@article{GraphTucker,

title = {Deciphering High-order Structures in Spatial Transcriptomes with Graph-guided Tucker Decomposition},

author = {Charles Broadbent and Tianci Song and Rui Kuang},

url = {https://academic.oup.com/bioinformatics/article/40/Supplement_1/i529/7700901},

doi = {doi.org/10.1093/bioinformatics/btae245},

year  = {2024},

date = {2024-07-12},

urldate = {2024-07-12},

journal = {Bioinformatics (Supplement Issue of the Proceedings of 32nd International Conference on Intelligent Systems for Molecular Biology (ISMB))↩},

volume = {40},

number = {Supplement_1},

pages = {i529-i538},

howpublished = {To appear In the Proceedings of International Conference on Intelligent Systems for Molecular Biology (ISMB) 2024},

keywords = {Multi-relational learning, Spatial Transcriptomics, Tensor Completion},

pubstate = {published},

tppubtype = {article}

}

@article{GNTD,

title = {GNTD: Reconstructing Spatial Transcriptomes with Graph-guided Neural Tensor Decomposition Informed by Spatial and Functional Relations},

author = {Tianci Song and Charles Broadbent and Rui Kuang},

url = {https://www.nature.com/articles/s41467-023-44017-0},

year  = {2023},

date = {2023-04-01},

urldate = {2023-04-01},

journal = {Nature Communications},

volume = {14},

number = {8276},

keywords = {Protein-Protein Interaction Network, Spatial Transcriptomics, Tensor Completion},

pubstate = {published},

tppubtype = {article}

}

@article{spatialGCNNb,

title = {Detecting Spatially Co-expressed Gene Clusters with Functional Coherence by Graph-regularized Convolutional Neural Network},

author = {Tianci Song and Kathleen K. Markham and Zhuliu Li and Kristen E. Muller and Kathleen Greenham and Rui Kuang},

url = {https://academic.oup.com/bioinformatics/article/38/5/1344/6448221},

year  = {2022},

date = {2022-03-01},

urldate = {2021-11-30},

journal = {Bioinformatics},

volume = {38},

number = {5},

pages = {1344–1352},

keywords = {Spatial Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{li2021imputation,

title = {Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion},

author = {Zhuliu Li and Tianci Song and Jeongsik Yong and Rui Kuang},

url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008218},

year  = {2021},

date = {2021-01-01},

journal = {PLoS computational biology},

volume = {17},

number = {4},

pages = {e1008218},

publisher = {Public Library of Science San Francisco, CA USA},

keywords = {Spatial Transcriptomics, Tensor Completion},

pubstate = {published},

tppubtype = {article}

}