Publications

71 entries « 2 of 2 »

2010

Fang, Gang; Kuang, Rui; Pandey, Gaurav; Steinbach, Michael; Myers, Chad L; Kumar, Vipin

Subspace differential coexpression analysis: problem definition and a general approach. Proceedings Article

In: Pacific symposium on biocomputing, pp. 145–56, 2010.

Abstract | Links | BibTeX | Tags: Gene Expression, Transcriptome

Jacko, Julie A.; Adam, Terrence; Westra, Bonnie; Witrak, Marty; Berkeland, Ron; Nelson, Andrew F.; Ali, Adel L.; Johnson, Layne; Kuang, Rui; LaTour, Kathy; Potthoff, Sandra; Watters, Amy

Launching: university partnership for health informatics Proceedings Article

In: Proceedings of the 1st ACM International Health Informatics Symposium, ACM 2010, ISBN: 978-1-4503-0030-8.

Abstract | Links | BibTeX | Tags:

2009

Gupta, Rohit; Agrawal, Smita; Rao, Navneet; Tian, Ze; Kuang, Rui; Kumar, Vipin

Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining Proceedings Article

In: Citeseer, 2009.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Gene Expression

Tian, Ze; Hwang, TaeHyun; Kuang, Rui

A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge Journal Article

In: Bioinformatics, vol. 25, no. 21, pp. 2831–2838, 2009, ISSN: 1460-2059.

Abstract | Links | BibTeX | Tags: DNA Copy Number Variation, Gene Expression, Semi-supervised Learning

Min, Martin Renqiang; Kuang, Rui; Bonner, Anthony J; Zhang, Zhaolei

Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery. Proceedings Article

In: SDM, pp. 133–144, SIAM 2009, ISBN: 978-0-89871-682-5.

Abstract | Links | BibTeX | Tags: Kernel Method, Protein Remote Homology Detection

Tian, Ze; Hwang, TaeHyun; Kuang, Rui

A hypergraph-based learning algorithm for classifying arraycgh data with spatial prior Proceedings Article

In: 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, pp. 1–4, IEEE IEEE, 2009, ISBN: 978-1-4244-4761-9.

Abstract | Links | BibTeX | Tags: DNA Copy Number Variation, Semi-supervised Learning

Ngo, Thanh; Kuang, Rui

Partial profile alignment kernels for protein classification Proceedings Article

In: 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, pp. 1–4, IEEE 2009, ISBN: 978-1-4244-4761-9.

Abstract | Links | BibTeX | Tags: Kernel Method, Protein Remote Homology Detection

2008

Hwang, TaeHyun; Tian, Ze; Kuang, Rui; Kocher, Jean-Pierre

Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction Proceedings Article

In: 2008 Eighth IEEE International Conference on Data Mining, pp. 293–302, IEEE 2008, ISBN: 978-0-7695-3502-9.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Gene Expression, Protein-Protein Interaction Network, Semi-supervised Learning

Kuang, Rui; Gu, Jianying; Cai, Hong; Wang, Yufeng

Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel Journal Article

In: Genetica, vol. 136, no. 1, pp. 189–209, 2008.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection

Hwang, TaeHyun; Kuang, Rui

A Comparative Study of Breast Cancer Microarray Gene Expression Profiles using Label Propagation Proceedings Article

In: Proceedings of the Workshop on Data Mining for Biomedical Informatics, held in conjunction with SIAM International Conference on Data Mining (SDM), 2008.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Semi-supervised Learning

Hwang, TaeHyun; Sicotte, Hugues; Tian, Ze; Wu, Baolin; Kocher, Jean-Pierre; Wigle, Dennis A; Kumar, Vipin; Kuang, Rui

Robust and efficient identification of biomarkers by classifying features on graphs Journal Article

In: Bioinformatics, vol. 24, no. 18, pp. 2023–2029, 2008, ISBN: 1460-2059.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Gene Expression, Semi-supervised Learning

2007

Melvin, Iain; Ie, Eugene; Kuang, Rui; Weston, Jason; Noble, William Stafford; Leslie, Christina

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition Journal Article

In: BMC bioinformatics, vol. 8, no. 4, 2007.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, String Kernels

2006

Weston, Jason; Kuang, Rui; Leslie, Christina; Noble, William Stafford

Protein ranking by semi-supervised network propagation Journal Article

In: BMC bioinformatics, vol. 7, no. 1, pp. 9, 2006.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, Semi-supervised Learning

2005

Noble, William Stafford; Kuang, Rui; Leslie, Christina; Weston, Jason

Idetifying remote protein homologs by network propagation Journal Article

In: FEBS J, vol. 272, no. 20, 2005.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, Semi-supervised Learning

Kuang, Rui; Ie, Eugene; Wang, Ke; Wang, Kai; Siddiqi, Mahira; Freund, Yoav; Leslie, Christina

Profile-based string kernels for remote homology detection and motif extraction Journal Article

In: Journal of bioinformatics and computational biology, vol. 3, no. 03, 2005.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, String Kernels

Kuang, Rui; Weston, Jason; Noble, William Stafford; Leslie, Christina

Motif-based protein ranking by network propagation Journal Article

In: Bioinformatics, vol. 21, no. 19, 2005.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, Semi-supervised Learning

2004

Leslie, Christina; Kuang, Rui

Fast string kernels using inexact matching for protein sequences Journal Article

In: Journal of Machine Learning Research, vol. 5, no. Nov, 2004.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, String Kernels

Kuang, Rui; Ie, Eugene; Wang, Ke; Wang, Kai; Siddiqi, Mahira; Freund, Yoav; Leslie, Christina

Profile-based string kernels for remote homology detection and motif extraction Proceedings Article

In: CSB 2004, IEEE, 2004, ISBN: 0-7695-2194-0.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, String Kernels

Kuang, Rui; Leslie, Christina; Yang, An-Suei

Protein backbone angle prediction with machine learning approaches Journal Article

In: Bioinformatics, vol. 20, no. 10, 2004.

Abstract | Links | BibTeX | Tags:

Leslie, Christina; Kuang, Rui; Eskin, Eleazar

Inexact matching string kernels for protein classification Book

MIT Press, Cambridge, MA, 2004, ISBN: 9780262256926.

BibTeX | Tags: Protein Remote Homology Detection, String Kernels

2003

Leslie, Christina; Kuang, Rui

Fast kernels for inexact string matching Proceedings Article

In: 16th Annual Conference on Computational Learning Theory and 7th Kernel Workshop (COLT/Kernel), Springer, 2003, ISBN: 978-3-540-45167-9.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection, String Kernels

71 entries « 2 of 2 »