[1] Azadeh Saffarian. Algorithmes de prédiction et de recherche de multi-structures d'ARN. These, Université Lille 1, November 2011. [ bib | http | .pdf ]
[2] Marie-Josée Cros, Antoine de Monte, Jérœme Mariette, Philippe Bardou, Benjamin Grenier-Boley, Daniel Gautheret, Helene Touzet, and Christine Gaspin. RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA, 17:1947-1956, September 2011. [ bib | DOI | http ]
[3] Jean-Frédéric Berthelot, Charles Deltel, Mathieu Giraud, Stéphane Janot, Laetitia Jourdan, Dominique Lavenier, Helene Touzet, and Jean-Stéphane Varré. biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics. In JOBIM 2011, Paris, France, July 2011. [ bib | http ]
[4] Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, and Eric Rivals. Querying Large Read Collections in Main Memory: A Versatile data Structure. BMC Bioinformatics, 12:242+, June 2011. [ bib | DOI | http ]
[5] Samuel Blanquart and Olivier Gascuel. Mitochondrial genes support a common origin of Plasmodium falciparum and relatives with rodent malaria parasites. BMC Evolutionary Biology, March 2011. [ bib | DOI | http ]
[6] Mathieu Giraud and Jean-Stéphane Varré. Parallel Position Weight Matrices Algorithms. Parallel Computing, 37:466-478, 2011. [ bib | DOI | http ]
[7] Anna Gambin, Slawomir Lasota, Michal Startek, Maciej Sykulski, Laurent Noé, and Gregory Kucherov. Subset seed extension to Protein BLAST. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2011), pages 149-158, 2011. [ bib | DOI | http ]
[8] Antoine Thomas, Jean-Stéphane Varré, and Aïda Ouangraoua. Genome Dedoubling by DCJ and Reversal. BMC Bioinformatics, 12(Suppl 9):S20, 2011. Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics. [ bib | DOI | http ]
[9] Aïda Ouangraoua, Eric Tannier, and Cedric Chauve. Reconstructing the architecture of the ancestral amniote genome. Bioinformatics, 27(19):2664-2671, 2011. [ bib | DOI | http ]
[10] Aïda Ouangraoua, Krister Swenson, and Cedric Chauve. A 2-Approximation for the Minimum Duplication Speciation Problem. Journal of Computational Biology, 18(9):1041-1053, 2011. [ bib | DOI | http ]
[11] Aïda Ouangraoua, Anne Bergeron, and Krister Swenson. Theory and practice of ultra-perfection. Journal of Computational Biology, 18(9):1219-1230, 2011. [ bib | DOI | http ]
[12] Aïda Ouangraoua, Valentin Guignon, Sylvie Hamel, and Cedric Chauve. A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes. Theoretical Computer Science, 412(8-10):753-764, 2011. [ bib | DOI | http ]
[13] Martine Léonard, Laurent Mouchard, and Mikaël Salson. On the number of elements to reorder when updating a suffix array. Journal of Discrete Algorithms, January 2011. [ bib | DOI | http ]
[14] Florence Levé, Richard Groult, Guillaume Arnaud, Cyril Séguin, Rémi Gaymay, and Mathieu Giraud. Rhythm extraction from polyphonic symbolic music. In 12th International Society for Music Information Retrieval Conference (ISMIR 2011), pages 375-380, United States, 2011. [ bib | http ]
[15] Mathieu Giraud, Stéphane Janot, Jean-Frédéric Berthelot, Charles Deltel, Laetitia Jourdan, Dominique Lavenier, Helene Touzet, and Jean-Stéphane Varré. Biomanycores, open-source parallel code for many-core bioinformatics. In Bioinformatics Open Source Conference (BOSC 2011), Vienne, Austria, 2011. [ bib | http ]
[16] Tuan Tu Tran, Mathieu Giraud, and Jean-Stéphane Varré. Bit-Parallel Multiple Pattern Matching. In Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11), Torun, Poland, 2011. [ bib | DOI | http ]
[17] Jean-Stéphane Varré, Bertil Schmidt, Stéphane Janot, and Mathieu Giraud. Manycore high-performance computing in bioinformatics. In Laura Elnitski, Helen Piontkivska, and Lonnie R Welch, editors, Advances in Genomic Sequence Analysis and Pattern Discovery, page chapter 8. World Scientific, 2011. [ bib | http ]