An introduction to spatial transcriptomics for biomedical research

CG Williams, HJ Lee, T Asatsuma, R Vento-Tormo… - Genome Medicine, 2022 - Springer
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over
the past decade, particularly in developmental biology, cancer, immunology, and …

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 …

Single-cell RNA sequencing technologies and bioinformatics pipelines

B Hwang, JH Lee, D Bang - Experimental & molecular medicine, 2018 - nature.com
Rapid progress in the development of next-generation sequencing (NGS) technologies in
recent years has provided many valuable insights into complex biological systems, ranging …

[HTML][HTML] A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

ATL Lun, DJ McCarthy, JC Marioni - F1000Research, 2016 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of
individual cells. This provides biological resolution that cannot be matched by bulk RNA …

TH2 cell development and function

JA Walker, ANJ McKenzie - Nature Reviews Immunology, 2018 - nature.com
Abstract T helper 2 (TH 2) cells orchestrate protective type 2 immune responses, such as
those that target helminths and facilitate tissue repair, but also contribute to chronic …

SC3: consensus clustering of single-cell RNA-seq data

VY Kiselev, K Kirschner, MT Schaub, T Andrews… - Nature …, 2017 - nature.com
Single-cell RNA-seq enables the quantitative characterization of cell types based on global
transcriptome profiles. We present single-cell consensus clustering (SC3), a user-friendly …

Single-cell transcriptomics to explore the immune system in health and disease

MJT Stubbington, O Rozenblatt-Rosen, A Regev… - Science, 2017 - science.org
The immune system varies in cell types, states, and locations. The complex networks,
interactions, and responses of immune cells produce diverse cellular ecosystems composed …

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

S Nestorowa, FK Hamey, B Pijuan Sala… - Blood, The Journal …, 2016 - ashpublications.org
Maintenance of the blood system requires balanced cell fate decisions by hematopoietic
stem and progenitor cells (HSPCs). Because cell fate choices are executed at the individual …

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

A Haque, J Engel, SA Teichmann, T Lönnberg - Genome medicine, 2017 - Springer
RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative
analysis of messenger RNA molecules in a biological sample and is useful for studying …

[HTML][HTML] The technology and biology of single-cell RNA sequencing

AA Kolodziejczyk, JK Kim, V Svensson, JC Marioni… - Molecular cell, 2015 - cell.com
The differences between individual cells can have profound functional consequences, in
both unicellular and multicellular organisms. Recently developed single-cell mRNA …