Ewan Birney

The paper imputes fluid intelligence scores in a large cohort, reducing ascertainment bias and increasing power to detect genetic associations with common and rare variants.

The paper maps heterochrony in zebrafish and medaka using single-cell genomics, revealing cell-level timing shifts that contribute to species-specific phenotypes.

This paper analyzes 100,526 GWAS to identify pleiotropic genes and their therapeutic implications, finding that highly pleiotropic genes are associated with safety liabilities and that combining PAV support with intermediate pleiotropy improves therapeutic success.

This paper introduces a high-throughput optomotor response platform for analyzing vision in medaka and zebrafish, finding that albino medaka show heightened sensitivity to visual stimuli.

The paper uses long-read sequencing to characterize structural variants in 1,019 samples from the 1000 Genomes Project, identifying 167,291 sequence-resolved SVs and highlighting their genomic and functional implications.

This study investigates the genetic and phenotypic relationships between retinal pigment epithelium thickness and various pigmentation traits, finding shared and divergent genetic factors.

The paper uses Nanopore duplex sequencing to analyze 5hmC and 5mC distribution in medaka brain DNA, revealing strand-specific patterns in CpG dinucleotides.

The paper uses direct RNA nanopore sequencing to identify RNA modification changes in human pancreatic beta-cells after glucose stimulation, finding 1,697 differentially modified sites linked to type 2 diabetes genes.

The paper develops a behavioral assay and uses a Hidden Markov Model to analyze bold-shy behaviors in medaka fish, identifying direct and social genetic effects on behavior.

The paper maps and validates key genetic loci influencing heart rate and function in fish, identifying potential targets for cardiac disease treatment.

The paper uses medaka fish to study genetic and environmental interactions in heart rate, identifying QTLs and validating genes, while showing limitations of GWAS in capturing complex genetic effects.

The paper uses genetic data from Denmark and Britain to infer historical North Sea migrations from the Middle Ages to the Industrial Revolution, identifying distinct population patterns and migration trends.

This study identifies 51 genome-wide significant loci associated with dosage changes in 42 drug pair phenotypes, revealing distinct genetic patterns in polypharmacy.

The paper uses an autoencoder to derive retinal phenotypes from OCT images, identifies 118 genetic loci, and shows their relevance to retinal morphology and disease prediction.

FEHAT automatically detects heart rates in Medaka fish embryos from high-resolution videos, showing reliable performance across temperature perturbations.

The paper introduces an IVT-based method with dRNA-seq to detect RNA modifications across the transcriptome, identifying 26,619 modification sites and revealing non-random co-occurrence and isoform-specific patterns.

This study shows that spatial and temporal control of axis segmentation in medaka fish are dissociable modules, identified through devQTL mapping and CRISPR validation.

The paper evaluates genotype imputation in F2 crosses of inbred medaka lines, finding that imputation performance plateaus with increased sequencing coverage and develops a computational pipeline for cost-benefit analysis.

The paper evaluates and optimizes computational tools for predicting the pathogenicity of PAX6 missense variants, finding that AlphaMissense performs best with an optimized threshold.

The paper identifies genetic variants associated with photoreceptor layer thickness using OCT data from UK Biobank, revealing a continuum between normal variation and rare disease.

This study uses Danish registries to estimate heritability and genetic correlations of disease phenotypes and trajectories, identifying novel genetic associations and sex-specific contributions.

The paper investigates the combined effect of TYR and OCA2 variants on albinism risk and finds synergistic effects increasing diagnosis odds.

This paper introduces BOSS-RUNS, a framework for dynamic nanopore sequencing that adapts in real-time to maximize information gain and reduce coverage bias.

The paper investigates the role of common regulatory and protein-coding TYR variants in albinism, finding a high-frequency promoter variant modulates penetrance of a missense change and a haplotype associated with increased albinism risk.

The paper describes the formation of the Gene Curation Coalition to standardize gene-disease validity terminology and create a unified database for curated gene-disease assertions.

The paper introduces the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel, a vertebrate genetic resource for genotype-to-phenotype studies, enabling controlled experiments on complex traits.

The paper analyzes genomic and epigenomic variation in the MIKK panel using long-read sequencing and pan-genome graphs, revealing novel structural variants and methylation patterns.

This study introduces NRCeq, a method to identify capped full-length SARS-CoV-2 transcripts, revealing new insights into sgRNA structure and expression.

The paper introduces Nanocompore, a method to detect RNA modifications using Nanopore direct RNA sequencing, validated on human polyA+ RNAs and non-coding RNAs.