Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells

SH Church, JL Mah, CW Dunn - Plos Biology, 2024 - journals.plos.org
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal
links between cellular gene expression and the evolution of cell functions, features, and …

[HTML][HTML] Cross-species analysis of single-cell transcriptomic data

MER Shafer - Frontiers in cell and developmental biology, 2019 - frontiersin.org
The ability to profile hundreds of thousands to millions of single cells using scRNA-
sequencing has revolutionized the fields of cell and developmental biology, providing …

Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data

JL Mah, CW Dunn - bioRxiv, 2023 - biorxiv.org
The origin and evolution of cell types has emerged as a key topic in evolutionary biology.
Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type …

Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data

JL Mah, CW Dunn - Nature Ecology & Evolution, 2024 - nature.com
The origin and evolution of cell types has emerged as a key topic in evolutionary biology.
Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type …

Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network

X Liu, Q Shen, S Zhang - Genome Research, 2023 - genome.cshlp.org
Cross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow
us to explore, at single-cell resolution, the origins of the cellular diversity and evolutionary …

[图书][B] Identification of cell types from single-cell transcriptomic data

K Shekhar, V Menon - 2019 - Springer
Unprecedented technological advances in single-cell RNA-sequencing (scRNA-seq)
technology have now made it possible to profile genome-wide expression in single cells at …

Phylogenetic comparative analysis of single-cell transcriptomes reveals constrained accumulation of gene expression heterogeneity during clonal expansion

F Chen, Z Li, X Zhang, P Wu, W Yang… - Molecular Biology …, 2023 - academic.oup.com
In the same way that a phylogeny summarizes the evolutionary history of species, a cell
lineage tree describes the process of clonal expansion, in which gene expression …

[PDF][PDF] Integration of single-cell genomics datasets

AC Adey - Cell, 2019 - cell.com
Welch et al. and Stuart et al. present novel techniques for the integration of single-cell RNA-
seq datasets across multiple platforms, individuals, and species. They both extend these …

[HTML][HTML] GeneMarkeR: a database and user interface for scRNA-seq marker genes

BM Paisley, Y Liu - Frontiers in Genetics, 2021 - frontiersin.org
Single-cell sequencing (scRNA-seq) has enabled researchers to study cellular
heterogeneity. Accurate cell type identification is crucial for scRNA-seq analysis to be valid …

Identifying cell types to interpret scRNA-seq data: how, why and more possibilities

Z Wang, H Ding, Q Zou - Briefings in functional genomics, 2020 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has generated numerous data and renewed our
understanding of biological phenomena at the cellular scale. Identification of cell types has …