Thibaut Hourlier
A5040491901- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- MicroRNA in disease regulation
- Genetic Mapping and Diversity in Plants and Animals
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- Genetic and phenotypic traits in livestock
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- CRISPR and Genetic Engineering
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Fish Biology and Ecology Studies
- Genomic variations and chromosomal abnormalities
- Genetic diversity and population structure
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Biomedical Text Mining and Ontologies
- Fish Ecology and Management Studies
- Livestock Farming and Management
- Pregnancy and preeclampsia studies
- Genetic factors in colorectal cancer
- Birth, Development, and Health
European Bioinformatics Institute
2015-2024
Wellcome Sanger Institute
2010-2016
Wellcome Trust
2014
Centre National de la Recherche Scientifique
2012
Laboratoire des Interactions Plantes Micro-Organismes
2011-2012
The accurate identification and description of the genes in human mouse genomes is a fundamental requirement for high quality analysis data informing both genome biology clinical genomics. Over last 15 years, GENCODE consortium has been producing reference gene annotations to provide this foundational resource. includes experimental computational groups who work together improve extend annotation. Specifically, we generate primary data, create bioinformatics tools support expert manual...
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...
Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed efficiently deliver annotation at scale all eukaryotic life, it also provides deep comprehensive key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the new assemblies. Here, report release greatest annual number newly annotated genomes history...
Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed comprehensive annotation of gene structures, regulatory elements variants, enable comparative genomics by inferring the evolutionary history genes genomes. Our integrated are made available in a variety ways, including genome browsers, search interfaces, specialist tools such as Variant Effect Predictor, download files programmatic interfaces....
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 gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based for human and mouse GENCODE sets. is based on alignment biological sequences, including cDNAs, proteins RNA-seq reads, target in order construct candidate transcript models. Careful assessment filtering these transcripts ultimately leads final set, which made available website. Here, we describe...
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 GENCODE project annotates human and mouse genes transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology clinical genomics. annotation processes make use of primary bioinformatic tools analysis generated both within the consortium externally to support creation transcript structures determination their function. Here, we present improvements our infrastructure, bioinformatics tools, analysis, advances they in...
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand molecular mechanisms underlying cichlid phenotypic diversity, we sequenced genomes transcriptomes five lineages African cichlids: Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; four members lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent Malawi), Pundamilia nyererei (very recent...
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 (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms more than twenty years. During that time, our resources, services tools have continually evolved in line with both the publicly available genome data downstream research applications utilise platform. In recent years we witnessed a dramatic shift landscape. There been large increase number of reference genomes through global biodiversity initiatives. parallel, there major...
The Ensembl project ( http://www.ensembl.org ) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations set of includes additional data focused variation, comparative, evolutionary, functional regulatory annotation. most advanced resources are provided for key including human, mouse, rat zebrafish...
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
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...
Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form wool represent distinct class animals that have specialized digestive organ, rumen, carries out initial digestion plant material. We developed analyzed high-quality reference sheep genome transcriptomes from 40 different tissues. identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. also involved lipid metabolism had been amplified and/or altered tissue expression...
GENCODE produces high quality gene and transcript annotation for the human mouse genomes. All is supported by experimental data serves as a reference genome biology clinical genomics. The consortium generates targeted data, develops bioinformatic tools carries out analyses that, along with externally produced methods, support identification of structures determination their function. Here, we present an update on genes, including developments in tools, major collaborations which underpin...
We have produced an mRNA expression time course of zebrafish development across 18 points from 1 cell to 5 days post-fertilisation sampling individual and pools embryos. Using poly(A) pulldown stranded RNA-seq a 3′ end transcript counting method we characterise temporal profiles 23,642 genes. identify functional co-variance that associates 5024 unnamed genes with distinct developmental points. Specifically, class over 100 previously uncharacterised zinc finger domain containing genes,...
Abstract Background The domestic pig (Sus scrofa) is important both as a food source and biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, pharmacology to humans. draft reference genome (Sscrofa10.2) of purebred Duroc female established using older clone-based sequencing methods was incomplete, unresolved redundancies, short-range order orientation errors, associated misassembled genes limited utility. Results We present 2 annotated highly contiguous...
Abstract Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates model organisms more than two decades. In recent years, there been dramatic shift in the landscape, with large increase number phylogenetic breadth of reference genomes, alongside major advances pan-genome representations higher species. order to support these efforts accelerate downstream research, continues focus on scaling rapid...