publications

2012 [bib]

[1]	Evguenia Kopylova, Laurent Noé, and Hélène Touzet. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics, pages 1-10, October 2012. [ bib \| DOI \| http ]
[2]	Ammar Abdo, Ségolène Caboche, Valérie Leclère, Philippe Jacques, and Maude Pupin. A new fingerprint to predict nonribosomal peptides activity. Journal of Computer-Aided Molecular Design, 26(10):1187-94, October 2012. [ bib \| DOI \| http ]
[3]	Max Béchet, Thibault Caradec, Walaa Hussein, Ahmed Abderrahmani, Marlène Chollet, Valérie Leclère, Thomas Dubois, Didier Lereclus, Maude Pupin, and Philippe Jacques. Structure, biosynthesis, and properties of kurstakins, nonribosomal lipopeptides from Bacillus spp. Applied Microbiology and Biotechnology, 95(3):593-600, August 2012. [ bib \| DOI \| http ]
[4]	Eric Rivals, Nicolas Philippe, Mikaël Salson, Martine Léonard, Thérèse Commes, and Thierry Lecroq. A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections. ERCIM News, 2012(89):20-21, April 2012. [ bib \| http ]
[5]	Martine Léonard, Laurent Mouchard, and Mikaël Salson. On the number of elements to reorder when updating a suffix array. Journal of Discrete Algorithms, 11:87-99, February 2012. [ bib \| DOI \| http ]
[6]	Azadeh Saffarian, Mathieu Giraud, Antoine De Monte, and Hélène Touzet. RNA Locally Optimal Secondary Structures. Journal of Computational Biology, 19(10):1120-1133, 2012. [ bib \| DOI \| http \| .pdf ]
[7]	Julien Allali, Cédric Saule, Cedric Chauve, Yves D'Aubenton-Carafa, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine De Monte, Aïda Ouangraoua, Marie-France Sagot, Michel Termier, Claude Thermes, and Hélène Touzet. BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms. Advances in Bioinformatics, pages accepted for publication (Feb, 2012), 2012. [ bib \| http ]
[8]	Michal Startek, Slawomir Lasota, Maciej Sykulski, Adam Bulak, Anna Gambin, Laurent Noé, and Gregory Kucherov. Efficient alternatives to PSI-BLAST. bulletin of the polish academy of sciences: technical sciences, 2012. [ bib \| http ]
[9]	Mathieu Giraud, Richard Groult, and Florence 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), pages 661-673, United Kingdom, 2012. [ bib \| http ]
[10]	Mathieu Giraud, Richard Groult, and Florence Levé. Detecting Episodes with Harmonic Sequences for Fugue Analysis. In ISMIR - International Society for Music Information Retrieval Conference - 2012, Porto, Portugal, 2012. [ bib \| http ]
[11]	Maude Pupin, Malika Smail-Tabbone, Philippe Jacques, Marie-Dominique Devignes, and Valérie Leclère. NRPS toolbox for the discovery of new nonribosomal peptides and synthetases. In François Coste and Denis Tagu, editors, Journées Ouvertes en Biologie, l'Informatique et les Mathématiques - JOBIM 2012, pages 89-93, Rennes, France, 2012. [ bib \| http ]
[12]	Antoine Thomas, Aïda Ouangraoua, and Jean-Stéphane Varré. Tandem Halving Problems by DCJ. In Workshop on Algorithms in Bioinformatics, volume 7534, pages 417-429, Ljubljana, Slovenia, 2012. Springer Berlin Heidelberg. [ bib \| DOI \| http ]
[13]	Antoine Thomas, Aïda Ouangraoua, and Jean-Stéphane Varré. Genome Halving by Block Interchange. In Jan Schier, Carlos Manuel B. A. Correia, Ana L. N. Fred, and Hugo Gamboa, editors, BIOINFORMATICS, pages 58-65, Lisboa, Portugal, 2012. SciTePress. [ bib \| http ]
[14]	Aïda Ouangraoua and Mathieu Raffinot. Faster and Simpler Minimal Conflicting Set Identification. In Combinatorial Pattern Matching, volume 7354, pages 41-55, Helsinki, Finland, 2012. Springer. [ bib \| http ]
[15]	Aïda Ouangraoua, Krister Swenson, and Anne Bergeron. On the comparison of sets of alternative transcripts. In International Symposium on Bioinformatics Research and Applications, volume 7292, pages 201-212, Dallas, Germany, 2012. Springer. [ bib \| http ]

2011 [bib]

[1]	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 \| http ]
[2]	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 ]
[3]	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 \| http ]
[4]	Mathieu Giraud and Jean-Stéphane Varré. Parallel Position Weight Matrices Algorithms. Parallel Computing, 37:466-478, 2011. [ bib \| DOI \| http ]
[5]	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 ]
[6]	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 \| http ]
[7]	Aïda Ouangraoua, Eric Tannier, and Cedric Chauve. Reconstructing the architecture of the ancestral amniote genome. Bioinformatics, (19):2664-2671, 2011. [ bib \| http ]
[8]	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 \| http ]
[9]	Aïda Ouangraoua, Anne Bergeron, and Krister Swenson. Theory and practice of ultra-perfection. Journal of Computational Biology, 18(9):1219-1230, 2011. [ bib \| http ]
[10]	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 \| http ]
[11]	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 ]
[12]	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 ]
[13]	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 ]
[14]	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 \| http ]
[15]	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 ]
[16]	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+, Jun 2011. [ bib \| DOI \| http ]
[17]	Azadeh Saffarian. Algorithmes de prédiction et de recherche de multi-structures d'ARN. PhD thesis, Université Lille 1, 2011. [ bib ]

2010 [bib]

[1]	S. Caboche, V. Leclère, M. Pupin, and P. Kucherov, G. Jacques. Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity. Journal of bacteriology, 192(19):5143-5150, October 2010. [ bib \| DOI \| http ]
[2]	A. Ouangraoua, K. Swenson, and C. Chauve. An approximation algorithm for computing a parsimonious first speciation in the gene duplication model. In E. Tannier, editor, RECOMB-Comparative Genomics, LNBI 6398, volume 6398 of Lecture Notes in Bioinformatics, pages 290-302, October 2010. [ bib ]
[3]	A. Ouangraoua, A. Bergeron, and K. Swenson. Ultra-perfect sorting scenarios. In E. Tannier, editor, RECOMB-Comparative Genomics, LNBI 6398, volume 6398 of Lecture Notes in Bioinformatics, pages 50-61, October 2010. [ bib ]
[4]	A. Ouangraoua and A. Bergeron. Combinatorial structure of genome rearrangements scenarios. Journal of Computational Biology, 2010:1129-1144, September 2010. [ bib \| DOI \| http \| http ]
[5]	C. Chauve, H. Gavranovic, A. Ouangraoua, and E. Tannier. Yeast ancestral genome reconstructions: the possibilities of computational methods. Journal of Computational Biology, 2010:1097-1112, September 2010. [ bib \| DOI \| http \| http ]
[6]	L. Noé, M. Gîrdea, and G. Kucherov. Designing efficient spaced seeds for SOLiD read mapping. Advances in Bioinformatics, 2010:ID 708501, July 2010. [ bib \| DOI \| .html \| .pdf ]
[7]	Laurie Tonon, Hélène Touzet, and Jean-Stéphane Varré. TFM-Explorer: mining cis-regulatory regions in genomes. Nucleic Acids Research, 38(suppl_2):W286-292, June 2010. [ bib \| DOI \| http \| .pdf ]
[8]	Aude Darracq, Jean-Stéphane Varré, and Pascal Touzet. A scenario of mitochondrial genome evolution in maize based on rearrangement events. BMC Genomics, 11(233), April 2010. [ bib \| DOI \| http \| .pdf ]
[9]	L. Noé, M. Gîrdea, and G. Kucherov. Seed design framework for mapping SOLiD reads. In B. Berger, editor, Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), April 25-28, 2010, Lisbon (Portugal), volume 6044 of Lecture Notes in Computer Science, pages 384-396. Springer, April 2010. [ bib \| DOI \| arXiv \| http \| .ps.gz \| .pdf ]
[10]	Jean-Stéphane Varré, Bertil Schmidt, Stéphane Janot, and Mathieu Giraud. Advances in Genomic Sequence Analysis and Pattern Discovery, chapter Manycore High-Performance Computing in Bioinformatics. World Scientific, 2010. to appear. [ bib \| .html ]
[11]	Nadia Pisanti, Mathieu Giraud, and Pierre Peterlongo. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, chapter Filters and Seeds Approaches for Fast Homology Searches in Large Datasets. Wiley, 2010. (to appear). [ bib \| .html ]
[12]	A. Ouangraoua, V. Guignon, S. Hamel, and C. Chauve. A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes. Theoretical Computer Science, 2010. to appear. [ bib ]
[13]	Mathieu Giraud and Jean-Stéphane Varré. Parallel position weight matrices algorithms. Parallel Computing, 2010. to appear. [ bib \| DOI \| http ]
[14]	M. Gîrdea, G. Kucherov, and L. Noé. Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms for Molecular Biology, 5(6), January 2010. [ bib \| DOI \| http \| .pdf ]
[15]	Hideo Bannai, Mathieu Giraud, Kazuhiko Kusano, Wataru Matsubara, Ayumi Shinohara, and Jamie Simpson. The number of runs in a ternary word. In Prague Stringology Conference 2010 (PSC 2010), 2010. [ bib \| .html ]
[16]	Aude Darracq. Evolution des génomes mitochondriaux de plantes - Approche de génomique comparative chez Zea mays et Beta vulgaris. PhD thesis, Université Lille 1, 2010. [ bib ]
[17]	Marta Gîrdea. New methods for biological sequence alignment. PhD thesis, Université Lille 1, 2010. [ bib ]

2009 [bib]

[1]	M. Gîrdea, G. Kucherov, and L. Noé. Back-translation for discovering distant protein homologies. In S.L. Salzberg and T. Warnow, editors, Proceedings of the 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia (USA), volume 5724 of Lecture Notes in Computer Science, pages 108-120. Springer Verlag, September 2009. [ bib \| DOI \| http \| .ps.gz \| .pdf ]
[2]	M. Gîrdea, L. Noé, and G. Kucherov. Read mapping tool for AB SOLiD data. In 9th Workshop on Algorithms in Bioinformatics (WABI), Philadelphia (USA), September 12-13, 2009, September 2009. poster. [ bib \| .pdf ]
[3]	S. Caboche, M. Pupin, V. Leclère, Ph. Jacques, and G. Kucherov. Structural pattern matching of nonribosomal peptides. BMC Structural Biology, 9:15, March 18 2009. [ bib \| DOI \| http ]
[4]	G. Kucherov and E. Ukkonen, editors. Combinatorial Pattern Matching: 20th Annual Symposium (CPM), Lille (France), June 2009. Proceedings, volume 5577 of Lecture Notes in Computer Science. Springer, 2009. [ bib \| DOI ]
[5]	R. Kolpakov and G. Kucherov. Searching for gapped palindromes. Theoretical Computer Science, 410(51):5365-5373, 2009. [ bib \| DOI ]
[6]	Arnaud Fontaine and Hélène Touzet. Computational identification of protein-coding sequences by comparative analysis. International Journal of Data Mining and Bioinformatics, 3(2):160-176, 2009. [ bib \| DOI \| http ]
[7]	M. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, and G. Kucherov. On subset seeds for protein alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(3):483-494, 2009. [ bib \| DOI \| .pdf \| .ps.gz ]
[8]	Mathieu Giraud. Asymptotic behavior of the number of runs and microruns. Information and Computation, 207(11):1221-1228, 2009. [ bib \| DOI \| http ]
[9]	R. Uricaru, C. Michotey, L. Noé, H. Chiapello, and É. Rivals. Improved sensitivity and reliability of anchor based genome alignment. In Proceedings of the 10th Open Days in Biology, Computer Science and Mathematics (JOBIM), June 9-11, 2009, Nantes (France), pages 31-36, 2009. [ bib \| .pdf ]
[10]	Peter Steffen, Robert Giegerich, and Mathieu Giraud. Gpu parallelization of algebraic dynamic programming. In Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 09), volume 6068 of Lecture Notes in Computer Science (LNCS), pages 290-299, 2009. [ bib ]
[11]	Mathieu Giraud and Jean-Stéphane Varré. Parallel Position Weight Matrices Algorithms. In Proceedings of the 8th International Symposium on Parallel and Distributed Computing, ISPDC'09, pages 65-69, 2009. [ bib \| DOI \| http ]
[12]	Aude Liefooghe, Hélène Touzet, and Jean-Stéphane Varré. Self-overlapping occurrences and Knuth-Morris-Pratt algorithm for weighted matching. In Proceedings of the 3rd International Conference on Language and Automata Theory and Applications, April 2-8, 2009 - Tarragona, Spain, volume 5457, pages 481-492, 2009. [ bib \| DOI \| http \| .pdf ]
[13]	E. Harris, T. Lecroq, G. Kucherov, and S. Lonardi. CPM's 20th anniversary: A statistical retrospective. In Proceedings of the 20th Annual Combinatorial Pattern Matching Symposium (CPM), Lille (France), June 22-24, 2009, volume 5577 of Lecture Notes in Computer Science, pages 1-11. Springer Verlag, 2009. [ bib \| DOI ]
[14]	Azadeh Saffarian, Mathieu Giraud, and Hélène Touzet. Paysage d'énergie et structures localement optimales d'un arn. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2009) (poster), 2009. poster. [ bib ]
[15]	Aude Darracq, Jean-Stéphane Varré, and Pascal Touzet. A study of genomic rearrangements in maize mitochondrial genomes. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2009), 2009. poster. [ bib ]
[16]	Aude Darracq, Jean-Stéphane Varré, and Pascal Touzet. A study of genomic rearrangements in maize mitochondrial genomes. In The 17th annual meeting of the Society for Molecular Biology and Evolution (SMBE 2009), 2009. poster. [ bib ]
[17]	Jean-Stéphane Varré, Stéphane Janot, and Mathieu Giraud. Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics. In Bioinformatics Open Source Conference (BOSC), 2009. [ bib ]
[18]	Ségolène Caboche. Mise en place d'une plateforme logicielle pour l'analyse des peptides non-ribosomiaux. PhD thesis, Université de Lille 1, 2009. [ bib ]
[19]	Arnaud Fontaine. Classification d'ARN codants et d'ARN non-codants. PhD thesis, Université de Lille 1, 2009. [ bib \| .pdf ]
[20]	A. Ouangraoua and P. Ferraro. A constrained edit distance algorithm between semi-ordered trees. Theor. Comput. Sci., 410(8-10):837-846, 2009. [ bib ]
[21]	A. Ouangraoua and P. Ferraro. A new constrained edit distance between quotiented ordered trees. J. Discrete Algorithms, 7(1):78-89, 2009. [ bib ]

2008 [bib]

[1]	Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, and Mathieu Giraud. Optimal neighborhood indexing for protein similarity search. BMC Bioinformatics, 9(534), 2008. [ bib \| DOI \| http \| .pdf ]
[2]	Aude Liefooghe. Matrices score-position, algorithmes et propriétés. PhD thesis, Université de Lille 1, 2008. [ bib ]
[3]	Jean-Stéphane Varré. Algorithmes pour la comparaison de génomes et la recherche de signaux cis-régulateurs. Habilitation à diriger des recherches, Université de Lille 1, 2008. [ bib ]
[4]	Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, and Hélène Touzet. Alignment of RNA structures. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008. [ bib \| DOI \| http ]
[5]	Arnaud Fontaine, Antoine de Monte, and Hélène Touzet. MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences. Nucleic Acids Research, Web Server Issue, Vol 36(suppl 2):W14-W18, 2008. [ bib \| DOI \| http \| .pdf ]
[6]	Anne Chenuil, Emilie Egea, Caroline Rocher, Hélène Touzet, and Jean-Pierre Féral. Does hybridization increase evolutionary rate ? Data from the 28S-rDNA D8 domain in echinoderms. Journal of Molecular Evolution, 67(5):539-550, 2008. [ bib \| DOI \| .html \| .pdf ]
[7]	M. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, and G. Kucherov. Efficient seeding techniques for protein similarity search. In M Elloumi, J. Küng, M. Linial, R.F. Murphy, K. Schneider, and C. Toma, editors, Proceedings of the 2nd Workshop on Algorithms in Molecular Biology (ALBIO'08), Vienna (Austria), July 7-9, 2008, volume 13 of Communications in Computer and Information Science, pages 466-478. Springer Verlag, 2008. [ bib \| DOI \| http \| .ps.gz \| .pdf ]
[8]	Mathieu Giraud. Not so many runs in strings. In Int. Conf. on Language and Automata Theory and Applications (LATA 08), volume 5196 of Lecture Notes in Computer Science (LNCS), pages 232-239, 2008. [ bib \| DOI \| .pdf ]
[9]	R. Kolpakov and G. Kucherov. Searching for gapped palindromes. In Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM), June 18-20, 2008, Pisa (Italy), volume 5029 of Lecture Notes in Computer Science, pages 18-30. Springer Verlag, 2008. [ bib \| DOI \| http \| .pdf ]
[10]	Jean-Émile Symphor, Alban Mancheron, Lionel Vinceslas, and Pascal Poncelet. Le fia : un nouvel automate permettant l'extraction efficace d'itemsets fréquents dans les flots de données. In Proceedings of the 8^th Extraction et Gestion des Connaissances (egc), volume RNTI-E-11 (1) of Revue des Nouvelles Technologies de l'Information, pages 157-168. Cépaduès-Éditions, 2008. [ bib \| .pdf ]
[11]	S. Guillemot. Parameterized complexity and approximability of the SLCS problem. In Proceedings of Parameterized and Exact Computation: Third International Workshop (IWPEC 2008), volume 5018 of Lecture Notes in Computer Science, pages 115-128, 2008. [ bib \| DOI \| http \| .pdf ]
[12]	S. Guillemot. FPT algorithms for path-transversals and cycle-transversals problems in graphs. In Proceedings of Parameterized and Exact Computation: Third International Workshop (IWPEC 2008), volume 5018 of Lecture Notes in Computer Science, pages 129-140, 2008. [ bib \| DOI \| http \| .pdf ]
[13]	J. Byrka, S. Guillemot, and J. Jansson. New Results on Optimizing Rooted Triplets Consistency. In Proceedings of the 19th International Symposium on Algorithms and Computation (ISAAC 2008), volume 5369 of Lecture Notes in Computer Science, pages 484-495, 2008. [ bib \| DOI \| http \| .pdf ]
[14]	Jesper Jansson and W.-K. Sung. New Topics in Theoretical Computer Science, chapter The Maximum Agreement of Two Nested Phylogenetic Networks, pages 119-141. NOVA Publishers, 2008. [ bib ]
[15]	Jesper Jansson. Encyclopedia of Algorithms, chapter Directed Perfect Phylogeny (Binary Characters) - 1991; Gusfield, pages 246-248. Springer, 2008. [ bib \| DOI \| http ]
[16]	Jesper Jansson. Encyclopedia of Algorithms, chapter Perfect Phylogeny (Bounded Number of States) - 1997; Kannan, Warnow, pages 644-647. Springer, 2008. [ bib \| DOI \| http ]
[17]	Jesper Jansson. Encyclopedia of Algorithms, chapter Phylogenetic Tree Construction from a Distance Matrix - 1989; Hein, pages 651-653. Springer, 2008. [ bib \| DOI \| http ]
[18]	G. Kucherov and D. Sokol. Encyclopedia of Algorithms, chapter Approximate Tandem Repeats, pages 48-51. Springer, 2008. [ bib \| DOI \| http ]
[19]	M. Gîrdea, G. Kucherov, and L. Noé. Protein sequence alignment via anti translation. In Proceedings of the 9th Open Days in Biology, Computer Science and Mathematics (JOBIM), June 30-July 2, 2008, Lille (France), pages 157-158, 2008. (short talk with poster). [ bib \| .pdf ]
[20]	Julien Allali, Yves d'Aubenton Carafa, Cédric Chauve, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine de Monte, Aida Ouangraoua, Marie-France Sagot, Cédric Saule, Michel Termier, Claude Thermes, and Hélène Touzet. Benchmarking RNA secondary structure comparison algorithms. In Proceedings of the 9th Open Days in Biology, Computer Science and Mathematics (JOBIM), June 30-July 2, 2008, Lille (France), pages 67-68, 2008. (short talk with poster). [ bib \| .pdf ]
[21]	Ségolène Caboche, Maude Pupin, Valérie Leclère, Philippe Jacques, and Gregory Kucherov. NORINE: a platform dedicated to nonribosomal peptides, 2008. 9th Open Days in Biology, Computer Science and Mathematics (JOBIM), June 30-July 2, 2008, Lille (France). [ bib ]
[22]	Ségolène Caboche, Maude Pupin, Valérie Leclère, Philippe Jacques, and Gregory Kucherov. NORINE: a public resource for nonribosomal peptides, 2008. EMBnet 2008 - 20th Anniversary Conference. [ bib \| http \| .pdf ]
[23]	Ségolène Caboche, Maude Pupin, Valérie Leclère, Philippe Jacques, and Gregory Kucherov. NORINE: database and efficient algorithms dedicated to nonribosomal peptides, 2008. ECCB08 European Conference on Computational Biology. [ bib \| http ]
[24]	A. Darracq, J.-S. Varré, A. Courseaux, L. Maréchal-Drouard, and P. Touzet. Evolution of the mitochondrial genome in beet. a comparative genomic study at the intra-specific level, 2008. XX International Congress of Genetics. [ bib ]
[25]	Lionel Vinceslas, Jean-Émile Symphor, Alban Mancheron, and Pascal Poncelet. FIASCO : un nouvel algorithme d'extraction d'itemsets fréquents dans les flots de données. In Proceedings of the 8th Extraction et Gestion des Connaissances (EGC), volume RNTI-E-11 (1) of Revue des Nouvelles Technologies de l'Information, pages 235-236. Cépaduès-Éditions, 2008. [ bib ]

2007 [bib]

[1]	Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gil les Georges, Julien Jacques, Gregory Kucherov, and Mathieu Giraud. Protein similarity search with subset seeds on a dedicated reconfigur able hardware. In R. Wyrzykowski, J. Dongarra, K. Karczewski, and J. Wasniewski, editors, Parallel Processing and Applied Mathematics / Parallel Biocomputi ng Conference (PPAM / PBC 07), volume 4967 of Lecture Notes in Computer Science (LNCS), pages 1240-1248, 2008. [ bib \| DOI \| http \| .pdf ]
[2]	M. Csürös, L. Noé, and G. Kucherov. Reconsidering the significance of genomic word frequencies. Trends in Genetics, 23(11):543-546, November 2007. [ bib \| DOI \| http \| .pdf ]
[3]	H. Touzet and J.-S. Varré. Efficient and accurate p-value computation for position weight matrices. Algorithms for Molecular Biology, 2(15), 2007. [ bib \| DOI \| http \| .pdf ]
[4]	G. Didier, L. Debomy, M. Pupin, M. Zhang, A. Grossmann, C. Devauchelle, and I. Laprevotte. Comparing sequences without using alignments: application to HIV/SIV subtyping. BMC Bioinformatics, 8(1), 2007. [ bib \| DOI \| http \| .pdf ]
[5]	H. Touzet. Comparing similar ordered trees in linear-time. Journal of Discrete Algorithms, 5(4):696-705, 2007. [ bib \| DOI \| http ]
[6]	H. Touzet. Comparative analysis of RNA genes: the CaRNAc software, volume Methods in Molecular Biology, Special issue on comparative genomics I, pages 465-473. Humana Press, 2007. [ bib \| DOI \| .pdf ]
[7]	Arnaud Fontaine and Hélène Touzet. Computational identification of protein-coding sequences by comparative analysis. In Proceedings of the 1st IEEE international conference on Bioinformatics and Biomedecine (BIBM), Silicon Valley, California, pages 95-102. IEEE Computer Society, 2007. [ bib \| DOI \| http \| http ]
[8]	Ségolène Caboche, Valérie Leclère, Maude Pupin, Gregory Kucherov, and Philippe Jacques. Norine: une nouvelle base de données qui met en exergue la biodiversité des structures et des activités des peptides synthétisés par la voie non-ribosomale (NRPS). In septième congrés de la Société Francaise de Microbiologie (SFM), 2007. (poster). [ bib ]
[9]	Ségolène Caboche, Maude Pupin, Valérie Leclère, Arnaud Fontaine, Philippe Jacques, and Gregory Kucherov. NORINE: a database of nonribosomal peptides. Nucleic Acids Research, 2007. [ bib \| DOI \| http \| http ]
[10]	G. Kucherov, L. Noé, and M. Roytberg. Subset seed automaton. In J. Holub and J. Zdarek, editors, Proceedings of the 12th International Conference on Implementation and Application of Automata (CIAA), Prague (Czech Republic), July 16-18, 2007, volume 4783 of Lecture Notes in Computer Science, pages 180-191. Springer Verlag, 2007. [ bib \| DOI \| http \| .ps.gz \| .pdf ]
[11]	Mathieu Giraud, Philippe Veber, and Dominique Lavenier. Path-equivalent developments in acyclic weighted automata. International Journal of Foundations of Computer Science, 18(4):799-812, 2007. [ bib \| DOI \| .pdf ]
[12]	Jean-Eudes Duchesne, Mathieu Giraud, and Nadia El Mabrouk. Seed-based exclusion method for non-coding rna gene search. In International Computing and Combinatorics Conference (COCOON), volume 4598 of Lecture Notes in Computer Science, pages 27-39. Springer, 2007. [ bib \| DOI \| http \| .pdf ]
[13]	Arnaud Fontaine, Mathieu Giraud, Laurent Noé, and Hélène Touzet. Graines espacées et recherche d'ARN non-codants. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), 2007. (poster). [ bib \| .pdf ]
[14]	D. Grzebelus, L. Lasota, T. Gambin, G. Kucherov, and A. Gambin. Diversity and structure of PIF/Harbinger-like elements in the genome of medicago truncatula. BMC Genomics, 8(409), 2007. [ bib \| DOI \| http \| .pdf ]
[15]	A. Fontaine and H. Touzet. Identification of protein-coding genes and RNA genes by comparative analysis. In Benelux Bioinformatics Conference (BBC), 2007. (poster). [ bib \| .pdf ]
[16]	Alban Mancheron and Jean-Émile Symphor. Finding Frequent Subsequences in a Set of Texts. HAL, 2007. [ bib \| http \| .pdf ]
[17]	Alban Mancheron and Jean-Émile Symphor. On-line & Incremental Update Properties of the Subsequence Automaton. HAL, 2007. [ bib \| http \| .pdf ]

2006 [bib]

[1]	Matthieu Defrance. Algorithmes pour l'analyse de régions régulatrices dans le génome d'eucaryotes supérieurs. PhD thesis, Université des Sciences et Technologies de Lille, December 2006. [ bib ]
[2]	Mathieu Giraud, Philippe Veber, and Dominique Lavenier. Path-equivalent removal of epsilon-transitions. In 11th International Conference on Implementation and Application of Automata (CIAA), volume 4094 of Lecture Notes in Computer Science, pages 23-33. Springer Verlag, August 2006. [ bib \| DOI \| http \| .pdf ]
[3]	G. Blin and H. Touzet. How to compare arc-annotated sequences: The alignment hierarchy. In 13th International Symposium on String Processing and Information Retrieval (SPIRE), volume 4209 of Lecture Notes in Computer Science, pages 291-303. Springer Verlag, 2006. [ bib \| DOI \| http \| .pdf ]
[4]	H. Touzet. Comparing similar ordered trees in linear-time. Journal of Discrete Algorithms, 2006. [ bib \| DOI \| http ]
[5]	H. Touzet. Comparative analysis of RNA genes: the CaRNAc software, volume Methods in Molecular Biology, Special issue on comparative genomics I. Humana Press, 2006. in press. [ bib ]
[6]	J. Cohen, F. Fomin, P. Heggernes, D. Kratsch, and G. Kucherov. Optimal linear arrangement of interval graphs. In Proceedings of the 13th International Symposium on Mathematical Foundations of Computer Science (MFCS 2006), High Tatras (Slovakia), August 28 - September 1, 2006, volume 4162 of Lecture Notes in Computer Science, pages 267-279. Springer Verlag, 2006. [ bib \| DOI \| http \| .pdf ]
[7]	G. Didier, I. Laprevotte, M. Pupin, and A. Henaut. Local decoding of sequences and alignment-free comparison. Journal of Computational Biology, 13(8):1465-1476, 2006. [ bib \| DOI \| http \| http ]
[8]	S. Caboche, V. Leclère, P. Jacques, M. Pupin, and G. Kucherov. Database and comparison of non ribosomal peptides. In 7th Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), 2006. [ bib \| .pdf \| .pdf ]
[9]	V. Leclère, S. Caboche, M. Pupin, G. Kucherov, and P. Jacques. NORINE: a recent database highlighting a large biodiversity among nrps peptide structures and activities. In RSC conference, Chemical Biology: directing biosynthesis (poster), 2006. [ bib \| .pdf ]
[10]	Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-César Lerman, Anne-Sophie Valin, Ivan Couée, Abdelhak El Amrani, and Jacques Nicolas. Domain organization within repeated dna sequences: application to the study of a family of transposable elements. Bioinformatics, 22(16):1948-1954, 2006. [ bib \| DOI \| http \| .pdf ]
[11]	A. Liefooghe, H. Touzet, and J.-S. Varré. Large scale matching for position weight matrices. In Proceedings 17th Annual Symposium on Combinatorial Pattern Matching (CPM), volume 4009 of Lecture Notes in Computer Science, pages 401-412. Springer Verlag, 2006. [ bib \| DOI \| http \| .pdf ]
[12]	M. Defrance and H. Touzet. Predicting transcription factor binding sites using local over-representation and comparative genomics. BMC Bioinformatics, 2006. [ bib \| DOI \| http \| .pdf ]
[13]	G. Kucherov, L. Noé, and M. Roytberg. A unifying framework for seed sensitivity and its application to subset seeds. Journal of Bioinformatics and Computational Biology, 4(2):553-569, 2006. [ bib \| DOI \| .html \| .pdf ]

2005 [bib]

[1]	M. Bouvel, V. Grebinski, and G. Kucherov. Combinatorial search on graphs motivated by bioinformatics applicaitons: a brief survey. In D. Kratsch, editor, Proceedings of the 31st International Workshop on Graph-Theoretic Concepts in Computer Science (WG), Metz (France), June 23-25, 2005, volume 3787 of Lecture Notes in Computer Science, pages 16-27. Springer Verlag, 2005. [ bib \| DOI \| http \| .pdf ]
[2]	Mathieu Giraud, Pascale Quignon, Élodie Retout, Emmanuelle Morin, Anne-Sophie Valin, Dominique Lavenier, Maud Rimbault, Francis Galibert, and Jacques Nicolas. Assemblage ciblé : recherche d'une famille de gènes sur un génome non assemblé. In Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2005), 2005. [ bib ]
[3]	Mathieu Giraud, Laurent Noé, Gregory Kucherov, and Dominique Lavenier. Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matérielles. In MajecSTIC, 2005. [ bib ]
[4]	Sébastien Tempel, Mathieu Giraud, Israël-César Lerman, Ivab Couée, Abdelhak El Amrani, and Jacques Nicolas. Domain organization within repeated DNA sequences : Application to the study of a new family of transposable elements in arabidopsis thaliana. In poster pour JOBIM 2005, 2005. [ bib ]
[5]	Dominique Lavenier and Mathieu Giraud. Reconfigurable Computing, chapter Bioinformatics Applications. Springer, 2005. [ bib \| DOI \| http \| http ]
[6]	Stéphane Guyetant, Mathieu Giraud, Ludovic L'Hours, Steven Derrien, Stéphane Rubini, Dominique Lavenier, and Frédéric Raimbault. Cluster of re-configurable nodes for scanning large genomic banks. Parallel Computing, 31(1):73-96, 2005. [ bib \| DOI \| http ]
[7]	Pascale Quignon, Mathieu Giraud, Maud Rimbault, Patricia Lavigne, Sandrine Tacher, Emmanuelle Morin, Élodie Retout, Anne-Sophie Valin, Kerstin Lindblad-Toh, Jacques Nicolas, and Francis Galibert. The dog and rat olfactory receptor repertoires. Genome Biology, 6(10):R83, 2005. [ bib \| DOI \| http \| http ]
[8]	Mathieu Giraud and Dominique Lavenier. Dealing with hardware space limits when removing epsilon-transitions in a genomic weighted finite automaton. Journal of Automata, Languages and Combinatorics, 10(2/3), 2005. [ bib \| .ps.gz ]
[9]	H. Touzet. A linear tree edit distance algorithm for similar ordered trees. In (CPM), volume 3537 of Lecture Notes in Computer Science, pages 334-345. Springer Verlag, 2005. [ bib \| DOI \| http \| .pdf ]
[10]	A. Fontaine and H. Touzet. How to detect non-coding RNAs ? In JOBIM, 2005. [ bib \| .pdf ]
[11]	Dulucq S. and Touzet H. Decomposition algorithms for the tree edit distance problem. Journal of Discrete Algorithms, pages 448-471, 2005. [ bib \| DOI \| http \| .pdf ]
[12]	H. Touzet. Structures combinatoires pour l'analyse de génomes. PhD thesis, Université des Sciences et Technologies de Lille, 2005. [ bib \| .pdf ]
[13]	G. Kucherov, L. Noé, and M. Roytberg. A unifying framework for seed sensitivity and its application to subset seeds. In R Casadio and G Myers, editors, Proceedings of the 5th International Workshop in Algorithms in Bioinformatics (WABI), Mallorca (Spain), volume 3692 of Lecture Notes in Computer Science, pages 251-263. Springer Verlag, 2005. [ bib \| DOI \| http \| .ps.gz \| .pdf ]
[14]	L. Noé and G. Kucherov. YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Research, 33 (web-server issue):W540-W543, 2005. [ bib \| DOI \| http \| .pdf ]
[15]	G. Kucherov, L. Noé, and M. Roytberg. Multiseed lossless filtration. IEEE Transactions on Computational Biology and Bioinformatics (TCBB), 2(1):51 - 61, 2005. [ bib \| DOI \| http \| .ps.gz \| .pdf ]
[16]	L Noé. Recherche de similarités dans les séquences d'ADN: modèles et algorithmes pour la conception de graines efficaces. PhD thesis, Université Henri Poincaré - Nancy, 2005. [ bib \| .ps.gz \| .pdf ]
[17]	A. Coppin, J.-S. Varré, L. Lienard, D. Dauvillée, Y. Guérardel, A. Soyer-Gobillard, M.-O.and Buléon, S. Ball, and S. Tomavo. Evolution of plant-like crystalline storage polysaccharide in the protozoan parasite toxoplasma gondii argues for a red alga ancestry. Journal of Molecular Evolution, 60(2):257-267, 2005. [ bib \| DOI \| http \| .pdf ]

2004 [bib]

[1]	Martin Figeac. Etude de l'ordre des gènes : clusters de gènes et algorithmique des réarrangements. PhD thesis, Université des Sciences et Technologies de Lille, 2004. [ bib ]
[2]	Martin Figeac and Jean-Stéphane Varré. Sorting by reversals with common intervals. In proceedings of WABI 2004. Lecture Notes in Computer Sciences, 2004. [ bib \| http ]
[3]	Hélène Touzet and Olivier Perriquet. Inférence de structure pour des familles d'ARN. 2004. [ bib ]
[4]	Hélène Touzet and Olivier Perriquet. CARNAC: folding families of related RNAs. Nucleic Acids Research, 32 (Supplement 2):142-145, 2004. [ bib \| http ]
[5]	Olivier Delgrange and Eric Rivals. STAR: an algorithm to search for tandem approximate repeats. Bioinformatics, 2004. [ bib \| http ]
[6]	Matthieu Defrance, Hélène Touzet, Karo Gosselin, and Corinne Abbadie. Recherche d'éléments régulateurs communs, application aux gènes cibles des facteurs de transcription rel/nf-kb. 2004. [ bib \| .pdf ]

2003 [bib]

[1]	Olivier Perriquet. approche algorithmique pour la prédiction de la structure secondaire des ARN. PhD thesis, Université des Sciences et Technologies de Lille, 2003. [ bib ]
[2]	O. Perriquet, H. Touzet, and M. Dauchet. Finding the common structure shared by two homologous rnas. Bioinformatics, 19:108-116, 2003. [ bib \| http ]
[3]	H. Touzet. Tree edit distance with gaps. Information Processing Letters, 85(3):123-129, 2003. [ bib \| .pdf ]
[4]	S.Dulucq and H. Touzet. Analysis of tree edit distance algorithms. Proceedings of CPM'03, 2676:83-95, 2003. [ bib \| .pdf ]
[5]	M. Defrance, H. Touzet, and S. Janot. A fast algorithm for analysing regulatory regions of related genes. Session poster ECCB 2003, 2003. [ bib \| .pdf ]
[6]	IG Boneca, H de Reuse, JC Epinat, M Pupin, A Labigne, and I Moszer. A revised annotation and comparative analysis of helicobacter pylori genomes. Nucleic acids research, 31(6):1704-1714, 2003. [ bib \| http ]
[7]	Matthieu Defrance, Hélène Touzet, and Stéphane Janot. A fast algorithm for analysing regulatory regions of related genes. 2003. [ bib ]

2002 [bib]

[1]	Olivier Perriquet and Hélène Touzet. Trouver la structure commune entre deux arn homologues. 2002. [ bib ]
[2]	Laurent Debomy, Maude Pupin, Gilles Didier, Ivan Laprevotte, and Alain Henaut. Phylogénie sans alignement pour les rétrovirus. 2002. [ bib ]
[3]	G Didier, I Laprevotte, and M Pupin. Codages de séquences. Gazette des Mathématiciens, 92:27-39, 2002. [ bib \| .pdf ]
[4]	H. Touzet. A characterisation of multiply recursive functions with higman's lemma. Information and Computation, 178:534-544, 2002. [ bib ]
[5]	L Debomy, M Pupin, G Didier, I Laprevotte, and A Henaut. Phylogénie sans alignement pour les rétrovirus. Session poster Jobim 2002, 2002. [ bib ]

2001 [bib]

[1]

I. Laprevotte, M. Pupin, E. Coward, G. Didier, C. Terzian, C. Devauchelle, and A. Henaut. Hiv-1 and hiv-2 ltr nucleotide sequences: assessment of the alignment by n-block presentation, "retroviral signatures" of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution. Molecular biology and evolution, 18(7):1231-1245, 2001. [ bib | http ]

[2]

G. Bonfante, A. Cichon, J.Y. Marion, and H. Touzet. Algorithms with polynomial interpretation termination proof. Journal of Functional Programming, 11(1):33-53, 2001. [ bib ]

2000 and before [bib]

[1]	E. Rocha, I. Moszer, A. Sekowska, M. Klaerr (Pupin), C. Médigue, A. Viari, and A. Danchin. chapter In silico genome analysis. John Wiley & Sons, 2000. [ bib ]
[2]	JS Varré. Concepts et algorithmes pour la comparaison de séquences génétiques : une approche informationnelle. PhD thesis, Université des Sciences et Technologies de Lille, 2000. [ bib ]
[3]	M Klaerr-Blanchard and E Coward H Chiapello. Detecting localized repeats in genomic sequences: a new strategy and its application to bacillus subtilis and arabidopsis thaliana sequences. Computers & Chemistry, 24(1):57-70, 2000. [ bib \| http \| .pdf ]
[4]	J.S. Varré, J.P. Delahaye, and E. Rivals. Transformation distances: A family of dissimilarity measures based on movements of segments. Bioinformatics, 1999. [ bib ]
[5]	Olivier Delgrange. Un algorithme rapide pour une compression modulaire optimale - Application a l'analyse de séquences génétiques. PhD thesis, Université des Sciences et Technologies de Lille, 1997. [ bib ]
[6]	Eric Rivals. Algorithmes de compression et applications à l'analyse de séquences génétiques. PhD thesis, Université des Sciences et Technologies de Lille, 1996. [ bib ]

PhD Thesis [bib]

[1]	Azadeh Saffarian. Algorithmes de prédiction et de recherche de multi-structures d'ARN. PhD thesis, Université Lille 1, 2011. [ bib ]
[2]	Marta Gîrdea. New methods for biological sequence alignment. PhD thesis, Université Lille 1, 2010. [ bib ]
[3]	Aude Darracq. Evolution des génomes mitochondriaux de plantes - Approche de génomique comparative chez Zea mays et Beta vulgaris. PhD thesis, Université Lille 1, 2010. [ bib ]
[4]	Ségolène Caboche. Mise en place d'une plateforme logicielle pour l'analyse des peptides non-ribosomiaux. PhD thesis, Université de Lille 1, 2009. [ bib ]
[5]	Arnaud Fontaine. Classification d'ARN codants et d'ARN non-codants. PhD thesis, Université de Lille 1, 2009. [ bib \| .pdf ]
[6]	Jean-Stéphane Varré. Algorithmes pour la comparaison de génomes et la recherche de signaux cis-régulateurs. Habilitation à diriger des recherches, Université de Lille 1, 2008. [ bib ]
[7]	A. Liefooghe. Matrices score-position, algorithmes et propriétés. PhD thesis, Université de Lille 1, 2008. [ bib ]
[8]	Matthieu Defrance. Algorithmes pour l'analyse de régions régulatrices dans le génome d'eucaryotes supérieurs. PhD thesis, Université des Sciences et Technologies de Lille, December 2006. [ bib ]
[9]	Hélène Touzet. Structures combinatoires pour l'analyse de génomes, 2005. [ bib \| .pdf ]
[10]	Martin Figeac. Etude de l'ordre des gènes : clusters de gènes et algorithmique des réarrangements. PhD thesis, Université des Sciences et Technologies de Lille, 2004. [ bib ]
[11]	Olivier Perriquet. approche algorithmique pour la prédiction de la structure secondaire des ARN. PhD thesis, Université des Sciences et Technologies de Lille, 2003. [ bib ]
[12]	JS Varré. Concepts et algorithmes pour la comparaison de séquences génétiques : une approche informationnelle. PhD thesis, Université des Sciences et Technologies de Lille, 2000. [ bib ]
[13]	Olivier Delgrange. Un algorithme rapide pour une compression modulaire optimale - Application a l'analyse de séquences génétiques. PhD thesis, Université des Sciences et Technologies de Lille, 1997. [ bib ]
[14]	Eric Rivals. Algorithmes de compression et applications à l'analyse de séquences génétiques. PhD thesis, Université des Sciences et Technologies de Lille, 1996. [ bib ]

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