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 …

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 …

Dictionary learning for integrative, multimodal and scalable single-cell analysis

Y Hao, T Stuart, MH Kowalski, S Choudhary… - Nature …, 2024 - nature.com
Map** single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

SARS-CoV-2 infection of the oral cavity and saliva

N Huang, P Pérez, T Kato, Y Mikami, K Okuda… - Nature medicine, 2021 - nature.com
Despite signs of infection—including taste loss, dry mouth and mucosal lesions such as
ulcerations, enanthema and macules—the involvement of the oral cavity in coronavirus …

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

RL Chua, S Lukassen, S Trump, BP Hennig… - Nature …, 2020 - nature.com
To investigate the immune response and mechanisms associated with severe coronavirus
disease 2019 (COVID-19), we performed single-cell RNA sequencing on nasopharyngeal …

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

DH Brann, T Tsukahara, C Weinreb, M Lipovsek… - Science …, 2020 - science.org
Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A
key question is whether SARS-CoV-2 (CoV-2)–the causal agent in COVID-19–affects …

A molecular cell atlas of the human lung from single-cell RNA sequencing

KJ Travaglini, AN Nabhan, L Penland, R Sinha… - Nature, 2020 - nature.com
Although single-cell RNA sequencing studies have begun to provide compendia of cell
expression profiles,,,,,,,–, it has been difficult to systematically identify and localize all …

Construction of a human cell landscape at single-cell level

X Han, Z Zhou, L Fei, H Sun, R Wang, Y Chen, H Chen… - Nature, 2020 - nature.com
Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex
systems. However, a comprehensive single-cell atlas has not been achieved for humans …

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

DT Montoro, AL Haber, M Biton, V Vinarsky, B Lin… - Nature, 2018 - nature.com
The airways of the lung are the primary sites of disease in asthma and cystic fibrosis. Here
we study the cellular composition and hierarchy of the mouse tracheal epithelium by single …