Publications by authors named "Stephen J Trevanion"

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity.

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Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades.

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Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years.

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The Ensembl Variant Effect Predictor (VEP) is a freely available, open-source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequences using the Ensembl/GENCODE or RefSeq gene sets. It also reports phenotype associations from databases such as ClinVar, allele frequencies from studies including gnomAD, and predictions of deleteriousness from tools such as Sorting Intolerant From Tolerant and Combined Annotation Dependent Depletion.

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Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.

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Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation.

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The COVID-19 pandemic has seen unprecedented use of SARS-CoV-2 genome sequencing for epidemiological tracking and identification of emerging variants. Understanding the potential impact of these variants on the infectivity of the virus and the efficacy of emerging therapeutics and vaccines has become a cornerstone of the fight against the disease. To support the maximal use of genomic information for SARS-CoV-2 research, we launched the Ensembl COVID-19 browser; the first virus to be encompassed within the Ensembl platform.

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Many gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified.

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The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species.

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The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms.

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Article Synopsis
  • Ensembl Genomes is an online resource that offers genome-scale data specifically for non-vertebrate species, complementing the vertebrate data available through the Ensembl project.
  • The resource provides a consistent interface for accessing various genomic data, including genome sequences, gene models, and genetic variations, which is updated four times a year.
  • Recent developments have focused on better organizing orthologues and paralogues, enhancing gene expression data, particularly in plants, and strengthening integration with the Ensembl project to manage the growing amount of genomic data.
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The major goal of sequencing humans and many other species is to understand the link between genomic variation, phenotype and disease. There are numerous valuable and well-established variation resources, but collating and making sense of non-homogeneous, often large-scale data sets from disparate sources remains a challenge. Without a systematic catalogue of these data and appropriate query and annotation tools, understanding the genome sequence of an individual and assessing their disease risk is impossible.

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Article Synopsis
  • The GWAS Catalog is a comprehensive resource for published genome-wide association studies, helping researchers identify disease-related genetic variants and develop new therapies.
  • The Catalog now includes data from targeted and exome arrays, with over 71000 associations from nearly 5700 studies, updating its content to support advanced research.
  • Recent enhancements include a RESTful API for easier data access, an upgraded user interface, and standardized formats for sharing summary statistics, significantly improving usability for the approximately 90,000 users who accessed the site in the last year.
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The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions.

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The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.

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Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes.

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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 and key model organisms.

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Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms.

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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 and farm animals.

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Article Synopsis
  • - The Consensus Coding Sequence (CCDS) project is a collaboration between NCBI, Ensembl, and other institutions to maintain high-quality, consistently annotated datasets of protein-coding regions in human and mouse genomes, identifiable by stable CCDS IDs.
  • - The project undergoes continuous review to ensure accuracy and has recently updated its web and FTP sites with clearer reporting on annotation releases, improved search and display functionalities, and additional biological information.
  • - The document highlights the current status of the CCDS dataset, recent expansions, and plans for future curation priorities to enhance the dataset's reliability and usefulness.
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