The advent of single-cell chromatin accessibility profiling has accelerated the ability to map
gene regulatory landscapes but has outpaced the development of scalable software to …

Disease-associated single-nucleotide polymorphisms (SNPs) generally do not implicate
target genes, as most disease SNPs are regulatory. Many SNP-to-gene (S2G) linking …

Single-cell atlases often include samples that span locations, laboratories and conditions,
leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets …

The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

INTRODUCTION In recent years, the single-cell genomics field has made incredible
progress toward disentangling the cellular heterogeneity of human tissues. However, the …

Genetic risk variants that have been identified in genome-wide association studies of
complex diseases are primarily non-coding. Translating these risk variants into mechanistic …

Genetic perturbations of cortical development can lead to neurodevelopmental disease,
including autism spectrum disorder (ASD). To identify genomic regions crucial to …

Genome-wide association studies of neurological diseases have identified thousands of
variants associated with disease phenotypes. However, most of these variants do not alter …

The human brain has undergone substantial change since humans diverged from
chimpanzees and the other great apes,. However, the genetic and developmental programs …

Understanding complex tissues requires single-cell deconstruction of gene regulation with
precision and scale. Here, we assess the performance of a massively parallel droplet-based …