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 …

Unraveling B cell trajectories at single cell resolution

D Morgan, V Tergaonkar - Trends in immunology, 2022 - cell.com
During adaptive immunity, B cells differentiate either into memory B cells or plasma cells and
produce antibodies against foreign antigens to fight infection. Additionally, they behave as …

CellRank for directed single-cell fate mapping

M Lange, V Bergen, M Klein, M Setty, B Reuter… - Nature …, 2022 - nature.com
Computational trajectory inference enables the reconstruction of cell state dynamics from
single-cell RNA sequencing experiments. However, trajectory inference requires that the …

FOXA2 drives lineage plasticity and KIT pathway activation in neuroendocrine prostate cancer

M Han, F Li, Y Zhang, P Dai, J He, Y Li, Y Zhu, J Zheng… - Cancer Cell, 2022 - cell.com
Prostate cancer adeno-to-neuroendocrine lineage transition has emerged as a mechanism
of targeted therapeutic resistance. Identifying the direct molecular drivers and developing …

Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction

C Li, MC Virgilio, KL Collins, JD Welch - Nature biotechnology, 2023 - nature.com
Multi-omic single-cell datasets, in which multiple molecular modalities are profiled within the
same cell, offer an opportunity to understand the temporal relationship between epigenome …

Enhancers in disease: molecular basis and emerging treatment strategies

A Claringbould, JB Zaugg - Trends in molecular medicine, 2021 - cell.com
Enhancers are genomic sequences that play a key role in regulating tissue-specific gene
expression levels. An increasing number of diseases are linked to impaired enhancer …

[HTML][HTML] Multi-omics analysis of human mesenchymal stem cells shows cell aging that alters immunomodulatory activity through the downregulation of PD-L1

Y Gao, Y Chi, Y Chen, W Wang, H Li, W Zheng… - Nature …, 2023 - nature.com
Mesenchymal stem cells (MSCs) possess potent immunomodulatory activity and have been
extensively investigated for their therapeutic potential in treating inflammatory disorders …

Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis

P Zeller, J Yeung, H Viñas Gaza, BA de Barbanson… - Nature Genetics, 2023 - nature.com
Post-translational histone modifications modulate chromatin activity to affect gene
expression. How chromatin states underlie lineage choice in single cells is relatively …

Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA

L Yang, J Wang, J Altreuter, A Jhaveri, CJ Wong… - Nature …, 2023 - nature.com
Abstract RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique
for molecular profiling and immune characterization of tumors. In the past decade, many …

Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

S Zhang, S Pyne, S Pietrzak, S Halberg… - Nature …, 2023 - nature.com
Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory
networks (GRNs) that connect transcription factors and signaling proteins to target genes …