Nana Wei

The paper introduces STARK, a toolkit for processing sc3DG-seq data, benchmarks 11 technologies, and establishes scNucleome as a resource for 3D genome research.

This study introduces FindMeta3D to analyze microbial 3D genomes and cross-domain interactions, revealing conserved chromatin patterns and infection-related hotspots with therapeutic implications.

Spider generates synthetic spatial transcriptomics data by simulating cell type proportions and transitions, enabling benchmarking of analysis tools.

The paper develops a protein large language model-based method to improve gene homology mapping in cross-species single-cell transcriptome integration, increasing homology pairs and identifying novel cell-type markers.

CellPatch is a lightweight foundation model for single-cell transcriptomics that achieves state-of-the-art performance with low computational costs.

STCC improves spatial domain detection in spatial transcriptomics by combining multiple clustering tools through consensus strategies, enhancing accuracy and stability across different data types.