Rui Kuang

Publications

Rui Kuang, Jianying Gu, Hong Cai and Yufeng Wang. Improved Prediction of Malaria Degradomes by Supervised Learning with SVM and Profile Kernel, [Paper] [Download] Accepted in Genetica

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] Accepted in the Eighth IEEE International Conference on Data Mining (ICDM), Dec. 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] [Download], 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 ][Download], 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 Homologs 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][Download] [Slides], 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] [Download], 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] [Download], 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][Download], Proc. of Conference on Learning Theory and Kernel Workshop (COLT/KW), 2003