Journal Papers

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.

Qian X., Sze S.-H. and Yoon B.-J. (2009) Querying pathways in protein interaction networks based on hidden Markov models. Journal of Computational Biology, 16, 145-157.

Lu Y. and Sze S.-H. (2008) Multiple sequence alignment based on profile alignment of intermediate sequences. Journal of Computational Biology, 15, 767-777.

Yang Q. and Sze S.-H. (2008) Large-scale analysis of gene clustering in bacteria. Genome Research, 18, 949-956.

Yang Q. and Sze S.-H. (2008) Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. BMC Bioinformatics, 9(320).

Lu S., Zhang F., Chen J. and Sze S.-H. (2007) Finding pathway structures in protein interaction networks. Algorithmica, 48, 363-374.

Yang Q. and Sze S.-H. (2007) Path matching and graph matching in biological networks. Journal of Computational Biology, 14, 56-67.

Yi G., Sze S.-H. and Thon M.R. (2007) Identifying clusters of functionally related genes in genomes. Bioinformatics, 23, 1053-1060.

Lee J.J., Hassan O.S.S., Gao W., Wei N.E., Kohel R.J., Chen X.-Y., Payton P., Sze S.-H., Stelly D.M. and Chen Z.J. (2006) Developmental and gene expression analyses of a cotton naked seed mutant. Planta, 223, 418-432.

Sze S.-H., Lu Y. and Yang Q. (2006) A polynomial time solvable formulation of multiple sequence alignment. Journal of Computational Biology, 13, 309-319.

Wang N., Lu S.-E., Yang Q., Sze S.-H. and Gross D.C. (2006) Identification of the syr-syp box in the promoter regions of genes dedicated to syringomycin and syringopeptin production by Pseudomonas syringae pv. syringae B301D. Journal of Bacteriology, 188, 160-168.

Yang S.S., Cheung F., Lee J.J., Ha M., Wei N.E., Sze S.-H., Stelly D.M., Thaxton P., Triplett B., Town C.D. and Chen Z.J. (2006) Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. The Plant Journal, 47, 761-775.

Wang J., Adelson D.L., Yilmaz, A., Sze S.-H., Jin Y. and Zhu J.J. (2005) Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics. BMC Genomics, 6(45).

Heber S., Alekseyev M., Sze S.-H., Tang H. and Pevzner P.A. (2002) Splicing graphs and EST assembly problem. Bioinformatics, 18, S181-188.

Lunyak V.V., Burgess R., Prefontaine G.G., Nelson C., Sze S.-H., Chenoweth J., Schwartz P., Pevzner P.A., Glass C., Mandel G. and Rosenfeld M.G. (2002) Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science, 298, 1747-1752.

Sze S.-H., Roytberg M.A., Gelfand M.S., Mironov A.A., Astakhova T.V. and Pevzner P.A. (1998) Algorithms and software for support of gene identification experiments. Bioinformatics, 14, 14-19.

Xu G., Sze S.-H., Liu C.-P., Pevzner P.A. and Arnheim N. (1998) Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs. Genomics, 47, 171-179.

Sze S.-H. and Pevzner P.A. (1997) Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. Journal of Computational Biology, 4, 297-309.


Conference Papers

Hsieh M.-F. and Sze S.-H. (2010) Graphlet alignment in protein interaction networks. Proceedings of the 9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'2010).

Qian X., Sze S.-H. and Yoon B.-J. (2008) Querying pathways in protein interaction networks based on hidden Markov models. Proceedings of the 4th Annual RECOMB Satellite Workshop on Systems Biology.

Chen J., Lu S., Sze S.-H. and Zhang F. (2007) Improved algorithms for path, matching, and packing problems. Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'2007), 298-307.

Lu Y. and Sze S.-H. (2007) Multiple sequence alignment based on profile alignment of intermediate sequences. Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB'2007), Lecture Notes in Bioinformatics, 4453, 283-295.

Liu Y., Lu S., Chen J. and Sze S.-H. (2006) Greedy localization and color-coding: improved matching and packing algorithms. Proceedings of the 2nd International Workshop on Parameterized and Exact Computation (IWPEC'2006), Lecture Notes in Computer Science, 4169, 84-95.

Sze S.-H. and Zhao X. (2006) Improved pattern-driven algorithms for motif finding in DNA sequences. Proceedings of the 2005 Joint RECOMB Satellite Workshops on Systems Biology and Regulatory Genomics, Lecture Notes in Bioinformatics, 4023, 198-211.

Sze S.-H., Lu Y. and Yang Q. (2005) A polynomial time solvable formulation of multiple sequence alignment. Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'2005), Lecture Notes in Bioinformatics, 3500, 204-216.

Sze S.-H., Lu S. and Chen J. (2004) Integrating sample-driven and pattern-driven approaches in motif finding. Proceedings of the 4th Workshop on Algorithms in Bioinformatics (WABI'2004), Lecture Notes in Bioinformatics, 3240, 438-449.

Heber S., Alekseyev M., Sze S.-H., Tang H. and Pevzner P.A. (2002) Splicing graphs and EST assembly problem. Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology (ISMB'2002).

Sze S.-H., Gelfand M.S. and Pevzner P.A. (2002) Finding weak motifs in DNA sequences. Pacific Symposium on Biocomputing (PSB'2002), 235-246.

Pevzner P.A. and Sze S.-H. (2000) Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB'2000), 269-278.

Sze S.-H. and Pevzner P.A. (1997) Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. Proceedings of the 1st Annual International Conference on Research in Computational Molecular Biology (RECOMB'1997), 300-309.


Book Chapters

Sze S.-H. (2008) Recent developments in sequence alignment and motif finding algorithms. In I. Mandoiu and A. Zelikovsky (Eds.), Bioinformatics Algorithms: Techniques and Applications, Wiley, 259-276.