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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

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OncotreeVIS-an interactive graphical user interface for visualizing mutation tree cohorts.

Monica-Andreea Baciu-Drăgan^1,2, Niko Beerenwinkel^1,2

¹Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland.

Bioinformatics Advances

|November 10, 2025

Summary

oncotreeVIS is a new tool for visualizing tumor evolution using mutation trees. It enables detailed inspection and comparison of cancer cell phylogenies at the cohort level, aiding computational oncology research.

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Area of Science:

Computational Biology
Cancer Research
Bioinformatics

Background:

Single-cell sequencing and computational methods allow tumor evolutionary history reconstruction via mutation trees.
Existing tools lack detailed visualization, cohort-level comparison, and analysis capabilities for mutation trees.

Purpose of the Study:

To develop oncotreeVIS, an interactive graphical user interface (GUI) for visualizing mutation tree cohorts.
To enable detailed inspection, comparison, and cohort-level analysis of tumor phylogenies.

Main Methods:

Developed oncotreeVIS as an interactive GUI for visualizing mutation tree cohorts and posterior distributions.
Implemented visualization of single and joint genetic events (point mutations, copy number changes).
Enabled highlighting of matching subclones, conserved trajectories, and drug-gene interactions.

Main Results:

oncotreeVIS facilitates visual inspection of mutation tree clusters and pairwise tree distances.
The tool supports cohort-level analysis of tumor evolutionary trajectories.
It integrates with existing mutation tree inference tools.

Conclusions:

oncotreeVIS enhances the analysis of tumor phylogenies by providing advanced visualization and comparison tools.
The tool supports computational oncology research by enabling cohort-level insights into cancer evolution.
oncotreeVIS is available as a JavaScript library and a web application, with example datasets provided.