Recherche - Archive ouverte HAL Accéder directement au contenu

Filtrer vos résultats

189 Résultats

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
Image document

MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences.

Arnaud Fontaine , Antoine de Monte , Hélène Touzet
Nucleic Acids Research, 2008, 36 (Web Server issue), pp.W14-8. ⟨10.1093/nar/gkn321⟩
Article dans une revue hal-00823594v1
Image document

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

Computational identification of protein-coding sequences by comparative analysis

Arnaud Fontaine , Hélène Touzet
International Journal of Data Mining and Bioinformatics, 2009, 3 (2), pp.160-76. ⟨10.1504/ijdmb.2009.024849⟩
Article dans une revue hal-00823601v1
Image document

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
Image document

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
Image document

ProCARs: Progressive Reconstruction of Ancestral Gene Orders

Amandine Perrin , Jean-Stéphane Varré , Samuel Blanquart , Aïda Ouangraoua
ISCB-Latin America, Oct 2014, Belo Horizonte, Brazil
Communication dans un congrès hal-01083841v1
Image document

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
Image document

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
Image document

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

Diagnostic et suivi des leucémies aiguës lymphoblastiques (LAL) par séquençage haut-débit (HTS)

Nathalie Grardel , Mikaël Salson , Aurélie Caillault , Marc Duez , Céline Villenet et al.
Congrès de la Société Française d'Hématologie (SFH), 2014, Paris, France
Communication dans un congrès hal-01100152v1
Image document

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
Image document

Prediction of New Bioactive Molecules using a Bayesian Belief Network

Ammar Abdo , Valérie Leclère , Philippe Jacques , Naomie Salim , Maude Pupin et al.
Journal of Chemical Information and Modeling, 2014, 54 (1), pp.30-36. ⟨10.1021/ci4004909⟩
Article dans une revue hal-01090611v1
Image document

Biomanycores, open-source parallel code for many-core bioinformatics

Mathieu Giraud , Stéphane Janot , Jean-Frédéric Berthelot , Charles Deltel , Laetitia Jourdan et al.
Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria
Communication dans un congrès inria-00623390v1

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
Image document

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
Image document

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
Image document

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
Image document

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

Subset seed extension to Protein BLAST

Anna Gambin , Slawomir Lasota , Michal Startek , Maciej Sykulski , Laurent Noé et al.
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

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
Image document

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

From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics

Annie Chateau , Mikaël Salson
Ouvrages hal-03920813v1
Image document

Indexer un ensemble de séquences ADN annotées

Tatiana Rocher , Mathieu Giraud , Mikael Salson
JOBIM, Jun 2016, Lyon, France
Communication dans un congrès hal-01576319v1

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
Image document

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
Image document

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