• Nguyen-Quoc-Khanh Le and Yu-Yen Ou, "Icorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins." BMC Bioinformatics, 17(Suppl 19):1369, 2016
  • Nguyen-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, 2016
  • M. Michael Gromiha, Yu-Yen Ou, "Bioinformatics approaches for functional annotation of membrane proteins." Briefings in Bioinformatics, Volume: 15 Issue: 2 Pages: 155-168 (SCI, 2/56, MATHEMATICAL & COMPUTATIONAL BIOLOGY), 2014
  • 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, 2013
  • 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, 2012.
  • Yu-Yen Ou*, "Predicting Protein Metal Binding Sites with RBF Networks based on PSSM Profiles and Additional Properties," Current Bioinformatics, 2012.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
  • 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