Nombre de documents

25

Julien Allali : algorithms on sequences and trees


Article dans une revue6 documents

  • Julien Allali, Cédric Saule, Cedric Chauve, Yves D'Aubenton-Carafa, Alain Denise, et al.. BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms. Advances in Bioinformatics, Hindawi Publishing Corporation, 2012, 2012 (893048), 5 p. 〈10.1155/2012〉. 〈hal-00647725〉
  • Julien Allali, Cedric Chauve, Pascal Ferraro, Anne-Laure Gaillard. Efficient chaining of seeds in ordered trees. Journal of Discrete Algorithms, Elsevier, 2012. 〈hal-00647714〉
  • Julien Allali, Pascal Ferraro, Pierre Hanna, C.S. Iliopoulos, Matthias Robine. Toward a general framework for polyphonic comparison. Fundamenta Informaticae, Polskie Towarzystwo Matematyczne, 2009, 97 (3), pp.331--346. 〈hal-00523428〉
  • Julien Allali, Marie-France Sagot. A multiple layer model to compare RNA secondary structures. Software: Practice and Experience, Wiley, 2008, 38 (8), pp.775-792. 〈hal-00306662〉
  • Pierre Peterlongo, Julien Allali, Marie-France Sagot. Indexing gapped-factors using a tree. International Journal of Foundations of Computer Science, World Scientific Publishing, 2007. 〈inria-00179719〉
  • Julien Allali, Marie-France Sagot. A new distance for high level RNA secondary structure comparison. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2005, 2, pp.3--14. 〈hal-00306658〉

Communication dans un congrès13 documents

  • Laetitia Bourgeade, Cedric Chauve, Julien Allali. Chaining Sequence/Structure Seeds for Computing RNA Similarity. First Workshop on Computational Methods for Structural RNAs - CMRS'14, Sep 2014, Strasbourg, France. 2014. 〈hal-01019797〉
  • Julien Allali, Pavlos Antoniou, Pascal Ferraro, C.S. Iliopoulos, Spiros Michalakopoulos. Combinatorial detection of arrhytmia. 3rd International Conference on Bio-inspired Systems and Signal Processing, Jan 2010, Valencia, Spain. pp.180--187, 2010. 〈hal-00523484〉
  • Julien Allali, Cédric Chauve, Pascal Ferraro, Anne-Laure Gaillard. Efficient chaining of seeds in ordered trees. 21st International Workshop on Combinatorial Algorithms, Jul 2010, London, United Kingdom. 2010. 〈hal-00490028〉
  • Pavlos Antoniou, Julien Allali, Costas Iliopoulos, Pascal Ferraro. Validation and Decomposition of Partially Occluded Images with Holes. Prague Stringology Conference, Aug 2009, Prague, Czech Republic. pp.129--136, 2009. 〈hal-00403709〉
  • Julien Allali, Pavlos Antoniou, Pascal Ferraro, Costas Iliopoulos, Spiros Michalakopoulos. Overlay problems for music and combinatorics. Mitsuko Aramaki and Richard Kronland-Martinet and Sølvi Ystad and Kristoffer Jensen. International Conference on Auditory Display, May 2009, Copenhagen, Denmark. pp.138--143, 2009. 〈hal-00411792〉
  • Pascal Ferraro, Julien Allali, Pierre Hanna, Matthias Robine. Extending Alignment Algorithm for Polyphonic Comparison. International Computer Music Modeling and Retrieval Conference (CMMR), 2009, Denmark. pp.206-209, 2009. 〈hal-00391094〉
  • Pierre Hanna, Matthias Robine, Pascal Ferraro, Julien Allali. Improvements of Alignment Algorithms for Polyphonic Music Retrieval. Computer Music Modeling and Retrieval 2008, 2008, Denmark. pp.244-251, 2008. 〈hal-00306949〉
  • Julien Allali, Yves D'Aubenton-Carafa, Cedric Chauve, Alain Denise, Christine Drevet, et al.. Benchmarking RNA secondary structure comparison algorithms. JOBIM'08, 2008, Lille, France. pp.67-68, 2008. 〈hal-00375710〉
  • Julien Allali, Pascal Ferraro, Pierre Hanna, Costas Iliopoulos. Local Transpositions in Alignment of Polyphonic Musical Sequences. Proceedings of the 14th String Processing and Information Retrieval Symposium (SPIRE07), 2007, Chile. pp.26-38, 2007. 〈hal-00307877〉
  • Matthias Robine, Pierre Hanna, Pascal Ferraro, Julien Allali. Adaptation of String Matching Algorithms for Identification of Near-Duplicate Music Documents. Workshop on Plagiarism Analysis, Authorship Identification, and Near-Duplicate Detection (PAN07), Jul 2007, Amsterdam, Netherlands. pp.37--43, 2007. 〈hal-00306567〉
  • Pierre Peterlongo, Julien Allali, Marie-France Sagot. The Gapped-Factor Tree. Prague Stringology Conference 2006, 2006, Czech Republic. pp.182--196, 2006. 〈hal-00306572〉
  • Julien Allali, Marie-France Sagot. A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison. String Processing and Information Retrieval 2005, Nov 2005, Argentina. Mariano Consens and Gonzalo Navarro, 3772, pp.348--359, 2005. 〈hal-00306660〉
  • Julien Allali, Marie-France Sagot. Novel tree edit operations for RNA secondary structure comparison. Workshop on Algorithms in Bioinformatics 2004, 2004, Bergen, Denmark. 3240, pp.412--425, 2004. 〈hal-00306661〉

Poster1 document

  • Joris Sansen, Romain Bourqui, Patricia Thebault, Julien Allali, David Auber. Visualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls. 5th Symposium on Biological Data Visualization, Jul 2015, Dublin, Ireland. 〈hal-01664524〉

Chapitre d'ouvrage2 documents

  • Pascal Ferraro, Matthias Robine, Julien Allali, Pierre Hanna, Rocher Thomas. Detection of Near-Duplicate Musical Documents from a Multi-Level Comparison of Tonal Information. Information Extraction from the Internet, iconcept press, pp.129--143, 2011. 〈hal-00643529〉
  • Julien Allali, Pascal Ferraro, Pierre Hanna, Matthias Robine. Polyphonic alignment algorithms for symbolic music retrieval. Ystad, S. and Aramaki, M. and Kronland-Martinet, R. and Jensen, K. Auditory Display, Springer Verlag Berlin, pp.466--482, 2010, LNCS, 〈10.1007/978-3-642-12439-6_24〉. 〈hal-00523486〉

Brevet1 document

  • Benjamin Martin, Pierre Hanna, Vinh Thong Ta, Myriam Desainte-Catherine, Julien Allali, et al.. Exemplar Based Assignment of Large Missing Audio Parts using String Matching on Tonal Features. United States, Patent n° : US61/547,854. 2011. 〈hal-01006489〉

Rapport1 document

  • Julien Allali, Marie-France Sagot. The at-most $k$-deep factor tree. 2004. 〈hal-00627813〉

Thèse1 document

  • Julien Allali. Comparaison de structures secondaires d'ARN. Informatique [cs]. Université de Marne la Vallée, 2004. Français. 〈tel-00637131〉