Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

[HTML][HTML] Single-cell multiomics: technologies and data analysis methods

J Lee, DY Hyeon, D Hwang - Experimental & Molecular Medicine, 2020 - nature.com
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …

Spatial transcriptomics at subspot resolution with BayesSpace

E Zhao, MR Stone, X Ren, J Guenthoer… - Nature …, 2021 - nature.com
Recent spatial gene expression technologies enable comprehensive measurement of
transcriptomic profiles while retaining spatial context. However, existing analysis methods …

Human distal airways contain a multipotent secretory cell that can regenerate alveoli

MC Basil, FL Cardenas-Diaz, JJ Kathiriya, MP Morley… - Nature, 2022 - nature.com
The human lung differs substantially from its mouse counterpart, resulting in a distinct distal
airway architecture affected by disease pathology in chronic obstructive pulmonary disease …

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

R Fang, C Xia, JL Close, M Zhang, J He, Z Huang… - Science, 2022 - science.org
The human cerebral cortex has tremendous cellular diversity. How different cell types are
organized in the human cortex and how cellular organization varies across species remain …

Unified one-step multi-view spectral clustering

C Tang, Z Li, J Wang, X Liu, W Zhang… - IEEE Transactions on …, 2022 - ieeexplore.ieee.org
Multi-view spectral clustering, which exploits the complementary information among graphs
of diverse views to obtain superior clustering results, has attracted intensive attention …

scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention

R Meng, S Yin, J Sun, H Hu, Q Zhao - Computers in biology and medicine, 2023 - Elsevier
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful
technique for investigating cellular heterogeneity and structure. However, analyzing scRNA …

[HTML][HTML] Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging

R Bogeska, AM Mikecin, P Kaschutnig, M Fawaz… - Cell stem cell, 2022 - cell.com
Hematopoietic stem cells (HSCs) mediate regeneration of the hematopoietic system
following injury, such as following infection or inflammation. These challenges impair HSC …

[HTML][HTML] Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

N Kim, HK Kim, K Lee, Y Hong, JH Cho… - Nature …, 2020 - nature.com
Advanced metastatic cancer poses utmost clinical challenges and may present molecular
and cellular features distinct from an early-stage cancer. Herein, we present single-cell …

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 …