Characterizing cis-regulatory elements using single-cell epigenomics
Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …
Single-cell multiomics: technologies and data analysis methods
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …
[HTML][HTML] ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
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 …
gene regulatory landscapes but has outpaced the development of scalable software to …
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell
Single-cell RNA sequencing can reveal the transcriptional state of cells, yet provides little
insight into the upstream regulatory landscape associated with open or accessible …
insight into the upstream regulatory landscape associated with open or accessible …
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data
C Bravo González-Blas, L Minnoye, D Papasokrati… - Nature …, 2019 - nature.com
We present cisTopic, a probabilistic framework used to simultaneously discover
coaccessible enhancers and stable cell states from sparse single-cell epigenomics data …
coaccessible enhancers and stable cell states from sparse single-cell epigenomics data …
Assessment of computational methods for the analysis of single-cell ATAC-seq data
Background Recent innovations in single-cell Assay for Transposase Accessible Chromatin
using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands …
using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands …
Chromatin accessibility profiling methods
L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO),
a comprehensive open-source computational workflow (http://github. com/liulab …
a comprehensive open-source computational workflow (http://github. com/liulab …
Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen
A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, ie, open chromatin
regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we …
regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we …
Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement
Formation and segregation of cell lineages forming the heart have been studied extensively
but the underlying gene regulatory networks and epigenetic changes driving cell fate …
but the underlying gene regulatory networks and epigenetic changes driving cell fate …