PARROT: Phase-Altering Regulatory Rewiring Over Time

Authors

Chen, C., Padi, M., Quackenbush, J.

Abstract

Motivation: Gene regulatory networks undergo dynamic restructuring during development and disease. Identifying when and how these networks change is crucial for understanding developmental and disease transitions, yet existing change-point detection methods often ignore network structure or lack interpretable community assignments. Results: We present PARROT (Phase-Altering Regulatory Rewiring Over Time), a framework for detecting change- points in dynamic networks using Stochastic Block Models. PARROT jointly estimates change-point locations and community structure across four network classes: unipartite and bipartite with either Gaussian or Bernoulli edge models. Simulations demonstrate improved performance and community recovery compared to other methods. Applications to human cardiac differentiation and mouse lung development data successfully recovered known phase boundaries. PARROT identifies both which genes are reassigned across modules and how the connections change between states.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 29 Jun 2026.

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