Publications

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Petegrosso, Raphael; Park, Sunho; Hwang, Tae Hyun; Kuang, Rui (2016): Transfer Learning across Ontologies for Phenome-Genome Association Prediction . In: Bioinformatics, pp. btw649, 2016. (Type: Journal Article | Abstract | Links | Tags: Phenome-genome Association, Semi-supervised Learning, Transfer Learning)
Vierra-Green, Cynthia; Roe, David; Jayaraman, Jyothi; Trowsdale, John; Traherne, James; Kuang, Rui; Spellman, Stephen; Maiers, Martin (2016): Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes . In: PloS one, 11 (10), pp. e0163973, 2016. (Type: Journal Article | Abstract | Links | Tags: Haplotype Inference, KIR)
Liang, Lining; Sun, Hao; Zhang, Wei; Zhang, Mengdan; Yang, Xiao; Kuang, Rui; Zheng, Hui (2016): Meta-Analysis of EMT Datasets Reveals Different Types of EMT. . In: PloS one, 11 (6), pp. e0156839–e0156839, 2016. (Type: Journal Article | Abstract | Links | Tags: EMT, Gene Expression, Transcriptome)
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)
Chang, Jae-Woong; Zhang, Wei; Yeh, Hsin-Sung; de Jong, Ebbing; Jun, Semo; Kim, Kwan-Hyun; Bae, Sun; Beckman, Kenneth; Hwang, Tae Hyun; Kim, Kye-Seong; others, (2015): mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation . In: Nature communications, 6 , 2015. (Type: Journal Article | Abstract | Links | Tags: 3'-UTR sequencing, 3'-UTR shortening, mTOR)
Cai, Hong; Lilburn, Timothy; Hong, Changjin; Gu, Jianying; Kuang, Rui; Wang, Yufeng (2015): Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments . In: BMC systems biology, 9 (4), pp. 1, 2015, ISSN: 1752-0509. (Type: Journal Article | Abstract | Links | Tags: Malaria, Network Alignment)
Xie, MaoQiang; Xu, YingJie; Zhang, YaoGong; Hwang, TaeHyun; Kuang, Rui (2015): Network-based Phenome-Genome Association Prediction by Bi-Random Walk . In: PloS one, 10 (5), pp. e0125138, 2015. (Type: Journal Article | Abstract | Links | Tags: Phenome-genome Association, Semi-supervised Learning)
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)
Cai, Hong; Lilburn, Timothy; Hong, Changjin; Gu, Jianying; Kuang, Rui; Wang, Yufeng (2015): Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments . In: BMC systems biology, 9 (4), pp. 1, 2015. (Type: Journal Article | Tags: Malaria, Network Alignment, Protein-Protein Interaction Network)
Sharma, Ankit; Kuang, Rui; Srivastava, Jaideep; Feng, Xiaodong; Singhal, Kartik (2015): Predicting small group accretion in social networks: A topology based incremental approach . In: 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), pp. 408–415, IEEE 2015, ISBN: 978-1-4503-3854-7/15/08. (Type: Inproceedings | Abstract | Links | Tags: Semi-supervised Learning, Social Network)
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)
Cai, Hong; Hong, Changjin; Lilburn, Timothy; Rodriguez, Armando; Chen, Sheng; Gu, Jianying; Kuang, Rui; Wang, Yufeng (2013): A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum . In: BMC bioinformatics, 14 (12), pp. 1, 2013, ISSN: 1471-2105. (Type: Journal Article | Abstract | Links | Tags: Malaria, Network Alignment)
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)
Tian, Ze; Zhang, Huanan; Kuang, Rui (2012): Sparse group selection on fused lasso components for identifying group-specific DNA copy number variations . In: 2012 IEEE 12th International Conference on Data Mining, pp. 665–674, IEEE IEEE, 2012, ISBN: 978-1-4673-4649-8. (Type: Inproceedings | Abstract | Links | Tags: DNA Copy Number Variation, LASSO Model, Sparse Group Learning)
Zhang, Wei; Johnson, Nicholas; Wu, Baolin; Kuang, Rui (2012): Signed network propagation for detecting differential gene expressions and DNA copy number variations . In: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 337–344, ACM 2012. (Type: Inproceedings | Abstract | Links | Tags: DNA Copy Number Variation, Gene Expression, Semi-supervised Learning)
Hwang, TaeHyun; Atluri, Gowtham; Xie, MaoQiang; Dey, Sanjoy; Hong, Changjin; Kumar, Vipin; Kuang, Rui (2012): Co-clustering phenome--genome for phenotype classification and disease gene discovery . In: Nucleic acids research, 40 (19), pp. e146–e146, 2012. (Type: Journal Article | Abstract | Links | Tags: Co-clustering, Network-based Learning, Phenome-genome Association, Semi-supervised Learning)
Xie, Maoqiang; Hwang, Taehyun; Kuang, Rui (2012): Prioritizing disease genes by bi-random walk . In: Pacific-Asia Conference on Knowledge Discovery and Data Mining, pp. 292–303, Springer 2012. (Type: Inproceedings | Abstract | Links | Tags: Phenome-genome Association, Semi-supervised Learning)
48 entries « 1 of 3 »