The triumphs and limitations of computational methods for scRNA-seq
PV Kharchenko - Nature Methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …
decade has been accompanied by equally impressive advances in the computational …
RNA sequencing: the teenage years
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 …
transcriptome-wide analysis of differential gene expression and differential splicing of …
Disease-associated astrocytes in Alzheimer's disease and aging
N Habib, C McCabe, S Medina, M Varshavsky… - Nature …, 2020 - nature.com
The role of non-neuronal cells in Alzheimer's disease progression has not been fully
elucidated. Using single-nucleus RNA sequencing, we identified a population of disease …
elucidated. Using single-nucleus RNA sequencing, we identified a population of disease …
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 …
[PDF][PDF] Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging
R Bogeska, AM Mikecin, P Kaschutnig, M Fawaz… - Cell Stem Cell, 2022 - cell.com
Hematopoietic stem cells (HSCs) mediate regeneration of the hematopoietic system
following injury, such as following infection or inflammation. These challenges impair HSC …
following injury, such as following infection or inflammation. These challenges impair HSC …
Single‐cell RNA sequencing technologies and applications: A brief overview
D Jovic, X Liang, H Zeng, L Lin, F Xu… - Clinical and …, 2022 - Wiley Online Library
Single‐cell RNA sequencing (scRNA‐seq) technology has become the state‐of‐the‐art
approach for unravelling the heterogeneity and complexity of RNA transcripts within …
approach for unravelling the heterogeneity and complexity of RNA transcripts within …
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 …
resolution. The promise of this technology is attracting a growing user base for single‐cell …
[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 …
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …
Challenges in unsupervised clustering of single-cell RNA-seq data
Single-cell RNA sequencing (scRNA-seq) allows researchers to collect large catalogues
detailing the transcriptomes of individual cells. Unsupervised clustering is of central …
detailing the transcriptomes of individual cells. Unsupervised clustering is of central …
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments
Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently
become technically feasible. While such analysis has the potential to accurately quantify …
become technically feasible. While such analysis has the potential to accurately quantify …