Sirui Liu

The paper introduces INF, an algorithm that integrates protein and gene level information to analyze regulatory circuits and their role in cellular responses and identity.

This paper introduces RASP, a deep learning model that improves structure prediction with restraints, and FAAST, a pipeline that accelerates NMR NOESY peak assignment and structure ensemble generation.

ColabDock improves protein-protein docking by integrating experimental restraints into a framework that outperforms existing methods in complex structure prediction.

This paper introduces a spectral regularizer to disentangle entropy from coevolution in sequence models, improving interpretability and reducing overfitting in contact map inference.

The paper examines chromatin structural changes and epigenetic reprogramming during mouse and human embryonic development, showing domain segregation correlates with genetic and epigenetic changes.

The paper quantifies the relationship between 3D chromatin structure and gene regulation by analyzing domain segregation and gene expression patterns in different tissues.