Eleven grand challenges in single-cell data science
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
Immune monitoring using mass cytometry and related high-dimensional imaging approaches
The cellular complexity and functional diversity of the human immune system necessitate the
use of high-dimensional single-cell tools to uncover its role in multifaceted diseases such as …
use of high-dimensional single-cell tools to uncover its role in multifaceted diseases such as …
Visualizing structure and transitions in high-dimensional biological data
The high-dimensional data created by high-throughput technologies require visualization
tools that reveal data structure and patterns in an intuitive form. We present PHATE, a …
tools that reveal data structure and patterns in an intuitive form. We present PHATE, a …
The art of using t-SNE for single-cell transcriptomics
Single-cell transcriptomics yields ever growing data sets containing RNA expression levels
for thousands of genes from up to millions of cells. Common data analysis pipelines include …
for thousands of genes from up to millions of cells. Common data analysis pipelines include …
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and
continuous cell transitions. Partition-based graph abstraction (PAGA) provides an …
continuous cell transitions. Partition-based graph abstraction (PAGA) provides an …
Guidelines for the use of flow cytometry and cell sorting in immunological studies
These guidelines are a consensus work of a considerable number of members of the
immunology and flow cytometry community. They provide the theory and key practical …
immunology and flow cytometry community. They provide the theory and key practical …
[HTML][HTML] A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
DJ Ahern, Z Ai, M Ainsworth, C Allan, A Allcock… - Cell, 2022 - cell.com
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete
description of specific immune biomarkers. We present here a comprehensive multi-omic …
description of specific immune biomarkers. We present here a comprehensive multi-omic …
Sialic acids in pancreatic cancer cells drive tumour-associated macrophage differentiation via the Siglec receptors Siglec-7 and Siglec-9
Abstract Changes in glycosylation during tumour progression are a key hallmark of cancer.
One of the glycan moieties generally overexpressed in cancer are sialic acids, which can …
One of the glycan moieties generally overexpressed in cancer are sialic acids, which can …
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
High-dimensional mass and flow cytometry (HDCyto) experiments have become a method
of choice for high-throughput interrogation and characterization of cell populations. Here, we …
of choice for high-throughput interrogation and characterization of cell populations. Here, we …
Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets
AC Belkina, CO Ciccolella, R Anno, R Halpert… - Nature …, 2019 - nature.com
Accurate and comprehensive extraction of information from high-dimensional single cell
datasets necessitates faithful visualizations to assess biological populations. A state-of-the …
datasets necessitates faithful visualizations to assess biological populations. A state-of-the …