An evolutionary perspective on complex neuropsychiatric disease

JM McClellan, AW Zoghbi, JD Buxbaum, C Cappi… - Neuron, 2024 - cell.com
The forces of evolution—mutation, selection, migration, and genetic drift—shape the genetic
architecture of human traits, including the genetic architecture of complex neuropsychiatric …

Three-dimensional genome rewiring in loci with human accelerated regions

KC Keough, S Whalen, F Inoue, PF Przytycki, T Fair… - Science, 2023 - science.org
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 …

Single-cell genomics and regulatory networks for 388 human brains

PS Emani, JJ Liu, D Clarke, M Jensen, J Warrell… - Science, 2024 - science.org
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 …

Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types

V Agarwal, F Inoue, M Schubach, BK Martin… - BioRxiv, 2023 - pmc.ncbi.nlm.nih.gov
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 …

Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids

D Capauto, Y Wang, F Wu, S Norton, J Mariani… - Scientific reports, 2024 - nature.com
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 …

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 …

Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity

M Kosicki, DL Cintrón, NF Page… - …, 2024 - pmc.ncbi.nlm.nih.gov
Genetic studies find hundreds of thousands of noncoding variants associated with
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 …

Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework

J Liu, T Ashuach, F Inoue, N Ahituv… - Nucleic acids …, 2024 - academic.oup.com
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 …

MPRAbase: a massively parallel reporter assay database

J Zhao, FA Baltoumas, MA Konnaris, I Mouratidis… - …, 2023 - pmc.ncbi.nlm.nih.gov
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 …