Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods
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 …
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
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 …
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
The treatment landscape of acute myeloid leukemia (AML) is evolving, with promising
therapies entering clinical translation, yet patient responses remain heterogeneous, and …
therapies entering clinical translation, yet patient responses remain heterogeneous, and …
[HTML][HTML] A transcription factor atlas of directed differentiation
Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular
processes and cell states. To comprehensively understand TFs and the programs they …
processes and cell states. To comprehensively understand TFs and the programs they …
Molecular logic of cellular diversification in the mouse cerebral cortex
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 …
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 …
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 …
cell types and functions, studies including large numbers of donors and multiple brain …
Large-scale foundation model on single-cell transcriptomics
Large pretrained models have become foundation models leading to breakthroughs in
natural language processing and related fields. Develo** foundation models for …
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 …
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
Background Single-cell transcriptomics is rapidly advancing our understanding of the
cellular composition of complex tissues and organisms. A major limitation in most analysis …
cellular composition of complex tissues and organisms. A major limitation in most analysis …