Hongcheng Yao

Integration of large, complex single-cell datasets with Harmony2

Harmony2 integrates large single-cell RNA-seq datasets efficiently and accurately, preventing overintegration in biologically diverse data.

Inferring CTCF binding patterns and anchored loops across human tissues and cell types

The paper develops DeepAnchor, a deep learning model to characterize CTCF binding patterns and predict CTCF-anchored loops across human tissues, revealing sequence and chromatin features that influence loop formation and disease mechanisms.

Endogenous fine-mapping of functional regulatory elements in complex genetic loci

The paper identifies causal regulatory elements in complex genetic loci using CRISPR perturbations and shows that many causal variants lack classical epigenetic markers.

Whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants

This paper develops regBase, a database of whole genome base-wise aggregations of regulatory variant predictions, and three composite models to score functional, pathogenic, and cancer driver variants, showing superior performance in fine-mapping causal variants.