Publications
Mallek Mziou-Sallami et al.
GNNenrich: a novel method for pathway enrichment analysis based on graph neural network
Bioinformatics 2025, vol. 41, issue 9
doi: 10.1093/bioinformatics/btaf478
Julie Bavais et al.
SciGeneX: enhancing transcriptional analysis through gene module detection in single-cell and spatial transcriptomics data
NAR Genomics and Bioinformatics 2025, vol. 7, issue 2
doi: 10.1093/nargab/lqaf043
Hugo Caro et al.
BioConvert: a comprehensive format converter for life sciences
NAR Genomics and Bioinformatics 2023, vol. 5, issue 3
doi: 10.1093/nargab/lqad074
Thomas Desvignes et al.
FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes
Molecular Biology and Evolution 2022, vol. 39, issue 2
doi: 10.1093/molbev/msac004
Andrea Di Gioacchino et al.
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
RNA 2021, vol. 28, issue 3
doi: 10.1261/rna.078969.121
Juan José Pierella Karlusich et al.
Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods
Nature Communications 2021, vol. 12, issue 1
doi: 10.1038/s41467-021-24299-y
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
Lucile Broseus et al.
TALC: Transcript-level Aware Long-read Correction
Bioinformatics 2020, vol. 36, issue 20
doi: 10.1093/bioinformatics/btaa634
Yousra Ben Zouari et al.
4See: A Flexible Browser to Explore 4C Data
Frontiers in Genetics 2020, vol. 10
doi: 10.3389/fgene.2019.01372
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
Mathias Lorieux et al.
NOISYmputer: genotype imputation in bi-parental populations for noisy low-coverage next-generation sequencing data
2019
doi: 10.1101/658237
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
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
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
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
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
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
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
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
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