Bayesian inference

Plasma Proteogenomics Identifies RGMB as a Candidate for Primary Open-Angle Glaucoma Detected Only in East Asians

The paper identifies RGMB as a potential risk factor for East Asian POAG through proteogenomic analysis, showing ancestry-specific associations and lack of colocalization with IOP traits.

Retinal arteriolar tortuosity as a candidate genetic window to inner-ear microvasculature: distributed sharing with blood pressure at CSK and PAWR and a roadmap for larger hearing GWAS

This paper investigates the genetic link between retinal arteriolar tortuosity and blood pressure, identifying potential shared genetic loci and suggesting retinal microvasculature as a candidate window for inner-ear microvasculature studies.

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy

StrainSpy fits zero-inflated beta mixed models to containment ANI, reaching >98% simulated sensitivity versus ~79% for logistic regression and detecting colorectal-cancer E. coli strain shifts.

Bayesian bacterial GWAS model reveals threshold-dependent genetic changes in antimicrobial resistance phenotypes

This paper introduces a Bayesian ordered logistic regression GWAS model for bacterial antimicrobial resistance phenotypes, showing improved variant discovery and MIC prediction by accounting for threshold-dependent effects.

Dissecting shared genetic susceptibility between gastroesophageal reflux disease and psychiatric disorders beyond body mass index

This study identifies shared genetic factors between GERD and psychiatric disorders, showing stronger links with internalizing disorders than with BMI.

An open field phenomics resource for multimodal maize yield prediction across divergent environments

Drone imagery from 356 flights in 19 Genomes to Fields maize environments; vegetation-index functional principal components complement genomic kernels, predicting yield of held-out hybrids at r up to 0.501.

Seven replicated genomic associations of myalgic encephalomyelitis/chronic fatigue syndrome: a biobank study

Targeted-learning GWAS of 1,268 UK Biobank ME/CFS cases found 176 FDR-significant variants; seven replicated in disjoint UK Biobank or All of Us cohorts.

Mammalian spermatogenesis at single-cell resolution downstream of genetic perturbations in meiotic double-strand break repair

Single-nucleus RNA+ATAC profiling of 32 mice shows asymmetric PRDM9 binding drives asynapsis, pachytene cell loss, aneuploidy and multi-megabase crossover redistribution, tuned by a chromosome 15 locus.

Shared genetic architecture between brain iron deposition and Alzheimer's disease

This study identifies shared genetic factors between brain iron deposition and Alzheimer's disease, revealing a polygenic basis and potential neuroimmune mechanisms.

Causal roles of phenotypic age and metabolic health on dementia: a Mendelian randomisation and structure learning study

This study uses Mendelian randomisation and causal network analysis to evaluate the causal effects of phenotypic age acceleration and metabolic health on dementia, finding no evidence of a causal effect but identifying key biomarkers.

Bayesian adaptive experimental design for efficient microbial genome-wide association studies

This paper introduces BASS-GWAS, a Bayesian method for efficient microbial GWAS, identifying causal loci with fewer phenotyped isolates than random sampling.

Causal inference for multiple risk factors and diseases from genomics data

The paper introduces CI-GWAS, a method to improve causal inference in GWAS by addressing confounding and pleiotropy, finding few suitable IVs and replicating some but not all previously reported causal links.

Genomic analysis identifies polygenic and region-specific contributions to ADHD-migraine comorbidity

This study identifies shared genetic variants and gene expression mechanisms between ADHD and migraine using genome-wide association data and multiple genetic analyses.

Representation in genetic studies affects inference about genetic architecture

Across UK Biobank, All of Us and FinnGen, the inferred mean direction (sign bias) of rare minor-allele effects varies and is largely explained by each cohort's trait skewness.

Benchmarking Bayesian colocalization methods in validating Mendelian randomization-identified targets

This study benchmarks four Bayesian colocalization methods to validate MR-identified protein-trait associations for cardiometabolic traits, finding SharePro most frequently supports significant associations.

Dissecting the Genetic Link Between Insulin Resistance and Coronary Heart Disease: A Multi-Trait GWAS and Proteomic-Metabolomic Mediation Analysis

This paper identifies a proteomic and metabolomic pathway linking insulin resistance to coronary heart disease through genetic analysis and mediation modeling.

Acute opioid responses are modulated by dynamic interactions of Oprm1 and Fgf12

This study identifies time-dependent epistatic interactions between Oprm1 and Fgf12 that modulate opioid-induced locomotion in mice and links Fgf12 to opioid behavior in humans.

Characterizing the impact of plasma protein levels on human brain structure and disorders leveraging integrative multi-omics analysis

This study identifies plasma proteins linked to brain structure and neurological disorders using multi-omics integration and Mendelian randomization.

Recalibrating Mendelian randomization under winner's curse, sample structure and polygenicity

This paper introduces a multivariable Rao-Blackwellization method to correct Mendelian randomization biases from winner's curse, polygenicity, and sample structure, improving type-I error control and inference robustness.

Disentangling adiposity-related and non-adiposity-related genetic pathways for type 2 diabetes

This paper identifies 29 circulating proteins associated with type 2 diabetes risk independent of BMI using GWAS-by-subtraction, proteome-wide Mendelian randomization, and colocalization analyses.

Investigating the Y chromosome in complex disease: Phenome-wide scan across 104,334 Finnish men

Phenome-wide scan of Y-chromosomal variants against 1,426 traits in 104,334 Finnish men finds no significant hits; kin-based validation supports haplogroup I1 increasing coronary heart disease risk.

A Multi-Context Regulome-Wide Association Atlas for Genetic Studies of Aging Brain Disorders

This paper introduces FGMB, a multi-context regulome-wide association atlas, and applies it to Alzheimer's disease to identify 327 regulatory associations and resolve 86 gene-molecular-trait pairs.

Unraveling the Genetic Overlap Between Parkinson's Disease and Schizophrenia Through Genome-wide Association and Cell-Type Specific Transcriptomic Analysis

This study identifies shared genetic loci between Parkinson's disease and schizophrenia using GWAS and scRNA-seq, highlighting RAI1's role in mitochondrial dysfunction and non-motor symptoms.

Evidence of Epistatic Interactive Effects of HK1 and GCK Genes on Circulating Hemoglobin A1c Levels

The paper identifies epistatic interactions between HK1 and GCK genes affecting HbA1c levels using Bayesian methods and confirms findings in independent studies.

Genetic and Proteomic Investigation of the Smoking-Parkinson Disease Association

This study investigates the causal relationship between smoking and Parkinson's disease using genetic and proteomic data, identifying shared biological pathways and potential therapeutic targets.

Shared Genetic Architecture Between Kidney Function and Alzheimer Disease Across Ancestries

This paper identifies shared genetic loci between kidney function and Alzheimer disease across ancestries, revealing both horizontal and vertical pleiotropy with APOE as the only shared locus.

A Bayesian multidimensional approach to decipher the genetic basis of dynamic phenotypes in multiple species

This paper introduces a Bayesian Varying Coefficient Model to analyze time-related phenotypic plasticity across species, revealing dynamic QTLs and improving phenotypic variance explanation.

Multi-trait colocalisation using MystraColoc: improved performance, deeper insights

The paper introduces MystraColoc, a Bayesian algorithm for multi-trait colocalisation, showing improved performance in clustering genetic association signals across GWAS datasets.

Cross-omic dissection reveals locus-specific heterogeneity and antagonistic pleiotropy between Alzheimer's disease and type 2 diabetes

This paper uses cross-omic analyses to show that Alzheimer's disease and type 2 diabetes share some genetic links but also exhibit locus-specific heterogeneity and antagonistic pleiotropy.

Genetically proxied inhibition of angiotensinogen synthesis is associated with lower cardiovascular risk

AGT variants mimicking hepatic angiotensinogen synthesis inhibition are linked, via drug-target Mendelian randomization, to lower coronary artery disease, stroke and heart failure risk and higher potassium.