Zhang, Wei, Jeremy Chien, Jeongsik Yong, and Rui Kuang. 2017. “Network-Based Machine Learning and Graph Theory Algorithms for Precision Oncology”. NPJ Precision Oncology 1. Nature Publishing Group UK London: 25.
Laplacian Graph-based Models
Tian, Ze, Taehyun Hwang, and Rui Kuang. 2009. “A Hypergraph-Based Learning Algorithm for Classifying Gene Expression and ArrayCGH Data With Prior Knowledge”. Bioinformatics 25. Oxford University Press: 2831-38.
Kuang, Rui, Jason Weston, William Stafford Noble, and Christina Leslie. 2005. “Motif-Based Protein Ranking by Network Propagation”. Bioinformatics 21. Oxford University Press: 3711-18.
Hwang, Taehyun, Hugues Sicotte, Ze Tian, Baolin Wu, Jean-Pierre Kocher, Dennis A Wigle, Vipin Kumar, and Rui Kuang. 2008. “Robust and Efficient Identification of Biomarkers by Classifying Features on Graphs”. Bioinformatics 24. Oxford University Press: 2023-29.
Zhang, Wei, Takayo Ota, Viji Shridhar, Jeremy Chien, Baolin Wu, and Rui Kuang. 2013. “Network-Based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment”. PLoS Computational Biology 9. Public Library of Science San Francisco, USA: e1002975.
Weston, Jason, Rui Kuang, Christina Leslie, and William Stafford Noble. 2006. “Protein Ranking by Semi-Supervised Network Propagation”. In BMC Bioinformatics, 7:1-9. Springer.
Hwang, Taehyun, Wei Zhang, Maoqiang Xie, Jinfeng Liu, and Rui Kuang. 2011. “Inferring Disease and Gene Set Associations With Rank Coherence in Networks”. Bioinformatics 27. Oxford University Press: 2692-99.
Tian, Ze, and Rui Kuang. 2012. “Global Linear Neighborhoods for Efficient Label Propagation”. In Proceedings of the 2012 SIAM International Conference on Data Mining, 863-72. SIAM.
Noble, William S, Rui Kuang, Christina Leslie, and Jason Weston. 2005. “Identifying Remote Protein Homologs by Network Propagation”. The FEBS Journal 272. Wiley Online Library: 5119-28.
Zhang, Wei, Jae-Woong Chang, Lilong Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng, and Rui Kuang. 2015. “Network-Based Isoform Quantification With RNA-Seq Data for Cancer Transcriptome Analysis”. PLoS Computational Biology 11. Public Library of Science San Francisco, CA USA: e1004465.