William S. Bush

Evaluating sequence-to-function deep learning models for ancestry-stratified regulatory variant effect prediction using multi-ancestry blood eQTLs

This study evaluates two sequence-to-function models for predicting regulatory variant effects across ancestries using blood eQTL data, finding better performance for high-confidence variants in African American populations.

A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease

This study identifies a MEF2C transcription factor network that regulates endothelial cell proliferation in diabetic kidney disease and shows that SGLT2i treatment can reverse its dysregulation.

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.

Early peripheral immune signaling precedes tau elevation and blood-brain barrier disruption in Alzheimer's disease

Local genetic correlation analysis of Alzheimer's disease and stroke implicates PHLPP1 as a shared locus in individuals of African ancestry

Neuroimaging PheWAS and molecular phenotyping implicate PSMC3 in Alzheimer's Disease

The paper links PSMC3 expression to Alzheimer's Disease through neuroimaging and genetic analyses, showing its association with brain structure changes and dementia family history.

Multi-ancestry Transcriptome-Wide Association Study Reveals Shared and Population-Specific Genetic Effects in Alzheimer's Disease

This study performs a multi-ancestry transcriptome-wide association study (TWAS) to identify shared and population-specific genetic effects in Alzheimer's disease using RNA-seq and genotype data from multiple cohorts.

A multi-ancestry polygenic risk score for Alzheimer disease is associated with cognitive decline, hippocampal atrophy and neuropathological hallmarks in diverse populations

This paper develops an APOE-independent polygenic risk score for Alzheimer's disease that shows associations with cognitive decline and neuropathological markers across diverse populations.

Alzheimer disease is (sometimes) highly heritable: Drivers of variation in heritability estimates for binary traits, a systematic review

This study reviews heritability estimates for late-onset Alzheimer's disease, showing significant variation across studies and highlighting the importance of population and methodological context.

A Specialized Reference Panel with Structural Variants Integration for Improving Genotype Imputation in Alzheimer's Disease and Related Dementias (ADRD)

The paper develops an imputation panel integrating structural variants for Alzheimer's disease and related dementias, improving genotype imputation and identifying new genetic associations.

Sex-Specific Genetic Drivers of Memory, Executive Functioning, and Language Performance in Older Adults

The paper identifies sex-specific genetic loci associated with memory, executive functioning, and language performance in older adults through genome-wide meta-analyses.

Alzheimer's Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset

The paper provides a whole-genome sequencing dataset of 36,361 ADSP participants, including variant annotations, phenotypes, and a linkage disequilibrium panel for Alzheimer's Disease research.

Brain and Blood Transcriptome-Wide Association Studies Identify Five Novel Genes Associated with Alzheimer's Disease

Evaluating the association of APOE genotype and cognitive resilience in SuperAgers

This study examines the association between APOE genotype and cognitive resilience in SuperAgers, finding lower APOE-ε4 and higher APOE-ε2 frequencies in non-Hispanic White SuperAgers compared to controls and Alzheimer's cases.

HORNET: Tools to find genes with causal evidence and their regulatory networks using eQTLs

HORNET identifies causal genes and their regulatory networks using eQTLs and GWAS data, showing differential gene expression causality in schizophrenia across brain tissues.

ANALYSIS OF GLOMERULAR TRANSCRIPTOMES FROM NEPHROTIC PATIENTS SUGGEST APOL1 RISK VARIANTS IMPACT PARIETAL EPITHELIAL CELLS

The paper analyzes glomerular transcriptomes to show APOL1 risk variants affect parietal epithelial cells in nephrotic patients, linking gene expression patterns to disease outcomes.

Association of Common and Rare Variants with Alzheimer's Disease in over 13,000 Diverse Individuals with Whole-Genome Sequencing from the Alzheimer's Disease Sequencing Project

The paper investigates the association of common and rare variants with Alzheimer's Disease in 13,371 diverse individuals using whole-genome sequencing, identifying significant genetic loci and population-specific associations.

Methylation Clocks Do Not Predict Age or Alzheimer's Disease Risk Across Genetically Admixed Individuals

The paper evaluates methylation clocks in genetically diverse populations and finds they are less accurate in admixed cohorts and fail to consistently predict age acceleration in Alzheimer's disease cases.

NIAGADS: A Comprehensive National Data Repository for Alzheimer's Disease and Related Dementia Genetics and Genomics Research

NIAGADS provides a national data repository for Alzheimer's Disease and related dementia genetics and genomics research, hosting genome and exome sequence data from over 209,000 samples.

An X Chromosome Transcriptome Wide Association Study Implicates ARMCX6 in Alzheimer's Disease

The paper models X chromosome gene expression in blood and brain cortex using elastic net and applies these models to sex-stratified AD GWAS data to identify ARMCX6 as a putative AD risk gene.

magpie: a power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing

magpie evaluates statistical power for differential RNA methylation analysis in m6A sequencing by simulating data and assessing factors like sample size and effect size.

The chromatin landscape of healthy and injured cell types in the human kidney

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

Extended genome-wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimers Disease in individuals of African ancestry

NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's Disease genetic and genomic knowledge

The paper introduces GenomicsDB, a public knowledgebase for Alzheimer's disease genetic datasets and annotations, enabling data sharing and discovery through harmonized GWAS summary statistics and functional annotations.

Spatial Distribution of Missense Variants within Complement Proteins Associates with Age Related Macular Degeneration

The paper analyzes missense variants in complement genes to identify spatial associations with AMD risk using structural and functional metrics.

A Haptoglobin (HP) Structural Variant Alters the Effect of APOE Alleles on Alzheimer's Disease

The paper investigates how a haptoglobin structural variant modifies the effect of APOE alleles on Alzheimer's disease risk and age of onset in European-descent and African American populations.

Tuberculosis severity associates with variants and eQTLs related to vascular biology and infection-induced inflammation

This paper identifies genetic variants and eQTLs associated with TB severity, linking them to vascular biology and inflammation, using GWAS and eQTL analyses in TB patients.

Somatic Loss of the Y Chromosome and Alzheimer's Disease Risk

This study validates the association between mosaic loss of the Y chromosome and Alzheimer's Disease using prospective analyses and Mendelian Randomization across multiple cohorts.

Data Descriptor: Human whole exome genotype data for Alzheimer's Disease

This paper presents a strategy to jointly analyze 20,504 whole-exome sequencing samples from nine studies, generating high-quality variant calls and addressing batch effects from different capture kits.

Allelic Transcription Factor binding shape transcriptional kinetics observed with scRNA-seq in human cell lines

The paper investigates how allelic transcription factor binding influences transcriptional kinetics in human cell lines using scRNA-seq, finding strong correlations between eQTL effect sizes and burst frequency.