Work

TIPS

Year: 2026

Type: software

Abstract: Understanding how developmental fate choices emerge within plastic, transition-prone progenitor states is crucial for early disease intervention. Transition-state detection identifies where fate decisions may emerge but not how gene interactions are associated with alternative stable descendants. We developed TIPS (Transcriptional Instability–guided Prediction of Subnetworks) to address this gap. Downstream of transition-state detection, TIPS reweights protein-interaction edges across a progenitor and candidate descendants, then uses supported transcription factor–target relationships to derive compact, descendant-associated modules. In hematopoietic lineage tracing, hematoendothelial differentiation, and cardaic developmental datasets, TIPS links detectable progenitor bottlenecks to prospective fate-informative, interpretable regulatory structure before commitment.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.22019706

Authors: Yang, Xinan Holly, Yu, Felix

Institution: University of Chicago

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: National Institutes of Health

Award: Hedgehog Signaling as a regulator of progenitor differentiation for organ maintenance and disease

OpenAlex ID: W7203944487

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