Gene regulatory network inference in the era of single-cell multi-omics
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome
Functional studies of the RNA N 6-methyladenosine (m6A) modification have been limited
by an inability to map individual m6A-modified sites in whole transcriptomes. To enable such …
by an inability to map individual m6A-modified sites in whole transcriptomes. To enable such …
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are
dynamically rewired during development and disease. Despite decades of advancement …
dynamically rewired during development and disease. Despite decades of advancement …
Landscape of stimulation-responsive chromatin across diverse human immune cells
A hallmark of the immune system is the interplay among specialized cell types transitioning
between resting and stimulated states. The gene regulatory landscape of this dynamic …
between resting and stimulated states. The gene regulatory landscape of this dynamic …
Prenatal immune stress blunts microglia reactivity, impairing neurocircuitry
Recent studies suggested that microglia, the primary brain immune cells, can affect circuit
connectivity and neuronal function,. Microglia infiltrate the neuroepithelium early in …
connectivity and neuronal function,. Microglia infiltrate the neuroepithelium early in …
Molecular diversification of regulatory T cells in nonlymphoid tissues
Foxp3+ CD4+ regulatory T cells (Tregs) accumulate in certain nonlymphoid tissues, where
they control diverse aspects of organ homeostasis. Populations of tissue Tregs, as they have …
they control diverse aspects of organ homeostasis. Populations of tissue Tregs, as they have …
Biomaterials-mediated regulation of macrophage cell fate
Endogenous regeneration aims to rebuild and reinstate tissue function through enlisting
natural self-repairing processes. Promoting endogenous regeneration by reducing tissue …
natural self-repairing processes. Promoting endogenous regeneration by reducing tissue …
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations
A major goal in the field of transcriptional regulation is the map** of changes in the
binding of transcription factors to the resultant changes in gene expression. Recently …
binding of transcription factors to the resultant changes in gene expression. Recently …
Biophysical regulation of macrophages in health and disease
Macrophages perform critical functions for homeostasis and immune defense in tissues
throughout the body. These innate immune cells are capable of recognizing and clearing …
throughout the body. These innate immune cells are capable of recognizing and clearing …