Hongyu Yu

This paper introduces ProCEDiS, a framework that generates representative protein conformations using neural surrogates and AlphaFold2, validated on four protein systems.

ArcFISH identifies 3D genome features from multiplexed DNA FISH data by modeling axis-specific measurement errors, showing reliable detection of chromatin loops, TAD boundaries, and A/B compartments.

This paper introduces CAPE, a model that improves promoter strength prediction by incorporating evolutionary information, achieving state-of-the-art results and enabling in silico directed evolution.

SnapFISH-IMPUTE imputes missing values in multiplexed DNA FISH data, improving downstream analysis by preserving pairwise distances and enhancing clustering and enhancer-promoter loop detection.

SnapFISH identifies chromatin loops from multiplexed DNA FISH data with high sensitivity and accuracy in mouse embryonic stem cells.

SnapHiC-D identifies differential chromatin contacts between two scHi-C datasets with high sensitivity and accuracy, showing correlation with cell-type-specific gene expression and epigenomic features.