Xuan He

This study introduces PULSE, a deep learning model that predicts pseudouridylation sites and characterizes their sequence features using convolutional neural networks.

This paper introduces GEM-FISH, a method that integrates Hi-C and FISH data to improve 3D chromosome modeling, showing better accuracy in TADs, compartments, and super-enhancer distributions than Hi-C alone.

ROSE predicts ribosome stalling from ribosome profiling data, showing better performance than conventional models and revealing regulatory factors and functional interactions.