Jian Yang

A proteome atlas of structural variation and VNTR effects on complex traits and diseases

The paper imputes structural variants and VNTRs in UK Biobank participants to identify their effects on plasma protein abundances and complex traits, finding significant associations and regulatory impacts.

Joint Bayesian modelling of molecular QTL and GWAS effects improves polygenic prediction for complex traits

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The paper introduces CIMA, a multi-omics atlas of human immune cells, identifying regulatory mechanisms and genetic associations across sex, age, and genetic factors.

The China Brain Multi-omics Atlas Project (CBMAP)

The China Brain Multi-omics Atlas Project (CBMAP) creates a comprehensive molecular reference map of over 1,000 human brains to address underrepresentation in East Asian populations and advance research on aging and neuropsychiatric disorders.

Transcriptional and translational genetic control in blood contributes significantly to complex trait heritability and polygenic prediction

The paper evaluates the contribution of expression, splicing, and protein QTL in blood to SNP-based heritability and polygenic prediction across 27 traits, finding they capture significant portions of genetic variation.

Benchmarking methods integrating GWAS and single-cell transcriptomic data for mapping trait-cell type associations

This paper benchmarks 20 methods for mapping trait-cell type associations by integrating GWAS and scRNA-seq data, finding CATCH to be the most robust approach.

Spatially resolved mapping of cells associated with human complex traits

The paper introduces gsMap, a method that maps disease-relevant cells to human complex traits using spatial transcriptomics and GWAS data, revealing spatial patterns of schizophrenia and depression-associated glutamatergic neurons.

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

This paper introduces SBayesRC, a method that improves polygenic prediction of complex traits by integrating GWAS summary statistics with functional genomic annotations, showing significant accuracy gains across ancestries.

Ggnbp2 regulates synaptic development and autophagy in motor neurons

This study investigates the function of the ALS risk variant GGNBP2 in Drosophila motor neurons, showing it regulates autophagy and synaptic development.

Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data

The paper introduces scPagwas, a method that integrates pathway activation transformation of scRNA-seq data with GWAS summary statistics to identify trait-relevant cell populations and pathways.

Sequencing of 19,219 exomes identifies a low-frequency variant in FKBP5 promoter predisposing to high myopia in a Han Chinese population

This study identifies low-frequency variants in FKBP5 and FOLH1 associated with high myopia in Han Chinese and European populations through whole-exome sequencing and functional experiments.

Larger cerebral cortex is genetically correlated with greater frontal area and dorsal thickness

The paper investigates the genetic architecture of cortical expansion and regionalization by comparing genome-wide association studies of 24 cortical regions with and without adjustment for global measures, finding distinct genetic loci associated with different regions.

OTTERS: A powerful TWAS framework leveraging summary-level reference data

OTTERS is a TWAS framework that uses summary-level eQTL reference data to estimate eQTL weights and perform omnibus TWAS, showing improved power and applicability.

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

mBAT-combo improves gene-trait association detection in GWAS by accounting for SNP effect directions, revealing masking effects in complex traits.

Ultra-Accurate Classification and Discovery of Functional Protein-Coding Genes from Microbiomes Using FunGeneTyper: an Expandable Deep Learning-Based Framework

FunGeneTyper is a deep learning framework for ultra-accurate classification and discovery of functional genes in microbiomes, outperforming existing methods in multiple environments.

Cold protection allows local cryotherapy in a clinical-relevant model of traumatic optic neuropathy

This paper develops a cold-protective treatment for traumatic optic neuropathy using a clinically relevant animal model, showing that combined hypothermia and cold protection reduces inflammation and metabolic stress without cellular damage.

Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors

This paper introduces DENTIST, a method to reduce errors and heterogeneity in GWAS summary data, improving analyses like COJO and fine-mapping.

Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals

This study estimates non-additive genetic variance in human complex traits using a large sample of unrelated individuals and finds that additive variance is predominant while dominance and epistatic variances are negligible.

Quantifying genetic heterogeneity between continental populations for human height and body mass index

The paper quantifies genetic heterogeneity between European and African populations for height and BMI, finding high shared genetic variation suggesting GWAS findings in Europeans are applicable to non-Europeans.

Cross-Species Integration of Transcriptomic Effects of Tobacco and Nicotine Exposure Helps to Prioritize Genetic Effects on Human Tobacco Consumption

The paper uses cross-species transcriptomic data to identify genetic factors influencing human tobacco consumption, finding heritability enrichment in co-regulated genes.

A parsimonious model for mass-univariate vertex-wise analysis

The paper compares GLM and LMM approaches for mass-univariate vertex-wise analysis, showing LMMs reduce false positives and cluster size but increase computation.

Genome-wide analyses of behavioural traits biased by misreports and longitudinal changes

The paper corrects biases in self-reported behavioural traits in UK Biobank data by addressing misreports and longitudinal changes, revealing previously hidden genetic associations.

Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations

This paper quantifies the accuracy loss of polygenic scores in non-European populations by modeling linkage disequilibrium, allele frequencies, and effect size correlations.

Widespread associations between grey matter structure and the human phenome

This paper identifies 58 significant associations between grey matter structure and diverse human phenotypes using large neuroimaging datasets and shows body size factors explain part of these associations.

Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data

This study predicts promoter-anchored chromatin interactions using DNA methylation QTL data from a human cohort, finding overlaps with experimental data and associations with complex traits.

Genomic evaluation of circulating proteins for drug target characterisation and precision medicine

The paper identifies pQTLs for cardiovascular proteins and uses them to evaluate drug targets and suggest new candidates for precision medicine.

Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration.

This study identifies 143 genetic loci associated with 25 hydroxyvitamin D concentration in Europeans, revealing biological pathways and causal relationships with health outcomes.

An epigenome-wide association study of sex-specific chronological ageing

This study identifies DNA methylation loci associated with age-by-sex interactions in a cohort of 2,586 individuals, finding most significant loci are X-linked and linked to disease-related genes.

Genotype-free demultiplexing of pooled single-cell RNA-Seq

scSplit demultiplexes pooled single-cell RNA-Seq samples using genetic differences inferred from the data, showing high accuracy and consistency with known truths.

A resource-efficient tool for mixed model association analysis of large-scale data

fastGWA is a resource-efficient mixed model tool for GWAS that addresses population stratification and relatedness in large biobank datasets.