[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 …

[HTML][HTML] 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 …

A curated database reveals trends in single-cell transcriptomics

V Svensson, E da Veiga Beltrame, L Pachter - Database, 2020 - academic.oup.com
The more than 1000 single-cell transcriptomics studies that have been published to date
constitute a valuable and vast resource for biological discovery. While various 'atlas' projects …

Single-cell biology: beyond the sum of its parts

AF Schier - Nature methods, 2020 - nature.com
The field of single-cell RNA sequencing (scRNA-seq) has been paired with genomics,
epigenomics, spatial omics, proteomics and imaging to achieve multimodal measurements …

[HTML][HTML] A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines

R Nayak, Y Hasija - Genomics, 2021 - Elsevier
Single-cell transcriptomics (SCT) is a tour de force in the era of big omics data that has led to
the accumulation of massive cellular transcription data at an astounding resolution of single …

Evaluating measures of association for single-cell transcriptomics

MA Skinnider, JW Squair, LJ Foster - Nature methods, 2019 - nature.com
Single-cell transcriptomics provides an opportunity to characterize cell-type-specific
transcriptional networks, intercellular signaling pathways and cellular diversity with …

[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 …

[HTML][HTML] Challenges and emerging directions in single-cell analysis

GC Yuan, L Cai, M Elowitz, T Enver, G Fan, G Guo… - Genome biology, 2017 - Springer
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular
information at the individual cell level. Development of single-cell technologies and …

Pervasive correlated evolution in gene expression shapes cell and tissue type transcriptomes

C Liang, JM Musser, A Cloutier… - Genome Biology and …, 2018 - academic.oup.com
The evolution and diversification of cell types is a key means by which animal complexity
evolves. Recently, hierarchical clustering and phylogenetic methods have been applied to …

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 …