Deciphering the multi-scale, quantitative cis-regulatory code
S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
[HTML][HTML] High-content CRISPR screening
CRISPR screens are a powerful source of biological discovery, enabling the unbiased
interrogation of gene function in a wide range of applications and species. In pooled …
interrogation of gene function in a wide range of applications and species. In pooled …
Systematic differences in discovery of genetic effects on gene expression and complex traits
Most signals in genome-wide association studies (GWAS) of complex traits implicate
noncoding genetic variants with putative gene regulatory effects. However, currently …
noncoding genetic variants with putative gene regulatory effects. However, currently …
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …
RNA polymerase II dynamics shape enhancer–promoter interactions
How enhancers control target gene expression over long genomic distances remains an
important unsolved problem. Here we investigated enhancer–promoter communication by …
important unsolved problem. Here we investigated enhancer–promoter communication by …
Roles of transposable elements in the regulation of mammalian transcription
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often
contain sequences capable of recruiting the host transcription machinery, which they use to …
contain sequences capable of recruiting the host transcription machinery, which they use to …
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics
Genome-wide association studies provide a powerful means of identifying loci and genes
contributing to disease, but in many cases, the related cell types/states through which genes …
contributing to disease, but in many cases, the related cell types/states through which genes …
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation
Sequence-based machine-learning models trained on genomics data improve genetic
variant interpretation by providing functional predictions describing their impact on the cis …
variant interpretation by providing functional predictions describing their impact on the cis …
Effective gene expression prediction from sequence by integrating long-range interactions
How noncoding DNA determines gene expression in different cell types is a major unsolved
problem, and critical downstream applications in human genetics depend on improved …
problem, and critical downstream applications in human genetics depend on improved …
Genome-wide enhancer maps link risk variants to disease genes
Genome-wide association studies (GWAS) have identified thousands of noncoding loci that
are associated with human diseases and complex traits, each of which could reveal insights …
are associated with human diseases and complex traits, each of which could reveal insights …