Single-cell multiomics connects 3D genome and transcriptome alterations in Alzheimer’s disease

Yang Zhang^†, Xinyue Lu^†, Alexander K. Kunisky^‡, Shahul Alam^‡, Junjie Tang^‡, Ruochi Zhang^‡, Shike Wang, Han Zhang, Jude Baroudi, Walid Ichcho, Deyong Jia, Sahar Ghorbanikalateh, Sahel Ghorbanikalateh, Shihan Wang, David A. Bennett, Hansruedi Mathys^*, Zhijun Duan^*, Jian Ma^*.

† Yang Zhang and Xinyue Lu contributed equally. ‡ Alexander K. Kunisky, Shahul Alam, Junjie Tang, and Ruochi Zhang contributed equally within a separate group.

A collaborative study integrating genome structure, gene expression, and spatial context in human brain tissue.

SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data

Siyuan Huang^†, Qinghua Ran^†, Junjie Tang^†, Xiaochen Wang^†, Junqing Xi, Shiyang Ma^*, Ruibin Xi^*.

Quantifying cellular neighborhoods to characterize tissue niches and patterns of spatial organization.

The interpretable multimodal dimension reduction framework SpaHDmap enhances resolution in spatial transcriptomics

Junjie Tang^†, Zihao Chen^†, Kun Qian^†, Siyuan Huang, Yang He, Shenyi Yin, Xinyu He, Buqing Ye, Yan Zhuang, Hongxue Meng^*, Jianzhong Jeff Xi^*, Ruibin Xi^*.

Hongxue Meng, Jianzhong Jeff Xi, and Ruibin Xi jointly supervised this work.

Integrating histology and spatial expression measurements to identify interpretable gene modules and resolve tissue structure.

Steamboat: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues

Shaoheng Liang^*, Junjie Tang, Guanghan Wang, Jian Ma^*.

Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics

Xuanwei Chen, Qinghua Ran, Junjie Tang, Zihao Chen, Siyuan Huang, Xingjie Shi^*, Ruibin Xi^*.

Lead contact: Ruibin Xi.

A Generic Family of Graphical Models: Diversity, Efficiency, and Heterogeneity

Yufei Huang^†, Changhu Wang^†, Junjie Tang, Weichi Wu^*, Ruibin Xi^*.

TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models

Sizhe Liu, Junjie Tang, Jian Ma^*, Shaoheng Liang^*.

Single-cell gene regulatory network analysis for mixed cell populations

Junjie Tang^†, Changhu Wang^†, Feiyi Xiao, Ruibin Xi^*.

A hierarchical graphical model jointly inferring cell populations and their gene networks.

Estimating graphical models for count data with applications to single-cell gene network

Feiyi Xiao^†, Junjie Tang^†, Huaying Fang, Ruibin Xi^*.