Publications

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Porechop_ABI: discovering unknown adapters in ONT sequencing reads for downstream trimming. 2022. <a target=\"_blank\" href=\"https://hal.science/hal-03865464\">⟨hal-03865464⟩</a>", "title_s":["Porechop_ABI: discovering unknown adapters in ONT sequencing reads for downstream trimming"], "authFullName_s":["Quentin Bonenfant", "Laurent Noé", "Hélène Touzet"], "halId_s":"hal-03865464", "docType_s":"UNDEFINED", "producedDateY_i":2022}, { "citationRef_s":"From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, 1, Wiley, 2022, <a target=\"_blank\" href=\"https://dx.doi.org/10.1002/9781394169641.ch3\">⟨10.1002/9781394169641.ch3⟩</a>", "citationFull_s":"Laurent Noé. Sequence Alignment. From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, 1, Wiley, 2022, <a target=\"_blank\" href=\"https://dx.doi.org/10.1002/9781394169641.ch3\">⟨10.1002/9781394169641.ch3⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03932710\">⟨hal-03932710⟩</a>", "title_s":["Sequence Alignment"], "authFullName_s":["Laurent Noé"], "halId_s":"hal-03932710", "docType_s":"COUV", "producedDateY_i":2022}, { "citationRef_s":"Bioinformatics, 2020, <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btaa1054\">⟨10.1093/bioinformatics/btaa1054⟩</a>", "citationFull_s":"Martin Frith, Laurent Noé, Gregory Kucherov. Minimally-overlapping words for sequence similarity search. Bioinformatics, 2020, <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btaa1054\">⟨10.1093/bioinformatics/btaa1054⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03087470\">⟨hal-03087470⟩</a>", "title_s":["Minimally-overlapping words for sequence similarity search"], "authFullName_s":["Martin Frith", "Laurent Noé", "Gregory Kucherov"], "halId_s":"hal-03087470", "docType_s":"ART", "producedDateY_i":2020}, { "citationRef_s":"2020", "citationFull_s":"Martin Frith, Laurent Noé, Gregory Kucherov. Minimally-overlapping words for sequence similarity search. 2020. <a target=\"_blank\" href=\"https://hal.science/hal-03049398\">⟨hal-03049398⟩</a>", "title_s":["Minimally-overlapping words for sequence similarity search"], "authFullName_s":["Martin Frith", "Laurent Noé", "Gregory Kucherov"], "halId_s":"hal-03049398", "docType_s":"UNDEFINED", "producedDateY_i":2020}, { "citationRef_s":"Journal of Computational Biology, 2020, 27 (2), pp.223-233. <a target=\"_blank\" href=\"https://dx.doi.org/10.1089/cmb.2019.0298\">⟨10.1089/cmb.2019.0298⟩</a>", "citationFull_s":"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, 2020, 27 (2), pp.223-233. <a target=\"_blank\" href=\"https://dx.doi.org/10.1089/cmb.2019.0298\">⟨10.1089/cmb.2019.0298⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02910076\">⟨hal-02910076⟩</a>", "title_s":["Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k -mer Hashing"], "authFullName_s":["Enrico Petrucci", "Laurent Noé", "Cinzia Pizzi", "Matteo Comin"], "halId_s":"hal-02910076", "docType_s":"ART", "producedDateY_i":2020}, { "citationRef_s":"15th International Symposium on Bioinformatics Research and Applications (ISBRA), Jun 2019, Barcelona, Spain. pp.208-219, <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/978-3-030-20242-2_18\">⟨10.1007/978-3-030-20242-2_18⟩</a>", "citationFull_s":"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, <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/978-3-030-20242-2_18\">⟨10.1007/978-3-030-20242-2_18⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02146404\">⟨hal-02146404⟩</a>", "title_s":["Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing"], "authFullName_s":["Enrico Petrucci", "Laurent Noé", "Cinzia Pizzi", "Matteo Comin"], "halId_s":"hal-02146404", "docType_s":"COMM", "producedDateY_i":2019}, { "citationRef_s":"BMC Bioinformatics, 2018, 19 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s12859-018-2215-1\">⟨10.1186/s12859-018-2215-1⟩</a>", "citationFull_s":"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, 2018, 19 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s12859-018-2215-1\">⟨10.1186/s12859-018-2215-1⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01881466\">⟨hal-01881466⟩</a>", "title_s":["DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data"], "authFullName_s":["Chadi Saad", "Laurent Noé", "Hugues Richard", "Julie Leclerc", "Marie-Pierre Buisine", "Hélène Touzet", "Martin Figeac"], "halId_s":"hal-01881466", "docType_s":"ART", "producedDateY_i":2018}, { "citationRef_s":"JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France", "citationFull_s":"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. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01574630\">⟨hal-01574630⟩</a>", "title_s":["DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors"], "authFullName_s":["Chadi Saad", "Laurent Noé", "Hugues Richard", "Julie Leclerc", "Marie-Pierre Buisine", "Helene Touzet", "Martin Figeac"], "halId_s":"hal-01574630", "docType_s":"COMM", "producedDateY_i":2017}, { "citationRef_s":"Algorithms for Molecular Biology, 2017, 12 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s13015-017-0092-1\">⟨10.1186/s13015-017-0092-1⟩</a>", "citationFull_s":"Laurent Noé. Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds. Algorithms for Molecular Biology, 2017, 12 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s13015-017-0092-1\">⟨10.1186/s13015-017-0092-1⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01467970\">⟨hal-01467970⟩</a>", "title_s":["Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds"], "authFullName_s":["Laurent Noé"], "halId_s":"hal-01467970", "docType_s":"ART", "producedDateY_i":2017}, { "citationRef_s":"Annals of the Institute of Statistical Mathematics, 2017, 69 (1), pp.231--248. <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/s10463-015-0540-y\">⟨10.1007/s10463-015-0540-y⟩</a>", "citationFull_s":"Donald E. K. Martin, Laurent Noé. Faster exact distributions of pattern statistics through sequential elimination of states. Annals of the Institute of Statistical Mathematics, 2017, 69 (1), pp.231--248. <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/s10463-015-0540-y\">⟨10.1007/s10463-015-0540-y⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01237045\">⟨hal-01237045⟩</a>", "title_s":["Faster exact distributions of pattern statistics through sequential elimination of states"], "authFullName_s":["Donald E. K. Martin", "Laurent Noé"], "halId_s":"hal-01237045", "docType_s":"ART", "producedDateY_i":2017}, { "citationRef_s":"Journal of Cheminformatics, 2015, 7, <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s13321-015-0111-5\">⟨10.1186/s13321-015-0111-5⟩</a>", "citationFull_s":"Yoann Dufresne, Laurent Noé, Valérie Leclère, Maude Pupin. Smiles2Monomers: a link between chemical and biological structures for polymers. Journal of Cheminformatics, 2015, 7, <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s13321-015-0111-5\">⟨10.1186/s13321-015-0111-5⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01250619\">⟨hal-01250619⟩</a>", "title_s":["Smiles2Monomers: a link between chemical and biological structures for polymers"], "authFullName_s":["Yoann Dufresne", "Laurent Noé", "Valérie Leclère", "Maude Pupin"], "halId_s":"hal-01250619", "docType_s":"ART", "producedDateY_i":2015}, { "citationRef_s":"Nucleic Acids Research, 2015, <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nar/gkv1143\">⟨10.1093/nar/gkv1143⟩</a>", "citationFull_s":"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, 2015, <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nar/gkv1143\">⟨10.1093/nar/gkv1143⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-01235996\">⟨hal-01235996⟩</a>", "title_s":["Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing"], "authFullName_s":["Areski Flissi", "Yoann Dufresne", "Juraj Michalik", "Laurie Tonon", "Stéphane Janot", "Laurent Noé", "Philippe Jacques", "Valérie Leclère", "Maude Pupin"], "halId_s":"hal-01235996", "docType_s":"ART", "producedDateY_i":2015}, { "citationRef_s":"Methods in Molecular Biology, 1269, Springer, pp.279-291, 2015, RNA Bioinformatics, 978-1-4939-2290-1. <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/978-1-4939-2291-8_17\">⟨10.1007/978-1-4939-2291-8_17⟩</a>", "citationFull_s":"Evguenia Kopylova, Laurent Noé, Corinne da Silva, Jean-Frédéric Berthelot, Adriana A. Alberti, et al.. Deciphering metatranscriptomic data. Methods in Molecular Biology, 1269, Springer, pp.279-291, 2015, RNA Bioinformatics, 978-1-4939-2290-1. <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/978-1-4939-2291-8_17\">⟨10.1007/978-1-4939-2291-8_17⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01104015\">⟨hal-01104015⟩</a>", "title_s":["Deciphering metatranscriptomic data"], "authFullName_s":["Evguenia Kopylova", "Laurent Noé", "Corinne da Silva", "Jean-Frédéric Berthelot", "Adriana A. Alberti", "Jean-Marc Aury", "Helene Touzet"], "halId_s":"hal-01104015", "docType_s":"COUV", "producedDateY_i":2015}, { "citationRef_s":"Journal of Computational Biology, 2014, 21 (12), pp.28. <a target=\"_blank\" href=\"https://dx.doi.org/10.1089/cmb.2014.0173\">⟨10.1089/cmb.2014.0173⟩</a>", "citationFull_s":"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, 2014, 21 (12), pp.28. <a target=\"_blank\" href=\"https://dx.doi.org/10.1089/cmb.2014.0173\">⟨10.1089/cmb.2014.0173⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01083204\">⟨hal-01083204⟩</a>", "title_s":["A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and $k$-Mer Distances"], "authFullName_s":["Laurent Noé", "Donald E. K. Martin"], "halId_s":"hal-01083204", "docType_s":"ART", "producedDateY_i":2014}, { "citationRef_s":"Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Sep 2014, Strasbourg, France", "citationFull_s":"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. <a target=\"_blank\" href=\"https://hal.science/hal-01094011\">⟨hal-01094011⟩</a>", "title_s":["SortMeRNA 2: ribosomal RNA classification for taxonomic assignation"], "authFullName_s":["Evguenia Kopylova", "Laurent Noé", "Pierre Pericard", "Mikaël Salson", "Hélène Touzet"], "halId_s":"hal-01094011", "docType_s":"COMM", "producedDateY_i":2014}, { "citationRef_s":"Nucleic Acids Research, 2014, 42 (7), pp.e59. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nar/gku104\">⟨10.1093/nar/gku104⟩</a>", "citationFull_s":"Martin Frith, Laurent Noé. Improved search heuristics find 20 000 new alignments between human and mouse genomes.. Nucleic Acids Research, 2014, 42 (7), pp.e59. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nar/gku104\">⟨10.1093/nar/gku104⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00958207\">⟨hal-00958207⟩</a>", "title_s":["Improved search heuristics find 20 000 new alignments between human and mouse genomes."], "authFullName_s":["Martin Frith", "Laurent Noé"], "halId_s":"hal-00958207", "docType_s":"ART", "producedDateY_i":2014}, { "citationRef_s":"JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. pp.143-150", "citationFull_s":"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. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00843827\">⟨hal-00843827⟩</a>", "title_s":["Non Ribosomal Peptides : A monomeric puzzle"], "authFullName_s":["Yoann Dufresne", "Valérie Leclère", "Philippe Jacques", "Laurent Noé", "Maude Pupin"], "halId_s":"hal-00843827", "docType_s":"COMM", "producedDateY_i":2013}, { "citationRef_s":"Bioinformatics, 2012, 28 (24), pp.3211-3217. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/bts611\">⟨10.1093/bioinformatics/bts611⟩</a>", "citationFull_s":"Evguenia Kopylova, Laurent Noé, Héléne Touzet. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.. Bioinformatics, 2012, 28 (24), pp.3211-3217. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/bts611\">⟨10.1093/bioinformatics/bts611⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00748990\">⟨hal-00748990⟩</a>", "title_s":["SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data."], "authFullName_s":["Evguenia Kopylova", "Laurent Noé", "Héléne Touzet"], "halId_s":"hal-00748990", "docType_s":"ART", "producedDateY_i":2012}, { "citationRef_s":"JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2012, Jul 2012, Rennes, France", "citationFull_s":"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. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00763792\">⟨hal-00763792⟩</a>", "title_s":["SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis"], "authFullName_s":["Evguenia Kopylova", "Laurent Noé", "Helene Touzet"], "halId_s":"hal-00763792", "docType_s":"COMM", "producedDateY_i":2012}, { "citationRef_s":"Bulletin of the Polish Academy of Sciences: Technical Sciences, 2012, 60 (3), pp.495-505. <a target=\"_blank\" href=\"https://dx.doi.org/10.2478/v10175-012-0063-0\">⟨10.2478/v10175-012-0063-0⟩</a>", "citationFull_s":"Michal Startek, Slawomir Lasota, Maciej Sykulski, Adam Bulak, Laurent Noé, et al.. Efficient alternatives to PSI-BLAST. 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Bioinformatics 2011 - International Conference on Bioinformatics Models, Methods and Algorithms, Jan 2011, Rome, Italy. pp.149-158, <a target=\"_blank\" href=\"https://dx.doi.org/10.5220/0003147601490158\">⟨10.5220/0003147601490158⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/inria-00609791\">⟨inria-00609791⟩</a>", "title_s":["Subset seed extension to Protein BLAST"], "authFullName_s":["Anna Gambin", "Slawomir Lasota", "Michal Startek", "Maciej Sykulski", "Laurent Noé", "Gregory Kucherov"], "halId_s":"inria-00609791", "docType_s":"COMM", "producedDateY_i":2011}, { "citationRef_s":"RECOMB, Aug 2010, Lisbon, Portugal. pp.384-396, <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/978-3-642-12683-3_25\">⟨10.1007/978-3-642-12683-3_25⟩</a>", "citationFull_s":"Laurent Noé, Marta L. Gîrdea, Gregory Kucherov. Seed design framework for mapping SOLiD reads. RECOMB, Aug 2010, Lisbon, Portugal. pp.384-396, <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/978-3-642-12683-3_25\">⟨10.1007/978-3-642-12683-3_25⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/inria-00484642\">⟨inria-00484642⟩</a>", "title_s":["Seed design framework for mapping SOLiD reads"], "authFullName_s":["Laurent Noé", "Marta L. Gîrdea", "Gregory Kucherov"], "halId_s":"inria-00484642", "docType_s":"COMM", "producedDateY_i":2010}, { "citationRef_s":"Algorithms for Molecular Biology, 2010, 5 (1), pp.6. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/1748-7188-5-6\">⟨10.1186/1748-7188-5-6⟩</a>", "citationFull_s":"Marta Gîrdea, Laurent Noé, Gregory Kucherov. Back-translation for discovering distant protein homologies in the presence of frameshift mutations. Algorithms for Molecular Biology, 2010, 5 (1), pp.6. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/1748-7188-5-6\">⟨10.1186/1748-7188-5-6⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00784444\">⟨hal-00784444⟩</a>", "title_s":["Back-translation for discovering distant protein homologies in the presence of frameshift mutations"], "authFullName_s":["Marta Gîrdea", "Laurent Noé", "Gregory Kucherov"], "halId_s":"hal-00784444", "docType_s":"ART", "producedDateY_i":2010}, { "citationRef_s":"Advances in Bioinformatics, 2010, <a target=\"_blank\" href=\"https://dx.doi.org/10.1155/2010/708501\">⟨10.1155/2010/708501⟩</a>", "citationFull_s":"Laurent Noé, Marta Gîrdea, Gregory Kucherov. Designing Efficient Spaced Seeds for SOLiD Read Mapping.. Advances in Bioinformatics, 2010, <a target=\"_blank\" href=\"https://dx.doi.org/10.1155/2010/708501\">⟨10.1155/2010/708501⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/inria-00527029\">⟨inria-00527029⟩</a>", "title_s":["Designing Efficient Spaced Seeds for SOLiD Read Mapping."], "authFullName_s":["Laurent Noé", "Marta Gîrdea", "Gregory Kucherov"], "halId_s":"inria-00527029", "docType_s":"ART", "producedDateY_i":2010}, { "citationRef_s":"the 9th International Workshop in Algorithms in Bioinformatics (WABI), Sep 2009, Philadelphia, United States. pp.108-120, <a target=\"_blank\" href=\"https://dx.doi.org/10.1007/978-3-642-04241-6_10\">⟨10.1007/978-3-642-04241-6_10⟩</a>", "citationFull_s":"Marta L. Gîrdea, Laurent Noé, Gregory Kucherov. 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Laurent Noé