Publications

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2019

Petegrosso, Raphael; Li, Zhuliu; Srour, Molly A.; Saad, Yousef; Zhang, Wei; Kuang, Rui

Scalable Remote Homology Detection and Fold Recognition in Massive Protein Networks Journal Article

In: PROTEINS: Structure, Function, and Bioinformatics, vol. 87, no. 6, pp. 478-491, 2019.

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

2009

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

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

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

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

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