Publications

2026

1. PR

   

   MoE-TCR: Mixture-of-experts framework for pan-specific TCR-epitope binding prediction

   Wei Qu, Jinxing Li, Zhentao He, Jiayi Wang, and Shanfeng Zhu

   Pattern Recognition, Nov 2026

   Abs DOI Code

   MoE-TCR is a sparsely gated mixture-of-experts framework for pan-specific TCR-epitope binding prediction. It combines diverse expert architectures, including the criss-cross attention-based TECC model, to improve predictive accuracy and generalizability across benchmark datasets.

2. Commun Biol

   

   SpaDC enables sequence-based integrative analysis and regulatory inference of spatial chromatin accessibility data

   Chuanlong Ma, Chenghui Yang, Caiwei Zhen, Zhentao He, Yong Luo, and Lihua Zhang

   Communications Biology, Jun 2026

   Published June 6, 2026

   Abs DOI Code

   SpaDC is a graph-regularized convolutional neural network that integrates DNA sequence, chromatin accessibility, and spatial location for spatial epigenomics data denoising, integration, spatial domain identification, and regulatory-network inference.

3. Cell Syst.

   

   Interpretable Data Integration for Single Cell and Spatial Multi-Omics

   Chenghui Yang, Zhentao He, Qing Nie, and Lihua Zhang

   Cell Systems, Feb 2026

   Published online February 4, 2026

   Abs DOI Code

   FGOT is a feature-guided optimal transport method for paired and unpaired single-cell multi-omics data as well as paired spatial multi-omics data. It jointly reveals cellular heterogeneity and transcriptional regulatory links, while providing post hoc interpretability for existing integration methods.