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Laurent Noé

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Présentation

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

Publications

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Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming

Quentin Bonenfant , Laurent Noé , Hélène Touzet
Bioinformatics Advances, 2022, 3 (1), pp.vbac085. ⟨10.1093/bioadv/vbac085⟩
Article dans une revue hal-03932719v1

Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k -mer Hashing

Enrico Petrucci , Laurent Noé , Cinzia Pizzi , Matteo Comin
Journal of Computational Biology, 2020, 27 (2), pp.223-233. ⟨10.1089/cmb.2019.0298⟩
Article dans une revue hal-02910076v1
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Minimally-overlapping words for sequence similarity search

Martin Frith , Laurent Noé , Gregory Kucherov
Article dans une revue hal-03087470v1
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DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

Chadi Saad , Laurent Noé , Hugues Richard , Julie Leclerc , Marie-Pierre Buisine
BMC Bioinformatics, 2018, 19 (1), ⟨10.1186/s12859-018-2215-1⟩
Article dans une revue hal-01881466v1

Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds

Laurent Noé
Algorithms for Molecular Biology, 2017, 12 (1), ⟨10.1186/s13015-017-0092-1⟩
Article dans une revue hal-01467970v1

Faster exact distributions of pattern statistics through sequential elimination of states

Donald E. K. Martin , Laurent Noé
Annals of the Institute of Statistical Mathematics, 2017, 69 (1), pp.231--248. ⟨10.1007/s10463-015-0540-y⟩
Article dans une revue hal-01237045v1
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Smiles2Monomers: a link between chemical and biological structures for polymers

Yoann Dufresne , Laurent Noé , Valérie Leclère , Maude Pupin
Journal of Cheminformatics, 2015, 7, ⟨10.1186/s13321-015-0111-5⟩
Article dans une revue hal-01250619v1
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Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing

Areski Flissi , Yoann Dufresne , Juraj Michalik , Laurie Tonon , Stéphane Janot
Nucleic Acids Research, 2015, ⟨10.1093/nar/gkv1143⟩
Article dans une revue hal-01235996v1
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A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and $k$-Mer Distances

Laurent Noé , Donald E. K. Martin
Journal of Computational Biology, 2014, 21 (12), pp.28. ⟨10.1089/cmb.2014.0173⟩
Article dans une revue hal-01083204v1

Improved search heuristics find 20 000 new alignments between human and mouse genomes.

Martin Frith , Laurent Noé
Nucleic Acids Research, 2014, 42 (7), pp.e59. ⟨10.1093/nar/gku104⟩
Article dans une revue hal-00958207v1
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SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

Evguenia Kopylova , Laurent Noé , Héléne Touzet
Bioinformatics, 2012, 28 (24), pp.3211-3217. ⟨10.1093/bioinformatics/bts611⟩
Article dans une revue hal-00748990v1

Efficient alternatives to PSI-BLAST

Michal Startek , Slawomir Lasota , Maciej Sykulski , Adam Bulak , Laurent Noé
Bulletin of the Polish Academy of Sciences: Technical Sciences, 2012, 60 (3), pp.495-505. ⟨10.2478/v10175-012-0063-0⟩
Article dans une revue hal-00749016v1

Designing Efficient Spaced Seeds for SOLiD Read Mapping.

Laurent Noé , Marta Gîrdea , Gregory Kucherov
Advances in Bioinformatics, 2010, ⟨10.1155/2010/708501⟩
Article dans une revue inria-00527029v1
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Back-translation for discovering distant protein homologies in the presence of frameshift mutations

Marta Gîrdea , Laurent Noé , Gregory Kucherov
Algorithms for Molecular Biology, 2010, 5 (1), pp.6. ⟨10.1186/1748-7188-5-6⟩
Article dans une revue hal-00784444v1
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On subset seeds for protein alignment

Mikhail A. Roytberg , Anna Gambin , Laurent Noé , Slawomir Lasota , Eugenia Furletova
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, 6 (3), pp.483-494. ⟨10.1109/TCBB.2009.4⟩
Article dans une revue inria-00354773v1
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Optimal neighborhood indexing for protein similarity search

Pierre Peterlongo , Laurent Noé , Dominique Lavenier , van Hoa Nguyen , Gregory Kucherov
BMC Bioinformatics, 2008, 9 (534), ⟨10.1186/1471-2105-9-534⟩
Article dans une revue inria-00340510v1

Reconsidering the significance of genomic word frequencies.

Miklós Csűrös , Laurent Noé , Gregory Kucherov
Trends in Genetics, 2007, 23 (11), pp.543-6. ⟨10.1016/j.tig.2007.07.008⟩
Article dans une revue inria-00448737v1
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A unifying framework for seed sensitivity and its application to subset seeds.

Gregory Kucherov , Laurent Noé , Mihkail Roytberg
Journal of Bioinformatics and Computational Biology, 2006, 4 (2), pp.553-69. ⟨10.1142/S0219720006001977⟩
Article dans une revue hal-00018114v2

Multi-seed lossless filtration

Gregory Kucherov , Laurent Noé , Mikhail Roytberg
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2005, 2 (1), pp.51--61. ⟨10.1109/TCBB.2005.12⟩
Article dans une revue inria-00000718v1
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Multiseed Lossless Filtration

Gregory Kucherov , Laurent Noé , Mikhail A. Roytberg
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2005, 2 (1), pp.51-61. ⟨10.1109/TCBB.2005.12⟩
Article dans une revue inria-00354810v1

YASS: enhancing the sensitivity of DNA similarity search.

Laurent Noé , Gregory Kucherov
Nucleic Acids Research, 2005, 33 (Web Server issue), pp.W540-W543. ⟨10.1093/nar/gki478⟩
Article dans une revue inria-00448742v1

Improved hit criteria for DNA local alignment.

Laurent Noé , Gregory Kucherov
BMC Bioinformatics, 2004, 5 (149), pp.1-9. ⟨10.1186/1471-2105-5-149⟩
Article dans une revue inria-00448743v1
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Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing

Enrico Petrucci , Laurent Noé , Cinzia Pizzi , Matteo Comin
15th International Symposium on Bioinformatics Research and Applications (ISBRA), Jun 2019, Barcelona, Spain. pp.208-219, ⟨10.1007/978-3-030-20242-2_18⟩
Communication dans un congrès hal-02146404v1
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DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors

Chadi Saad , Laurent Noé , Hugues Richard , Julie Leclerc , Marie-Pierre Buisine
JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France
Communication dans un congrès hal-01574630v1

SortMeRNA 2: ribosomal RNA classification for taxonomic assignation

Evguenia Kopylova , Laurent Noé , Pierre Pericard , Mikaël Salson , Hélène Touzet
Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Sep 2014, Strasbourg, France
Communication dans un congrès hal-01094011v1
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Non Ribosomal Peptides : A monomeric puzzle

Yoann Dufresne , Valérie Leclère , Philippe Jacques , Laurent Noé , Maude Pupin
JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. pp.143-150
Communication dans un congrès hal-00843827v1

SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis

Evguenia Kopylova , Laurent Noé , Helene Touzet
JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2012, Jul 2012, Rennes, France
Communication dans un congrès hal-00763792v1

Subset seed extension to Protein BLAST

Anna Gambin , Slawomir Lasota , Michal Startek , Maciej Sykulski , Laurent Noé
Bioinformatics 2011 - International Conference on Bioinformatics Models, Methods and Algorithms, Jan 2011, Rome, Italy. pp.149-158, ⟨10.5220/0003147601490158⟩
Communication dans un congrès inria-00609791v1
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Seed design framework for mapping SOLiD reads

Laurent Noé , Marta L. Gîrdea , Gregory Kucherov
RECOMB, Aug 2010, Lisbon, Portugal. pp.384-396, ⟨10.1007/978-3-642-12683-3_25⟩
Communication dans un congrès inria-00484642v1
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Back-translation for discovering distant protein homologies

Marta L. Gîrdea , Laurent Noé , Gregory Kucherov
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⟩
Communication dans un congrès inria-00448741v1
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Improved sensitivity and reliability of anchor based genome alignment

Raluca Uricaru , Célia Michotey , Laurent Noé , Helene H. Chiapello , Eric Rivals
JOBIM - Journées Ouvertes en Biologie Informatique Mathématiques2009 - Nantes :, Jun 2009, Nantes, France. 259 p
Communication dans un congrès hal-02751358v1
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Improved Sensitivity And Reliability Of Anchor Based Genome Alignment

Raluca Uricaru , Célia Michotey , Laurent Noé , Hélène Chiapello , Eric Rivals
JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36
Communication dans un congrès lirmm-00407215v1
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Efficient seeding techniques for protein similarity search

Mihkail Roytberg , Anna Gambin , Laurent Noé , Slawomir Lasota , Eugenia Furletova
Proceedings of the 2nd International Conference BIRD, Jul 2008, Vienna, Austria. pp.466-478, ⟨10.1007/978-3-540-70600-7⟩
Communication dans un congrès inria-00335564v1
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Protein similarity search with subset seeds on a dedicated reconfigurable hardware

Pierre Peterlongo , Laurent Noé , Dominique Lavenier , Gilles Georges , Julien Jacques
Parallel Bio-Computing, Sep 2007, Gdansk,, Poland
Communication dans un congrès inria-00178325v1
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Subset seed automaton

Gregory Kucherov , Laurent Noé , Mihkail Roytberg
CIAA 2007, Jul 2007, Prague, Czech Republic. pp.180-191, ⟨10.1007/978-3-540-76336-9_18⟩
Communication dans un congrès inria-00170414v1
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Recherches de motifs et de similarités en bioinformatique : modélisations, solutions logicielles et matérielles

Mathieu Giraud , Laurent Noé , Gregory Kucherov , Dominique Lavenier
MajecSTIC 2005 : Manifestation des Jeunes Chercheurs francophones dans les domaines des STIC, IRISA – IETR – LTSI, Nov 2005, Rennes/France, pp.18--37
Communication dans un congrès inria-00001036v1
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A unifying framework for seed sensitivity and its application to subset seeds (Extended abstract)

Gregory Kucherov , Laurent Noé , Mikhail Roytberg
WABI, 2005, Majorca/Spain, Spain
Communication dans un congrès inria-00001164v1
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Multi-seed lossless filtration (Extended abstract)

Gregory Kucherov , Laurent Noé , Mikhail A. Roytberg
Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching - CPM'2004, Jul 2004, Istambul, Turkey. pp.297-310, ⟨10.1007/11557067_21⟩
Communication dans un congrès inria-00001162v1

Computer analysis of multiple repeats in bacteria

Alexey Vitreschak , Laurent Noé , Gregory Kucherov
The fourth International Conference on Bioinformatics of Genome Regulation and Structure - BGRS'2004, 2004, Novosibirsk, Russia, 5 p
Communication dans un congrès inria-00100088v1

Improved hit criteria for DNA local alignment

Laurent Noé , Gregory Kucherov
Proceedings of the 5th Open Days in Biology, Computer Science and Mathematics - JOBIM'2004, 2004, Montreal, Canada, 11 p
Communication dans un congrès inria-00099999v1

YASS : Enhancing the sensitivity of DNA similarity search

Laurent Noé , Gregory Kucherov
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
Communication dans un congrès inria-00100004v1
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Estimating seed sensitivity on homogeneous alignments

Gregory Kucherov , Laurent Noé , Yann Ponty
4th Symposium on Bioinformatics and bioengineering - BIBE'2004, May 2004, Taichung, Taiwan. pp.387-394, ⟨10.1109/BIBE.2004.1317369⟩
Communication dans un congrès inria-00001163v1

YASS : similarity search in DNA sequences

Gregory Kucherov , Laurent Noé
The Seventh Annual International Conference on Research in Computational Molecular Biology - RECOMB'03, Apr 2003, Berlin, Germany, 1 p
Communication dans un congrès inria-00099599v1

A new method of finding similarity regions in DNA sequences

Laurent Noé , Gregory Kucherov
European Conference on Computational Biology - ECCB'2002, Oct 2002, Saarbrücken, Germany, pp.173-174
Communication dans un congrès inria-00100859v1

Sequence Alignment

Laurent Noé
From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, 3, Wiley, 2022, 9781789450668. ⟨10.1002/9781394169641.ch3⟩
Chapitre d'ouvrage hal-04304829v1

Sequence Alignment

Laurent Noé
From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, 1, Wiley, 2022, ⟨10.1002/9781394169641.ch3⟩
Chapitre d'ouvrage hal-03932710v1

Deciphering metatranscriptomic data

Evguenia Kopylova , Laurent Noé , Corinne da Silva , Jean-Frédéric Berthelot , Adriana A. Alberti
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⟩
Chapitre d'ouvrage hal-01104015v1