Stéfan Engelen
A5002907739- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Genetic and phenotypic traits in livestock
- RNA modifications and cancer
- Genetic diversity and population structure
- Protist diversity and phylogeny
- Plant Disease Resistance and Genetics
- Environmental DNA in Biodiversity Studies
- Advanced biosensing and bioanalysis techniques
- Coral and Marine Ecosystems Studies
- Plant Virus Research Studies
- Genetic Mapping and Diversity in Plants and Animals
- Machine Learning in Bioinformatics
- Banana Cultivation and Research
- Plant tissue culture and regeneration
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- DNA Repair Mechanisms
- Yeasts and Rust Fungi Studies
- Plant Pathogenic Bacteria Studies
- Wildlife Ecology and Conservation
- Cancer Genomics and Diagnostics
- Biosensors and Analytical Detection
Université Paris-Saclay
2018-2025
Genoscope
2016-2025
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2015-2024
CEA Paris-Saclay
2018-2024
Centre National de la Recherche Scientifique
2009-2024
Direction de la Recherche Fondamentale
2020-2024
CEA Paris-Saclay - Etablissement de Fontenay-aux-roses
2024
Université d'Évry Val-d'Essonne
2007-2019
Centre National de Recherche en Génomique Humaine
2014
Génomique Métabolique du Genoscope
2012
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture functional diversity, microbial community structure, and their ecological determinants remains grand challenge. We analyzed 7.2 terabases metagenomic data from 243 Tara Oceans samples 68 locations in epipelagic mesopelagic waters across the globe to generate an ocean reference gene catalog with >40 million nonredundant, mostly novel sequences viruses, prokaryotes, picoeukaryotes. Using 139...
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted not accounted for the full range size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone communities collected across tropical temperate oceans during circumglobal Tara Oceans expedition. analyzed 18S ribosomal DNA sequences intermediate plankton-size spectrum smallest unicellular eukaryotes (protists, >0.8 micrometers) to small...
Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report whole-genome sequencing and phenotyping 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture variants that shape species-wide landscape this yeast. Genomic analyses support a single ‘out-of-China’ origin for species, followed by several independent domestication events. Although domesticated isolates exhibit high variation...
MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and comparative analysis. The resource provides data from completed ongoing projects (automatic expert annotations), together with sources post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users perfect improve understanding gene functions. (http://www.genoscope.cns.fr/agc/microscope) combines tools graphical interfaces analyse genomes perform manual...
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic genomic compositions, little is known about how transcriptomes vary globally. Here, we present a dataset 187 metatranscriptomes 370 metagenomes from 126 globally distributed sampling stations establish resource 47 million genes to study community-level across depth layers pole-to-pole. We examine gene expression changes community...
While our knowledge about the roles of microbes and viruses in ocean has increased tremendously due to recent advances genomics metagenomics, research on marine microbial eukaryotes zooplankton benefited much less from these new technologies because their larger genomes, enormous diversity, largely unexplored physiologies. Here, we use a metatranscriptomics approach capture expressed genes open Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster...
The initial outcome of genome sequencing is the creation long text strings written in a four letter alphabet. role silico sequence analysis to assist biologists act associating biological knowledge with these sequences, allowing investigators make inferences and predictions that can be tested experimentally. A wide variety software available scientific community, used identify genomic objects, before predicting their functions. However, only limited number biologically interesting features...
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as domestic species become genome-enabled. Before established worldwide, sheep goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence genomes Asiatic mouflon Bezoar ibex goat center compare with that domestics from local, traditional, improved breeds. Among genomic regions carrying...
Long-read sequencing technologies were launched a few years ago, and in contrast with short-read technologies, they offered promise of solving assembly problems for large complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read still have several limitations that complicate their use most research laboratories, as well and/or genome projects. In 2014, Oxford Nanopore released the MinION® device, small low-cost...
Abstract A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks recent advances in field genomics, extensive sequencing has been performed for a deep genomic analysis this huge samples. strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics metatranscriptomics, chosen size-fractionated...
Transposable elements (TEs) are mobile parasitic sequences that have been repeatedly coopted during evolution to generate new functions and rewire gene regulatory networks. Yet, the contribution of active TEs creation heritable mutations remains unknown. Using TE accumulation lines in Arabidopsis thaliana we show once initiated, transposition produces an exponential spread copies, which rapidly leads high mutation rates. Most insertions occur near or within genes targets differ between...
Abstract Background: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from genomes in matter seconds. The technology is truly disruptive; it has potential to revolutionize genomic applications due its portability, low cost, and ease use compared with existing reads technologies. MinION sequencer enables rapid eukaryotic genomes, such as yeast genome....
The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access the gene catalogue given species but also reveals architecture organization chromosomes, including complex regions such telomeres centromeres. Brassica genus exempt, many based on are available. reference for napus, Darmor-bzh, which was published in 2014, produced using short its contiguity extremely low compared with current genus....
Abstract Background The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining reference cultivar Chinese Spring have launched in past it was achieved 2018 as result huge effort combine short-read with other resources. Reference-quality assemblies were then produced accessions, but rapid evolution technologies offers opportunities reach...
Since the time of their domestication, goats (Capra hircus) have evolved in a large variety locally adapted populations response to different human and environmental pressures. In present era, many indigenous are threatened with extinction due substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial characterize neutral adaptive genetic diversity populations. A fine characterization whole genome variation farm animals now possible...
Abstract Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased intermediates from Saccharomyces cerevisiae , orient 58,651 tracks reproducing population-based directionality profiles and 4964 4485 individual initiation termination events, respectively. Although most events cluster...
Abstract Little is known about replication fork velocity variations along eukaryotic genomes, since reference techniques to determine speed either provide no sequence information or suffer from low throughput. Here we present NanoForkSpeed, a nanopore sequencing-based method map and extract the of individual forks detected as tracks thymidine analogue bromodeoxyuridine incorporated during brief pulse-labelling asynchronously growing cells. NanoForkSpeed retrieves previous Saccharomyces...
Abstract Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience devise strategies slow loss resulting from environmental stresses. Key are symbiotic interactions established within complex holobiont, i.e . multipartite assemblages comprising host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, viruses. Tara Pacific an ambitious project built upon experience of previous Oceans expeditions, leveraging...
The Joint Evolutionary Trees (JET) method detects protein interfaces, the core residues involved in folding process, and susceptible to site-directed mutagenesis relevant molecular recognition. approach, based on Trace (ET) method, introduces a novel way treat evolutionary information. Families of homologous sequences are analyzed through Gibbs-like sampling distance trees reduce effects erroneous multiple alignment impacts weakly tree construction. makes sequence analysis more sensitive...
Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities. However, to cope with the challenges environmental sampling, various rRNA removal cDNA synthesis methods have been applied published metatranscriptomic studies, making comparisons arduous. Whereas efficiency biases introduced by relatively well explored, impact library preparation on transcript abundance remains poorly characterized. The evaluation...
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, goal was assess the efficiency several SNP genotyping strategies by testing their accurately estimate parameters describing neutral diversity detect signatures selection. We analysed 110 at 12× coverage four different...
Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed understand the consequences on diversity domestic goats elucidate how speciation hybridization modeled genomes set species representative genus Capra.A dataset comprising 652 sequenced 507 public sequences, including 35 animals representing...
Nanopore adaptive sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Here we designed and validated an experiment to enrich set of resistance genes several melon cultivars as proof concept. Using the same reference guide read acceptance or rejection with NAS, successfully accurately reconstructed 15 regions two newly assembled ssp. melo genomes third agrestis cultivar. We obtained fourfold enrichment regardless tested samples, but some...