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Updated: Jan 9, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Pseudotimecascade visualizes gene expression cascade in pseudotime analysis.

Changxin Wan^1,2, Beijie Ji³, Zhicheng Ji^1,2

¹Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.

Biorxiv : the Preprint Server for Biology

|December 3, 2025

Summary

This summary is machine-generated.

Pseudotimecascade visualizes multi-gene expression cascades during cell differentiation. This tool reveals coordinated gene programs and stage-specific pathways, enhancing understanding of cell fate decisions.

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Last Updated: Jan 9, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

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Published on: July 1, 2020

Area of Science:

Computational Biology
Genomics
Cell Biology

Background:

Single-cell transcriptomics reveals dynamic biological processes like cell development.
Current pseudotime methods analyze individual gene expression, missing coordinated gene programs.
Understanding coordinated gene regulation is crucial for cell fate determination.

Purpose of the Study:

To introduce Pseudotimecascade, a novel computational tool.
To enable visualization and comparison of multi-gene expression cascades along pseudotime.
To link gene cascades to biological functions via stage-specific pathway identification.

Main Methods:

Development of the Pseudotimecascade software package.
Application of Pseudotimecascade to analyze hematopoietic stem cell differentiation.
Integration of gene expression data with pathway analysis.

Main Results:

Pseudotimecascade effectively visualizes multi-gene expression dynamics.
The tool identifies coordinated gene programs driving cellular transitions.
Analysis of hematopoietic stem cell differentiation revealed regulatory hierarchies and stage-specific processes.

Conclusions:

Pseudotimecascade offers a deeper understanding of gene programs governing cell fate.
The tool facilitates the study of coordinated gene regulation in biological processes.
Pseudotimecascade enhances the analysis of single-cell transcriptomic data for developmental studies.