Sing-Hoi Sze

Associate Professor

Image of Sing Hoi Sze

Office: 328B HRBB
Phone: 979.845.5009

Personal Website
Google Scholar Profile

Research Interests

  • Bioinformatics/Computational Biology
  • Multiple sequence alignment
  • Motif finding with applications to predicting transcription factor binding sites
  • Biological network analysis
  • Identification of gene clusters within genomes

Awards & Honors

  • Undergraduate Faculty Teaching Award: Computer Science Department, 2006


  • Ph.D. Computer Science, University of Southern California, 2000
  • M.S. Computer Science, Pennsylvania State University, 1995
  • B.S. Computer Science, Chinese University of Hong Kong, 1990

Selected Publications

Chen J., Liu Y., Lu S., Sze S.-H. and Zhang F. (2012) Iterative expansion and color coding: an improved algorithm for 3D-matching. ACM Transactions on Algorithms, 8(6).

Fan J.-H., Chen J. and Sze S.-H. (2012) Identifying complexes from protein interaction networks according to different types of neighborhood density. Journal of Computational Biology, 19, 1284-1294.

Sze S.-H., Dunham J.P., Carey B., Chang P.L., Li F., Edman R.M., Fjeldsted C., Scott M.J., Nuzhdin S.V. and Tarone A.M. (2012) A de novo transcriptome assembly of Lucilia sericata (Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms, and transcript expression estimates. Insect Molecular Biology, 21, 205-221.

Yi G., Thon M.R. and Sze S.-H. (2012) Supervised protein family classification and new family construction. Journal of Computational Biology, 19, 957-967.

Madina B.R., Kuppan G., Vashisht A.A., Liang Y.-H., Downey K.M., Wohlschlegel J.A., Ji X., Sze S.-H., Sacchettini J.C., Read L.K. and Cruz-Reyes J. (2011) Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei. RNA, 17, 1821-1830.

Zhao X. and Sze S.-H. (2011) Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains. Journal of Computational Biology, 18, 759-770.

Zhu H., Hu F., Wang R., Zhou X., Sze S.-H., Liou L.W., Barefoot A., Dickman M. and Zhang X. (2011) Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell, 145, 242-256.

Yang Q., Yi G., Zhang F., Thon M.R. and Sze S.-H. (2010) Identifying gene clusters within localized regions in multiple genomes. Journal of Computational Biology, 17, 657-668.

Chen J., Kneis J., Lu S., Mölle D., Richter S., Rossmanith P., Sze S.-H. and Zhang F. (2009) Randomized divide-and-conquer: improved path, matching, and packing algorithms. SIAM Journal on Computing, 38, 2526-2547.

Lu Y. and Sze S.-H. (2009) Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Research, 37, 463-472.