Laurent Gil
A5078770916- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Metabolomics and Mass Spectrometry Studies
- Nutrition, Genetics, and Disease
- Genomic variations and chromosomal abnormalities
- RNA and protein synthesis mechanisms
- Biomedical Text Mining and Ontologies
- Antioxidant Activity and Oxidative Stress
- Genetic Syndromes and Imprinting
- Rural development and sustainability
- Genetic Mapping and Diversity in Plants and Animals
- Research Data Management Practices
- Ginseng Biological Effects and Applications
- Digestive system and related health
- Race, Genetics, and Society
- Chromosomal and Genetic Variations
- Congenital heart defects research
- Molecular Biology Techniques and Applications
- Social Capital and Networks
Wellcome Sanger Institute
2011-2024
Health Data Research UK
2020-2024
University of Cambridge
2020-2024
European Bioinformatics Institute
2011-2022
British Heart Foundation
2020-2021
Wellcome Trust
2013-2014
National Center for Biotechnology Information
2013
University of Leicester
2013
Université de Bordeaux
2009-2011
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing diverse individuals from multiple populations. Here we report completion the project, having reconstructed genomes 2,504 26 populations using combination low-coverage sequencing, deep exome and dense microarray genotyping. We characterized broad spectrum variation, in total over 88 million variants (84.7 single nucleotide polymorphisms (SNPs), 3.6...
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding non-coding regions. It provides access to an extensive collection with variety interfaces suit different requirements, simple options configuring extending analysis. open source, free use, supports full reproducibility results. can simplify accelerate variant interpretation wide range study designs.
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of draft human genome, with aim accelerating genomics research through rapid open distribution public data. Large amounts raw data are thus transformed into knowledge, which is made available via a multitude channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded multiple directions. First, resources describe fields genomics, gene...
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. new infrastructure includes a graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality an improved curation interface. These developments have release frequency by increasing automation of providing scaling improvements. range available also been extended with structured ancestry recruitment...
The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates key model organisms. It provides data 87 species across our main early Pre! websites. This year we introduced three newly annotated released numerous updates supported with concentration on latest assemblies human, mouse, zebrafish rat. We also provided two previous human assembly, GRCh37, through dedicated...
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms farm animals. Over the past year we have increased number of that support 77 expanded our genome browser a new scrollable overview improved variation phenotype views. We also report updates core datasets improvements gene homology relationships from addition species. Our REST service has been extended additional for...
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions variation) on new human assembly, GRCh38, although continue to support researchers using GRCh37.p13 assembly through dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped identify of interest...
The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation comparative genomics across the vertebrate subphylum key model organisms. pipeline capable of integrating experimental reference data from multiple providers into single integrated resource. Here, we present 94 newly annotated re-annotated genomes, bringing total number genomes offered by to 227. This represents largest expansion resource since its...
Abstract The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare industry. contains variant-trait associations supporting metadata for >45 published across >5000 human traits, >40 full P-value summary statistics datasets. Content curated publications or acquired via author submission...
The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. seeks be a fundamental resource driving progress by creating, maintaining and updating reference genome annotation comparative genomics resources. This year we describe our new expanded gene, variant capabilities, which led 50% increase in number of vertebrate genomes support. We have also doubled human variants added regulatory regions for many mouse...
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets all supported species; large-scale whole multiple species alignments across vertebrates clade-specific eutherian mammals, primates, birds fish; variation data 17 regulation annotations based ENCODE other sets. are accessible through the browser at http://www.ensembl.org tools...
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human data as well key model organisms such mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) Tasmanian devil (Sarcophilus harrisii) bringing total number of supported to 61 release 64 (September 2011). Of these, 55 appear main website six are provided preview site (Pre!Ensembl; http://pre.ensembl.org)...
Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate integrate diverse collection of large-scale reference data to create more comprehensive view biology than would be possible from any individual dataset. Our extensive resources include evidence-based gene regulatory region annotation, variation trees. An accompanying suite tools, infrastructure programmatic access methods ensure uniform analysis distribution all...
The major goal of sequencing humans and many other species is to understand the link between genomic variation, phenotype disease. There are numerous valuable well-established variation resources, but collating making sense non-homogeneous, often large-scale data sets from disparate sources remains a challenge. Without systematic catalogue these appropriate query annotation tools, understanding genome sequence an individual assessing their disease risk impossible. In Ensembl, we...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in context of project (http://www.ensembl.org). Together, two provide a consistent set interfaces to genomic across tree life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform...
ABSTRACT The Ensembl Variant Effect Predictor (VEP) is a powerful toolset for the analysis, annotation and prioritization of genomic variants, including in non-coding regions. VEP accurately predicts effects sequence variants on transcripts, protein products, regulatory regions binding motifs by leveraging high quality, broad scope, integrated nature databases. In addition, it enables comparison with large collection existing publicly available variation data within to provide insights into...
Abstract Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, absence a standard for clinical reporting and browser display complicates process consistent interpretation reporting. To address these challenges, Ensembl/GENCODE 1 RefSeq 2 launched joint initiative, Matched Annotation from NCBI EMBL-EBI (MANE) collaboration, converge on human gene transcript jointly define high-value set transcripts corresponding proteins. Here, we...
Abstract Polygenic scores (PGS) have transformed human genetic research and multiple potential clinical applications, including risk stratification for disease prevention prediction of treatment response. Here, we present a series recent enhancements to the PGS Catalog ( www.PGSCatalog.org ), largest findable, accessible, interoperable, reusable (FAIR) repository PGS. These include expansions in data content ancestral diversity as well addition new features. We further Calculator pgsc_calc ,...
Locus Reference Genomic (LRG; http://www.lrg-sequence.org/) records contain internationally recognized stable reference sequences designed specifically for reporting clinically relevant sequence variants. Each LRG is contained within a single file consisting of 'fixed' section and regularly updated 'updatable' section. The fixed contains genomic DNA region, essential transcripts proteins variant an exon numbering system. updatable mapping information, annotation all overlapping genes in the...
Abstract Background Improvements in the techniques for metabolomics analyses and growing interest metabolomic approaches are resulting generation of increasing numbers profiles. Platforms required profile management, as a function experimental design, metabolite identification, to facilitate mining corresponding data. Various databases have been created, including organism-specific knowledgebases analytical technique-specific spectral databases. However, there is currently no platform...
Polygenic [risk] scores (PGS) can enhance prediction and understanding of common diseases traits. However, the reproducibility PGS their subsequent applications in biological clinical research have been hindered by several factors, including: inadequate incomplete reporting development, heterogeneity evaluation techniques, inconsistent access to, distribution of, information necessary to calculate themselves. To address this we present Catalog (www.PGSCatalog.org), an open resource for...