ESTmapper: Efficiently Aligning DNA Sequences to Genomes. - Xue Wu 002; Woei-Jyh Lee; Chau-Wen Tseng (IPDPS, 2005)

BioBench: A Benchmark Suite of Bioinformatics Applications. - Kursad Albayraktaroglu; Aamer Jaleel; Xue Wu 002; Manoj Franklin; Bruce L. Jacob; Chau-Wen Tseng; Donald Yeung (ISPASS, 2005)

Peptide Identification via Tandem Mass Spectrometry. - Xue Wu 002; Nathan Edwards; Chau-Wen Tseng (Adv. Comput., 2006)

HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models. - Xue Wu 002; Chau-Wen Tseng; Nathan Edwards (J. Comput. Biol., 2007)

Improving the Performance and Precision of Bioinformatics Algorithms. - Xue Wu 002 (2008)