[HTML][HTML] Automatic cell-type harmonization and integration across Human Cell Atlas datasets

C Xu, M Prete, S Webb, L Jardine, BJ Stewart, R Hoo… - Cell, 2023 - cell.com
Harmonizing cell types across the single-cell community and assembling them into a
common framework is central to building a standardized Human Cell Atlas. Here, we present …

Mapping and analysis of chromatin state dynamics in nine human cell types

J Ernst, P Kheradpour, TS Mikkelsen, N Shoresh… - Nature, 2011 - nature.com
Chromatin profiling has emerged as a powerful means of genome annotation and detection
of regulatory activity. The approach is especially well suited to the characterization of non …

Simultaneous profiling of multiple chromatin proteins in the same cells

S Gopalan, Y Wang, NW Harper, M Garber, TG Fazzio - Molecular cell, 2021 - cell.com
Methods derived from CUT&RUN and CUT&Tag enable genome-wide mapping of the
localization of proteins on chromatin from as few as one cell. These and other mapping …

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

AW Zhang, C O'Flanagan, EA Chavez, JLP Lim… - Nature …, 2019 - nature.com
Single-cell RNA sequencing has enabled the decomposition of complex tissues into
functionally distinct cell types. Often, investigators wish to assign cells to cell types through …

Using single‐cell genomics to understand developmental processes and cell fate decisions

JA Griffiths, A Scialdone, JC Marioni - Molecular systems biology, 2018 - embopress.org
High‐throughput‐omics techniques have revolutionised biology, allowing for thorough and
unbiased characterisation of the molecular states of biological systems. However, cellular …

OpenCell: Endogenous tagging for the cartography of human cellular organization

NH Cho, KC Cheveralls, AD Brunner, K Kim… - Science, 2022 - science.org
Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era.
We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data …

Droplet-based single-cell joint profiling of histone modifications and transcriptomes

Y Xie, C Zhu, Z Wang, M Tastemel, L Chang… - Nature Structural & …, 2023 - nature.com
Abstract We previously reported Paired-Tag, a combinatorial indexing-based method that
can simultaneously map histone modifications and gene expression at single-cell resolution …

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

M Plass, J Solana, FA Wolf, S Ayoub, A Misios… - Science, 2018 - science.org
INTRODUCTION Understanding the differentiation of stem cells into the vast amount of cell
types that form the human body is a central problem of basic and medical science. The …

The scverse project provides a computational ecosystem for single-cell omics data analysis

I Virshup, D Bredikhin, L Heumos, G Palla… - Nature …, 2023 - nature.com
Single-cell omics technologies have enabled the creation of comprehensive cell atlases
across tissues and species and delivered key insights into the biological mechanisms …

Cross-species analysis of single-cell transcriptomic data

MER Shafer - Frontiers in cell and developmental biology, 2019 - frontiersin.org
The ability to profile hundreds of thousands to millions of single cells using scRNA-
sequencing has revolutionized the fields of cell and developmental biology, providing …