European Bioinformatics Institute

ERGA-BGE genome of Valencia hispanica (Valenciennes, 1826): a critically endangered Iberian toothcarp

The reference genome of Valencia hispanica , a critically endangered actinopterygian species endemic to the Iberian Peninsula, is key to unravelling its genetic architecture and adaptation to freshwater ecosystems. This genomic resource will enable targeted conservation efforts a...

Federated EGA in the European and Global Human Data Ecosystem

This Federated EGA in the European and Global Human Data Ecosystem white paper sets out our vision for the future role of Federated EGA (FEGA) in supporting secure, responsible and FAIR reuse of controlled-access human data. It describes how FEGA has developed into an operational...

SpaCEy links spatial tissue patterns to clinical outcomes using explainable graph neural networks

Abstract Tissues are complex ecosystems organised in space, and alterations in this organisation underpin multiple diseases. Spatial omics enables molecular profiling of tissue organisation, but linking these patterns to clinical outcomes remains challenging. We present SpaCEy (...

The Onychomys pangenome reveals the unique molecular adaptations that confer toxin resistance

Abstract Background Predatory grasshopper mice ( Onychomys sp.) have co-evolved resistance to painful and lethal neurotoxins produced by their scorpion prey. Previous studies have reported that structural and functional modifications of the sodium channel Nav1.8 block the effect...

Deciphering the genomic signatures of climate vulnerability across 77 sheep breeds

Abstract Among domesticated species, sheep ( Ovis aries ) have achieved a wide geographic distribution due to their mobility, rusticity and ability to adapt to diverse environments and climatic conditions. Here, we characterise the genome-wide diversity of >1,000 sheep representi...

Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa

Abstract Streptococcus pneumoniae is highly diverse, comprising over 100 serotypes and hundreds of genomic lineages amid widespread vaccination. While it can cause invasive pneumococcal disease (IPD) which exhibits pronounced seasonal spikes, the interplay between pneumococcal di...

Extensive and differential platinum chemotherapy mutagenesis in livers of children

Childhood cancer survivors often experience late adverse effects that may be linked to chemotherapy mutagenesis. We studied chemotherapy mutagenesis in normal pediatric tissues using duplex sequencing (NanoSeq) to enable the detection of mutations from single DNA molecules. We fo...

α-Latrotoxin and Pain: A Nociceptor Perspective on Latrodectism

Alpha-latrotoxin (α-LTX) is the principal vertebrate-specific neurotoxin in widow spider (Latrodectus) venom and a powerful presynaptic secretagogue. Although its receptors, pore-forming activity and stimulation of neurotransmitter release have been studied extensively in central...

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions

Abstract Background The human pathogen Streptococcus pneumoniae is a major cause of disease, including pneumonia and meningitis. The introduction of Pneumococcal Conjugate Vaccines (PCVs) initially reduced the burden of disease through a reduction of colonisation by vaccine-targe...

Programmatic access to ICTV virus taxonomy through a public ontology API

Abstract Background The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespre...

Order–disorder interfaces in viral pRb inactivation: molecular dynamics insights into SLiM-mediated recognition and implications for interaction databases

Intrinsically disordered regions (IDRs) mediate protein interactions through poorly understood mechanisms. We studied the retinoblastoma protein (pRb) and its interaction with the SV40 Large T antigen (LTSV40), a viral oncoprotein that displaces E2F factors. Using molecular dynam...

Order–disorder interfaces in viral pRb inactivation: molecular dynamics insights into SLiM-mediated recognition and implications for interaction databases

Intrinsically disordered regions (IDRs) mediate protein interactions through poorly understood mechanisms. We studied the retinoblastoma protein (pRb) and its interaction with the SV40 Large T antigen (LTSV40), a viral oncoprotein that displaces E2F factors. Using molecular dynam...

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcriptomics, delineating higher-order anatomical structures is critical for understand...

Paediatric therapeutic development workshop on osteosarcoma

The fourth Paediatric Therapeutic Development Workshop focused on osteosarcoma, the most common primary bone cancer in children and young adults. Current treatment of osteosarcoma comprises surgery and chemotherapy. Outcome has shown very little improvement over the last four dec...

Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz

ABSTRACT With the growing number of metabolomics and lipidomics studies, robust strategies for bioinformatic analyses are increasingly important. However, the absence of standardized and reproducible workflows, coupled with ambiguous metabolite annotations, hampers effective anal...

A compendium of next-generation patient-derived models for diverse cancers

Abstract The development of new therapeutics and the validation of pathogenetic cancer mechanisms require representative laboratory models 1,2 . However, existing collections represent only a fraction of the diversity observed in human cancer 2–4 . Recent technologies have enable...

EFECT enables reliable and reproducible stochastic simulations across disciplines

Stochastic simulations underpin computational research in fields from systems biology and epidemiology to finance and physics-informed machine learning, yet their reproducibility is hard to quantify because each run yields different outcomes. Existing practices to improve computa...