Spaceland reconstructs high-resolution 3D molecular atlases from sparse spatial transcriptomics and histology, improving resolution and accuracy across multiple biological contexts.

bioRxiv · Jul 27, 2026 · PreprintBioinformatics

Intraperitoneal programming of tailored CAR macrophages via mRNA-LNP to boost cancer immunotherapy

Kedan Gu, Ting Liang, Luting Hu, Yifan Zhao, Weiyang Ying, Mengke Zhang, Yashuang Chen, Benmeng Liang, Xinrui Lin, Yanqi Zhang, Hongyu Wu, Meng Wang, Yuping Zhu, Wenxi Wang, Y. Zhang, , Weihong Tan

This study develops an mRNA-LNP delivery system to program CAR-Ms in vivo, showing enhanced antitumor effects through immune activation and synergy with PD-1/L1 therapy.

Nature Communications · Dec 24, 2025Peer-reviewedBioengineering

Well-Paired-Seq2: High-Throughput and High-Sensitivity Strategy for Characterizing Low RNA-Content Cell/Nucleus Transcriptomes

Kun Yin, Meijuan Zhao, Yiling Xu, Zhong Zheng, Shanqing Huang, Dianyi Liang, He Dong, Ye Guo, Li Lin, Jia Tao Song, Huimin Zhang, Junhua Zheng, Zhi Zhu, Chaoyong James Yang

The paper introduces WPS2, a high-throughput and high-sensitivity scRNA-seq method, which improves gene and transcript detection in low RNA-content cells and nuclei.

Analytical Chemistry · Apr 10, 2024Peer-reviewedGenetics

mitoSplitter: A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq

Xinrui Lin, Yingwen Chen, Li Lin, Kun Yin, Rui Cheng, Xin Lin, Xiaoyu Wang, Ye Guo, Zhaorun Wu, Yingkun Zhang, Jin Li, Chaoyong James Yang, Jia Tao Song

mitoSplitter uses mitochondrial RNA variants to demultiplex pooled single-cell RNA-seq data, enabling efficient analysis of multiple samples without batch effects.

Proceedings of the National Academy of Sciences · Sep 19, 2023Peer-reviewedBioinformatics

Dendrimeric DNA Coordinate Barcoding Design for Spatial RNA Sequencing

Jiao Cao, Zhong Zheng, Di Sun, Xin Chen, Rui Cheng, Tianpeng Lv, Yu An, Junhua Zheng, Jia Tao Song, Lingling Wu, Chaoyong James Yang

Decoder-seq is a spatial RNA sequencing method that provides high-resolution, cost-effective, and sensitive spatial transcriptomic analysis, revealing detailed spatial gene expression patterns in mouse hippocampus and renal cancer.

bioRxiv · Jun 26, 2023 · PreprintGenomics

Single-cell transcriptome lineage tracing of human pancreatic development identifies distinct developmental trajectories of alpha and beta cells

Li Lin, Yufeng Zhang, Weizhou Qian, Yao Liu, Yingkun Zhang, Fanghe Lin, Cenxi Liu, Guangxing Lu, Yanling Song, Jia Tao Song, Chaoyong James Yang, Jin Li

This study uses single-cell RNA-seq and mitochondrial variants to trace lineage differences between alpha and beta cells in human pancreatic development, revealing distinct developmental trajectories not seen in mice.

bioRxiv · Jan 14, 2021 · PreprintDevelopmental Biology

Evolutionary patterns of 64 vertebrate genomes (species) revealed by phylogenomics analysis of protein-coding gene families

Jia Tao Song, Xia Han, Kui Lin

The paper develops a phylogenomics workflow to analyze 64 vertebrate genomes, revealing evolutionary patterns and duplication/loss events with high accuracy.

bioRxiv · Mar 31, 2020 · PreprintBioinformatics