Recherche - Archive ouverte HAL Accéder directement au contenu

Filtrer vos résultats

189 Résultats
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
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

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

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

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

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

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

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

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

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

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
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
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

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

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

Bipartite Graphs of Small Readability

Rayan Chikhi , Vladan Jovičić , Stefan Kratsch , Paul Medvedev , Martin Milanic et al.
COCOON 2018 - The 24th International Computing and Combinatorics Conference, Jul 2018, Qingdao, China
Communication dans un congrès hal-01935562v1

Genome scaffolding with PE-contaminated mate-pair libraries

Kristoffer Sahlin , Rayan Chikhi , Lars Arvestad.
WABI 2015, 2015, Atlanta, United States. ⟨10.1101/025650⟩
Communication dans un congrès hal-01236176v1
Image document

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

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

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
Image document

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
Image document

Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome

Jean-Stéphane Varré , Nunzio d'Agostino , Pascal Touzet , Sophie Gallina , Rachele Tamburino et al.
International Journal of Molecular Sciences, 2019, 20, ⟨10.3390/ijms20194788⟩
Article dans une revue hal-02298474v1
Image document

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
Image document

Tandem Halving Problems by DCJ

Antoine Thomas , Aïda Ouangraoua , Jean-Stéphane Varré
Workshop on Algorithms in Bioinformatics, Sep 2012, Ljubljana, Slovenia. pp.417-429, ⟨10.1007/978-3-642-33122-0_33⟩
Communication dans un congrès hal-00749019v1
Image document

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
Image document

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

Algorithms for bioinformatics

Hélène Touzet
Mihai Pop; Hélène Touzet. WABI, Sep 2015, Atlanta, United States. 9289, Springer Verlag, 2015, 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings, ⟨10.1007/978-3-662-48221-6⟩
Proceedings/Recueil des communications hal-01228138v1