Publications

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Zhang, Wei; Chang, Jae-Woong; Lin, Lilong; Minn, Kay; Wu, Baolin; Chien, Jeremy; Yong, Jeongsik; Zheng, Hui; Kuang, Rui (2015): Network-based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis . In: PLoS Computational Biology, e1004465 , 2015. (Type: Journal Article | Abstract | Links | Tags: Cancer Genomics, Isoform Quantification, Network-based Learning, Protein Domain-Domain Interactions, RNA-Seq)
Chien, Jeremy; Sicotte, Hugues; Fan, Jian-Bing; Humphray, Sean; Cunningham, Julie; Kalli, Kimberly; Oberg, Ann; Hart, Steven; Li, Ying; Davila, Jaime; others, (2015): TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer . In: Nucleic acids research, pp. gkv111, 2015. (Type: Journal Article | Abstract | Links | Tags: Cancer Genomics, Ovarian Cancer)
Johnson, Nicholas; Zhang, Huanan; Fang, Gang; Kumar, Vipin; Kuang, Rui (2015): SubPatCNV: approximate subspace pattern mining for mapping copy-number variations . In: BMC bioinformatics, 16 (1), pp. 1, 2015, ISSN: 1471-2105. (Type: Journal Article | Abstract | Links | Tags: Approximate pattern mining, Cancer Genomics, DNA Copy Number Variation)
Zhang, Huanan; Tian, Ze; Kuang, Rui (2013): Transfer learning across cancers on DNA copy number variation analysis . In: 2013 IEEE 13th International Conference on Data Mining, pp. 1283–1288, IEEE IEEE, 2013, ISBN: 978-0-7695-5108-1. (Type: Inproceedings | Abstract | Links | Tags: Cancer Genomics, DNA Copy Number Variation, Transfer Learning)
Chien, Jeremy; Kuang, Rui; Landen, Charles; Shridhar, Viji (2013): Platinum-sensitive recurrence in ovarian cancer: the role of tumor microenvironment . In: Frontiers in oncology, 3 , pp. 251, 2013. (Type: Journal Article | Abstract | Links | Tags: Cancer Genomics, Ovarian Cancer)
Hwang, TaeHyun; Atluri, Gowtham; Kuang, Rui; Kumar, Vipin; Starr, Timothy; Silverstein, Kevin AT; Haverty, Peter; Zhang, Zemin; Liu, Jinfeng (2013): Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers . In: BMC genomics, 14 (1), pp. 440, 2013. (Type: Journal Article | Abstract | Links | Tags: Cancer Genomics, DNA Copy Number Variation, Network-based Learning)
Zhang, Wei; Ota, Takayo; Shridhar, Viji; Chien, Jeremy; Wu, Baolin; Kuang, Rui (2013): Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment . In: PLoS Comput Biol, 9 (3), pp. e1002975, 2013. (Type: Journal Article | Abstract | Links | Tags: Cancer Genomics, Network-based Learning, Ovarian Cancer, Survival Analysis, Transcriptome)
Zhang, Wei; Hwang, Baryun; Wu, Baolin; Kuang, Rui (2010): Network propagation models for gene selection . In: 2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), IEEE, 2010, ISBN: 978-1-61284-791-7. (Type: Inproceedings | Abstract | Links | Tags: Cancer Genomics, Gene Expression, Semi-supervised Learning)
Gupta, Rohit; Agrawal, Smita; Rao, Navneet; Tian, Ze; Kuang, Rui; Kumar, Vipin (2009): Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining . In: Citeseer, 2009. (Type: Inproceedings | Abstract | Links | Tags: Approximate pattern mining, Cancer Genomics, Gene Expression)
Hwang, TaeHyun; Tian, Ze; Kuang, Rui; Kocher, Jean-Pierre (2008): Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction . In: 2008 Eighth IEEE International Conference on Data Mining, pp. 293–302, IEEE 2008, ISBN: 978-0-7695-3502-9. (Type: Inproceedings | Abstract | Links | Tags: Cancer Genomics, Gene Expression, Protein-Protein Interaction Network, Semi-supervised Learning)
Hwang, TaeHyun; Kuang, Rui (2008): A Comparative Study of Breast Cancer Microarray Gene Expression Profiles using Label Propagation . In: Proceedings of the Workshop on Data Mining for Biomedical Informatics, held in conjunction with SIAM International Conference on Data Mining (SDM), 2008. (Type: Inproceedings | Abstract | Links | Tags: Cancer Genomics, Semi-supervised Learning)
Hwang, TaeHyun; Sicotte, Hugues; Tian, Ze; Wu, Baolin; Kocher, Jean-Pierre; Wigle, Dennis; Kumar, Vipin; Kuang, Rui (2008): Robust and efficient identification of biomarkers by classifying features on graphs . In: Bioinformatics, 24 (18), pp. 2023–2029, 2008, ISBN: 1460-2059. (Type: Journal Article | Abstract | Links | Tags: Cancer Genomics, Gene Expression, Semi-supervised Learning)