A5021690242- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Cell Image Analysis Techniques
- Gut microbiota and health
- COVID-19 and Mental Health
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Psychological Well-being and Life Satisfaction
- Mental Health Research Topics
- CRISPR and Genetic Engineering
- COVID-19 epidemiological studies
- Microbial Community Ecology and Physiology
- Advanced biosensing and bioanalysis techniques
- Bacteriophages and microbial interactions
- Plant Disease Resistance and Genetics
- Yeasts and Rust Fungi Studies
- Artificial Intelligence in Healthcare
- Plant Pathogens and Fungal Diseases
- Quantum-Dot Cellular Automata
- Bacterial Genetics and Biotechnology
- Agriculture and Rural Development Research
- Behavioral Health and Interventions
- Scientific Computing and Data Management
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2023-2025
Université Paris-Saclay
2019-2025
Mathématiques et Informatique Appliquées du Génome à l'Environnement
2023-2024
Laboratoire d'Analyses Génétiques pour les Espèces Animales
2023-2024
Centre National de la Recherche Scientifique
2019-2020
Genoscope
2019-2020
CEA Paris-Saclay
2019-2020
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2016-2020
Infectious Disease Models and Innovative Therapies
2016-2017
Inserm
2016-2017
Abstract Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount new information that completely transforms our understanding thousands microbial species. However, despite development powerful bioinformatics approaches, full interpretation content these genomes remains difficult task. Launched in 2005, MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous provides analysis for prokaryotic...
The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms occurrence a given species. These usually lack multivariate statistical models infer the partitions optimal number classes don't account genome organization. We introduce graph structure model pangenomes which nodes represent edges genomic neighborhood. Our method, named PPanGGOLiN, using an Expectation-Maximization algorithm based on Bernoulli Mixture...
The COVIDiSTRESS global survey collects data on early human responses to the 2020 COVID-19 pandemic from 173 429 respondents in 48 countries. open science study was co-designed by an international consortium of researchers investigate how psychological differ across countries and cultures, this has impacted behaviour, coping trust government efforts slow spread virus. Starting March 2020, leveraged convenience unpaid online recruitment generate public data. objective present analysis is...
Abstract This N = 173,426 social science dataset was collected through the collaborative COVIDiSTRESS Global Survey – an open effort to improve understanding of human experiences 2020 COVID-19 pandemic between 30th March and May, 2020. The allows a cross-cultural study psychological behavioural responses Coronavirus associated government measures like cancellation public functions stay at home orders implemented in many countries. contains demographic background variables as well Asian...
The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance thousands stored in public databanks. MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is integrative resource supports systematic and efficient revision microbial annotation, data management comparative analysis. Starting from results our syntactic, functional relational pipelines, provides integrated...
Metagenomic sequencing provides profound insights into microbial communities, but it is often compromised by technical biases, including cross-sample contamination. This underexplored phenomenon arises when content inadvertently exchanged among concurrently processed samples. Such contamination that distort profiles, poses significant risks to the reliability of metagenomic data and downstream analyses. Despite its critical impact, this issue remains insufficiently addressed. To fill gap, we...
Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions genome plasticity (RGPs) are clusters genes located highly variable genomic regions. Most them arise from HGT and correspond to islands (GIs). The study those regions at the species level has become increasingly difficult with data deluge To date, no methods available identify GIs using hundreds genomes explore their diversity. Results We present here panRGP method that...
Flow, hyperspectral and mass cytometry are experimental techniques measuring cell marker expressions at the single level. The recent increase of number markers simultaneously measurable has led to development new automatic gating algorithms. Especially, SPADE algorithm been proposed as a novel way identify clusters cells having similar phenotypes in high-dimensional data. While or other clustering algorithms powerful approaches, complementary analysis features needed better characterize...
Cytometry is an experimental technique used to measure molecules expressed by cells at a single cell resolution. Recently, several technological improvements have made possible increase greatly the number of markers that can be simultaneously measured. Many computational methods been proposed identify clusters having similar phenotypes. Nevertheless, only limited permits compare phenotypes identified different clustering approaches. These phenotypic comparisons are necessary choose...
This N=173,426 social science dataset was collected through the collaborative COVIDiSTRESS Global Survey – an open effort to improve understandings of human experiences 2020 COVID-19 pandemic between 30th March and May, 2020. The allows a cross-cultural study psychological behavioural responses Coronavirus associated government measures like cancellation public functions stay at home orders implemented in many countries. contains demographic background variables as well perceived stress...
Abstract The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms occurrence a given species. These usually lack multivariate statistical models infer the partitions optimal number classes don’t account genome organization. We introduce graph structure model pangenomes which nodes represent edges genomic neighborhood. Our method, named PPanGGOLiN, using an Expectation-Maximization algorithm based on...
Graph databases are increasingly used to handle complex data pipelines, in which interconnected is exploited for visualization and analytics. We propose a novel method, PanGraph-DB, performing inter-pangenomic analysis within graph database. As case study, we focus on the antibiotic resistance sequenced genomes. Over past decade, volumes of genomic stored public have grown exponentially, point hindering comparative genomics algorithms. show that, due nature data, enable accurate metadata...
Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions Genome Plasticity (RGPs) are clusters genes located highly variable genomic regions. Most them arise from HGT and correspond to Genomic Islands (GIs). The study those regions at the species level has become increasingly difficult with data deluge To date no methods available identify GIs using hundreds genomes explore their diversity. Results We present here panRGP method that...
Motivation Flow, hyperspectral and mass cytometry are experimental techniques measuring cell marker expressions at the single level. The recent increase of number markers simultaneously measurable has led to development new automatic gating algorithms. Especially, SPADE algorithm been proposed as a novel way identify clusters cells having similar phenotypes in high-dimensional data. While or other clustering algorithms powerful approaches, complementary analysis features needed better...