Laboratory of Bioinformatics Analyses for Genomics and Metabolism
Prokaryotes —bacteria and archaea— are diverse, ubiquitous organisms with vast impacts on health, soil, and ocean ecosystems. Large-scale genome sequencing and pangenomics have revealed their molecular diversity, especially the role of Mobile Genetic Elements (MGEs). Pangenomics analyzes genetic variability across
Prokaryotes (i.e. bacteria and archaea) constitute a fascinating field of living organisms, representing remarkable diversity and ubiquity. Their impact on the biosphere is immense, influencing human and animal health, soil and ocean biogeochemistry, and much more. Large-scale exploration of microbial
Abstract The emergence of eukaryotes (eukaryogenesis) is one of the central, extensively debated and yet unanswered questions in biology. It was proposed that informational genes as well as cytoskeleton and membrane remodelling/cell division machineries of eukaryotes have been inherited from
The aim of the DREAM project is to study whether diet, through its impact on the digestive microbiota, can modulate the selection of antibiotic resistance during treatment. Multiple observations suggest that, from one individual to another, the intensity of selective
The aim of this PhD thesis is to achieve new methodological developments for the comparative study of pangenomes. This will involve the development of new bioinformatic methods for inter-pangenome comparisons, which will be particularly based on the developments carried out
PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes.
Abstract The project focuses on a poorly known carbon-sequestering environmental process by a group of diverse bacteria forming intracellular carbonates, occurring at oxic/anoxic boundaries (OAB) in aquatic environments. The molecular and geochemical processes of bacterial biomineralization will be studied by
Abstract The project aims to decipher the biodiversity, ecology and evolution of a group of unicellular eukaryotes ubiquitous in marine anoxic sediments that sense the Earth’s magnetic field thanks to their symbiotic bacteria. This exploration will be done with a combination of
Description Contexte scientifique : Les Thermococcales sont un ordre d’archées anaérobies et hyperthermophiles, qui vivent au niveau des cheminées océaniques hydrothermales et au niveau de sources chaudes terrestres à pH neutre 1–3. Elles sont utilisées comme organisme modèle pour l’étude
Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of Genome Plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to Genomic Islands (GIs).
Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria An international consortium coordinated by the Marine Glycobiology team (UMR8227 – CNRS/UPMC) has just published the discovery of the complete system for the utilization of carrageenans, sulfated
In order to extend the range of tools available to MicroScope users, we aim to develop the platform functionalities dedicated prediction, annotation and exploration of genomic regions. These genomic regions include specialized gene clusters (ie, encoding for secretion systems, CRISPR
Cyanobacteria are an ancient lineage of photosynthetic bacteria, which are prolific producers of secondary metabolites. Hundreds of bioactive compounds with diverse chemical structures , such as toxins and molecules of pharmaceutical interest, have been characterized from cyanobacteria.
Prokaryotes —bacteria and archaea— are diverse, ubiquitous organisms with vast impacts on health, soil, and ocean ecosystems. Large-scale genome sequencing and pangenomics have revealed their molecular diversity, especially the role of Mobile Genetic Elements (MGEs). Pangenomics analyzes genetic variability across
Localisé au CEA/Genoscope, un centre de recherche scientifique dédié à la génomique environnementale, le Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme (LABGeM, UMR8030, labgem.genoscope.cns.fr) s’intéresse à l’analyse et à l’exploration de la diversité des microorganismes et de leur