Publications
Bertrand Theulot et al.
Genome-wide mapping of individual replication fork velocities using nanopore sequencing
Nature Communications 2022, vol. 13, issue 1
doi: 10.1038/s41467-022-31012-0
Juan José Pierella Karlusich et al.
Coupling Imaging and Omics in Plankton Surveys: State-of-the-Art, Challenges, and Future Directions
Frontiers in Marine Science 2022, vol. 9
doi: 10.3389/fmars.2022.878803
Maëlle Daunesse et al.
ePeak: from replicated chromatin profiling data to epigenomic dynamics
NAR Genomics and Bioinformatics 2022, vol. 4, issue 2
doi: 10.1093/nargab/lqac041
Maxime Wack et al.
viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome
Studies in Health Technology and Informatics 2022
doi: 10.3233/shti220602
Rémi Tournebize et al.
Ecological and genomic vulnerability to climate change across native populations of Robusta coffee ( Coffea canephora )
Global Change Biology 2022, vol. 28, issue 13
doi: 10.1111/gcb.16191
Quentin Piet et al.
A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly
Plant Communications 2022, vol. 3, issue 5
doi: 10.1016/j.xplc.2022.100330
Stefano Gnan et al.
Kronos scRT: a uniform framework for single-cell replication timing analysis
Nature Communications 2022, vol. 13, issue 1
doi: 10.1038/s41467-022-30043-x
Antoine Régimbeau et al.
Contribution of genome‐scale metabolic modelling to niche theory
Ecology Letters 2022
doi: 10.1111/ele.13954
Théophile Grébert et al.
Diversity and Evolution of Pigment Types in MarineSynechococcusCyanobacteria
Genome Biology and Evolution 2022, vol. 14, issue 4
doi: 10.1093/gbe/evac035
C. M. Singleton et al.
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide
The ISME Journal 2022
doi: 10.1038/s41396-022-01212-z
Charles Pouchon et al.
ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications
Molecular Ecology Resources 2022
doi: 10.1111/1755-0998.13584
Dounia Saleh et al.
Genome‐wide evolutionary response of European oaks during the Anthropocene
Evolution Letters 2022, vol. 6, issue 1
doi: 10.1002/evl3.269
Ali Janbain et al.
TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules
NAR Genomics and Bioinformatics 2021, vol. 3, issue 4
doi: 10.1093/nargab/lqab103
Juliette Coursimault et al.
MYT1L-associated neurodevelopmental disorder: description of 40 new cases and literature review of clinical and molecular aspects
Human Genetics 2021, vol. 141, issue 1
doi: 10.1007/s00439-021-02383-z
Nathalie Lehmann et al.
Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses
2021
doi: 10.1101/2021.10.13.464219
Nathalie Lehmann et al.
Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses
2021
doi: 10.1101/2021.10.13.464219
Charles-Elie Rabier et al.
On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo
PLOS Computational Biology 2021, vol. 17, issue 9
doi: 10.1371/journal.pcbi.1008380
Manoela C. Brandão et al.
Macroscale patterns of oceanic zooplankton composition and size structure
Scientific Reports 2021, vol. 11, issue 1
doi: 10.1038/s41598-021-94615-5
Benjamin Istace et al.
Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case
Biology 2021, vol. 10, issue 8
doi: 10.3390/biology10080732
Julien Vibert et al.
Identification of Tissue of Origin and Guided Therapeutic Applications in Cancers of Unknown Primary Using Deep Learning and RNA Sequencing (TransCUPtomics)
The Journal of Molecular Diagnostics 2021, vol. 23, issue 10
doi: 10.1016/j.jmoldx.2021.07.009
Julien Vibert et al.
Identification of Tissue of Origin and Guided Therapeutic Applications in Cancers of Unknown Primary Using Deep Learning and RNA Sequencing (TransCUPtomics)
The Journal of Molecular Diagnostics 2021, vol. 23, issue 10
doi: 10.1016/j.jmoldx.2021.07.009
Sébastien Riquier et al.
Long non-coding RNA exploration for mesenchymal stem cell characterisation
BMC Genomics 2021, vol. 22, issue 1
doi: 10.1186/s12864-020-07289-0
Miriam I. Brandt et al.
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding
Molecular Ecology Resources 2021
doi: 10.1111/1755-0998.13398
Léa Meunier et al.
DNA Methylation Signatures Reveal the Diversity of Processes Remodeling Hepatocellular Carcinoma Methylomes
Hepatology 2021, vol. 74, issue 2
doi: 10.1002/hep.31796
Caroline Vernette et al.
The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms
Molecular Ecology Resources 2021, vol. 21, issue 4
doi: 10.1111/1755-0998.13322
Alexis Hardy et al.
DNAModAnnot: a R toolbox for DNA modification filtering and annotation
Bioinformatics 2021, vol. 37, issue 17
doi: 10.1093/bioinformatics/btab032
Ozvan Bocher et al.
Extension of SKAT to multi-category phenotypes through a geometrical interpretation
European Journal of Human Genetics 2021 vol.29
doi: 10.1038/s41431-020-00792-8
Dimitra Sakoula et al.
Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification
The ISME Journal 2020
doi: 10.1038/s41396-020-00827-4
Agnès Barbance et al.
Genetic Analysis of Citrobacter sp.86 Reveals Involvement of Corrinoids in Chlordecone and Lindane Biotransformations
Frontiers in Microbiology 2020, vol. 11
doi: 10.3389/fmicb.2020.590061
Benjamin Istace et al.
BiSCoT: improving large eukaryotic genome assemblies with optical maps
PeerJ 2020, vol. 8
doi: 10.7717/peerj.10150