Welcome to Yu-Yen Ou's Homepage

 

Dept. of Computer Science and Engineering,
Yuan Ze University (No. 135 Yuan-Tung Road, Chungli),
Taoyuan, Taiwan, 320
Tel: (886) 3-463-8800 x 2185
Fax: (886) 3-463-8850
Email: yien@csie.org or yien@saturn.yzu.edu.tw

I am now a professor in the Department of Computer Science and Engineering, Yuan-Ze University, Taiwan. My fields of professional interest are Bioinformatics, Machine Learning and Data Mining.

Research

About My Publications in Google Scholar Search

Software Publication

  1. Nguyen Quoc Khanh Le, Green Arther Sandag, Yu-Yen Ou, "Incorporating post translational modification information for enhancing the predictive performance of membrane transport proteins," Computational Biology and Chemistry , Volume 77, December 2018, Pages 251-260.
  2. Semmy Wellem Taju, Trinh-Trung-Duong Nguyen, Nguyen-Quoc-Khanh Le, Rosdyana Mangir Irawan Kusuma, Yu-Yen Ou, "DeepEfflux: a 2D Convolutional Neural Network Model for Identifying Families of Efflux Proteins in Transporters," BIOINFORMATICS, Volume 34, Issue 18, Pages 3111¡V3117
  3. Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou, "Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks," Analytical Biochemistry, Volume 555, Pages 33- 41.
  4. Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou. "Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins," Journal of Computational Chemistry, Volume:38, 23
  5. Nguyen-Quoc-Khanh Le, Trinh-Trung-Duong Nguyen and Yu-Yen Ou, "Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties," Journal of Molecular Graphics and Modelling, Volume 73, Pages 166-178.
  6. Nguyen-Quoc-Khanh Le and Yu-Yen Ou, "Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins," BMC Bioinformatics, 17(Suppl 19):1369.
  7. guyen-Quoc-Khanh Le and Yu-Yen Ou, "Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs," BMC Bioinformatics, 17:298.
  8. M. Michael Gromiha, Yu-Yen Ou, "Bioinformatics approaches for functional annotation of membrane proteins," Briefings in Bioinformatics, Volume: 15 Issue: 2 Pages: 155-168
  9. Yu-Yen Ou, Shu-An Chen, Yun-Min Chang, Devadasan Velmurugan, Kazuhiko Fukui, M. Michael Gromiha. "Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties," Proteins: Structure, Function, and Bioinformatics, Vol: 81:9 pages: 1634-1643.
  10. Yu-Yen Ou*, Shu-An Chen, Sheng-Cheng Wu, "ETMB-RBF: Discrimination of metal-binding sites in electron transporters based on RBF Networks with PSSM profiles and significant amino acid pairs," PLoS ONE, Volume: 8 Issue: 2 Article Number: e46572. 2012.
  11. Yu-Yen Ou*, "Predicting Protein Metal Binding Sites with RBF Networks based on PSSM Profiles and Additional Properties," Current Bioinformatics, 2012.
  12. Shu-An Chen, Yu-Yen Ou*, Tzong-Yi Lee, M.Michael Gromiha*, "Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties," Bioinformatics, 27(15):2062-7, 2011.
  13. Tzong-Yi Lee, Shu-An Chen, Hsin-Yi Hung and Yu-Yen Ou*, "Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites," PLoS ONE, 2011.
  14. Shu-An Chen, Tzong-Yi Lee, and Yu-Yen Ou*, "Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins," BMC Bioinformatics. 11:536. 2010.
  15. Yu-Yen Ou, Shu-An Chen, M.Michael Gromiha, "Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties," PROTEINS: Structure, Function, and Bioinformatics. 2010.
  16. Yu-Yen Ou, Shu-An Chen, M.Michael Gromiha, "Prediction of Membrane Spanning Segments and Topology in beta-barrel Membrane Proteins at Better Accuracy," Journal of Computational Chemistry. Volume 31 Issue 1, Pages 217 - 223. 2010.
  17. Darby Tien-Hao Chang, Yu-Yen Ou, Hao-Geng Hung, Meng-Han Yang, Chien-Yu Chen and Yen-Jen Oyang, "Prediction of protein secondary structures with a novel kernel density estimation based classifier", BMC Research Notes, 1:51, 2008.
  18. Yu-Yen Ou, M.Michael Gromiha, Shu-An Chen, and Makiko Suwa, "TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles," Computational Biology and Chemistry, Volume 32, Issue 3, Pages 227-231, 2008
  19. Yu-Yen Ou, Shu-An Chen, Chung-Lu Shao, and Hao-Geng Hung, "Using Efficient RBF Network to Identify Interface Residues Based on PSSM Profiles and Biochemical Properties," Lecture Notes in Bioinformatics, 4774, 2007
  20. Chung-Tsai Su, Tong-Ming Hsu, Chien-Yu Chen, Yu-Yen Ou, Yen-Jen Oyang, "Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction," Lecture Notes in Bioinformatics, 4414, pp. 395-409, 2007
  21. Chung-Tsai Su, Chien-Yu Chen, and Yu-Yen Ou, "Protein disorder prediction by condensed PSSM considering propensity for order or disorder," BMC Bioinformatics, 7, pp. 319, 2006
  22. Yu-Yen Ou, Guan-Hau Chen, and Yen-Jen Oyang, "Expediting Model Selection for Support Vector Machines Based on an Advanced Data Reduction Algorithm, "Lecture Notes in Artificial Intelligence, 4099, pp. 1017-1021, 2006
  23. Yen-Jen Oyang, Shien-Ching Hwang, Yu-Yen Ou, Chien-Yu Chen, and Zhi-Wei Chen, Data Classification with the Radial Basis Function Network Based on a Novel Kernel Density Estimation Algorithm, IEEE Transactions on Neural Networks, pp. 225-236, 2005.[pdf]

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Yu-Yen Ou