[HTML][HTML] 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 …

[HTML][HTML] Stem cells and the differentiation hierarchy in mammary gland development

NY Fu, E Nolan, GJ Lindeman… - Physiological …, 2020 - journals.physiology.org
The mammary gland is a highly dynamic organ that undergoes profound changes within its
epithelium during puberty and the reproductive cycle. These changes are fueled by …

A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast

B Pal, Y Chen, F Vaillant, BD Capaldo, R Joyce… - The EMBO …, 2021 - embopress.org
To examine global changes in breast heterogeneity across different states, we determined
the single‐cell transcriptomes of> 340,000 cells encompassing normal breast, preneoplastic …

Single-cell transcriptional diversity is a hallmark of developmental potential

GS Gulati, SS Sikandar, DJ Wesche, A Manjunath… - Science, 2020 - science.org
Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular
differentiation trajectories. However, inferring both the state and direction of differentiation is …

[HTML][HTML] Cell clustering for spatial transcriptomics data with graph neural networks

J Li, S Chen, X Pan, Y Yuan, HB Shen - Nature Computational Science, 2022 - nature.com
Spatial transcriptomics data can provide high-throughput gene expression profiling and the
spatial structure of tissues simultaneously. Most studies have relied on only the gene …

Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity

QH Nguyen, N Pervolarakis, K Blake, D Ma… - Nature …, 2018 - nature.com
Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to
subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been …

[HTML][HTML] A human breast atlas integrating single-cell proteomics and transcriptomics

GK Gray, CMC Li, JM Rosenbluth, LM Selfors… - Developmental cell, 2022 - cell.com
The breast is a dynamic organ whose response to physiological and pathophysiological
conditions alters its disease susceptibility, yet the specific effects of these clinical variables …

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures

S Ruiz García, M Deprez, K Lebrigand… - …, 2019 - journals.biologists.com
The upper airway epithelium, which is mainly composed of multiciliated, goblet, club and
basal cells, ensures proper mucociliary function and can regenerate in response to assaults …

[HTML][HTML] Heterotypic cell–cell communication regulates glandular stem cell multipotency

A Centonze, S Lin, E Tika, A Sifrim, M Fioramonti… - Nature, 2020 - nature.com
Glandular epithelia, including the mammary and prostate glands, are composed of basal
cells (BCs) and luminal cells (LCs),. Many glandular epithelia develop from multipotent …

[HTML][HTML] Aging-associated alterations in mammary epithelia and stroma revealed by single-cell RNA sequencing

CMC Li, H Shapiro, C Tsiobikas, LM Selfors, H Chen… - Cell reports, 2020 - cell.com
Aging is closely associated with increased susceptibility to breast cancer, yet there have
been limited systematic studies of aging-induced alterations in the mammary gland. Here …