| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2006 | OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures | Shih, E. S.; Gan, R. C.; Hwang, M. J. | Nucleic Acids Res 34(Web Server issue), W95-W98 | | | |
| 2003 | Protein structure comparison by probability-based matching of secondary structure elements | Shih, E. S.; Hwang, M. J. | Bioinformatics 19, 735-741 | | | |
| 2002 | Single nucleotide polymorphism mapping using genome-wide unique sequences | Chen, L. Y.; Lu, S. H.; Shih, E. S.; Hwang, M. J. | Genome Res 12, 1106-1111 | | | |
