From reads to insight: a hitchhiker's guide to ATAC-seq data analysis

F Yan, DR Powell, DJ Curtis, NC Wong - Genome biology, 2020 - Springer
Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …

Mechanisms of synaptic transmission dysregulation in the prefrontal cortex: pathophysiological implications

Z Yan, B Rein - Molecular psychiatry, 2022 - nature.com
The prefrontal cortex (PFC) serves as the chief executive officer of the brain, controlling the
highest level cognitive and emotional processes. Its local circuits among glutamatergic …

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases

MR Corces, A Shcherbina, S Kundu, MJ Gloudemans… - Nature …, 2020 - nature.com
Genome-wide association studies of neurological diseases have identified thousands of
variants associated with disease phenotypes. However, most of these variants do not alter …

Identification of common genetic risk variants for autism spectrum disorder

J Grove, S Ripke, TD Als, M Mattheisen, RK Walters… - Nature …, 2019 - nature.com
Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of
neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic …

Comprehensive functional genomic resource and integrative model for the human brain

D Wang, S Liu, J Warrell, H Won, X Shi, FCP Navarro… - Science, 2018 - science.org
INTRODUCTION Strong genetic associations have been found for a number of psychiatric
disorders. However, understanding the underlying molecular mechanisms remains …

Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

AW Turner, SS Hu, JV Mosquera, WF Ma… - Nature …, 2022 - nature.com
Coronary artery disease (CAD) is a complex inflammatory disease involving genetic
influences across cell types. Genome-wide association studies have identified over 200 loci …

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

PF Sullivan, JRS Meadows, S Gazal, BDN Phan, X Li… - Science, 2023 - science.org
Thousands of genomic regions have been associated with heritable human diseases, but
attempts to elucidate biological mechanisms are impeded by an inability to discern which …

Comparative genetic architectures of schizophrenia in East Asian and European populations

M Lam, CY Chen, Z Li, AR Martin, J Bryois, X Ma… - Nature …, 2019 - nature.com
Schizophrenia is a debilitating psychiatric disorder with approximately 1% lifetime risk
globally. Large-scale schizophrenia genetic studies have reported primarily on European …

Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses

C Wallace - PLoS genetics, 2020 - journals.plos.org
Horizontal integration of summary statistics from different GWAS traits can be used to
evaluate evidence for their shared genetic causality. One popular method to do this is a …

Genetics of the human microglia regulome refines Alzheimer's disease risk loci

R Kosoy, JF Fullard, B Zeng, J Bendl, P Dong… - Nature …, 2022 - nature.com
Microglia are brain myeloid cells that play a critical role in neuroimmunity and the etiology of
Alzheimer's disease (AD), yet our understanding of how the genetic regulatory landscape …