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An evolutionary perspective on complex neuropsychiatric disease
The forces of evolution—mutation, selection, migration, and genetic drift—shape the genetic
architecture of human traits, including the genetic architecture of complex neuropsychiatric …
architecture of human traits, including the genetic architecture of complex neuropsychiatric …
Three-dimensional genome rewiring in loci with human accelerated regions
Human accelerated regions (HARs) are conserved genomic loci that evolved at an
accelerated rate in the human lineage and may underlie human-specific traits. We …
accelerated rate in the human lineage and may underlie human-specific traits. We …
Single-cell genomics and regulatory networks for 388 human brains
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the
brain. Yet little is understood about how genetic variants influence cell-level gene …
brain. Yet little is understood about how genetic variants influence cell-level gene …
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types
The human genome contains millions of candidate cis-regulatory elements (CREs) with cell-
type-specific activities that shape both health and myriad disease states. However, we lack a …
type-specific activities that shape both health and myriad disease states. However, we lack a …
Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids
Regulation of gene expression through enhancers is one of the major processes sha**
the structure and function of the human brain during development. High-throughput assays …
the structure and function of the human brain during development. High-throughput assays …
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models
K Gjoni, KS Pollard - Bioinformatics, 2024 - academic.oup.com
The increasing development of sequence-based machine learning models has raised the
demand for manipulating sequences for this application. However, existing approaches to …
demand for manipulating sequences for this application. However, existing approaches to …
Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity
Genetic studies find hundreds of thousands of noncoding variants associated with
psychiatric disorders. Massively parallel reporter assays (MPRAs) and in vivo transgenic …
psychiatric disorders. Massively parallel reporter assays (MPRAs) and in vivo transgenic …
Rapid and quantitative functional interrogation of human enhancer variant activity in live mice
EW Hollingsworth, TA Liu, JA Alcantara… - Nature …, 2025 - nature.com
Functional analysis of non-coding variants associated with congenital disorders remains
challenging due to the lack of efficient in vivo models. Here we introduce dual-enSERT, a …
challenging due to the lack of efficient in vivo models. Here we introduce dual-enSERT, a …
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework
The advent of perturbation-based massively parallel reporter assays (MPRAs) technique
has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating …
has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating …
MPRAbase: a massively parallel reporter assay database
Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies
that measure the functional effects of thousands of sequences/variants on gene regulatory …
that measure the functional effects of thousands of sequences/variants on gene regulatory …