Rui Kuang

Publications

Hwang, TaeHyun; Atluri, Gowtham; Xie, Maoqiang; Dey, Sanjoy; Hong, Changjin; Kumar, Vipin; Kuang, Rui, Co-clustering Phenome-genome for Phenotype Classification and Disease Gene Discovery, Nucleic Acids Research, In Press, 2012

Ze Tian and Rui Kuang. Global Linear Neighborhood for Efficient Label Propagation, Proc. of SIAM International Conference on Data Mining (SDM), [Paper] In Press, 2012

Jacko, JA, Johnson, JM, Adam, T, Ali, AL, Chan, D, Kuang, R, Nelson, AF, Watters, A, Westra, B, Fauchald, S, Potthoff, S, Witrak, M., Co-creating management education: Moving toward emergent education in a complex world. International Journal of Information and Operations Management Education. , [Paper] the International Journal of Information and Operations Management Education (IJIOME) - Special Issue on: "The Emerging Healthcare Education Revolution". Vol. 4, No. 3-4, 284-308, 2012

TaeHyun Hwang, Wei Zhang, MaoQiang Xie, Jinfeng Liu and Rui Kuang. Inferring Disease and Gene Set Associations with Rank Coherence in Networks, [Paper] [WebTool] Bioinformatics, Vol. 27, No. 19, 2692-2699, 2011

Hong Cai, Rui Kuang, Jianying Gu and Yufeng Wang. Proteases in Malaria Parasites - a Phylogenomic Perspective, Current Genomics, Vol. 12, No. 6, pp. 417-427, 2011

Jacko, J. A., Adam, T., Westra, B., Witrak, M., Berkeland, R., Nelson, A. F., Ali, A. L., Johnson, L., Kuang, R., LaTour, K., Potthoff, S., & Watters, A. Launching: University Partnership for Health Informatics, [Paper] Proceedings of the ACM International Health Informatics Symposium, Arlington, VA. 521-525. 2011

Wei Zhang, Baryun Hwang, Baolin Wu and Rui Kuang. Label Propagation Models for Gene Selection, [Paper] Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2011

Ze Tian and Rui Kuang. Integrative Classification and Analysis of Multiple ArrayCGH Datasets with Probe Alignment, [Paper] [Download] Bioinformatics, Vol. 26, No. 18, pages: 2313-2320, 2010

TaeHyun Hwang and Rui Kuang. A Heterogeneous Label Propagation Algorithm for Disease Gene Discovery, [Paper] Proc. of SIAM International Conference on Data Mining (SDM), pages 583-594, 2010

Rohit Gupta, Smita Agrawal, Navneet Rao, Ze Tian, Rui Kuang and Vipin Kumar. Integrative biomarker discovery for breast cancer metastasis from gene expression and protein interaction data using error-tolerant pattern mining, [Paper] Proc. of International Conference on Bioinformatics and Computational Biology (BICoB), 2010

Gang Fang, Rui Kuang, Gaurav Pandey, Michael Steinbach, Chad L. Myers and Vipin Kumar. Subspace Differential Coexpression Analysis: Problem Definition and a General Approach, [Paper] Proc. of Pacific Symposium on Biocomputing (PSB), Vol. 15, pages: 145-156, 2010

Ze Tian, TaeHyun Hwang and Rui Kuang. A Hypergraph-based Learning Algorithm for Classifying Gene Expression and ArrayCGH Data with Prior Knowledge, [Paper] [Download] Bioinformatics, Vol. 25, No. 21, pages: 2831-2838, 2009

Rui Kuang, Jianying Gu, Hong Cai and Yufeng Wang. Improved Prediction of Malaria Degradomes by Supervised Learning with SVM and Profile Kernel, [Paper] Genetica 36(1):189-209, 2009

Renqiang Min, Rui Kuang, Anthony Bonner and Zhaolei Zhang. Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery, [Paper] Proc. of SIAM International Conference on Data Mining (SDM),pages 133-144, 2009

Thanh Ngo and Rui Kuang. Partial Profile Alignment Kernels fro Protein Classification, [Paper] Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009

Ze Tian, TaeHyun Hwang, and Rui Kuang. A Hypergraph-based Learing Algorithm for Classifying ArrayCGH Data with Spatial Prior, [Paper] Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2009

TaeHyun Hwang, Ze Tian, Jean-Pierre Kocher, and Rui Kuang. Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction, [Paper] [Download] Proc. of Eighth IEEE International Conference on Data Mining (ICDM), pages 293-302, 2008

TaeHyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Dennis Wigle, Jean-Pierre Kocher, Vipin Kumar and Rui Kuang. Robust and Efficient Identification of Biomarkers by Classifying Features on Graphs, [Paper] [Download] Bioinformatics, Vol. 24, No. 18, pages 2023-2029, 2008

TaeHyun Hwang, Hugues Sicotte, Dennis Wigle, Jean-Pierre Kocher, Vipin Kumar and Rui Kuang. Identifying Clinical and Genetic Markers of Human Disease by Classifying Features on Graphs, [Paper] Technical Report UMN-CS-07-021, Sept. 2007

Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble and Christina Leslie, SVM-fold: a tool for discriminative multi-class protein fold and superfamily recognition [Paper], BMC Bioinformatics 2007, 8 (Suppl 4) : S2

Rui Kuang, Inferring Protein Structure with Discriminative Learning and Network Diffusion [Manuscript], Ph.D. Thesis (Columbia University), 2006

Jason Weston, Rui Kuang, Christina Leslie and William Stafford Noble, Protein Ranking by Semi-Supervised Network Propagation[Paper], BMC Bioinformatics 2006, 7 (Suppl 1) : S10

Rui Kuang , Jason Weston, William Stafford Noble and Christina Leslie, Motif-based Protein Ranking by Network Propagation [Paper], Bioinformatics Vol.21 No.19, pages 3711-3718, 2005

Rui Kuang ,Eugene Ie, Ke Wang, Kai Wang,Mahira Siddiqi, Yoav Freund and Christina Leslie, Profile-based String Kernels for Remote Homology Detection and Motif Extraction[Paper ], Journal of Bioinformatics and Computational Biology Vol. 3, No. 3 527-550, 2005 (Journal version of CSB 2004 paper)

William Stafford Noble, Rui Kuang , Christina Leslie and Jason Weston, Identifying Remote Protein Homology by Network Propagation [Paper], The FEBS Journal. 272(20):5119-5128, 2005

Rui Kuang ,Eugene Ie, Ke Wang, Kai Wang,Mahira Siddiqi, Yoav Freund and Christina Leslie, Profile-based String Kernels for Remote Homology Detection and Motif Extraction [Paper], Proc. of the Computational Systems Bioinformatics Conference (IEEE CSB), 2004

Christina Leslie and Rui Kuang, Fast String Kernels Using Inexact Matching for Protein Sequences [Paper] , Journal of Machine Learning Research Vol. 5, pages 1435--1455, 2004 (Journal version of COLT/KW 2003 paper)

Rui Kuang , Christina Leslie and An-Suei Yang, Protein Backbone Angle Prediction with Machine Learning Approaches [Paper] , Bioinformatics Vol.20 No.10, pages 1612-1621, 2004

Christina Leslie, Rui Kuang and Eleazar Eskin, Inexact Matching String Kernels for Protein Classification [Chapter], Kernel Methods in Computational Biology, B. Schoelkopf, K. Tsuda and J.-P. Vert, ed. MIT Press, 2004

Christina Leslie and Rui Kuang, Fast Kernels for Inexact String Matching [Paper], Proc. of Conference on Learning Theory and Kernel Workshop (COLT/KW), 2003