[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 ]