Multi-species functional genomic data from various high-throughput assays are highly informative for the comparative analysis of gene regulation to better understand the molecular mechanisms of phenotypic diversity between human and other mammalian species. Continuous-trait models, which are key to the modeling of functional genomic signals, are gaining increasing attention in genome-wide comparative genomic studies. However, computational models are currently under-explored to fully capture continuous features in the context of multi-species comparisons. There have been several types of continuous-trait evolutionary models, including Brownian motion and Ornstein-Uhlenbeck (OU) process. However, to the best of our knowledge, there are no existing computational methods available to simultaneously infer heterogeneous continuous-trait evolutionary models along the genome based on functional genomic signals.
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