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Genome Halving by Block Interchange

Antoine Thomas , Aïda Ouangraoua , Jean-Stéphane Varré
BIOINFORMATICS, Feb 2012, Lisboa, Portugal. pp.58-65
Communication dans un congrès hal-00749026v1
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CRAC: an integrated approach to the analysis of RNA-seq reads

Nicolas Philippe , Mikaël Salson , Thérèse Commes , Eric Rivals
Genome Biology, 2013, 14 (3), pp.R30. ⟨10.1186/gb-2013-14-3-r30⟩
Article dans une revue inserm-00850972v1
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A new fingerprint to predict nonribosomal peptides activity.

Ammar Hasan Abdo , Ségolène Caboche , Valérie Leclère , Philippe Jacques , Maude Pupin et al.
Journal of Computer-Aided Molecular Design, 2012, 26 (10), pp.1187-94. ⟨10.1007/s10822-012-9608-4⟩
Article dans une revue hal-00750002v1

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Marta Tomaszkiewicz , Samarth Rangavittal , Monika Cechova , Rebeca Campos Sanchez , Howard William Fescemyer et al.
Genome Research, 2016, 26 (4), pp.530 - 540. ⟨10.1101/gr.199448.115⟩
Article dans une revue hal-01395702v1

Nonribosomal peptide synthetase with a unique iterative-alternative-optional mechanism catalyzes amonabactin synthesis in Aeromonas

Qassim Esmaeel , Mickael Chevalier , Gabrielle Chataigne , Rathinasamy Subashkumar , Philippe Jacques et al.
Applied Microbiology and Biotechnology, 2016, 100 (19), pp.8453-8463. ⟨10.1007/s00253-016-7773-4⟩
Article dans une revue hal-01601408v1
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One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia

Patrick Villarese , Chrystelle Abdo , Matthieu Bertrand , Florian Thonier , Mathieu Giraud et al.
Anton W. Langerak. Immunogenetics. Methods and Protocols, 2453, Springer, pp.43-59, 2022, Methods in Molecular Biology, 978-1-0716-2115-8. ⟨10.1007/978-1-0716-2115-8_3⟩
Chapitre d'ouvrage hal-03684695v1

Traitement des données - introduction

Iovka Boneva , Héléne Touzet
Les Big Data à découvert, 2016
Chapitre d'ouvrage hal-01574692v1
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A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections

Eric Rivals , Nicolas Philippe , Mikael Salson , Martine Léonard , Thérèse Commes et al.
ERCIM News, 2012, 2012 (89), pp.20-21
Article dans une revue lirmm-00712653v1

TFM-Explorer: mining cis-regulatory regions in genomes

Tonon Laurie , Hélène Touzet , Jean-Stéphane Varré
Nucleic Acids Research, 2010, 38 (S2), pp.W286-W292. ⟨10.1093/nar/gkq473⟩
Article dans une revue hal-00823465v1
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Indexing De Bruijn graphs with minimizers

Camille Marchet , Maël Kerbiriou , Antoine Limasset
Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Whashinton, United States. pp.1-16, ⟨10.1101/546309⟩
Communication dans un congrès hal-02435086v1
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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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On the Levenshtein Automaton and the Size of the Neighborhood of a Word

Hélène Touzet
LATA 2016 - 10th International Conference on Language and Automata Theory and Applications, Mar 2016, Prague, Czech Republic. pp.207-218, ⟨10.1007/978-3-319-30000-9_16⟩
Communication dans un congrès hal-01360482v1
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Searching for alternate RNA structures in genomic sequences

Azadeh Saffarian , Mathieu Giraud , Hélène Touzet
Computational Methods for Structural RNAs, CMSR'14, Sep 2014, Strasbourg, France. pp.13-24, ⟨10.15455/CMSR.2014.0002⟩
Communication dans un congrès hal-01084319v1
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SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

Jérôme Audoux , Mikaël Salson , Christophe Grosset , Sacha Beaumeunier , Jean-Marc Holder et al.
BMC Bioinformatics, 2017, 18 (1), pp.428. ⟨10.1186/s12859-017-1831-5⟩
Article dans une revue inserm-02437931v1
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Critical Assessment of Metagenome Interpretation: the second round of challenges

Fernando Meyer , Adrian Fritz , Zhi-Luo Deng , David Koslicki , Till Robin Lesker et al.
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Article dans une revue hal-03832903v1
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Scalable long read self-correction and assembly polishing with multiple sequence alignment

Pierre Morisse , Camille Marchet , Antoine Limasset , Thierry Lecroq , Arnaud Lefebvre et al.
Scientific Reports, 2021, 11 (1), pp.1-13. ⟨10.1038/s41598-020-80757-5⟩
Article dans une revue hal-03210290v1

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

Chadi Saad , Laurent Noé , Hugues Richard , Julie Leclerc , Marie-Pierre Buisine et al.
BMC Bioinformatics, 2018, 19 (1), ⟨10.1186/s12859-018-2215-1⟩
Article dans une revue hal-01881466v1
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Algebraic Dynamic Programming 2.0

Robert Giegerich , Hélène Touzet
Workshop Haskell-Treffen an der Universität Leipzig, Jun 2013, Leipzig, Germany
Communication dans un congrès hal-00857801v1
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On the readability of overlap digraphs

Rayan Chikhi , Paul Medvedev , Martin Milanič , Sofya Raskhodnikova
Discrete Applied Mathematics, 2016, 205, pp.35-44. ⟨10.1016/j.dam.2015.12.009⟩
Article dans une revue hal-01729749v1
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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 et al.
Nucleic Acids Research, 2015, ⟨10.1093/nar/gkv1143⟩
Article dans une revue hal-01235996v1
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Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide Discovery

Thibault Caradec , Maude Pupin , Aurélien Vanvlassenbroeck , Marie-Dominique Devignes , Malika Smaïl-Tabbone et al.
PLoS ONE, 2014, 9 (1), pp.e85667. ⟨10.1371/journal.pone.0085667⟩
Article dans une revue hal-01090619v1
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Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia

Anne Langlois de Septenville , Myriam Boudjoghra , Clotilde Bravetti , Marine Armand , Mikaël Salson et al.
Anton W. Langerak. Immunogenetics, 2453, Springer, pp.153-167, 2022, Methods in Molecular Biology, 978-1-0716-2115-8. ⟨10.1007/978-1-0716-2115-8_10⟩
Chapitre d'ouvrage hal-03684717v1

A dataset of sequences with manually curated V(D)J designations

Mikael Salson , Aurélie Caillault , Marc Duez , Yann Ferret , Alice Fievet et al.
2016
Autre publication scientifique hal-01331556v1
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Solutions d'amélioration des études de métagénomique ciblée

Léa Siegwald
Médecine humaine et pathologie. Université du Droit et de la Santé - Lille II, 2017. Français. ⟨NNT : 2017LIL2S006⟩
Thèse tel-01575747v2
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ELECTOR : evaluator for long reads correction methods

Camille Marchet , Pierre Morisse , Lolita Lecompte , Arnaud Lefebvre , Thierry Lecroq et al.
NAR Genomics and Bioinformatics, 2020, 2 (1), pp.1-12. ⟨10.1093/nargab/lqz015⟩
Article dans une revue hal-02371117v1

A survey of mapping algorithms in the long-reads era

Kristoffer Sahlin , Thomas Baudeau , Bastien Cazaux , Camille Marchet
2023
Pré-publication, Document de travail hal-03934299v1
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REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

Camille Marchet , Zamin Iqbal , Daniel Gautheret , Mikaël Salson , Rayan Chikhi et al.
Bioinformatics, 2020, 36 (Supplement_1), pp.i177-i185. ⟨10.1093/bioinformatics/btaa487⟩
Article dans une revue hal-03413006v1
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AllSome Sequence Bloom Trees

Chen Sun , Robert S. Harris , Rayan Chikhi , Paul Medvedev
RECOMB 2017 - 21st Annual International Conference on Research in Computational Molecular Biology, May 2017, Hong Kong, China. ⟨10.1007/978-3-319-56970-3_17⟩
Communication dans un congrès hal-01575350v1

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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Improved Sensitivity And Reliability Of Anchor Based Genome Alignment

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