Research

Our lab is interested in developing general machine learning models and algorithms for integrative analysis of large-scale genomic data to understand the molecular characteristics of biological functions and phenotypes. We design mathematically principled methods in the categories of graph-based semi-supervised learning, transfer learning, string kernels and other kernel methods, sequence alignment methods and various statistical models for a unified analysis of heterogeneous biological data. Our current projects center around the following topics,

  • Cancer genomics: Development of graph-based learning algorithms, sequence alignment algorithms and association rule-mining algorithms for building predictive models and mining biomarkers of cancer phenotypes from microarray or sequencing transcriptome data, DNA copy number variations, SNPs and protein-protein interactions.
    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)
    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)
  • Phenome-genome association analysis: Development of graph-based learning algorithms for analyzing disease and gene associations in a network context.
    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)
  • Protein remote homology detection: Development of string kernel algorithms and label propagation algorithms to infer the protein remote homologys and study their protein structures and functions.
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    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)
    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)
    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 | )
    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)
    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)
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  • Semi-supervised and transfer learning algorithms: Development of general and scalable graph-based learning, transfer learning, sparse group learning and kernel learning method.
    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)
    Kuang, Rui; Weston, Jason; Noble, William Stafford; Leslie, Christina (2005): Motif-based protein ranking by network propagation . In: Bioinformatics, 21 (19), 2005. (Type: Journal Article | Abstract | Links)