Characterizing cis-regulatory elements using single-cell epigenomics

S Preissl, KJ Gaulton, B Ren - Nature Reviews Genetics, 2023 - nature.com
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 …

Single-cell multiomics: technologies and data analysis methods

J Lee, DY Hyeon, D Hwang - Experimental & Molecular Medicine, 2020 - nature.com
Advances in single-cell isolation and barcoding technologies offer unprecedented
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

JM Granja, MR Corces, SE Pierce, ST Bagdatli… - Nature …, 2021 - nature.com
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 …

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

S Chen, BB Lake, K Zhang - Nature biotechnology, 2019 - nature.com
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 …

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 …

Assessment of computational methods for the analysis of single-cell ATAC-seq data

H Chen, C Lareau, T Andreani, ME Vinyard, SP Garcia… - Genome biology, 2019 - Springer
Background Recent innovations in single-cell Assay for Transposase Accessible Chromatin
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 …

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

C Wang, D Sun, X Huang, C Wan, Z Li, Y Han, Q Qin… - Genome biology, 2020 - Springer
Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO),
a comprehensive open-source computational workflow (http://github. com/liulab …

Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen

Z Li, C Kuppe, S Ziegler, M Cheng, N Kabgani… - Nature …, 2021 - nature.com
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 …

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

G Jia, J Preussner, X Chen, S Guenther, X Yuan… - Nature …, 2018 - nature.com
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 …