The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims
to unravel the complex relationships between genes and their regulators. Deciphering these …

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 …

In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based
on their location within the liver lobule. However, it is unclear whether this spatial variation …

Following gastrulation, the three primary germ layers develop into the major organs in a
process known as organogenesis. Single-cell RNA sequencing has enabled the profiling of …

The immune system comprises diverse specialized cell types that cooperate to defend the
host against a wide range of pathogenic threats. Recent advancements in single-cell and …

Histone modifications are associated with distinct transcriptional states, but it is unclear
whether they instruct gene expression. To investigate this, we mutate histone H3. 3 K9 and …

Eukaryotic gene regulation is a combinatorial, dynamic, and quantitative process that plays
a vital role in development and disease and can be modeled at a systems level in gene …

Motivation Profiling of gene expression and chromatin accessibility by single-cell multi-
omics approaches can help to systematically decipher how transcription factors (TFs) …

Differential gene expression in response to perturbations is mediated at least in part by
changes in binding of transcription factors (TFs) and other proteins at specific genomic …