2026

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

Xinyi Yu, Xiaomeng Wan, Leqi Tian, Yuheng Chen, Yuyao Liu, Tianwei Yu*, Can Yang*, Jiashun Xiao* (* corresponding author)

Nature Cell Biology (In revision) 2026

[Paper] [Code]

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

Xinyi Yu, Xiaomeng Wan, Leqi Tian, Yuheng Chen, Yuyao Liu, Tianwei Yu*, Can Yang*, Jiashun Xiao* (* corresponding author)

Nature Cell Biology (In revision) 2026

[Paper] [Code]

CellART: a unified framework for extracting single-cell information from high-resolution spatial transcriptomics
CellART: a unified framework for extracting single-cell information from high-resolution spatial transcriptomics

Yuheng Chen, Yuyao Liu, Zhiwei Wang, Yeqin Zeng, Zitong Chao, Peiqi Jiang, Hao Chen, Jiguang Wang, Jiashun Xiao*, Can Yang* (* corresponding author)

Nature Computational Science (In revision) 2026

[Code]

CellART: a unified framework for extracting single-cell information from high-resolution spatial transcriptomics

Yuheng Chen, Yuyao Liu, Zhiwei Wang, Yeqin Zeng, Zitong Chao, Peiqi Jiang, Hao Chen, Jiguang Wang, Jiashun Xiao*, Can Yang* (* corresponding author)

Nature Computational Science (In revision) 2026

[Code]

2025

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

Xinyi Yu, Xianghong Hu, Xiaomeng Wan, Zhiyong Zhang, Xiang Wan, Mingxuan Cai, Tianwei Yu*, Jiashun Xiao* (* corresponding author)

The American Journal of Human Genetics 2025

[Paper] [Code]

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

Xinyi Yu, Xianghong Hu, Xiaomeng Wan, Zhiyong Zhang, Xiang Wan, Mingxuan Cai, Tianwei Yu*, Jiashun Xiao* (* corresponding author)

The American Journal of Human Genetics 2025

[Paper] [Code]

UCS: A Unified Approach to Cell Segmentation for Subcellular Spatial Transcriptomics
UCS: A Unified Approach to Cell Segmentation for Subcellular Spatial Transcriptomics

Yuheng Chen, Xin Xu, Xiaomeng Wan, Jiashun Xiao*, Can Yang* (* corresponding author)

Small Methods 2025

[Paper] [Code]

UCS: A Unified Approach to Cell Segmentation for Subcellular Spatial Transcriptomics

Yuheng Chen, Xin Xu, Xiaomeng Wan, Jiashun Xiao*, Can Yang* (* corresponding author)

Small Methods 2025

[Paper] [Code]

2024

A Robust Statistical Approach for Finding Informative Spatially Associated Pathways
A Robust Statistical Approach for Finding Informative Spatially Associated Pathways

Leqi Tian, Jiashun Xiao*, Tianwei Yu* (* corresponding author)

Briefings in Bioinformatics 2024

[Paper] [Code]

A Robust Statistical Approach for Finding Informative Spatially Associated Pathways

Leqi Tian, Jiashun Xiao*, Tianwei Yu* (* corresponding author)

Briefings in Bioinformatics 2024

[Paper] [Code]

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

Xianghong Hu, Mingxuan Cai, Jiashun Xiao, Xiaomeng Wan, Zhiwei Wang, Hongyu Zhao, Can Yang* (* corresponding author)

The American Journal of Human Genetics 2024

[Paper] [Code]

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

Xianghong Hu, Mingxuan Cai, Jiashun Xiao, Xiaomeng Wan, Zhiwei Wang, Hongyu Zhao, Can Yang* (* corresponding author)

The American Journal of Human Genetics 2024

[Paper] [Code]

Endothelial pyroptosis-driven microglial activation in choroid plexus mediates neuronal apoptosis in hemorrhagic stroke rats
Endothelial pyroptosis-driven microglial activation in choroid plexus mediates neuronal apoptosis in hemorrhagic stroke rats

Lingui Gu, Hualin Chen, Ruxu Geng, Tingyu Liang, Yihao Chen, Zhuo Wang, Liguo Ye, Mingjiang Sun, Qinglei Shi, Gui Wan, Jianbo Chang, Junji Wei, Wenbin Ma*, Jiashun Xiao*, Xinjie Bao*, Renzhi Wang* (* corresponding author)

Neurobiology of Disease 2024

[Paper]

Endothelial pyroptosis-driven microglial activation in choroid plexus mediates neuronal apoptosis in hemorrhagic stroke rats

Lingui Gu, Hualin Chen, Ruxu Geng, Tingyu Liang, Yihao Chen, Zhuo Wang, Liguo Ye, Mingjiang Sun, Qinglei Shi, Gui Wan, Jianbo Chang, Junji Wei, Wenbin Ma*, Jiashun Xiao*, Xinjie Bao*, Renzhi Wang* (* corresponding author)

Neurobiology of Disease 2024

[Paper]

Single-cell and Spatial Transcriptomics Reveals Ferroptosis as The Most Enriched Programmed Cell Death Process in Hemorrhage Stroke-induced Oligodendrocyte-mediated White Matter Injury
Single-cell and Spatial Transcriptomics Reveals Ferroptosis as The Most Enriched Programmed Cell Death Process in Hemorrhage Stroke-induced Oligodendrocyte-mediated White Matter Injury

Lingui Gu, Hualin Chen, Ruxu Geng, Mingjiang Sun, Qinglei Shi, Yihao Chen, Jianbo Chang, Junji Wei, Wenbin Ma, Jiashun Xiao, Xinjie Bao*, Renzhi Wang* (* corresponding author)

International Journal of Biological Sciences 2024

[Paper]

Single-cell and Spatial Transcriptomics Reveals Ferroptosis as The Most Enriched Programmed Cell Death Process in Hemorrhage Stroke-induced Oligodendrocyte-mediated White Matter Injury

Lingui Gu, Hualin Chen, Ruxu Geng, Mingjiang Sun, Qinglei Shi, Yihao Chen, Jianbo Chang, Junji Wei, Wenbin Ma, Jiashun Xiao, Xinjie Bao*, Renzhi Wang* (* corresponding author)

International Journal of Biological Sciences 2024

[Paper]

2023

Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope
Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope

Xiaomeng Wan#, Jiashun Xiao#, Sindy Sing Ting Tam, Mingxuan Cai, Ryohichi Sugimura, Yang Wang, Xiang Wan, Zhixiang Lin, Angela Ruohao Wu, Can Yang* (# equal contribution, * corresponding author)

Nature Communications 2023

[Paper] [Code]

Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope

Xiaomeng Wan#, Jiashun Xiao#, Sindy Sing Ting Tam, Mingxuan Cai, Ryohichi Sugimura, Yang Wang, Xiang Wan, Zhixiang Lin, Angela Ruohao Wu, Can Yang* (# equal contribution, * corresponding author)

Nature Communications 2023

[Paper] [Code]

XMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias
XMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias

Mingxuan Cai, Zhiwei Wang, Jiashun Xiao, Xianghong Hu, Gang Chen, Can Yang* (* corresponding author)

Nature Communications 2023

[Paper] [Code]

XMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias

Mingxuan Cai, Zhiwei Wang, Jiashun Xiao, Xianghong Hu, Gang Chen, Can Yang* (* corresponding author)

Nature Communications 2023

[Paper] [Code]

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

Yiming Chao, Yang Xiang, Jiashun Xiao, Weizhong Zheng, Mo R Ebrahimkhani, Can Yang, Angela Ruohao Wu, Pentao Liu, Yuanhua Huang, Ryohichi Sugimura* (* corresponding author)

Signal transduction and targeted therapy 2023

[Paper]

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

Yiming Chao, Yang Xiang, Jiashun Xiao, Weizhong Zheng, Mo R Ebrahimkhani, Can Yang, Angela Ruohao Wu, Pentao Liu, Yuanhua Huang, Ryohichi Sugimura* (* corresponding author)

Signal transduction and targeted therapy 2023

[Paper]

PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations

Xinyi Yu, Jiashun Xiao, Mingxuan Cai, Yuling Jiao, Xiang Wan, Jin Liu, Can Yang

Bioinformatics 2023

[Paper] [Code]

PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations

Xinyi Yu, Jiashun Xiao, Mingxuan Cai, Yuling Jiao, Xiang Wan, Jin Liu, Can Yang

Bioinformatics 2023

[Paper] [Code]

2022

Leveraging the local genetic structure for trans-ancestry association mapping
Leveraging the local genetic structure for trans-ancestry association mapping

Jiashun Xiao#, Mingxuan Cai#, Xinyi Yu, Xianghong Hu, Gang Chen, Xiang Wan, Can Yang* (# equal contribution, * corresponding author)

The American Journal of Human Genetics 2022

[Paper] [Code]

Leveraging the local genetic structure for trans-ancestry association mapping

Jiashun Xiao#, Mingxuan Cai#, Xinyi Yu, Xianghong Hu, Gang Chen, Xiang Wan, Can Yang* (# equal contribution, * corresponding author)

The American Journal of Human Genetics 2022

[Paper] [Code]

XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis
XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis

Jiashun Xiao#, Mingxuan Cai#, Xianghong Hu, Xiang Wan, Gang Chen, Can Yang* (# equal contribution, * corresponding author)

Bioinformatics 2022

[Paper] [Code]

XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis

Jiashun Xiao#, Mingxuan Cai#, Xianghong Hu, Xiang Wan, Gang Chen, Can Yang* (# equal contribution, * corresponding author)

Bioinformatics 2022

[Paper] [Code]

2021

A unified framework for cross-population trait prediction by leveraging the genetic correlation of polygenic traits
A unified framework for cross-population trait prediction by leveraging the genetic correlation of polygenic traits

Mingxuan Cai#, Jiashun Xiao#, Shunkang Zhang#, Xiang Wan, Hongyu Zhao, Gang Chen, Can Yang* (# equal contribution, * corresponding author)

The American Journal of Human Genetics 2021

[Paper] [Code]

A unified framework for cross-population trait prediction by leveraging the genetic correlation of polygenic traits

Mingxuan Cai#, Jiashun Xiao#, Shunkang Zhang#, Xiang Wan, Hongyu Zhao, Gang Chen, Can Yang* (# equal contribution, * corresponding author)

The American Journal of Human Genetics 2021

[Paper] [Code]