Xiaomeng Wan

Hierarchical distribution matching enables comprehensive characterization of common and condition-specific cell niches in spatial omics data

This paper introduces Harmonics, a framework for identifying common and condition-specific cell niches in spatial omics data, demonstrating its effectiveness across diverse datasets and diseases.

Characterizing dynamic tissue architectures by identifying cell-type-specific spatiotemporal gene programs with stGP

This paper introduces stGP, a statistical framework to identify cell-type-specific spatiotemporal gene programs, revealing how gene programs are influenced by time and spatial structure in tissues.

NicheScope: Identifying Multicellular Niches and Niche-Regulated Cell States in Spatial Transcriptomics

NicheScope identifies multicellular niches and their regulated cell states from spatial transcriptomics data, revealing tissue structures and clinically relevant tumor niches.

A unified framework for cell-type-specific eQTLs prioritization by integrating bulk and scRNA-seq data

This paper introduces IBSEP, a statistical framework that integrates bulk and scRNA-seq data to prioritize cell-type-specific eQTLs, showing improved performance over existing methods.

UCS: a unified approach to cell segmentation for subcellular spatial transcriptomics

UCS improves cell segmentation for subcellular spatial transcriptomics by integrating nuclei and transcript data, enhancing accuracy and enabling downstream analyses.

Benchmarking Mendelian Randomization methods for causal inference using genome-wide association study summary statistics

This study benchmarks 15 Mendelian Randomization methods using real genetic data to evaluate their performance in causal inference under various confounding scenarios.

SpatialScope: A unified approach for integrating spatial and single-cell transcriptomics data using deep generative models

SpatialScope integrates spatial and single-cell transcriptomics data using deep generative models to achieve single-cell resolution and infer transcriptome-wide expression levels.

Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis

The paper defines the single-cell spatiotemporal gene expression landscape of human embryonic development using stem-cell-derived organoids and identifies key developmental signatures and signaling pathways.