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Publication

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,

is accepted in Proceedings of the 15th Pacific Symposium on Biocomputing (PSB), in press, 2010.

 

2009

Ze Tian*, TaeHyun Hwang*, and Rui Kuang.

A Hypergraph-based Learning Algorithm for Classifying Gene Expression and arrayCGH data with Prior Knowledge, [Paper] [Download], is accepted in Bioinformatics 2009,

(*Joint first authors)

Rui Kuang, Jianying Gu, Hong Cai and Yufeng Wang. Improved Prediction of Malaria Degradomes by Supervised Learning with SVM and Profile Kernel, [Paper] [Download], Genetica, Volume 136, Number 1 / May, 2009.

Renqiang Min, Rui Kuang, Anthony Bonner , and Zhaolei Zhang. Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery, [Paper] [Download] accepted in SIAM International Conference on Data Mining (SDM). 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

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

 

2008

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), Dec. 2008. (*Joint first authors)

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, and Rui Kuang. A Comparative Study of Breast Cancer Microarray Gene Expression Profiles using Label Propagation , [Paper] Proc. of the Workshop on Data Mining for Biomedical Informatics, held in conjunction with SIAM International Conference on Data Mining, 2008.

 

2007

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

 

2006

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

 

2005

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

 

2004

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)

 

2003

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