Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

[HTML][HTML] Comparison and evaluation of statistical error models for scRNA-seq

S Choudhary, R Satija - Genome biology, 2022 - Springer
Background Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple
sources, including biological variation in cellular state as well as technical variation …

Direct cell reprogramming: approaches, mechanisms and progress

H Wang, Y Yang, J Liu, L Qian - Nature Reviews Molecular Cell Biology, 2021 - nature.com
The reprogramming of somatic cells with defined factors, which converts cells from one
lineage into cells of another, has greatly reshaped our traditional views on cell identity and …

[HTML][HTML] Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Determining cell type abundance and expression from bulk tissues with digital cytometry

AM Newman, CB Steen, CL Liu, AJ Gentles… - Nature …, 2019 - nature.com
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing
cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be …

[HTML][HTML] Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

C Hafemeister, R Satija - Genome biology, 2019 - Springer
Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to
technical factors, including the number of molecules detected in each cell, which can …

[HTML][HTML] Single-cell RNA-seq technologies and related computational data analysis

G Chen, B Ning, T Shi - Frontiers in genetics, 2019 - frontiersin.org
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …

Challenges in unsupervised clustering of single-cell RNA-seq data

VY Kiselev, TS Andrews, M Hemberg - Nature Reviews Genetics, 2019 - nature.com
Single-cell RNA sequencing (scRNA-seq) allows researchers to collect large catalogues
detailing the transcriptomes of individual cells. Unsupervised clustering is of central …