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Number of documents

50

Laurent Noe Homepage


http://cristal.univ-lille.fr/~noe


Journal articles21 documents

  • Enrico Petrucci, Laurent Noé, Cinzia Pizzi, Matteo Comin. Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k -mer Hashing. Journal of Computational Biology, Mary Ann Liebert, 2020, 27 (2), pp.223-233. ⟨10.1089/cmb.2019.0298⟩. ⟨hal-02910076⟩
  • Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, et al.. DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data. BMC Bioinformatics, BioMed Central, 2018, 19 (1), ⟨10.1186/s12859-018-2215-1⟩. ⟨hal-01881466⟩
  • Laurent Noé. Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds. Algorithms for Molecular Biology, BioMed Central, 2017, 12 (1), ⟨10.1186/s13015-017-0092-1⟩. ⟨hal-01467970⟩
  • Donald E. K. Martin, Laurent Noé. Faster exact distributions of pattern statistics through sequential elimination of states. Annals of the Institute of Statistical Mathematics, Springer Verlag, 2017, 69 (1), pp.231--248. ⟨10.1007/s10463-015-0540-y⟩. ⟨hal-01237045⟩
  • Yoann Dufresne, Laurent Noé, Valérie Leclère, Maude Pupin. Smiles2Monomers: a link between chemical and biological structures for polymers. Journal of Cheminformatics, Chemistry Central Ltd. and BioMed Central, 2015, 7, ⟨10.1186/s13321-015-0111-5⟩. ⟨hal-01250619⟩
  • Areski Flissi, Yoann Dufresne, Juraj Michalik, Laurie Tonon, Stéphane Janot, et al.. Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. Nucleic Acids Research, Oxford University Press, 2015, ⟨10.1093/nar/gkv1143⟩. ⟨hal-01235996⟩
  • Laurent Noé, Donald E. K. Martin. A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k-Mer Distances. Journal of Computational Biology, Mary Ann Liebert, 2014, 21 (12), pp.28. ⟨10.1089/cmb.2014.0173⟩. ⟨hal-01083204⟩
  • Martin Frith, Laurent Noé. Improved search heuristics find 20 000 new alignments between human and mouse genomes.. Nucleic Acids Research, Oxford University Press, 2014, 42 (7), pp.e59. ⟨10.1093/nar/gku104⟩. ⟨hal-00958207⟩
  • Evguenia Kopylova, Laurent Noé, Héléne Touzet. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.. Bioinformatics, Oxford University Press (OUP), 2012, 28 (24), pp.3211-3217. ⟨10.1093/bioinformatics/bts611⟩. ⟨hal-00748990⟩
  • Michal Startek, Slawomir Lasota, Maciej Sykulski, Adam Bulak, Laurent Noé, et al.. Efficient alternatives to PSI-BLAST. Bulletin of the Polish Academy of Sciences: Technical Sciences, Polish Academy of Sciences, 2012, 60 (3), pp.495-505. ⟨10.2478/v10175-012-0063-0⟩. ⟨hal-00749016⟩
  • Marta Gîrdea, Laurent Noé, Gregory Kucherov. Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms for Molecular Biology, BioMed Central, 2010, 5 (1), pp.6. ⟨10.1186/1748-7188-5-6⟩. ⟨hal-00784444⟩
  • Laurent Noé, Marta Gîrdea, Gregory Kucherov. Designing Efficient Spaced Seeds for SOLiD Read Mapping.. Advances in Bioinformatics, Hindawi Publishing Corporation, 2010, ⟨10.1155/2010/708501⟩. ⟨inria-00527029⟩
  • Mikhail Roytberg, Anna Gambin, Laurent Noé, Slawomir Lasota, Eugenia Furletova, et al.. On subset seeds for protein alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2009, 6 (3), pp.483-494. ⟨10.1109/TCBB.2009.4⟩. ⟨inria-00354773⟩
  • Pierre Peterlongo, Laurent Noé, Dominique Lavenier, van Hoa Nguyen, Gregory Kucherov, et al.. Optimal neighborhood indexing for protein similarity search. BMC Bioinformatics, BioMed Central, 2008, 9 (534), ⟨10.1186/1471-2105-9-534⟩. ⟨inria-00340510⟩
  • Miklós Csűrös, Laurent Noé, Gregory Kucherov. Reconsidering the significance of genomic word frequencies.. Trends in Genetics, Elsevier, 2007, 23 (11), pp.543-6. ⟨10.1016/j.tig.2007.07.008⟩. ⟨inria-00448737⟩
  • Gregory Kucherov, Laurent Noé, Mihkail Roytberg. A unifying framework for seed sensitivity and its application to subset seeds.. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2006, 4 (2), pp.553-69. ⟨10.1142/S0219720006001977⟩. ⟨hal-00018114v2⟩
  • Gregory Kucherov, Laurent Noé, Mikhail Roytberg. Multiseed Lossless Filtration. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2005, 2 (1), pp.51-61. ⟨10.1109/TCBB.2005.12⟩. ⟨inria-00354810⟩
  • Gregory Kucherov, Laurent Noé, Mikhail Roytberg. Multi-seed lossless filtration. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2005, 2 (1), pp.51--61. ⟨10.1109/TCBB.2005.12⟩. ⟨inria-00000718⟩
  • Laurent Noé, Gregory Kucherov. YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Research, Oxford University Press, 2005, 33 (Web server issue), pp.W540--W543. ⟨10.1093/nar/gki478⟩. ⟨inria-00000721⟩
  • Laurent Noé, Gregory Kucherov. YASS: enhancing the sensitivity of DNA similarity search.. Nucleic Acids Research, Oxford University Press, 2005, 33 (Web Server issue), pp.W540-3. ⟨10.1093/nar/gki478⟩. ⟨inria-00448742⟩
  • Laurent Noé, Gregory Kucherov. Improved hit criteria for DNA local alignment.. BMC Bioinformatics, BioMed Central, 2004, 5 (149), pp.1-9. ⟨10.1186/1471-2105-5-149⟩. ⟨inria-00448743⟩

Conference papers23 documents

  • Enrico Petrucci, Laurent Noé, Cinzia Pizzi, Matteo Comin. Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing. 15th International Symposium on Bioinformatics Research and Applications (ISBRA), Jun 2019, Barcelona, Spain. pp.208-219, ⟨10.1007/978-3-030-20242-2_18⟩. ⟨hal-02146404⟩
  • Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, et al.. DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. ⟨hal-01574630⟩
  • Evguenia Kopylova, Laurent Noé, Pierre Pericard, Hélène Touzet. SortMeRNA 2: ribosomal RNA classification for taxonomic assignation. Bioinformatics for Environmental Genomics, May 2014, Lyon, France. ⟨hal-01094029⟩
  • Evguenia Kopylova, Laurent Noé, Pierre Pericard, Mikaël Salson, Hélène Touzet. SortMeRNA 2: ribosomal RNA classification for taxonomic assignation. Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Sep 2014, Strasbourg, France. ⟨hal-01094011⟩
  • Yoann Dufresne, Valérie Leclère, Philippe Jacques, Laurent Noé, Maude Pupin. Non Ribosomal Peptides : A monomeric puzzle. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. pp.143-150. ⟨hal-00843827⟩
  • Evguenia Kopylova, Laurent Noé, Helene Touzet. SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2012, Jul 2012, Rennes, France. ⟨hal-00763792⟩
  • Anna Gambin, Slawomir Lasota, Michal Startek, Maciej Sykulski, Laurent Noé, et al.. Subset seed extension to Protein BLAST. Bioinformatics 2011 - International Conference on Bioinformatics Models, Methods and Algorithms, Jan 2011, Rome, Italy. pp.149-158, ⟨10.5220/0003147601490158⟩. ⟨inria-00609791⟩
  • Laurent Noé, Marta Gîrdea, Gregory Kucherov. Seed design framework for mapping SOLiD reads. RECOMB, Aug 2010, Lisbon, Portugal. pp.384-396, ⟨10.1007/978-3-642-12683-3_25⟩. ⟨inria-00484642⟩
  • Marta Gîrdea, Laurent Noé, Gregory Kucherov. Back-translation for discovering distant protein homologies. the 9th International Workshop in Algorithms in Bioinformatics (WABI), Sep 2009, Philadelphia, United States. pp.108-120, ⟨10.1007/978-3-642-04241-6_10⟩. ⟨inria-00448741⟩
  • Raluca Uricaru, Célia Michotey, Laurent Noé, Hélène Chiapello, Eric Rivals. Improved Sensitivity And Reliability Of Anchor Based Genome Alignment. JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36. ⟨lirmm-00407215⟩
  • Raluca Uricaru, Célia Michotey, Laurent Noé, Helene Chiapello, Eric Rivals. Improved sensitivity and reliability of anchor based genome alignment. JOBIM - Journées Ouvertes en Biologie Informatique Mathématiques2009 - Nantes :, Jun 2009, Nantes, France. 259 p. ⟨hal-02751358⟩
  • Mihkail Roytberg, Anna Gambin, Laurent Noé, Slawomir Lasota, Eugenia Furletova, et al.. Efficient seeding techniques for protein similarity search. Proceedings of the 2nd International Conference BIRD, Jul 2008, Vienna, Austria. pp.466-478, ⟨10.1007/978-3-540-70600-7⟩. ⟨inria-00335564⟩
  • Gregory Kucherov, Laurent Noé, Mihkail Roytberg. Subset seed automaton. CIAA 2007, Jul 2007, Prague, Czech Republic. pp.180-191, ⟨10.1007/978-3-540-76336-9_18⟩. ⟨inria-00170414⟩
  • Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, et al.. Protein similarity search with subset seeds on a dedicated reconfigurable hardware. Parallel Bio-Computing, Sep 2007, Gdansk,, Poland. ⟨inria-00178325⟩
  • Gregory Kucherov, Laurent Noé, Mikhail Roytberg. A unifying framework for seed sensitivity and its application to subset seeds (Extended abstract). WABI, 2005, Majorca/Spain, Spain. ⟨inria-00001164⟩
  • Mathieu Giraud, Laurent Noé, Gregory Kucherov, Dominique Lavenier. Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matérielles. MajecSTIC 2005 : Manifestation des Jeunes Chercheurs francophones dans les domaines des STIC, IRISA – IETR – LTSI, Nov 2005, Rennes/France, pp.18--37. ⟨inria-00001036⟩
  • Laurent Noé, Gregory Kucherov. YASS : Enhancing the sensitivity of DNA similarity search. Proceedings of the 4th International conference on Bioinformatics of Genome Regulation and Structure - BGRS'2004, Institute of Cytology and Genetics, 2004, Novosibirsk, Russia, pp.289-292. ⟨inria-00100004⟩
  • Laurent Noé, Gregory Kucherov. Improved hit criteria for DNA local alignment. Proceedings of the 5th Open Days in Biology, Computer Science and Mathematics - JOBIM'2004, 2004, Montreal, Canada, 11 p. ⟨inria-00099999⟩
  • Alexey Vitreschak, Laurent Noé, Gregory Kucherov. Computer analysis of multiple repeats in bacteria. The fourth International Conference on Bioinformatics of Genome Regulation and Structure - BGRS'2004, 2004, Novosibirsk, Russia, 5 p. ⟨inria-00100088⟩
  • Gregory Kucherov, Laurent Noé, Mikhail Roytberg. Multi-seed lossless filtration (Extended abstract). Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching - CPM'2004, Jul 2004, Istambul, Turkey. pp.297-310, ⟨10.1007/11557067_21⟩. ⟨inria-00001162⟩
  • Gregory Kucherov, Laurent Noé, Yann Ponty. Estimating seed sensitivity on homogeneous alignments. 4th Symposium on Bioinformatics and bioengineering - BIBE'2004, May 2004, Taichung, Taiwan. pp.387-394, ⟨10.1109/BIBE.2004.1317369⟩. ⟨inria-00001163⟩
  • Gregory Kucherov, Laurent Noé. YASS : similarity search in DNA sequences. The Seventh Annual International Conference on Research in Computational Molecular Biology - RECOMB'03, Apr 2003, Berlin, Germany, 1 p. ⟨inria-00099599⟩
  • Laurent Noé, Gregory Kucherov. A new method of finding similarity regions in DNA sequences. European Conference on Computational Biology - ECCB'2002, Oct 2002, Saarbrücken, Germany, pp.173-174. ⟨inria-00100859⟩

Book sections1 document

  • Evguenia Kopylova, Laurent Noé, Corinne da Silva, Jean-Frédéric Berthelot, Adriana Alberti, et al.. Deciphering metatranscriptomic data. Methods in Molecular Biology, 1269, Springer, pp.279-291, 2015, RNA Bioinformatics, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_17⟩. ⟨hal-01104015⟩

Reports4 documents

  • Gregory Kucherov, Laurent Noé, Mikhail Roytberg. A unifying framework for seed sensitivity and its application to subset seeds. [Research Report] RR-5374, INRIA. 2004, pp.21. ⟨inria-00070629⟩
  • Laurent Noé, Gregory Kucherov. YASS: Similarity search in DNA sequences. [Research Report] RR-4852, INRIA. 2003, pp.20. ⟨inria-00071731⟩
  • Gregory Kucherov, Laurent Noé, Yann Ponty. Estimating seed sensitivity on homogeneous alignments. [Research Report] RR-5047, INRIA. 2003, pp.17. ⟨inria-00071536⟩
  • Laurent Noé. Recherche de répétitions distantes dans les séquences. [Stage] A02-R-296 || noe02b, 2002, 30 p. ⟨inria-00100902⟩

Theses1 document

  • Laurent Noé. Recherche de similarités dans les séquences d'ADN : modèles et algorithmes pour la conception de graines efficaces. Autre [cs.OH]. Université Henri Poincaré - Nancy 1, 2005. Français. ⟨NNT : 2005NAN10118⟩. ⟨tel-01748141v3⟩