Publications
(*) joint first authors with equal contribution
(#) corresponding authors
Preprints
I-Uen Hsu, Jia Zhao, Yingxin Lin, Yunshan Guo, Qian Xu, Yuancheng Shao, Ruiqi Wang, Dominc Yin, Kakali Ghoshal, Rida Mourad, Ambra Pozzi, Carmen Halabi, Lawrence Young, Hongyu Zhao, Le Zhang (#), Rui Chang (#). Lineage Prepatterning and Organ Instructions Sequentially Build Organ Intrinsic Nervous Systems. Preprint. 2026+.
Jia Zhao, Xiangyu Zhang, Gefei Wang, Yingxin Lin, Tianyu Liu, Rui B. Chang, Hongyu Zhao (#). INSPIRE: interpretable, flexible and spatially-aware integration of multiple spatial transcriptomics datasets from diverse sources. Preprint. 2026+. [bioRxiv] [Software] [Website]
Gefei Wang, Tianyu Liu, Jia Zhao, Youshu Cheng, Hongyu Zhao (#). Modeling and predicting single-cell multi-gene perturbation responses with scLAMBDA. Preprint. 2026+. [bioRxiv] [Software]
Yunshan Guo, Jia Zhao, Rui B. Chang, Hongyu Zhao (#). scGPD: single-cell informed gene panel design for targeted spatial transcriptomics. Preprint. 2026+. [bioRxiv] [Software]
Publications
Leqi Xu, Wangjie Zheng, Jiaqi Hu, Yingxin Lin, Jia Zhao, Gefei Wang, Tianyu Liu, Hongyu Zhao (#). Improving polygenic risk prediction performance by integrating electronic health records by phenotype embedding. The American Journal of Human Genetics. 112(12), 3030-3045, 2025. [AJHG] [bioRxiv] [Software]
The Tabula Microcebus Consortium†, Camille Ezran (*), Shixuan Liu (*), Stephen Chang (*), Jingsi Ming, Olga Botvinnik, Lolita Penland, Alexander Tarashansky, Antoine de Morree, Kyle J. Travaglini, Jia Zhao, Gefei Wang, Kazuteru Hasegawa, Hosu Sin, Rene Sit, Jennifer Okamoto, Rahul Sinha, Yue Zhang, Caitlin J. Karanewsky, Jozeph L. Pendleton, Maurizio Morri, Martine Perret, Fabienne Aujard, Lubert Stryer, Steven Artandi, Margaret Fuller, Irving L. Weissman, Thomas A. Rando, James E. Ferrell, Jr., Bo Wang, Iwijn De Vlaminck, Can Yang, Kerriann M. Casey, Megan A. Albertelli, Angela Oliveira Pisco, Jim Karkanias, Norma Neff, Angela Ruohao Wu, Stephen R. Quake (#), Mark A. Krasnow (#). †Jia Zhao is a member of the Tabula Microcebus Consortium. A molecular cell atlas of mouse lemur, an emerging model primate. Nature. 644(8075), 173-184, 2025. [Nature] [bioRxiv] [Website]
In this project, our computational method Portal facilitates evolutionary comparisons of cell types and gene expression patterns across human, macaque, lemur and mouse, using mouse as a non-primate outgroup to investigate gene expression changes during primate evolution..
Camille Ezran (*), Shixuan Liu (*), Stephen Chang (*), Jingsi Ming, Lisbeth A. Guethlein, Michael F.Z. Wang, Roozbeh Dehghannasiri, Julia Olivieri, Hannah K. Frank, Alexander Tarashansky, Winston Koh, Qiuyu Jing, Olga Botvinnik, Jane Antony, The Tabula Microcebus Consortium†, Angela Oliveira Pisco, Jim Karkanias, Can Yang, James E. Ferrell Jr., Scott D. Boyd, Peter Parham, Jonathan Z. Long, Bo Wang, Julia Salzman, Iwijn De Vlaminck, Angela Wu, Stephen R. Quake (#), Mark A. Krasnow (#). †Jia Zhao is a member of the Tabula Microcebus Consortium. Mouse lemur cell atlas informs primate genes, physiology, and disease. Nature. 644(8075), 185-196, 2025. [Nature] [bioRxiv] [Website]
Tianyu Liu, Jia Zhao, Hongyu Zhao (#). SuperGLUE facilitates an explainable training framework for multi-modal data analysis. Cell Reports Methods. 5(9), 2025. [Cell Reports Methods] [bioRxiv] [Software]
Xiangyu Zhang, Lijun Wang, Jia Zhao, Hongyu Zhao (#). Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies. The American Journal of Human Genetics. 112(10), 2476-2492, 2025. [AJHG] [bioRxiv] [Software] [Website]
Gefei Wang, Jia Zhao, Yingxin Lin, Tianyu Liu, Yize Zhao, Hongyu Zhao (#). scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links. Nature Communications. 16(1), 4994, 2025. [Nature Communications] [bioRxiv] [Software] [Website]
Shixuan Liu, Camille Ezran, Michael F. Z. Wang, Zhengda Li, The Tabula Microcebus Consortium†, Jonathon Z. Long, Iwijn De Vlaminck, Sheng Wang, Christin Kuo, Jacques Epelbaum, Jeremy Terrien, Mark A. Krasnow (#), James E. Ferrell, Jr. (#). †Jia Zhao is a member of the Tabula Microcebus Consortium. An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nature Communications. 15(1), 2188, 2024. [Nature Communications] [Project website]
Gefei Wang (*), Jia Zhao (*), Yan Yan, Yang Wang, Angela Ruohao Wu (#), Can Yang (#). Construction of a 3D whole organism spatial atlas by joint modelling of multiple slices with deep neural networks. Nature Machine Intelligence. 5(11), 1200-1213, 2023. [Nature Machine Intelligence] [Full text] [bioRxiv] [Software] [Website]
Jingsi Ming, Jia Zhao, Can Yang (#). scPI: a scalable framework for probabilistic inference in single-cell RNA-sequencing data analysis. Statistics in Biosciences. 15, 633–656, 2023. [Statistics in Biosciences] [PDF] [Software]
Winner of the 2024 Statistics in Biosciences Best Paper Award.
Jia Zhao (*), Gefei Wang (*), Jingsi Ming, Zhixiang Lin, Yang Wang, The Tabula Microcebus Consortium†, Angela Ruohao Wu (#), Can Yang (#). †Jia Zhao is a member of the Tabula Microcebus Consortium. Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets. Nature Computational Science. 2(5), 317–330, 2022. [Nature Computational Science] [Full text] [bioRxiv] [Software] [Blog]
The proposed computational method contributes to the mouse lemur cell atlas project, led by the Tabula Microcebus Consortium.
Jingsi Ming (*), Zhixiang Lin (*), Jia Zhao, Xiang Wan, The Tabula Microcebus Consortium†, Can Yang (#), Angela Ruohao Wu (#). †Jia Zhao is a member of the Tabula Microcebus Consortium. FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets. Briefings in Bioinformatics. bbac167, 2022. [Briefings in Bioinformatics] [bioRxiv] [Software]
Xianghong Hu (*), Jia Zhao (*), Zhixiang Lin, Yang Wang, Heng Peng, Hongyu Zhao (#), Xiang Wan (#), Can Yang (#). Mendelian Randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics. Proceedings of the National Academy of Sciences. 119(28), e2106858119, 2022. [PNAS] [bioRxiv] [Software]
Jia Zhao, Jingsi Ming, Xianghong Hu, Gang Chen, Jin Liu, Can Yang (#). Bayesian weighted Mendelian randomization for causal inference based on summary statistics. Bioinformatics. 36(5), 1501-1508, 2020. [Bioinformatics] [Software]