Publications
* Joint first authors. # Corresponding authors. † Consortium membership.
2025
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. 2025. [Paper] [bioRxiv] [Software] [Website]
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. Nature Genetics. 2025+, in press. [bioRxiv] [Software] [Website]
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 through phenotype embedding. The American Journal of Human Genetics. 2025. [Paper] [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#. A molecular cell atlas of mouse lemur, an emerging model primate. Nature. 2025. [Paper] [News] [bioRxiv] [Website]
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 Ruohao Wu, Stephen R. Quake#, Mark A. Krasnow#. Mouse lemur cell atlas informs primate genes, physiology, and disease. Nature. 2025. [Paper] [News] [bioRxiv] [Website]
Chenxi Li*, Xinyuan Tian*, Simiao Gao, Selena Wang, Gefei Wang, Yi Zhao, Yize Zhao#. Bayesian longitudinal network regression with application to brain connectome genetics. Statistics in Medicine. 2025. [Paper]
Simiao Gao*, Zhiling Gu*, Shengxian Ding*, Gefei Wang, Zhengwu Zhang, Hongyu Zhao, Yize Zhao#. medRxiv. 2025. Brain functional-structural gradient coupling reflects development, behavior and genetic influences. [medRxiv]
2024
Gefei Wang, Tianyu Liu, Jia Zhao, Youshu Cheng, Hongyu Zhao#. Modeling and predicting single-cell multi-gene perturbation responses with scLAMBDA. bioRxiv. 2024. [bioRxiv] [Software]
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.#. An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nature Communications. 2024. [Paper]
2023
- 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. 2023. [Paper] [bioRxiv] [Software] [Website]
2022
- Jia Zhao*, Gefei Wang*, Jingsi Ming, Zhixiang Lin, Yang Wang, The Tabula Microcebus Consortium†, Angela Ruohao Wu#, Can Yang#. Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets. Nature Computational Science. 2022. [Paper] [bioRvix] [Blog] [Software]