Alignment of cell lineage trees elucidates genetic programs for the development and evolution of cell types

M Yuan, X Yang, J Lin, X Cao, F Chen, X Zhang, Z Li… - Iscience, 2020 - cell.com
A full understanding of the developmental process requires fine-scale characterization of
cell divisions and cell types, which are naturally organized as the developmental cell …

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

CT Hittinger, M Johnston… - Proceedings of the …, 2010 - National Acad Sciences
Assembling the tree of life is a major goal of biology, but progress has been hindered by the
difficulty and expense of obtaining the orthologous DNA required for accurate and fully …

Meta-analysis of RNA-seq expression data across species, tissues and studies

PH Sudmant, MS Alexis, CB Burge - Genome biology, 2015 - Springer
Background Differences in gene expression drive phenotypic differences between species,
yet major organs and tissues generally have conserved gene expression programs. Several …

Dissecting genomic diversity, one cell at a time

PC Blainey, SR Quake - Nature methods, 2014 - nature.com
Dissecting genomic diversity, one cell at a time | Nature Methods Skip to main content Thank
you for visiting nature.com. You are using a browser version with limited support for CSS. To …

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

L Zappia, FJ Theis - Genome biology, 2021 - Springer
Recent years have seen a revolution in single-cell RNA-sequencing (scRNA-seq)
technologies, datasets, and analysis methods. Since 2016, the scRNA-tools database has …

Single-cell RNA sequencing elucidates the structure and organization of microbial communities

MA Brennan, AZ Rosenthal - Frontiers in Microbiology, 2021 - frontiersin.org
Clonal bacterial populations exhibit various forms of heterogeneity, including co-occurrence
of cells with different morphological traits, biochemical properties, and gene expression …

Mapping the mouse cell atlas by microwell-seq

X Han, R Wang, Y Zhou, L Fei, H Sun, S Lai… - Cell, 2018 - cell.com
Single-cell RNA sequencing (scRNA-seq) technologies are poised to reshape the current
cell-type classification system. However, a transcriptome-based single-cell atlas has not …

Principles of transcriptome analysis and gene expression quantification: an RNA‐seq tutorial

JBW Wolf - Molecular ecology resources, 2013 - Wiley Online Library
Genome‐wide analyses and high‐throughput screening was long reserved for biomedical
applications and genetic model organisms. With the rapid development of massively parallel …

scmap: projection of single-cell RNA-seq data across data sets

VY Kiselev, A Yiu, M Hemberg - Nature methods, 2018 - nature.com
Single-cell RNA-seq (scRNA-seq) allows researchers to define cell types on the basis of
unsupervised clustering of the transcriptome. However, differences in experimental methods …

[HTML][HTML] Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq

B Lieberman, M Kusi, CN Hung, CW Chou… - Journal of …, 2021 - ncbi.nlm.nih.gov
Among single-cell analysis technologies, single-cell RNA-seq (scRNA-seq) has been one of
the front runners in technical inventions. Since its induction, scRNA-seq has been well …