The technological landscape and applications of single-cell multi-omics

A Baysoy, Z Bai, R Satija, R Fan - Nature Reviews Molecular Cell …, 2023 - nature.com
Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

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 chromatin state analysis with Signac

T Stuart, A Srivastava, S Madad, CA Lareau, R Satija - Nature methods, 2021 - nature.com
The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

Rolling back human pluripotent stem cells to an eight-cell embryo-like stage

MA Mazid, C Ward, Z Luo, C Liu, Y Li, Y Lai, L Wu, J Li… - Nature, 2022 - nature.com
After fertilization, the quiescent zygote experiences a burst of genome activation that initiates
a short-lived totipotent state. Understanding the process of totipotency in human cells would …

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

R Vaisvila, VKC Ponnaluri, Z Sun… - Genome …, 2021 - genome.cshlp.org
Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite
treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing …

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 …

Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention

X Zhu, Z Chen, W Shen, G Huang, JM Sedivy… - Signal transduction and …, 2021 - nature.com
Remarkable progress in ageing research has been achieved over the past decades.
General perceptions and experimental evidence pinpoint that the decline of physical …

Integrative single-cell analysis

T Stuart, R Satija - Nature reviews genetics, 2019 - nature.com
The recent maturation of single-cell RNA sequencing (scRNA-seq) technologies has
coincided with transformative new methods to profile genetic, epigenetic, spatial, proteomic …

Current best practices in single‐cell RNA‐seq analysis: a tutorial

MD Luecken, FJ Theis - Molecular systems biology, 2019 - embopress.org
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

R Argelaguet, D Arnol, D Bredikhin, Y Deloro, B Velten… - Genome biology, 2020 - Springer
Technological advances have enabled the profiling of multiple molecular layers at single-
cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a …