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Data structures based on k -mers for querying large collections of sequencing data sets

Camille Marchet , Christina Boucher , Simon Puglisi , Paul Medvedev , Mikaël Salson et al.
Genome Research, 2021, 31 (1), pp.1-12. ⟨10.1101/gr.260604.119⟩
Article dans une revue hal-03165261v1
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Assisted transcriptome reconstruction and splicing orthology

Samuel Blanquart , Jean-Stéphane Varré , Paul Guertin , Amandine Perrin , Anne Bergeron et al.
BMC Genomics, 2016, Proceedings of the 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: genomics, 17 (Suppl 10), pp.786. ⟨10.1186/s12864-016-3103-6⟩
Article dans une revue hal-01396410v1
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DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Jérôme Audoux , Nicolas Philippe , Rayan Chikhi , Mikael Salson , Mélina Gallopin et al.
Genome Biology, 2017, 18 (1), pp.1-15. ⟨10.1186/s13059-017-1372-2⟩
Article dans une revue hal-01728770v1

BLight: efficient exact associative structure for k-mers

Antoine Limasset , Camille Marchet , Mael Kerbiriou
Bioinformatics, 2021, 37 (18), pp.2858-2865. ⟨10.1093/bioinformatics/btab217⟩
Article dans une revue hal-03443183v1
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MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

Pierre Pericard , Yoann Dufresne , Loïc Couderc , Samuel Blanquart , Hélène Touzet et al.
Article dans une revue hal-01646297v1
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STRONG: metagenomics strain resolution on assembly graphs

Antoine Limasset , Christopher Quince , Sergey Nurk , Sebastien Raguideau , Robert James et al.
Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩
Article dans une revue hal-03443171v1
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TgAP2IX-5 is a key transcriptional regulator of the asexual cell cycle division in Toxoplasma gondii

Asma S. Khelifa , Cecilia Guillen Sanchez , Kevin M. Lesage , Ludovic Huot , Thomas Mouveaux et al.
Nature Communications, 2021, 12, pp.116. ⟨10.1038/s41467-020-20216-x⟩
Article dans une revue hal-03107529v2
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Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis

Yann Ferret , Aurélie Caillault , Shéhérazade Sebda , Marc Duez , Nathalie Grardel et al.
British Journal of Haematology, 2016, 173 (3), pp.413-420. ⟨10.1111/bjh.13981⟩
Article dans une revue hal-01279160v1
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Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

Leandro Lima , Camille Marchet , Ségolène Caboche , Corinne da Silva , Benjamin Istace et al.
Briefings in Bioinformatics, 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩
Article dans une revue hal-02394395v1
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Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

Léa Siegwald , Hélène Touzet , Yves Lemoine , David Hot , Christophe Audebert et al.
PLoS ONE, 2017, 12 (1), pp.e0169563. ⟨10.1371/journal.pone.0169563⟩
Article dans une revue hal-01575755v1

Bioinformatics tools for the discovery of new lipopeptides with biocontrol applications

Maude Pupin , Areski Flissi , Philippe Jacques , Valérie Leclère
European Journal of Plant Pathology, 2018, ⟨10.1007/s10658-018-1544-2⟩
Article dans une revue hal-01937890v1

Compacting de Bruijn graphs from sequencing data quickly and in low memory

Rayan Chikhi , Antoine Limasset , Paul Medvedev
Bioinformatics, 2016, 32 (12), pp.i201 - i208. ⟨10.1093/bioinformatics/btw279⟩
Article dans une revue hal-01395704v1
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Médiation Scientifique : une facette de nos métiers de la recherche

Antoine Rousseau , Aurélie Darnaud , Brice Goglin , Céline Acharian , Christine Leininger et al.
[Interne] Inria. 2013, pp.34
Rapport hal-00804915v1
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CONSENT: Scalable self-correction of long reads with multiple sequence alignment

Pierre Morisse , Camille Marchet , Antoine Limasset , Thierry Lecroq , Arnaud Lefebvre et al.
Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Washinton, United States. pp.1-9, ⟨10.1101/546630⟩
Communication dans un congrès hal-02435116v1

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Monika Brüggemann , Michaela Kotrova , Henrik Knecht , Jack Bartram , Myriam Boudjogrha et al.
Article dans une revue hal-02169053v1

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges.

Anton W Langerak , Monika Brüggemann , Frédéric Davi , Nikos Darzentas , Jacques J M van Dongen et al.
Journal of Immunology, 2017, pp.1602050. ⟨10.4049/jimmunol.1602050⟩
Article dans une revue hal-01516289v1

From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics

Annie Chateau , Mikaël Salson
Ouvrages hal-03920813v1

String Processing and Information Retrieval

Thierry Lecroq , Hélène Touzet
Springer International Publishing, 12944, 2021, Lecture Notes in Computer Science, ⟨10.1007/978-3-030-86692-1⟩
Ouvrages hal-03368750v1
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Indexing labeled sequences

Tatiana Rocher , Mathieu Giraud , Mikaël Salson
PeerJ Computer Science, 2018, 4, pp.1-14. ⟨10.7717/peerj-cs.148⟩
Article dans une revue hal-01743104v1

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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Fast and scalable minimal perfect hashing for massive key sets

Antoine Limasset , Guillaume Rizk , Rayan Chikhi , Pierre Peterlongo
16th International Symposium on Experimental Algorithms, Jun 2017, London, United Kingdom. pp.1 - 11
Communication dans un congrès hal-01566246v1

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
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Indexer un ensemble de séquences ADN annotées

Tatiana Rocher , Mathieu Giraud , Mikael Salson
JOBIM, Jun 2016, Lyon, France
Communication dans un congrès hal-01576319v1
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Efficient approximations of RNA kinetics landscape using non-redundant sampling

Juraj Michálik , Hélène Touzet , Yann Ponty
ISMB/ECCB - 25th Annual international conference on Intelligent Systems for Molecular Biology/16th European Conference on Computational Biology - 2017, Jul 2017, Prague, Czech Republic. pp.i283 - i292, ⟨10.1093/bioinformatics/btx269⟩
Communication dans un congrès hal-01500115v1
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Practical dynamic de Bruijn graphs

Alan Kuhnle , Victoria G. Crawford , Christina Boucher , Rayan Chikhi , Travis Gagie et al.
Article dans une revue hal-01935559v1
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Algorithmes pour la reconstruction de séquences de marqueurs conservés dans des données de métagénomique

Pierre Pericard
Bio-informatique [q-bio.QM]. Université de Lille, 2017. Français. ⟨NNT : 2017LIL10084⟩
Thèse tel-01738687v2
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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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Debugging long-read genome and metagenome assemblies using string graph analysis

Pierre Marijon , Jean-Stéphane Varré , Rayan Chikhi
JOBIM 2017- Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France.
Poster de conférence hal-01574824v1
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Norine: update of the nonribosomal peptide resource

Areski Flissi , Emma Ricart , Clémentine Campart , Mickael Chevalier , Yoann Dufresne et al.
Nucleic Acids Research, 2019, ⟨10.1093/nar/gkz1000⟩
Article dans une revue hal-02376009v1
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Sneak peek at the -tig sequences: useful sequences built from nucleic acid data

Camille Marchet
2022
Pré-publication, Document de travail hal-03768446v2