Publications

* Joint first authors. # Corresponding authors. † Consortium membership.

Selected Publications

• scMODAL: A general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links. [Paper] [bioRxiv] [Software] [Website]

  Gefei Wang, Jia Zhao, Yingxin Lin, Tianyu Liu, Yize Zhao, Hongyu Zhao#.

  Nature Communications. 2025, 16(1): 4994.

• Construction of a 3D whole organism spatial atlas by joint modelling of multiple slices with deep neural networks. [Paper] [bioRxiv] [Software] [Website]

  Gefei Wang*, Jia Zhao*, Yan Yan, Yang Wang, Angela Ruohao Wu#, Can Yang#.

  Nature Machine Intelligence. 2023, 5(11): 1200–1213.

• Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets. [Paper] [bioRvix] [Blog] [Software]

  Jia Zhao*, Gefei Wang*, Jingsi Ming, Zhixiang Lin, Yang Wang, The Tabula Microcebus Consortium†, Angela Ruohao Wu#, Can Yang#. †Gefei Wang is a member of the Tabula Microcebus Consortium.

  Nature Computational Science. 2022, 2(5): 317-330.

• Deep generative learning via Schrödinger bridge. [Paper] [Code]

  Gefei Wang, Yuling Jiao#, Qian Xu, Yang Wang, Can Yang#.

  International Conference on Machine Learning. 2021, 10794-10804.

Other Publications

• A molecular cell atlas of mouse lemur, an emerging model primate. [Paper] [News] [bioRxiv] [Website]

  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#.

  Nature. 2025, 644(8075): 173-184.

• Mouse lemur cell atlas informs primate genes, physiology, and disease. [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#.

  Nature. 2025, 644(8075): 185-196.

• Bayesian longitudinal network regression with application to brain connectome genetics. [Paper]

  Chenxi Li*, Xinyuan Tian*, Simiao Gao, Selena Wang, Gefei Wang, Yi Zhao, Yize Zhao#.

  Statistics in Medicine. 2025, 44(8-9): e70069.

• An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. [Paper]

  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.#.

  Nature Communications. 2024, 15(1): 2188.

Preprints

• Brain functional-structural gradient coupling reflects development, behavior and genetic influences. [medRxiv]

  Simiao Gao*, Zhiling Gu*, Shengxian Ding*, Gefei Wang, Zhengwu Zhang, Hongyu Zhao, Yize Zhao#.

  medRxiv 2025; https://doi.org/10.1101/2025.09.16.25335918.

• Improving polygenic risk prediction performance through integrating electronic health records by phenotype embedding. [bioRxiv] [Software]

  Leqi Xu, Wangjie Zheng, Jiaqi Hu, Yingxin Lin, Jia Zhao, Gefei Wang, Tianyu Liu, Hongyu Zhao#.

  bioRxiv 2025; https://doi.org/10.1101/2025.08.05.668705.

• Modeling and predicting single-cell multi-gene perturbation responses with scLAMBDA. [bioRxiv] [Software]

  Gefei Wang, Tianyu Liu, Jia Zhao, Youshu Cheng, Hongyu Zhao#.

  bioRxiv 2024; https://doi.org/10.1101/2024.12.04.626878.

• 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#.

  bioRxiv 2024; doi: https://doi.org/10.1101/2024.09.23.614539.