PARROT: Phase-Altering Regulatory Rewiring Over Time.

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. Availability: PARROT is available as an R package at https://github.com/cchen22/PARROT. Contact: chenchen9945@gmail.com. Supplementary information: Supplementary data are available at Bioinformatics online.