Yang Liu

Integrated multi-omic and functional evidence uncover substantial strain-specific divergence in zebrafish

The paper compares two zebrafish strains using multi-omic data to identify genetic and regulatory differences affecting circadian rhythms and immune response.

Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping

Spatial tri-omic sequencing (DBiT ARP-seq and DBiT CTRP-seq) and CODEX imaging map chromatin, RNA, and protein dynamics across mammalian brain development and lysolecithin-induced neuroinflammation.

Binding Site-enhanced Sequence Pretraining and Out-of-cluster Meta-learning Predict Genome-Wide Chemical-Protein Interactions for Dark Proteins

PortalCG predicts chemical-protein interactions for dark proteins using a deep learning framework that integrates binding site information and meta-learning, outperforming existing methods in out-of-distribution scenarios.

DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework Towards Predicting Out-of-distribution Receptor Activity of Ligand Binding

DeepREAL predicts genome-scale receptor activity of ligand binding for novel chemicals using deep learning, addressing data scarcity and distribution shifts.