Publications 2021

Aimeric Bruno et al.
BoardION: real-time monitoring of Oxford Nanopore sequencing instruments
BMC Bioinformatics 2021, vol. 22, issue 1
doi: 10.1186/s12859-021-04161-0

Romain Feron et al.
RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data
Molecular Ecology Resources 2021
doi: 10.1111/1755-0998.13360

Morgane Pierre-Jean et al.
Clustering and variable selection evaluation of 13 unsupervised methods for multi-omics data integration
Briefings in Bioinformatics 2019
doi: 10.1093/bib/bbz138

Mickaël Canouil et al.
NACHO: an R package for quality control of NanoString nCounter data
Bioinformatics 2019
doi: 10.1093/bioinformatics/btz647

Nathalie Grafféo et al.
ipcwswitch: An R package for inverse probability of censoring weighting with an application to switches in clinical trials
Computers in Biology and Medicine 2019, vol. 111
doi: 10.1016/j.compbiomed.2019.103339

Royer G et al.
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level
Microbial Genomics 2018 4(9)
doi: 10.1099/mgen.0.000211

Belser C et al.
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
Nature Plants 2018 4(11)
doi: 10.1038/s41477-018-0289-4

Varet H et al.
checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes
Bioinformatics 2018 35(5)
doi: 10.1093/bioinformatics/bty706

Varet H et al.
Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica
Scientific Reports 2018 8(1)
doi: 10.1038/s41598-018-27086-w

Randrianjatovo-Gbalou I et al.
Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries
Nucleic Acids Research 2018 46(12)
doi: 10.1093/nar/gky413

Krin E et al.
Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
BMC Genomics 2018 19(1)
doi: 10.1186/s12864-018-4716-8

Claverie JM et al.
Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes
Viruses 2018 10(9)
doi: 10.3390/v10090506

Kojadinovic-Sirinelli M et al.
Exploring the microbiome of the “star” freshwater diatom Asterionella formosa
in a laboratory context
Environmental Microbiology 2018 20(10)
doi: 10.1111/1462-2920.14337

Belahbib H et al.
New genomic data and analyses challenge the traditional vision of animal epithelium evolution
BMC Genomics 2018 19(1)
doi: 10.1186/s12864-018-4715-9

Mercier J et al.
GROOLS: reactive graph reasoning for genome annotation through biological processes
BMC Bioinformatics 2018 19(1)
doi: 10.1186/s12859-018-2126-1

Leandro Lima et al.
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data
Briefings in Bioinformatics 2019
doi: 10.1093/bib/bbz058

Florian Thibord et al.
OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis
RNA 2019, vol. 25, issue 6
doi: 10.1261/rna.069708.118

Alice Fiévet et al.
ART-DeCo: easy tool for detection and characterization of cross-contamination of DNA samples in diagnostic next-generation sequencing analysis
European Journal of Human Genetics 2019, vol. 27, issue 5
doi: 10.1038/s41431-018-0317-x

Eglantine Mathieu-Bégné et al.
De novo transcriptome assembly for Tracheliastes polycolpus, an invasive ectoparasite of freshwater fish in western Europe
Marine Genomics 2019, vol. 46
doi: 10.1016/j.margen.2018.12.001

Caroline Belser et al.
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
Nature Plants 2018, vol. 4, issue 11
doi: 10.1038/s41477-018-0289-4

Sara Masachis et al.
FASTBAC-Seq: Functional Analysis of Toxin–Antitoxin Systems in Bacteria by Deep Sequencing
Methods in Enzymology 2018
doi: 10.1016/bs.mie.2018.08.033

Camille Marchet et al.
De novoclustering of long reads by gene from transcriptomics data
Nucleic Acids Research 2018, vol. 47, issue 1
doi: 10.1093/nar/gky834

Hugo Varet et al.
checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes
Bioinformatics 2018, vol. 35, issue 5
doi: 10.1093/bioinformatics/bty706

Bellenguez C. et al.
Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls.
Neurobiol. Aging (2017) Jul. pii: S0197-4580(17)30232-4.
doi: 10.1016/j.neurobiolaging.2017.07.001

Guillem Rigaill et al.
Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis
Briefings in Bioinformatics 2016
doi: 10.1093/bib/bbw092