Publications
Ali Hamraoui et al.
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Bioinformatics 2025, vol. 41, issue 3
doi: 10.1093/bioinformatics/btaf087
Arthur Monjot et al.
Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes
Microbiome 2025, vol. 13, issue 1
doi: 10.1186/s40168-024-02027-0
Alexandra Cerqueira de Araujo et al.
Genome sequences of four Ixodes species expands understanding of tick evolution
BMC Biology 2025, vol. 23, issue 1
doi: 10.1186/s12915-025-02121-1
Kaj Chokeshaiusaha et al.
Development of a deep learning-based 1D convolutional neural network model for cross-species natural killer T cell identification using peripheral blood mononuclear cell single-cell RNA sequencing data
Veterinary World 2024
doi: 10.14202/vetworld.2024.2846-2857
Anthony F Herzig et al.
SURFBAT: a surrogate family based association test building on large imputation reference panels
G3: Genes, Genomes, Genetics 2024
doi: 10.1093/g3journal/jkae287
Laure Lemée et al.
Check My Sample Sheet: a Web Application for Validating Illumina Sample Sheets Before Demultiplexing
2024
doi: 10.21203/rs.3.rs-5268893/v1
Lisa Mazéas et al.
Candidate genes involved in biosynthesis and degradation of the main extracellular matrix polysaccharides of brown algae and their probable evolutionary history
BMC Genomics 2024, vol. 25, issue 1
doi: 10.1186/s12864-024-10811-3
Ali Hamraoui et al.
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
2024
doi: 10.1101/2024.09.20.613625
Jean Mainguy et al.
metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads
2024
doi: 10.1101/2024.09.13.612854
Marinna Gaudin et al.
Ecological associations distribution modelling of marine plankton at a global scale
Philosophical Transactions of the Royal Society B: Biological Sciences 2024, vol. 379, issue 1909
doi: 10.1098/rstb.2023.0169
Roberta Gargiulo et al.
Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets
Evolutionary Applications 2024, vol. 17, issue 5
doi: 10.1111/eva.13691
Nils Giordano et al.
Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities
Nature Communications 2024, vol. 15, issue 1
doi: 10.1038/s41467-024-46374-w
Téo Lemane et al.
Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA
Nature Computational Science 2024, vol. 4, issue 2
doi: 10.1038/s43588-024-00596-6
Roy El Hourany et al.
Linking satellites to genes with machine learning to estimate phytoplankton community structure from space
Ocean Science 2024, vol. 20, issue 1
doi: 10.5194/os-20-217-2024
Céline Loot et al.
Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites
Nature Microbiology 2024, vol. 9, issue 1
doi: 10.1038/s41564-023-01548-y
Sofia Rigou et al.
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses
Molecular Biology and Evolution 2023, vol. 40, issue 11
doi: 10.1093/molbev/msad244
Fabien Girka et al.
Tensor generalized canonical correlation analysis
Information Fusion 2023, vol. 102
doi: 10.1016/j.inffus.2023.102045
Hiroto Kaneko et al.
Predicting global distributions of eukaryotic plankton communities from satellite data
ISME Communications 2023, vol. 3, issue 1
doi: 10.1038/s43705-023-00308-7
Maryam Karimi et al.
A Case-Only Genome-Wide Interaction Study of Smoking and Bladder Cancer Risk: Results from the COBLAnCE Cohort
Cancers 2023, vol. 15, issue 17
doi: 10.3390/cancers15174218
Angelina Beavogui et al.
The defensome of complex bacterial communities
2023
doi: 10.1101/2023.08.12.553040
Thomas Cokelaer et al.
Reprohackathons: promoting reproducibility in bioinformatics through training
Bioinformatics 2023, vol. 39, issue Supplement_1
doi: 10.1093/bioinformatics/btad227
Gaëlle Munsch et al.
Genome-wide association study of a semicontinuous trait: illustration of the impact of the modeling strategy through the study of Neutrophil Extracellular Traps levels
NAR Genomics and Bioinformatics 2023, vol. 5, issue 2
doi: 10.1093/nargab/lqad062
Lisa Sikkema et al.
An integrated cell atlas of the lung in health and disease
Nature Medicine 2023, vol. 29, issue 6
doi: 10.1038/s41591-023-02327-2
Guillaume Martin et al.
Shared pedigree relationships and transmission of unreduced gametes in cultivated banana
Annals of Botany 2023
doi: 10.1093/aob/mcad065
Ricardo Cortez Cardoso Penha et al.
Common genetic variations in telomere length genes and lung cancer: a Mendelian randomisation study and its novel application in lung tumour transcriptome
eLife 2023, vol. 12
doi: 10.7554/elife.83118
François Lecoquierre et al.
High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders
Human Genetics 2023, vol. 142, issue 6
doi: 10.1007/s00439-023-02553-1
Lény Calvez et al.
Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks
Plants 2023, vol. 12, issue 8
doi: 10.3390/plants12081630
Miriam Riquelme-Perez et al.
DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data
F1000Research 2023, vol. 11
doi: 10.12688/f1000research.122949.2
Sophie Mieszkin et al.
Scleromatobacter humisilvae gen. nov., sp. nov., a novel bacterium isolated from oak forest soil
International Journal of Systematic and Evolutionary Microbiology 2023, vol. 73, issue 3
doi: 10.1099/ijsem.0.005793
Hugo Doré et al.
Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies
The ISME Journal 2023
doi: 10.1038/s41396-023-01386-0