Helen Parkinson

The paper introduces an interactive Data Integrator for uniform processing and integration of bulk RNA-seq datasets from the MorPhiC program and external sources.

PEGASUS defines a community reporting standard for GWAS predicted effector genes: a metadata record, a full locus-by-gene evidence matrix, and a derived author-prioritised gene list.

This paper describes an AI semantics workflow using LLM agents to integrate multimodal biomedical data through ontologies and knowledge graphs.

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.

The paper presents tools to validate and simplify ontology term hierarchies for better usability in biomedical research.

The paper develops a public ontology API for programmatic access to ICTV virus taxonomy, enabling semantic and machine-actionable retrieval of taxonomic data across releases.

The paper describes the International Mouse Phenotyping Consortium's data portal, its expansion to over 100 million data points, and improvements to its web interface and data access tools.

This study develops and validates LLM-based methods to extract PDCM-related entities from scientific texts, showing soft prompting improves small open LLMs' performance.

This study establishes TTE reference ranges for mice, showing anesthesia significantly affects cardiac function, with minimal sex differences and modest age-related changes.

The paper introduces uPheno, a framework for cross-species phenomics integration by harmonizing phenotype data across species and ontologies.

The GWAS Catalog now holds 625,113 curated SNP-trait associations from 6,921 publications plus >85K summary statistics datasets, with a new GWAS-SSF submission standard and GRCh38 harmonisation.

The paper analyzes 3,313 genetically engineered mouse lines to identify gene essentiality as the main factor affecting Cas9-based genome editing success.

The paper introduces new features and tools for the PGS Catalog to enhance FAIR research, enabling reproducible and equitable polygenic score calculations.

The paper visualises molecular QTLs to better understand genetic effects on gene expression and identifies causal genes at GWAS loci.

The paper develops genetic scores for 17,227 molecular traits using multi-omic data from INTERVAL and validates them across ancestries, demonstrating their utility in pathway analysis and disease association discovery.

The paper identifies novel Mendelian genes by analyzing mouse embryo lethality and linking them to human disease phenotypes and genetic variants.

The paper defines a standard format for GWAS summary statistics to improve data sharing and analysis.

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.

PGS Catalog standardizes 192 curated polygenic scores and metadata (86 traits); reapplied in UK Biobank, eight of nine colorectal cancer scores predicted disease in European-ancestry participants.

ClinGen and the PGS Catalog expand the GRIPS guideline into a 22-item Polygenic Risk Score Reporting Statement covering study populations, model construction, evaluation, and clinical interpretation.

OpenStats improves speed and scalability for high-throughput phenotypic data analysis, showing significant performance gains in the International Mouse Phenotyping Consortium.

The paper integrates gene essentiality data from human and mouse screens to classify genes into FUSIL categories, identifying developmental lethal genes associated with rare diseases.

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

The paper introduces a method called soft windowing to improve analysis of high-throughput phenotyping data by reducing false positives and increasing significant results.

This study analyzes 70 EHR phenotyping algorithms from CALIBER and UK Biobank to understand their heterogeneity and identify common implementation patterns for developing a minimum information standard.

The paper introduces a standardized framework for ancestry data representation in genomics studies and applies it to the NHGRI-EBI GWAS Catalog to improve data integration and analysis.

The paper outlines ten lessons for designing, provisioning, and reusing persistent identifiers to improve data integration in life sciences.