Peng Ye

Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement

This paper introduces scMRDR, a framework for integrating unpaired single-cell and spatial multi-omics data, showing strong performance in batch correction and spatial mapping.

scDNAm-GPT Captures Genome-wide CpG Dependencies in Single-cell DNA methylomes to Revolutionize Epigenetic Analysis

scDNAm-GPT is a foundation model for single-cell DNA methylation analysis that improves clustering, trajectory inference, and deconvolution using context-aware tokenization and attention mechanisms.

Genomics-FM: Universal Foundation Model for Versatile andData-Efficient Functional Genomic Analysis

Genomics-FM is a foundation model that reduces reliance on labeled data and outperforms existing models in genome annotation, epigenomic prediction, and variant effect assessment.