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 …

[HTML][HTML] Automated methods for cell type annotation on scRNA-seq data

G Pasquini, JER Arias, P Schäfer… - Computational and …, 2021 - Elsevier
The advent of single-cell sequencing started a new era of transcriptomic and genomic
research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type …

A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia

AGX Zeng, S Bansal, L **, A Mitchell, WC Chen… - Nature medicine, 2022 - nature.com
The treatment landscape of acute myeloid leukemia (AML) is evolving, with promising
therapies entering clinical translation, yet patient responses remain heterogeneous, and …

[HTML][HTML] A transcription factor atlas of directed differentiation

J Joung, S Ma, T Tay, KR Geiger-Schuller… - Cell, 2023 - cell.com
Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular
processes and cell states. To comprehensively understand TFs and the programs they …

Molecular logic of cellular diversification in the mouse cerebral cortex

DJ Di Bella, E Habibi, RR Stickels, G Scalia, J Brown… - Nature, 2021 - nature.com
The mammalian cerebral cortex has an unparalleled diversity of cell types, which are
generated during development through a series of temporally orchestrated events that are …

Transformer for one stop interpretable cell type annotation

J Chen, H Xu, W Tao, Z Chen, Y Zhao… - Nature …, 2023 - nature.com
Consistent annotation transfer from reference dataset to query dataset is fundamental to the
development and reproducibility of single-cell research. Compared with traditional …

A brain cell atlas integrating single-cell transcriptomes across human brain regions

X Chen, Y Huang, L Huang, Z Huang, ZZ Hao, L Xu… - Nature Medicine, 2024 - nature.com
While single-cell technologies have greatly advanced our comprehension of human brain
cell types and functions, studies including large numbers of donors and multiple brain …

Large-scale foundation model on single-cell transcriptomics

M Hao, J Gong, X Zeng, C Liu, Y Guo, X Cheng… - Nature …, 2024 - nature.com
Large pretrained models have become foundation models leading to breakthroughs in
natural language processing and related fields. Develo** foundation models for …

Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis

S Gribaudo, R Robert, B van Sambeek, C Mirdass… - Nature …, 2024 - nature.com
Integrated in vitro models of human organogenesis are needed to elucidate the multi-
systemic events underlying development and disease. Here we report the generation of …

A comparison of automatic cell identification methods for single-cell RNA sequencing data

T Abdelaal, L Michielsen, D Cats, D Hoogduin, H Mei… - Genome biology, 2019 - Springer
Background Single-cell transcriptomics is rapidly advancing our understanding of the
cellular composition of complex tissues and organisms. A major limitation in most analysis …