Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

ZA Clarke, TS Andrews, J Atif, D Pouyabahar… - Nature protocols, 2021 - nature.com
Single-cell transcriptomics can profile thousands of cells in a single experiment and identify
novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard …

Cell type ontologies of the Human Cell Atlas

D Osumi-Sutherland, C Xu, M Keays, AP Levine… - Nature cell …, 2021 - nature.com
Massive single-cell profiling efforts have accelerated our discovery of the cellular
composition of the human body while at the same time raising the need to formalize this new …

Cells of the adult human heart

M Litviňuková, C Talavera-López, H Maatz, D Reichart… - Nature, 2020 - nature.com
Cardiovascular disease is the leading cause of death worldwide. Advanced insights into
disease mechanisms and therapeutic strategies require a deeper understanding of the …

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

J Wang, A Ma, Y Chang, J Gong, Y Jiang, R Qi… - Nature …, 2021 - nature.com
Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and
dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from …

Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations

ZZ Hao, JR Wei, D Xiao, R Liu, N Xu, L Tang… - Nature …, 2022 - nature.com
The extent to which neurogenesis occurs in adult primates remains controversial. In this
study, using an optimized single-cell RNA sequencing pipeline, we profiled 207,785 cells …

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

H Liu, Q Zeng, J Zhou, A Bartlett, BA Wang, P Berube… - Nature, 2023 - nature.com
Cytosine DNA methylation is essential in brain development and is implicated in various
neurological disorders. Understanding DNA methylation diversity across the entire brain in a …

Single-cell transcriptomics for the assessment of cardiac disease

AMA Miranda, V Janbandhu, H Maatz… - Nature Reviews …, 2023 - nature.com
Cardiovascular disease is the leading cause of death globally. An advanced understanding
of cardiovascular disease mechanisms is required to improve therapeutic strategies and …

Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

Clustering by measuring local direction centrality for data with heterogeneous density and weak connectivity

D Peng, Z Gui, D Wang, Y Ma, Z Huang, Y Zhou… - Nature …, 2022 - nature.com
Clustering is a powerful machine learning method for discovering similar patterns according
to the proximity of elements in feature space. It is widely used in computer science …

Guided construction of single cell reference for human and mouse lung

M Guo, MP Morley, C Jiang, Y Wu, G Li, Y Du… - Nature …, 2023 - nature.com
Accurate cell type identification is a key and rate-limiting step in single-cell data analysis.
Single-cell references with comprehensive cell types, reproducible and functionally …