Song, Tianci, Quoc Nguyen, Charles Broadbent, and Rui Kuang. 2026. “CTFacTomo: Reconstructing 3D Spatial Structures of RNA Tomography Transcriptomes by Collapsed Tensor Factorization”. PLOS Computational Biology 22. Public Library of Science: e1013457.
Spatial and Single-cell Genomics
Broadbent, Charles, Tianci Song, and Rui Kuang. 2024. “Deciphering High-Order Structures in Spatial Transcriptomes With Graph-Guided Tucker Decomposition”. Bioinformatics 40 (Special Issue of The Proceedings of The 32nd International Conference on Intelligent Systems for Molecular Biology (ISMB). Oxford University Press: i529-i538.
Song, Tianci, Eric Cosatto, Gaoyuan Wang, Rui Kuang, Mark Gerstein, Martin Renqiang Min, and Jonathan Warrell. 2024. “Predicting Spatially Resolved Gene Expression via Tissue Morphology Using Adaptive Spatial GNNs”. Bioinformatics 40 (Special Issue of The Proceedings of The 23rd European Conference on Computational Biology (ECCB). Oxford University Press: ii111-ii119.
Song, Tianci, Charles Broadbent, and Rui Kuang. 2023. “GNTD: Reconstructing Spatial Transcriptomes With Graph-Guided Neural Tensor Decomposition Informed by Spatial and Functional Relations”. Nature Communications 14. Nature Publishing Group UK London: 8276.
Song, Tianci, Kathleen K Markham, Zhuliu Li, Kristen E Muller, Kathleen Greenham, and Rui Kuang. 2022. “Detecting Spatially Co-Expressed Gene Clusters With Functional Coherence by Graph-Regularized Convolutional Neural Network”. Bioinformatics 38. Oxford University Press: 1344-52.
Li, Zhuliu, Tianci Song, Jeongsik Yong, and Rui Kuang. 2021. “Imputation of Spatially-Resolved Transcriptomes by Graph-Regularized Tensor Completion”. PLoS Computational Biology 17. Public Library of Science San Francisco, CA USA: e1008218.
Petegrosso, Raphael, Zhuliu Li, and Rui Kuang. 2020. “Machine Learning and Statistical Methods for Clustering Single-Cell RNA-Sequencing Data”. Briefings in Bioinformatics 21. Oxford University Press: 1209-23.
Zhang, Huanan, Catherine AA Lee, Zhuliu Li, John R Garbe, Cindy R Eide, Raphael Petegrosso, Rui Kuang, and Jakub Tolar. 2018. “A Multitask Clustering Approach for Single-Cell RNA-Seq Analysis in Recessive Dystrophic Epidermolysis Bullosa”. PLoS Computational Biology 14. Public Library of Science San Francisco, CA USA: e1006053.