Weize Xu

U-Chrom: a unified framework for single-cell and spatial 3D genome data

U-Chrom provides a unified framework for analyzing single-cell and spatial 3D genome data, showing consistent cell-type differences across assays.

Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems

Bio-Babel reconstructs computational biology software in new ecosystems, enabling agent-callable usage and revealing pancreatic differentiation defects under SWI/SNF loss.

U-Probe: universal agentic probe design for imaging-based spatial-omics

U-Probe is a universal probe design platform that enables agentic, AI-assisted creation of FISH probes for spatial-omics applications, validated across multiple scenarios.

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery

PantheonOS introduces a multi-agent framework for automated genomics analysis, achieving super-human performance in batch correction and gene panel selection across diverse biological tasks.

U-FISH: a universal deep learning approach for accurate FISH spot detection across diverse datasets

U-FISH improves FISH spot detection accuracy and generalization using a deep learning approach with a U-Net model and a large annotated dataset.

Robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing (MGA-Seq)

This study introduces MGA-Seq, a method to detect multiple genomic abnormalities, and finds that focal amplification in tumors is heterogeneous and reveals ecDNA network architecture.

Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics

The paper develops MiP-Seq, a multiomics in situ sequencing method, to analyze spatial gene profiles, mutations, and RNA modifications at single-cell resolution.

CoolBox: A flexible toolkit for visual analysis of genomics data

CoolBox is a flexible open-source toolkit for visualizing genomics data, compatible with Python, offering customization and integration with Jupyter and web browsers.

DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

The paper introduces DLO Hi-C Tool for analyzing DLO Hi-C data, providing a pipeline from raw reads to contact maps with quality controls and efficient processing.

CoolBox: a interactive genomic data explorer for Jupyter Notebook

CoolBox provides an interactive genomic data exploration tool for Jupyter Notebook with a ggplot2-like API and GUI support for multi-omics data.