This paper develops Deep-STARmap and Deep-RIBOmap for 3D spatial transcriptomics and translatomics in thick tissue blocks, enabling analysis of gene expression and immune interactions in human skin cancer.

Nature Methods · Nov 24, 2025Peer-reviewedGenomics

Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo

Zuwan Lin, Wenbo Wang, Arnau Marin‐Llobet, Qifu Li, Samuel D. Pollock, Xin Sui, Almir Aljović, Jaeyong Lee, Jongmin Baek, Ningyue Liang, Xinhe Zhang, Connie Kangni Wang, Jiahao Huang, Mai Liu, Zihan Gao, , Jia Liu B

The paper introduces STAgent, an AI tool that automates spatial transcriptomics analysis, revealing in vivo maturation of human stem cell-derived pancreatic cells.

bioRxiv · Apr 1, 2025 · PreprintGenomics

Search and Match across Spatial Omics Samples at Single-cell Resolution

Zefang Tang, Shuchen Luo, Hu Zeng, Jiahao Huang, Xin Sui, Morgan Wu, Xiao Wang

CAST enables spatial-to-spatial searching and matching of single-cell spatial omics data across technologies and conditions, identifying disease-associated pathways and translational efficiency variations.

Nature Methods · Sep 18, 2024Peer-reviewedBioinformatics

Diversity of ribosomes at the level of rRNA variation associated with human health and disease

Daphna Rothschild, Teodorus Theo Susanto, Xin Sui, Jeffrey P. Spence, Ramya Rangan, Naomi R. Genuth, Nasa Sinnott-Armstrong, Xiao Wang, Jonathan K. Pritchard, Maria Barna

This study identifies and characterizes rRNA variants in human tissues and cancer, revealing tissue-specific ribosome subtypes and cancer-specific ribosome variations.

Cell Genomics · Aug 6, 2024Peer-reviewedGenetics

Spatially Resolved Single-cell Translatomics at Molecular Resolution

Hu Zeng, Jiahao Huang, Jingyi Ren, Connie Kangni Wang, Zefang Tang, Haowen Zhou, Yiming Zhou, Hailing Shi, Abhishek J. Aditham, Xin Sui, Hongyu Chen, Jennifer A. Lo, Xiao Wang

The paper introduces RIBOmap, a 3D in situ method to profile mRNA translation at single-cell and spatial resolutions, revealing translation dependencies on cell cycle and subcellular localization in brain tissue.

Science · Jun 29, 2023Peer-reviewedGenomics

Spatiotemporally resolved transcriptomics reveals subcellular RNA kinetic landscape

Jingyi Ren, Haowen Zhou, Hu Zeng, Connie Kangni Wang, Jiahao Huang, Xiaojie Qiu, Xin Sui, Qiang Li, Xunwei Wu, Zuwan Lin, Jennifer A. Lo, Kamal Maher, Yichun He, Xin Tang, Judson Lam, , Xiao Wang

This paper introduces TEMPOmap, a method to profile subcellular RNA kinetics in single cells, revealing kinetic gene clusters with distinct functional roles.

Nature Methods · Apr 10, 2023Peer-reviewedGenomics

In situ electro-sequencing in three-dimensional tissues

Qiang Li, Zuwan Lin, Ren Liu, Xin Tang, Jiahao Huang, Yichun He, Xin Sui, Weiwen Tian, Hao Shen, Haowen Zhou, Hao Sheng, Hailing Shi, Ling Xiao, Xiao Wang, Jia Liu B

This paper introduces in situ electro-sequencing to map gene expression and electrophysiology in 3D tissues, improving cell type analysis and developmental trajectory reconstruction.

Cell · Apr 1, 2023Peer-reviewedGenomics