Hua‐Jun Wu

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.

Hi-Compass predicts chromatin organization from single-cell and spatial ATAC-seq data, outperforming existing methods and enabling analysis across biological scales.

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

The paper constructs a single-cell-resolution spatial transcriptomic atlas of mouse cochlear development, revealing molecular gradients and tonotopic organization along the cochlear axis.

This study identifies convergent therapeutic targets for chemoresistance in cancer using CRISPR screens across multiple drug conditions and cancer models.

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

The paper introduces BendNet, a neural network that predicts DNA bending at base-resolution from sequences, revealing stiffness patterns and TF binding preferences in the human genome.

The paper identifies and characterizes LNCSOX17, a lncRNA essential for human endoderm formation, showing its role in regulating transcriptome and differentiation.

CopyKit is a computational tool that resolves clonal substructure and reconstructs genetic lineages in tumors using single cell copy number data.