[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 ]