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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1A. Abdo, S. Caboche, V. Leclère, P. Jacques, M. Pupin.

    A new fingerprint to predict nonribosomal peptides activity., in: Journal of Computer-Aided Molecular Design, October 2012, vol. 26, no 10, p. 1187-94. [ DOI : 10.1007/s10822-012-9608-4 ]

    http://hal.inria.fr/hal-00750002
  • 2J. Allali, C. Saule, C. Chauve, Y. D'Aubenton-Carafa, A. Denise, C. Drevet, P. Ferraro, D. Gautheret, C. Herrbach, F. Leclerc, A. De Monte, A. Ouangraoua, M.-F. Sagot, M. Termier, C. Thermes, H. Touzet.

    BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms, in: Advances in Bioinformatics, 2012, accepted for publication (Feb, 2012).

    http://hal.inria.fr/hal-00647725
  • 3M. Béchet, T. Caradec, W. Hussein, A. Abderrahmani, M. Chollet, V. Leclère, T. Dubois, D. Lereclus, M. Pupin, P. Jacques.

    Structure, biosynthesis, and properties of kurstakins, nonribosomal lipopeptides from Bacillus spp., in: Applied Microbiology and Biotechnology, August 2012, vol. 95, no 3, p. 593-600. [ DOI : 10.1007/s00253-012-4181-2 ]

    http://hal.inria.fr/hal-00749819
  • 4E. Kopylova, L. Noé, H. Touzet.

    SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data., in: Bioinformatics, October 2012, p. 1-10. [ DOI : 10.1093/bioinformatics/bts611 ]

    http://hal.inria.fr/hal-00748990
  • 5M. Léonard, L. Mouchard, M. Salson.

    On the number of elements to reorder when updating a suffix array, in: Journal of Discrete Algorithms, February 2012, vol. 11, p. 87-99. [ DOI : 10.1016/j.jda.2011.01.002 ]

    http://hal.inria.fr/inria-00636066
  • 6E. Rivals, N. Philippe, M. Salson, M. Léonard, T. Commes, T. Lecroq.

    A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections, in: ERCIM News, April 2012, vol. 2012, no 89, p. 20-21.

    http://hal.inria.fr/lirmm-00712653
  • 7A. Saffarian, M. Giraud, A. De Monte, H. Touzet.

    RNA Locally Optimal Secondary Structures, in: Journal of Computational Biology, 2012, vol. 19, no 10, p. 1120-1133. [ DOI : 10.1089/cmb.2010.0178 ]

    http://hal.inria.fr/hal-00756249
  • 8M. Startek, S. Lasota, M. Sykulski, A. Bulak, A. Gambin, L. Noé, G. Kucherov.

    Efficient alternatives to PSI-BLAST, in: bulletin of the polish academy of sciences: technical sciences, 2012.

    http://hal.inria.fr/hal-00749016

International Conferences with Proceedings

  • 9M. Giraud, R. Groult, F. Levé.

    Detecting Episodes with Harmonic Sequences for Fugue Analysis, in: ISMIR - International Society for Music Information Retrieval Conference - 2012, Porto, Portugal, 2012.

    http://hal.inria.fr/hal-00712565
  • 10M. Giraud, R. Groult, F. Levé.

    Subject and counter-subject detection for analysis of the Well-Tempered Clavier fugues, in: International Symposium on Computer Music Modelling and Retrieval (CMMR 2012), United Kingdom, 2012, p. 661-673.

    http://hal.inria.fr/hal-00712554
  • 11A. Ouangraoua, M. Raffinot.

    Faster and Simpler Minimal Conflicting Set Identification., in: Combinatorial Pattern Matching, Helsinki, Finland, Springer, 2012, vol. 7354, p. 41-55.

    http://hal.inria.fr/hal-00750028
  • 12A. Ouangraoua, K. Swenson, A. Bergeron.

    On the comparison of sets of alternative transcripts, in: International Symposium on Bioinformatics Research and Applications, Dallas, Germany, Springer, 2012, vol. 7292, p. 201-212.

    http://hal.inria.fr/hal-00750031
  • 13A. Thomas, A. Ouangraoua, J.-S. Varré.

    Genome Halving by Block Interchange, in: BIOINFORMATICS, Lisboa, Portugal, J. Schier, C. M. B. A. Correia, A. L. N. Fred, H. Gamboa (editors), SciTePress, 2012, p. 58-65.

    http://hal.inria.fr/hal-00749026
  • 14A. Thomas, A. Ouangraoua, J.-S. Varré.

    Tandem Halving Problems by DCJ, in: Workshop on Algorithms in Bioinformatics, Ljubljana, Slovenia, Springer Berlin Heidelberg, 2012, vol. 7534, p. 417-429. [ DOI : 10.1007/978-3-642-33122-0_33 ]

    http://hal.inria.fr/hal-00749019

National Conferences with Proceeding

  • 15E. Kopylova, L. Noé, H. Touzet.

    SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis, in: JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2012, Rennes, France, 2012.

    http://hal.inria.fr/hal-00763792
  • 16M. Pupin, M. Smail-Tabbone, P. Jacques, M.-D. Devignes, V. Leclère.

    NRPS toolbox for the discovery of new nonribosomal peptides and synthetases, in: Journées Ouvertes en Biologie, l'Informatique et les Mathématiques - JOBIM 2012, Rennes, France, F. Coste, D. Tagu (editors), 2012, p. 89-93.

    http://hal.inria.fr/hal-00734312
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
  • 18S. 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
  • 19P. Gardner, R. Giegerich.

    A comprehensive comparison of comparative RNA structure prediction approaches, in: BMC Bioinformatics, 2004, vol. 5(140).
  • 20G. 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/
  • 21F. 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.
  • 22L. Noé, M. Gîrdea, G. Kucherov.

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

    http://www.hindawi.com/journals/abi/2010/708501/
  • 23L. 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/
  • 24A. 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.
  • 25A. Ouangraoua, P. Ferraro.

    A new constrained edit distance between quotiented ordered trees, in: J. Discrete Algorithms, 2009, vol. 7, no 1, p. 78-89.
  • 26A. 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.
  • 27P. 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
  • 28P. 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
  • 29M. 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
  • 30M. 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.
  • 31M. Salson, T. Lecroq, M. Léonard, L. Mouchard.

    Dynamic Extended Suffix Array, in: Journal of Discrete Algorithms, 2010, vol. 8, p. 241–257.
  • 32H. 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