Publications
Publications
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(*) joint first authors with equal contribution
(#) corresponding authors
Preprints
Preprints
INSPIRE: interpretable, flexible and spatially-aware integration of multiple spatial transcriptomics datasets from diverse sources.
[bioRxiv] [Software] [Website]
Jia Zhao, Xiangyu Zhang, Gefei Wang, Yingxin Lin, Tianyu Liu, Rui B. Chang, Hongyu Zhao (#).
Preprint. 2025+.
Modeling and predicting single-cell multi-gene perturbation responses with scLAMBDA.
Gefei Wang, Tianyu Liu, Jia Zhao, Youshu Cheng, Hongyu Zhao (#).
Preprint. 2025+.
Improving polygenic risk prediction performance through integrating electronic health records by phenotype embedding.
Leqi Xu, Wangjie Zheng, Jiaqi Hu, Yingxin Lin, Jia Zhao, Gefei Wang, Tianyu Liu, Hongyu Zhao (#).
Preprint. 2025+.
Publications
Publications
A molecular cell atlas of mouse lemur, an emerging model primate.
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.
Nature. 644(8075), 173-184, 2025.
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.
Mouse lemur cell atlas informs primate genes, physiology, and disease.
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.
Nature. 644(8075), 185-196, 2025.
SuperGLUE facilitates an explainable training framework for multi-modal data analysis.
[Cell Reports Methods] [bioRxiv] [Software]
Tianyu Liu, Jia Zhao, Hongyu Zhao (#).
Cell Reports Methods. 2025.
Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies.
[AJHG] [bioRxiv] [Software] [Website]
Xiangyu Zhang, Lijun Wang, Jia Zhao, Hongyu Zhao (#).
The American Journal of Human Genetics. 2025.
scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links.
[Nature Communications] [bioRxiv] [Software] [Website]
Gefei Wang, Jia Zhao, Yingxin Lin, Tianyu Liu, Yize Zhao, Hongyu Zhao (#).
Nature Communications. 16(1), 4994, 2025.
An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome.
[Nature Communications] [Project 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.
Nature Communications. 15(1), 2188, 2024.
Construction of a 3D whole organism spatial atlas by joint modelling of multiple slices with deep neural networks.
[Nature Machine Intelligence] [Full text] [bioRxiv] [Software] [Website]
Gefei Wang (*), Jia Zhao (*), Yan Yan, Yang Wang, Angela Ruohao Wu (#), Can Yang (#).
Nature Machine Intelligence. 5(11), 1200-1213, 2023.
scPI: a scalable framework for probabilistic inference in single-cell RNA-sequencing data analysis.
[Statistics in Biosciences] [PDF] [Software]
Jingsi Ming, Jia Zhao, Can Yang (#).
Statistics in Biosciences. 15, 633–656, 2023.
Winner of the 2024 Statistics in Biosciences Best Paper Award.
Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets.
[Nature Computational Science] [Full text] [bioRxiv] [Software] [Blog]
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.
Nature Computational Science. 2(5), 317–330, 2022.
The proposed computational method contributes to the mouse lemur cell atlas project, led by the Tabula Microcebus Consortium.
FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets.
[Briefings in Bioinformatics] [bioRxiv] [Software]
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.
Briefings in Bioinformatics. bbac167, 2022.
Mendelian Randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics.
Xianghong Hu (*), Jia Zhao (*), Zhixiang Lin, Yang Wang, Heng Peng, Hongyu Zhao (#), Xiang Wan (#), Can Yang (#).
Proceedings of the National Academy of Sciences. 119(28), e2106858119, 2022.
Bayesian weighted Mendelian randomization for causal inference based on summary statistics.
Jia Zhao, Jingsi Ming, Xianghong Hu, Gang Chen, Jin Liu, Can Yang (#).
Bioinformatics. 36(5), 1501-1508, 2020.
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