A Multi-strategy Approach to Protein Structural Alphabet Design. - Shih-Yen Ku; Yuh-Jyh Hu (BIOCOMP, 2006)

Using Protein Structural Alphabet to Characterize Local Structure Features. - Shih-Yen Ku; Yuh-Jyh Hu (BIOCOMP, 2008)

Protein structure search and local structure characterization. - Shih-Yen Ku; Yuh-Jyh Hu (BMC Bioinform., 2008)

Discovery of Structural Motifs in Metalloproteins Using Protein Structural Alphabets and 1D Motif-finding Methods. - Shih-Yen Ku; Chih-Ying Wei; Yuh-Jyh Hu (BIOCOMP, 2009)

SA-Motifbase: A Database of Protein Structural Alphabet Motifs. - Shih-Yen Ku; Yuh-Jyh Hu (BIOCOMP, 2010)

The Power of Detecting Enriched Patterns: An HMM Approach. - Zhiyuan Zhai; Shih-Yen Ku; Yihui Luan; Gesine Reinert; Michael S. Waterman; Fengzhu Sun (J. Comput. Biol., 2010)

Structural alphabet motif discovery and a structural motif database. - Shih-Yen Ku; Yuh-Jyh Hu (Comput. Biol. Medicine, 2012)