation à Diriger des Recherches.

    http://hal.inria.fr/tel-00918918

Articles in International Peer-Reviewed Journals

  • 3M. Groussin, B. Boussau, S. Charles, S. Blanquart, M. Gouy.

    The molecular signal for the adaptation to cold temperature during early life on Earth, in: Biol Lett, October 2013, vol. 9, no 5.

    http://hal.inria.fr/hal-00918283
  • 4A. Ouangraoua, M. Raffinot.

    On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction, in: Journal of Computational Biology, 2013, pp. 1-16. [ DOI : 10.1089/cmb.2013.0086 ]

    http://hal.inria.fr/hal-00913212
  • 5N. Philippe, M. Salson, T. Commes, E. Rivals.

    CRAC: an integrated approach to the analysis of RNA-seq reads, in: Genome Biology, March 2013, vol. 14, no 3. [ DOI : 10.1186/gb-2013-14-3-r30 ]

    http://hal.inria.fr/inserm-00850972
  • 6B. Reisinger, J. Sperl, A. Holinski, V. Schmid, C. Rajendran, L. Carstensen, S. Schlee, S. Blanquart, R. Merkl, R. Sterner.

    Evidence for the Existence of Elaborate Enzyme Complexes in the Paleoarchean Era, in: Journal of the American Chemical Society, December 2013. [ DOI : 10.1021/ja4115677 ]

    http://hal.inria.fr/hal-00924047

National Conferences with Proceedings

  • 7Y. Dufresne, V. Leclère, P. Jacques, L. Noé, M. Pupin.

    Non Ribosomal Peptides : A monomeric puzzle, in: JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Toulouse, France, July 2013, pp. 143-150.

    http://hal.inria.fr/hal-00843827
  • 8M. Giraud, M. Salson, M. Duez, J.-S. Varré, C. Villenet, S. Quief, A. Caillault, N. Grardel, C. Roumier, C. Preudhomme, m. Figeac.

    Suivi de la leucémie résiduelle par séquençage haut-débit, in: JOBIM, Toulouse, France, July 2013.

    http://hal.inria.fr/hal-00857581

Conferences without Proceedings

  • 9R. Giegerich, H. Touzet.

    Algebraic Dynamic Programming 2.0, in: Workshop Haskell-Treffen an der Universität Leipzig, Leipzig, Germany, June 2013.

    http://hal.inria.fr/hal-00857801

Internal Reports

  • 10A. Rousseau, A. Darnaud, B. Goglin, C. Acharian, C. Leininger, C. Godin, C. Holik, C. Kirchner, D. Rives, E. Darquie, E. Kerrien, F. Neyret, F. Masseglia, F. Dufour, G. Berry, G. Dowek, H. Robak, H. Xypas, I. Illina, I. Gnaedig, J. Jongwane, J. Ehrel, L. Viennot, L. Guion, L. Calderan, L. Kovacic, M. Collin, M.-A. Enard, M.-H. Comte, M. Quinson, M. Olivi, M. Giraud, M. Dorémus, M. Ogouchi, M. Droin, N. Lacaux, N. Rougier, N. Roussel, P. Guitton, P. Peterlongo, R.-M. Cornus, S. Vandermeersch, S. Maheo, S. Lefebvre, S. Boldo, T. Viéville, V. Poirel, A. Chabreuil, A. Fischer, C. Farge, C. Vadel, I. Astic, J.-P. Dumont, L. Féjoz, P. Rambert, P. Paradinas, S. De Quatrebarbes, S. Laurent.

    Médiation Scientifique : une facette de nos métiers de la recherche, March 2013, 34 p.

    http://hal.inria.fr/hal-00804915
References in notes
  • 11G. 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
  • 12S. 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
  • 13G. 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, pp. 180–191. [ DOI : 10.1007/978-3-540-76336-9_18 ]

    http://www.springerlink.com/content/y824l20554002756/
  • 14F. 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, pp. 1–34.
  • 15L. 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/
  • 16L. 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, pp. 384–396. [ DOI : 10.1007/978-3-642-12683-3_25 ]

    http://www.springerlink.com/content/41535x341gu34131/
  • 17A. Ouangraoua, P. Ferraro.

    A constrained edit distance algorithm between semi-ordered trees, in: Theor. Comput. Sci., 2009, vol. 410, no 8-10, pp. 837-846.
  • 18A. Ouangraoua, P. Ferraro.

    A new constrained edit distance between quotiented ordered trees, in: J. Discrete Algorithms, 2009, vol. 7, no 1, pp. 78-89.
  • 19A. Ouangraoua, P. Ferraro, L. Tichit, S. Dulucq.

    Local similarity between quotiented ordered trees, in: J. Discrete Algorithms, 2007, vol. 5, no 1, pp. 23-35.
  • 20P. Peterlongo, L. Noé, D. Lavenier, G. 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, pp. 1240-1248. [ DOI : 10.1007/978-3-540-68111-3 ]

    http://www.lifl.fr/~giraud/publis/peterlongo-pbc-07.pdf
  • 21P. 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
  • 22M. 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, pp. 483–494.

    http://www.lifl.fr/~noe/files/pp_TCBB09_preprint.pdf
  • 23M. 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, pp. 4350–4359.
  • 24M. Salson, T. Lecroq, M. Léonard, L. Mouchard.

    Dynamic Extended Suffix Array, in: Journal of Discrete Algorithms, 2010, vol. 8, pp. 241–257.
  • 25H. Touzet.

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

    http://linkinghub.elsevier.com/retrieve/pii/S1570866706000700