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Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

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Published on: September 5, 2019

Single-cell trajectory inference for detecting transient events in biological processes.

Alexandre Hutton¹, Jesús Muñoz-Estrada¹, Jesse G Meyer¹

¹Department of Computational Biomedicine, Board of Governors Innovation Center, Cedars Sinai Medical Center, Los Angeles CA 90048, United States.

Nucleic Acids Research

|April 25, 2026

Summary

scTransient identifies transient gene expression events in single-cell data. This method detects short-lived regulatory programs crucial for cell development and differentiation.

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Area of Science:

Single-cell omics
Computational biology
Systems biology

Background:

Transient gene or protein expression changes are critical regulatory checkpoints in cellular transitions.
These short-lived expression events are often missed in sparse and noisy single-cell omics data.

Purpose of the Study:

To introduce scTransient, a novel computational method for detecting transient molecular events in single-cell expression data.
To enhance the analysis of dynamic cellular processes by quantifying fleeting regulatory programs.

Main Methods:

scTransient transforms single-cell expression profiles into continuous pseudotime signals.
It employs wavelet-based signal processing to isolate short-lived gene activity bursts.
A continuous wavelet transform is applied to assign a transient-event score (TES) to each gene.

Main Results:

Synthetic benchmarks show TES robustly recovers transient events across various parameters.
scTransient successfully detected transient events in induced neuron development and single-cell cell cycle datasets.
The method identified key proteins, including stem cell regulators and S-phase DNA replication factors.

Conclusions:

scTransient effectively detects transient molecular events that are often missed in traditional analyses.
The method extends trajectory inference beyond descriptive ordering to quantitative detection of regulatory programs.
scTransient provides a practical approach to uncover transient events driving cell development, differentiation, and disease.