Publication

  1. Cang, Zixuan, Yaqi Wu, Yanxiang Zhao. "Supervised Gromov-Wasserstein Optimal Transport" (2024).
    Preprint
  2. Huynh, Tram, Zixuan Cang. "Topological and geometric analysis of cell states in single-cell transcriptomic data." Briefings in Bioinformatics (2024).
    Preprint
  3. Chen, Jiahui, Yongjia Xu, Xin Yang, Zixuan Cang, Weihua Geng, Guo-Wei Wei. "Poisson-Boltzmann based machine learning (PBML) model for electrostatic analysis." Biophysical Journal (2024).
    Published Version | Preprint
  4. Dover, Kathryn, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin. "AVIDA: Alternating method for visualizing and integrating data." Journal of Computational Science 68, (2023): 101998.
    Published Version | Preprint
  5. Cang, Zixuan, Yanxiang Zhao, Axel A. Almet, Adam Stabell, Raul Ramos, Maksim V. Plikus, Scott X. Atwood, 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
  6. Cang, Zixuan, Qing Nie, Yanxiang Zhao. "Supervised optimal transport." SIAM Journal on Applied Mathematics 82, no. 5 (2022): 1851-1877.
    Published Version | Preprint
  7. Ren, Honglei, Benjamin L. Walker, Zixuan Cang, Qing Nie. "Identifying multicellular spatiotemporal organization of cells with SpaceFlow." Nature Communications 13, no. 1 (2022): 4076.
    Published Version
  8. Walker, Benjamin L., Zixuan Cang, Honglei Ren, Eric Bourgain-Chang, Qing Nie. "Deciphering tissue structure and function using spatial transcriptomics." Communications Biology 5, no. 1 (2022): 1-10.
    Published Version
  9. Tatarakis, David, Zixuan Cang, Xiaojun Wu, Praveer P. Sharma, Matthew Karkomi, Adam L. Maclean, Qing Nie, 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
  10. Cang, Zixuan, Xinyi Ning, Annika Nie, Min Xu, and Jing Zhang. "Scan-IT: Domain segmentation of spatial transcriptomics images by graph neural network." In BMVC. (2021).
    Published Version
  11. Mehrabi, Mehrsa, Tessa A. Morris, Zixuan Cang, Cecilia HH 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 (2021): 1-16.
    Published Version
  12. 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
  13. 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
  14. Cang, Zixuan, Yangyang Wang, Qixuan Wang, Ken WY 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
  15. 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): 636743.
    Published Version
  16. 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, no. 4 (2020): 481-507.
    Published Version | Preprint
  17. Guo, Ruiqiong, Zixuan Cang, Jiaqi Yao, Miyeon Kim, Erin Deans, Guowei 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
  18. Cang, Zixuan, and Qing Nie. "Inferring spatial and signaling relationships between cells from single cell transcriptomic data." Nature communications 11, no. 1 (2020): 1-13.
    Published Version | UCI News
  19. Haensel, Daniel, Suoqin Jin, Peng Sun, Rachel Cinco, Morgan Dragan, Quy Nguyen, Zixuan Cang et al. "Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics." Cell reports 30, no. 11 (2020): 3932-3947.
    Published Version | Preprint
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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 34, no. 2 (2018): e2914.
    Published Version | Preprint
  26. 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
  27. 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
  28. 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
  29. Cang, Zixuan, Lin Mu, Kedi Wu, Kristopher Opron, Kelin Xia, and Guo-Wei Wei. "A topological approach for protein classification." Computational and Mathematical Biophysics 3, no. 1 (2015).
    Published Version | Preprint