publications

Book chapters

[1]

E. Kopylova, L. Noé, C. Da Silva, J.-F. Berthelot, A. Alberti, J.-M. Aury, and H. Touzet, RNA Bioinformatics, vol. 1269 of Methods in Molecular Biology, ch. Deciphering metatranscriptomic data, pp. 279--291. January 2015. [ DOI | pubmed | hal ]

Peer-reviewed journals

[1]

M. C. Frith, L. Noé, and G. Kucherov, “Minimally-overlapping words for sequence similarity search,” Bioinformatics, December 2020. [ DOI | pubmed | hal | http ]

[2]

E. Petrucci, L. Noé, C. Pizzi, and M. Comin, “Iterative spaced seed hashing: Closing the gap between spaced seed hashing,” Journal of Computational Biology, vol. 27, pp. 223--233, February 2020. [ DOI | pubmed | hal | http ]

[3]

C. Saad, L. Noé, H. Richard, J. Leclerc, M.-P. Buisine, H. Touzet, and M. Figeac, “DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data,” BMC Bioinformatics, vol. 19, June 2018. [ DOI | pmc | pubmed | hal | http ]

[4]

L. Noé, “Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds,” Algorithms for Molecular Biology, vol. 12, February 2017. [ DOI | pmc | pubmed | hal | http | .pdf ]

[5]

D. E. K. Martin and L. Noé, “Faster exact distributions of pattern statistics through sequential elimination of states,” Annals of the Institute of Statistical Mathematics, vol. 69, pp. 231--248, February 2017. [ DOI | hal | http | .pdf ]

[6]

A. Flissi, Y. Dufresne, J. Michalík, L. Tonon, S. Janot, L. Noé, P. Jacques, V. Leclère, and M. Pupin, “Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing,” Nucleic Acids Research, vol. 44, pp. D1113--D1118, January 2016. [ DOI | pmc | pubmed | hal | http | .pdf ]

[7]

Y. Dufresne, L. Noé, V. Leclère, and M. Pupin, “Smiles2Monomers: a link between chemical and biological structures for polymers,” Journal of Cheminformatics, vol. 7, December 2015. [ DOI | pmc | pubmed | hal | http | .pdf ]

[8]

[9]

M. C. Frith and L. Noé, “Improved search heuristics find 20 000 new alignments between human and mouse genomes,” Nucleic Acids Research, vol. 42, p. e59, February 2014. [ DOI | pmc | pubmed | hal | http | .pdf ]

[10]

E. Kopylova, L. Noé, and H. Touzet, “SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data,” Bioinformatics, vol. 28, pp. 3211--3217, December 2012. [ DOI | pubmed | hal | http | .pdf ]

[11]

M. Startek, S. Lasota, M. Sykulski, A. Bulak, L. Noé, G. Kucherov, and A. Gambin, “Efficient alternatives to PSI-BLAST,” Bulletin of the Polish Academy of Sciences: Technical Sciences, vol. 60, pp. 495--505, December 2012. [ DOI | hal | http | .pdf ]

[12]

L. Noé, M. Gîrdea, and G. Kucherov, “Designing efficient spaced seeds for SOLiD read mapping,” Advances in Bioinformatics, vol. 2010, p. ID 708501, July 2010. [ DOI | pmc | pubmed | hal | http | .pdf ]

[13]

M. Gîrdea, L. Noé, and G. Kucherov, “Back-translation for discovering distant protein homologies in the presence of frameshift mutations,” Algorithms for Molecular Biology, vol. 5, January 2010. [ DOI | pmc | pubmed | hal | http | .pdf ]

[14]

[15]

P. Peterlongo, L. Noé, D. Lavenier, V.-H. Nguyen, G. Kucherov, and M. Giraud, “Optimal neighborhood indexing for protein similarity search,” BMC Bioinformatics, vol. 9, p. 534, December 2008. [ DOI | pmc | pubmed | hal | http | .pdf ]

[16]

[17]

[18]

L. Noé and G. Kucherov, “YASS: enhancing the sensitivity of DNA similarity search,” Nucleic Acids Research, vol. 33 (web-server issue), pp. W540--W543, April 2005. [ DOI | pmc | pubmed | hal | http | .pdf ]

[19]

[20]

L. Noé and G. Kucherov, “Improved hit criteria for DNA local alignment,” BMC Bioinformatics, vol. 5, p. 149, October 2004. [ DOI | pmc | pubmed | hal | http | .pdf ]

Peer-reviewed conferences

[1]

E. Petrucci, L. Noé, C. Pizzi, and M. Comin, “Iterative spaced seed hashing: Closing the gap between spaced seed hashing and k-mer hashing,” in Proceedings of the 15th International Symposium on Bioinformatics Research and Applications (ISBRA), June 3-6, 2019, Barcelona (Catalonia) (Z. Cai, P. Skums, and M. Li, eds.), vol. 11490 of Lecture Notes in Computer Science, pp. 208--219, May 2019. [ DOI | hal | http ]

[2]

Y. Dufresne, V. Leclère, P. Jacques, L. Noé́, and M. Pupin, “Non Ribosomal Peptides : A monomeric puzzle,” in Proceedings of the 14th Open Days in Biology, Computer Science and Mathematics (JOBIM), July 1 - 4, 2013, Toulouse (France), pp. 143--150, 2013. [ hal | http ]

[3]

A. Gambin, S. Lasota, M. Startek, M. Sykulski, L. Noé, and G. Kucherov, “Subset seed extension to Protein BLAST,” in Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2011), January 26-29 2011, Rome (Italy), pp. 149--158, SciTePress Digital Library, January 2011. [ DOI | hal | http ]

[4]

L. Noé, M. Gîrdea, and G. Kucherov, “Seed design framework for mapping SOLiD reads,” in Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), April 25-28, 2010, Lisbon (Portugal) (B. Berger, ed.), vol. 6044 of Lecture Notes in Computer Science, pp. 384--396, Springer, April 2010. [ DOI | arXiv | hal | http | http | http ]

[5]

M. Gîrdea, G. Kucherov, and L. Noé, “Back-translation for discovering distant protein homologies,” in Proceedings of the 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia (USA) (S. Salzberg and T. Warnow, eds.), vol. 5724 of Lecture Notes in Computer Science, pp. 108--120, Springer, September 2009. [ DOI | arXiv | hal | http | http | http ]

[6]

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), pp. 31--36, June 2009. [ hal | .pdf ]

[7]

M. A. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, and G. Kucherov, “Efficient seeding techniques for protein similarity search,” in Bioinformatics Research and Development, Proceedings of the 2nd International Conference BIRD 2008, Vienna (Austria), July 7-9, 2008 (M. Elloumi, J. Küng, M. Linial, R. Murphy, K. Schneider, and C. Toma, eds.), vol. 13 of Communications in Computer and Information Science, pp. 466--478, Springer, July 2008. [ DOI | arXiv | hal | http | http | http ]

[8]

G. Kucherov, L. Noé, and M. A. Roytberg, “Subset seed automaton,” in Proceedings of the 12th International Conference on Implementation and Application of Automata (CIAA), July 16-18, 2007, Prague (Czech Republic) (J. Holub and J. Zdarek, eds.), vol. 4783 of Lecture Notes in Computer Science, pp. 180--191, Springer, July 2007. [ DOI | arXiv | hal | http | http | http ]

[9]

P. Peterlongo, L. Noé, D. Lavenier, G. Georges, J. Jacques, G. Kucherov, and M. Giraud, “Protein similarity search with subset seeds on a dedicated reconfigurable hardware,” in Proceedings of the 2nd Workshop on Parallel Bio-Computing (PBC), September 9-12, 2007 Gdansk (Poland) (R. Wyrzykowski, J. Dongarra, K. Karczewski, and J. Wasniewski, eds.), vol. 4967 of Lecture Notes in Computer Science, pp. 1240--1248, Springer, September 2008. [ DOI | hal | http | .pdf ]

[10]

G. Kucherov, L. Noé, and M. A. Roytberg, “A unifying framework for seed sensitivity and its application to subset seeds (extended abstract),” in Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (WABI), October 3-6, 2005, Mallorca (Spain) (R. Casadio and G. Myers, eds.), vol. 3692 of Lecture Notes in Computer Science, pp. 251--263, Springer, October 2005. [ DOI | arXiv | hal | http | http | http ]

[11]

G. Kucherov, L. Noé, and M. A. Roytberg, “Multi-seed lossless filtration (extended abstract),” in Proceedings of the 15th Annual Combinatorial Pattern Matching Symposium (CPM), July 5-7, 2004, Istanbul (Turkey) (S. Sahinalp, S. Muthukrishnan, and U. Dogrusoz, eds.), vol. 3109 of Lecture Notes in Computer Science, pp. 297--310, Springer, July 2004. [ DOI | hal | http | http | http ]

[12]

G. Kucherov, L. Noé, and Y. Ponty, “Estimating seed sensitivity on homogeneous alignments,” in Proceedings of the IEEE 4th Symposium on Bioinformatics and Bioengineering (BIBE), May 19-21, 2004, Taichung (Taiwan), pp. 387--394, IEEE Computer Society Press, April 2004. [ DOI | arXiv | hal | http | http | http ]

[13]

L. Noé and G. Kucherov, “Improved hit criteria for DNA local alignment,” in Proceedings of the 5th Open Days in Biology, Computer Science and Mathematics (JOBIM), June 28-30, 2004, Montréal (Canada), June 2004. [ hal | http | http ]

Phd

[1]

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, September 2005. [ hal | http | http ]

[2]

L. Noé, “Recherche de répétitions distantes dans les séquences,” rapport de DEA, LORIA, Université Henri Poincaré Nancy 1, July 2002. [ http | http ]

Miscellaneous

[1]

E. Kopylova, L. Noé, and H. Touzet, “SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis,” in Proceedings of the 13th Open Days in Biology, Computer Science and Mathematics (JOBIM), July 3 - 6, 2012, Rennes (France), 2012. [ hal ]

[2]

M. Gîrdea, L. Noé, and G. Kucherov, “Read mapping tool for AB SOLiD data,” in 9th Workshop on Algorithms in Bioinformatics (WABI), September 12-13, 2009, Philadelphia (USA), September 2009. (poster). [ http | http ]

[3]

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), pp. 157--158, June 2008. (short talk with poster). [ http ]

[4]

E. Furletova, G. Kucherov, L. Noé, M. A. Roytberg, and I. Tsitovich, “Transitive subset seeds for protein alignment,” in Proceedings of the 6th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS), July 22-28, 2008, Novosibirsk (Russia), p. 77, July 2008. [ http ]

[5]

A. Fontaine, M. Giraud, L. Noé, and H. Touzet, “Graines espacées et recherche d'ARN non-codants,” in Proceedings of the 8th Open Days in Biology, Computer Science and Mathematics (JOBIM), July 10-12, 2007, Marseille (France), pp. 389--390, July 2007. (poster). [ http ]

[6]

E. Furletova, G. Kucherov, L. Noé, M. A. Roytberg, and I. Tsitovich, “Statisical approach to the design of subset seeds for protein alignment,” in Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB), July 27-31, 2007, Moscow (Russia), pp. 94--95, July 2007. [ http ]

[7]

M. Giraud, L. Noé, G. Kucherov, and D. Lavenier, “Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matérielles (tutoriel),” in in MajecSTIC : Manifestation des Jeunes Chercheurs francophones dans les domaines des STIC , Rennes, pp. 18--37, 2005. [ hal ]

[8]

G. Kucherov, L. Noé, and M. A. Roytberg, “A unifying framework for seed sensitivity and its application to subset seeds,” in Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB), July 18-21, 2005, Moscow (Russia), pp. 195--196, July 2005. [ bib ]

[9]

G. Kucherov, L. Noé, and M. A. Roytberg, “A unifying framework for seed sensitivity and its application to subset seeds,” in Proceedings of the 6th Open Days in Biology, Computer Science and Mathematics (JOBIM), July 6-8, 2005, Lyon (France), 2005. (poster). [ .pdf ]

[10]

A. G. Vitreschak, L. Noé, and G. Kucherov, “Computer analysis of multiple repeats in bacteria,” in Proceedings of the 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS), July 25-30, 2004, Novosibirsk (Russia), vol. 2, pp. 297--299, Institute of Cytology and Genetics, July 2004. [ http ]

[11]

L. Noé and G. Kucherov, “YASS : Enhancing the sensitivity of DNA similarity search,” in Proceedings of the 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS), July 25-30, 2004, Novosibirsk (Russia), vol. 2, pp. 289--292, Institute of Cytology and Genetics, July 2004. [ hal | http ]

[12]

L. Noé and G. Kucherov, “A new method of finding similarity regions in DNA sequences,” in European Conference on Computational Biology (ECCB), Saarbrücken, Germany, European Conference on Computational biology - ECCB'2002. Poster Abstracts, pp. 173--174, October 2002. (poster). [ http | http | http ]

[13]

G. Kucherov and L. Noé, “Yass : similarity search in DNA sequences,” in The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (Germany), pp. 81--82, April 2003. (poster). [ http | http ]

[14]

G. Kucherov, L. Noé, and M. A. Roytberg, “A unifying framework for seed sensitivity and its application to subset seeds,” Research Report RR-5374, INRIA, November 2004. [ hal | http | http ]

[15]

G. Kucherov, L. Noé, and Y. Ponty, “Estimating seed sensitivity on homogeneous alignments,” Research Report RR-5047, INRIA, Novemnber 2003. [ hal | http | http ]

[16]

L. Noé and G. Kucherov, “YASS: Similarity search in DNA sequences,” Research Report RR-4852, INRIA, June 2003. [ hal | http | http ]