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 importance …

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

TS Andrews, VY Kiselev, D McCarthy, M Hemberg - Nature protocols, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows
you to profile the whole transcriptome of a large number of individual cells. However, the …

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

ZA Clarke, TS Andrews, J Atif, D Pouyabahar… - Nature protocols, 2021 - nature.com
Single-cell transcriptomics can profile thousands of cells in a single experiment and identify
novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard …

[PDF][PDF] Single‐cell, single‐nucleus, and spatial RNA sequencing of the human liver identifies cholangiocyte and mesenchymal heterogeneity

TS Andrews, J Atif, JC Liu, CT Perciani… - Hepatology …, 2022 - Wiley Online Library
The critical functions of the human liver are coordinated through the interactions of hepatic
parenchymal and non‐parenchymal cells. Recent advances in single‐cell transcriptional …

[HTML][HTML] Identifying cell populations with scRNASeq

TS Andrews, M Hemberg - Molecular aspects of medicine, 2018 - Elsevier
Single-cell RNASeq (scRNASeq) has emerged as a powerful method for quantifying the
transcriptome of individual cells. However, the data from scRNASeq experiments is often both …

M3Drop: dropout-based feature selection for scRNASeq

TS Andrews, M Hemberg - Bioinformatics, 2019 - academic.oup.com
Motivation Most genomes contain thousands of genes, but for most functional responses,
only a subset of those genes are relevant. To facilitate many single-cell RNASeq (scRNASeq) …

[HTML][HTML] False signals induced by single-cell imputation

TS Andrews, M Hemberg - F1000Research, 2018 - ncbi.nlm.nih.gov
… The authors Andrews and Hemberg provided an insightful analysis assessing whether or
not false positives (or capturing false signals) are introduced by imputation methods into scRNA…

Phosphorylation switches Bax from promoting to inhibiting apoptosis thereby increasing drug resistance

…, TS Andrews, B Leber, A Letai, DW Andrews - EMBO …, 2018 - embopress.org
Akt is a pro‐survival kinase frequently activated in human cancers and is associated with
more aggressive tumors that resist therapy. Here, we connect Akt pathway activation to …

[HTML][HTML] Sulfate-based anionic diblock copolymer nanoparticles for efficient occlusion within zinc oxide

Y Ning, LA Fielding, TS Andrews, DJ Growney… - Nanoscale, 2015 - pubs.rsc.org
Occlusion of copolymer particles within inorganic crystalline hosts not only provides a
model for understanding the crystallisation process, but also may offer a direct route for the …

[HTML][HTML] Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver

TS Andrews, D Nakib, CT Perciani, XZ Ma, L Liu… - Journal of …, 2024 - Elsevier
Background Primary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver
disease characterized by bile retention, biliary tree destruction, and progressive fibrosis …