Andrew D. Yates

Taming the reference genome jungle: the refget sequence collection standard

The paper introduces a standard for unambiguously representing, retrieving, and comparing reference genomes and transcriptomes, revealing inconsistencies across 60 human and 36 mouse references.

A comprehensive AMR genotype-phenotype database (CABBAGE)

The paper introduces CABBAGE, a large-scale AMR genotype-phenotype database linking bacterial genomes to antibiotic susceptibility data and metadata, enabling analysis of resistance trends and predictive method benchmarks.

Development and application of a computable genotype model in the GA4GH Variation Representation Specification

The paper develops and applies a computable genotype model within the GA4GH Variation Representation Specification to enable precise and interoperable representation of genomic variation data.

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

The paper introduces the GA4GH Variation Representation Specification (VRS), a framework for precise and federated representation of molecular variation, with a reference implementation and community resources available online.

The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

The paper presents the eQTL Catalogue, a resource containing uniformly processed eQTLs from 21 studies, enabling integrative analysis and identification of cell-type-specific eQTLs and disease colocalisations.

Refget: standardised access to reference sequences

The paper introduces refget, an API for standardized access to reference sequences using identifiers derived from the sequences themselves.

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.

MuGVRE. A virtual research environment for 3D/4D genomics

MuGVRE provides a cloud-based infrastructure for 3D/4D genomics analysis, supporting both high-computational and high-throughput applications.

Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation

The paper describes the Ensembl Core software infrastructure for storing and accessing genome assemblies and annotations, supporting multiple species and providing APIs for programmatic access.