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Julien Allali

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A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets

Aarón Ayllón-Benítez , Fleur Mougin , Julien Allali , Rodolphe Thiébaut , Patricia Thebault
PLoS ONE, 2018, 13 (11), pp.e0208037. ⟨10.1371/journal.pone.0208037⟩
Journal articles hal-01938961v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Journal articles hal-00647725v1

Efficient chaining of seeds in ordered trees

Julien Allali , Cedric Chauve , Pascal Ferraro , Anne-Laure Gaillard
Journal of Discrete Algorithms, 2012
Journal articles hal-00647714v1

Toward a general framework for polyphonic comparison

Julien Allali , Pascal Ferraro , Pierre Hanna , C.S. Iliopoulos , Matthias Robine
Fundamenta Informaticae, 2009, 97 (3), pp.331--346
Journal articles hal-00523428v1
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Indexing gapped-factors using a tree

Pierre Peterlongo , Julien Allali , Marie-France Sagot
International Journal of Foundations of Computer Science, 2008, 19 (1), pp.71-87. ⟨10.1142/S0129054108005541⟩
Journal articles inria-00179719v1
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A multiple layer model to compare RNA secondary structures

Julien Allali , Marie-France Sagot
Software: Practice and Experience, 2008, 38 (8), pp.775-792
Journal articles hal-00306662v1
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A new distance for high level RNA secondary structure comparison

Julien Allali , Marie-France Sagot
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2005, 2, pp.3--14
Journal articles hal-00306658v1
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Chaining Sequence/Structure Seeds for Computing RNA Similarity

Laetitia Bourgeade , Cedric Chauve , Julien Allali
First Workshop on Computational Methods for Structural RNAs - CMRS'14, Sep 2014, Strasbourg, France
Conference papers hal-01019797v1

Combinatorial detection of arrhytmia

Julien Allali , Pavlos Antoniou , Pascal Ferraro , C.S. Iliopoulos , Spiros Michalakopoulos
3rd International Conference on Bio-inspired Systems and Signal Processing, Jan 2010, Valencia, Spain. pp.180--187
Conference papers hal-00523484v1
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Efficient chaining of seeds in ordered trees

Julien Allali , Cédric Chauve , Pascal Ferraro , Anne-Laure Gaillard
21st International Workshop on Combinatorial Algorithms, Jul 2010, London, United Kingdom
Conference papers hal-00490028v1

Overlay problems for music and combinatorics

Julien Allali , Pavlos Antoniou , Pascal Ferraro , Costas Iliopoulos , Spiros Michalakopoulos
International Conference on Auditory Display, May 2009, Copenhagen, Denmark. pp.138--143
Conference papers hal-00411792v1

Validation and Decomposition of Partially Occluded Images with Holes

Pavlos Antoniou , Julien Allali , Costas Iliopoulos , Pascal Ferraro
Prague Stringology Conference, Aug 2009, Prague, Czech Republic. pp.129--136
Conference papers hal-00403709v1

Extending Alignment Algorithm for Polyphonic Comparison

Pascal Ferraro , Julien Allali , Pierre Hanna , Matthias Robine
International Computer Music Modeling and Retrieval Conference (CMMR), 2009, Denmark. pp.206-209
Conference papers hal-00391094v1

Benchmarking RNA secondary structure comparison algorithms

Julien Allali , Yves d'Aubenton-Carafa , Cedric Chauve , Alain Denise , Christine Drevet
JOBIM'08, 2008, Lille, France. pp.67-68
Conference papers hal-00375710v1
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Improvements of Alignment Algorithms for Polyphonic Music Retrieval

Pierre Hanna , Matthias Robine , Pascal Ferraro , Julien Allali
Computer Music Modeling and Retrieval 2008, 2008, Denmark. pp.244-251
Conference papers hal-00306949v1
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Adaptation of String Matching Algorithms for Identification of Near-Duplicate Music Documents

Matthias Robine , Pierre Hanna , Pascal Ferraro , Julien Allali
Workshop on Plagiarism Analysis, Authorship Identification, and Near-Duplicate Detection (PAN07), Jul 2007, Amsterdam, Netherlands. pp.37--43
Conference papers hal-00306567v1

Local Transpositions in Alignment of Polyphonic Musical Sequences

Julien Allali , Pascal Ferraro , Pierre Hanna , Costas Iliopoulos
Proceedings of the 14th String Processing and Information Retrieval Symposium (SPIRE07), 2007, Chile. pp.26-38
Conference papers hal-00307877v1
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The Gapped-Factor Tree

Pierre Peterlongo , Julien Allali , Marie-France Sagot
Prague Stringology Conference 2006, 2006, Prague, Czech Republic. pp.182--196
Conference papers hal-00306572v1
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A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison

Julien Allali , Marie-France Sagot
String Processing and Information Retrieval 2005 (SPIRE 2005), Nov 2005, Buenos Aires, Argentina. pp.348--359
Conference papers hal-00306660v1
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Novel tree edit operations for RNA secondary structure comparison

Julien Allali , Marie-France Sagot
Workshop on Algorithms in Bioinformatics 2004, 2004, Bergen, Denmark. pp.412--425, ⟨10.1007/978-3-540-30219-3_35⟩
Conference papers hal-00306661v1

Detection of Near-Duplicate Musical Documents from a Multi-Level Comparison of Tonal Information

Pascal Ferraro , Matthias Robine , Julien Allali , Pierre Hanna , Rocher Thomas
Information Extraction from the Internet, iconcept press, pp.129--143, 2011
Book sections hal-00643529v1

Polyphonic alignment algorithms for symbolic music retrieval

Julien Allali , Pascal Ferraro , Pierre Hanna , Matthias Robine
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⟩
Book sections hal-00523486v1
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Comparaison de structures secondaires d'ARN

Julien Allali
Informatique [cs]. Université de Marne la Vallée, 2004. Français. ⟨NNT : ⟩
Theses tel-00637131v1