Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Choroidal endothelial and macrophage gene expression in atrophic and neovascular macular degeneration

AP Voigt, NK Mullin, K Mulfaul… - Human molecular …, 2022 - academic.oup.com
The human choroid is a heterogeneous, highly vascular connective tissue that dysfunctions
in age-related macular degeneration (AMD). In this study, we performed single-cell RNA …

Typical development of synaptic and neuronal properties can proceed without microglia in the cortex and thalamus

M O'Keeffe, SA Booker, D Walsh, M Li, C Henley… - Nature …, 2025 - nature.com
Brain-resident macrophages, microglia, have been proposed to have an active role in
synaptic refinement and maturation, influencing plasticity and circuit-level connectivity. Here …

Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data

S Junttila, J Smolander, LL Elo - Briefings in bioinformatics, 2022 - academic.oup.com
Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of
thousands of cells simultaneously and study transcriptomic changes between cells. scRNA …

Mitochondrial uncoupling proteins protect human airway epithelial ciliated cells from oxidative damage

A Jain, BR Kim, W Yu, TO Moninger… - Proceedings of the …, 2024 - National Acad Sciences
Apical cilia on epithelial cells defend the lung by propelling pathogens and particulates out
of the respiratory airways. Ciliated cells produce ATP that powers cilia beating by densely …

Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies

X Guo, J Ning, Y Chen, G Liu, L Zhao… - Briefings in …, 2024 - academic.oup.com
Differential expression (DE) analysis is a necessary step in the analysis of single-cell RNA
sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data. Unlike …

Robustness of single-cell RNA-seq for identifying differentially expressed genes

Y Liu, J Huang, R Pandey, P Liu, B Therani, Q Qiu… - BMC genomics, 2023 - Springer
Background A common feature of single-cell RNA-seq (scRNA-seq) data is that the number
of cells in a cell cluster may vary widely, ranging from a few dozen to several thousand. It is …

Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation

LT Vu, F Ahmed, H Zhu, DSH Iu, EA Fogarty… - Cell Reports …, 2024 - cell.com
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious and poorly
understood disease. To understand immune dysregulation in ME/CFS, we use single-cell …

Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation

F Ahmed, LT Vu, H Zhu, DSH Iu, EA Fogarty, Y Kwak… - BioRxiv, 2022 - biorxiv.org
SUMMARY ME/CFS is a serious and poorly understood disease. To understand immune
dysregulation in ME/CFS, we used single-cell RNA-seq (scRNA-seq) to examine immune …

A single-cell atlas of large and small airways at birth in a porcine model of cystic fibrosis

AL Thurman, X Li, R Villacreses, W Yu… - American journal of …, 2022 - atsjournals.org
Lack of CFTR (cystic fibrosis transmembrane conductance regulator) affects the
transcriptome, composition, and function of large and small airway epithelia in people with …