Publication

  1. Wu, Yaqi, Jingfeng Wang, Xin Maizie Zhou, Yanxiang Zhao, Zixuan Cang. "RAFT-UP: Robust Alignment for Spatial Transcriptomics with Explicit Control of Spatial Distortion." arXiv preprint arXiv:2603.18249 (2026).
    Preprint
  2. Cang, Zixuan, Jingfeng Wang, Xiaoqi Wei, Yanxiang Zhao. "Synchronization of Unbalanced Dynamical Optimal Transport across Multiple Spaces." arXiv preprint arXiv:2602.18725 (2026).
    Preprint
  3. Beamer, Perry Z., and Zixuan Cang. "Multiscale domain identification for spatial transcriptomics via persistent homology." Cell Reports Methods 6, no. 5 (2026): 101376.
    Published Version | Preprint
  4. Bourgain-Chang, Eric, Xiangyu Kuang, Zixuan Cang, and Qing Nie. "Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner." Nature Communications 17 (2026): 3304.
    Published Version
  5. Wei, Xiaoqi, Xuhang Dai, Yaqi Wu, Yanxiang Zhao, Yingkai Zhang, and Zixuan Cang. "OTMol: Robust molecular structure comparison via optimal transport." Journal of Chemical Information and Modeling 65, no. 20 (2025): 11013-11028.
    Published Version | Preprint
  6. Cang, Zixuan, Yaqi Wu, and Yanxiang Zhao. "Supervised Gromov-Wasserstein optimal transport with metric-preserving constraints." SIAM Journal on Mathematics of Data Science 7, no. 1 (2025): 301-328.
    Published Version | Preprint
  7. Cang, Zixuan, and Yanxiang Zhao. "Synchronized optimal transport for joint modeling of dynamics across multiple spaces." SIAM Journal on Applied Mathematics 85, no. 1 (2025): 341-365.
    Published Version | Preprint
  8. Zaragoza, Michael V., Thuy-Anh Bui, Halida P. Widyastuti, Mehrsa Mehrabi, Zixuan Cang, Yutong Sha, Anna Grosberg, and Qing Nie. "LMNA-related dilated cardiomyopathy: Single-cell transcriptomics during patient-derived iPSC differentiation support cell type and lineage-specific dysregulation of gene expression and development for cardiomyocytes and epicardium-derived cells with Lamin A/C haploinsufficiency." Cells 13, no. 17 (2024): 1479.
    Published Version | Preprint
  9. Chen, Jiahui, Yongjia Xu, Xin Yang, Zixuan Cang, Weihua Geng, and Guo-Wei Wei. "Poisson-Boltzmann based machine learning (PBML) model for electrostatic analysis." Biophysical Journal 123, no. 17 (2024): 2807-2814.
    Published Version | Preprint
  10. Huynh, Tram, and Zixuan Cang. "Topological and geometric analysis of cell states in single-cell transcriptomic data." Briefings in Bioinformatics 25, no. 3 (2024): bbae176.
    Published Version | Preprint
  11. Dover, Kathryn, Zixuan Cang, Anna Ma, Qing Nie, and Roman Vershynin. "Avida: An alternating method for visualizing and integrating data." Journal of Computational Science 68 (2023): 101998.
    Published Version | Preprint
  12. Cang, Zixuan, Yanxiang Zhao, Axel A. Almet, Adam Stabell, Raul Ramos, Maksim V. Plikus, Scott X. Atwood, and Qing Nie. "Screening cell-cell communication in spatial transcriptomics via collective optimal transport." Nature Methods 20, no. 2 (2023): 218-228.
    Published Version | Nature Methods Research Briefing
  13. Cang, Zixuan, Qing Nie, and Yanxiang Zhao. "Supervised optimal transport." SIAM Journal on Applied Mathematics 82, no. 5 (2022): 1851-1877.
    Published Version | Preprint
  14. Ren, Honglei, Benjamin L. Walker, Zixuan Cang, and Qing Nie. "Identifying multicellular spatiotemporal organization of cells with SpaceFlow." Nature Communications 13, no. 1 (2022): 4076.
    Published Version
  15. Walker, Benjamin L., Zixuan Cang, Honglei Ren, Eric Bourgain-Chang, and Qing Nie. "Deciphering tissue structure and function using spatial transcriptomics." Communications Biology 5, no. 1 (2022): 220.
    Published Version
  16. Tatarakis, David, Zixuan Cang, Xiaojun Wu, Praveer P. Sharma, Matthew Karikomi, Adam L. MacLean, Qing Nie, and Thomas F. Schilling. "Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development." Cell Reports 37, no. 12 (2021): 110140.
    Published Version
  17. Cang, Zixuan, Xinyi Ning, Annika Nie, Min Xu, and Jing Zhang. "SCAN-IT: Domain segmentation of spatial transcriptomics images by graph neural network." In British Machine Vision Conference (2021).
    Published Version
  18. Mehrabi, Mehrsa, Tessa A. Morris, Zixuan Cang, Cecilia H. H. Nguyen, Yutong Sha, Mira N. Asad, Nyree Khachikyan, Taylor L. Greene, Danielle M. Becker, Qing Nie, Michael V. Zaragoza, and Anna Grosberg. "A study of gene expression, structure, and contractility of iPSC-derived cardiac myocytes from a family with heart disease due to LMNA mutation." Annals of Biomedical Engineering 49 (2021): 3524-3539.
    Published Version
  19. Zhu, Qing, Yuzhe Du, Yoshiko Nomura, Rong Gao, Zixuan Cang, Guo-Wei Wei, Dalia Gordon, Michael Gurevitz, James Groome, and Ke Dong. "Charge substitutions at the voltage-sensing module of domain III enhance actions of site-3 and site-4 toxins on an insect sodium channel." Insect Biochemistry and Molecular Biology 137 (2021): 103625.
    Published Version
  20. Almet, Axel A., Zixuan Cang, Suoqin Jin, and Qing Nie. "The landscape of cell-cell communication through single-cell transcriptomics." Current Opinion in Systems Biology 26 (2021): 12-23.
    Published Version
  21. Maseda, Floyd, Zixuan Cang, and Qing Nie. "Deepsc: A deep learning-based map connecting single-cell transcriptomics and spatial imaging data." Frontiers in Genetics 12 (2021): 348.
    Published Version
  22. Cang, Zixuan*, Yangyang Wang*, Qixuan Wang, Ken W. Y. Cho, William Holmes, and Qing Nie. "A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development." PLOS Computational Biology 17, no. 3 (2021): e1008571.
    Published Version
  23. Cang, Zixuan, Elizabeth Munch, and Guo-Wei Wei. "Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis." Journal of Applied and Computational Topology 4 (2020): 481-507.
    Published Version | Preprint
  24. Guo, Ruiqiong, Zixuan Cang, Jiaqi Yao, Miyeon Kim, Erin Deans, Guo-Wei Wei, Seung-gu Kang, and Heedeok Hong. "Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme." Proceedings of the National Academy of Sciences 117, no. 36 (2020): 22146-22156.
    Published Version
  25. Cang, Zixuan, and Qing Nie. "Inferring spatial and signaling relationships between cells from single cell transcriptomic data." Nature Communications 11, no. 1 (2020): 2084.
    Published Version | UCI News
  26. Cang, Zixuan, and Guo-Wei Wei. "Persistent cohomology for data with multicomponent heterogeneous information." SIAM Journal on Mathematics of Data Science 2, no. 2 (2020): 396-418.
    Published Version
  27. Haensel, Daniel, Suoqin Jin, Peng Sun, Rachel Cinco, Morgan Dragan, Quy Nguyen, Zixuan Cang, Yanwen Gong, Remy Vu, Adam L. MacLean, Kai Kessenbrock, Enrico Gratton, Qing Nie, and Xing Dai. "Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics." Cell Reports 30, no. 11 (2020): 3932-3947.e6.
    Published Version | Preprint
  28. Nguyen, Duc Duy, Zixuan Cang, and Guo-Wei Wei. "A review of mathematical representations of biomolecular data." Physical Chemistry Chemical Physics 22, no. 8 (2020): 4343-4367.
    Published Version | Preprint
  29. Wang, Menglun, Zixuan Cang, and Guo-Wei Wei. "A topology-based network tree for the prediction of protein-protein binding affinity changes following mutation." Nature Machine Intelligence 2, no. 2 (2020): 116-123.
    Published Version
  30. Nguyen, Duc Duy, Zixuan Cang, Kedi Wu, Menglun Wang, Yin Cao, and Guo-Wei Wei. "Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges." Journal of Computer-Aided Molecular Design 33, no. 1 (2019): 71-82.
    Published Version | Preprint
  31. Zhao, Rundong, Zixuan Cang, Yiying Tong, and Guo-Wei Wei. "Protein pocket detection via convex hull surface evolution and associated Reeb graph." Bioinformatics 34, no. 17 (2018): i830-i837.
    Published Version
  32. Cang, Zixuan, Lin Mu, and Guo-Wei Wei. "Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening." PLOS Computational Biology 14, no. 1 (2018): e1005929.
    Published Version | Preprint
  33. Cang, Zixuan, and Guo-Wei Wei. "TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions." PLOS Computational Biology 13, no. 7 (2017): e1005690.
    Published Version | Preprint | SIAM News | ICCM Best Paper Award 2019
  34. Cang, Zixuan, and Guo-Wei Wei. "Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction." International Journal for Numerical Methods in Biomedical Engineering (2017): e2914.
    Published Version | Preprint
  35. Cang, Zixuan, and Guo-Wei Wei. "Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology." Bioinformatics 33, no. 22 (2017): 3549-3557.
    Published Version | Preprint
  36. Cang, Zixuan, Lin Mu, Kedi Wu, Kristopher Opron, Kelin Xia, and Guo-Wei Wei. "A topological approach for protein classification." Molecular Based Mathematical Biology 3, no. 1 (2015): 140-162.
    Published Version | Preprint