HR job title
- Associate Professor
- Contact Info
- 1 979 845 5009
- Websites
Sze, Sing-Hoi Associate Professor - Term Appoint
Positions
- Associate Professor - Term Appoint, Computer Science and Engineering, College of Engineering
Our work focuses on the application of computational techniques to solve problems in biology. Current research projects cover diverse areas in computational biology, including multiple sequence alignment, motif finding with applications to predicting transcription factor binding sites, biological network analysis, and identification of gene clusters within genomes.
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- Works By Students
- Background
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Overview
Publications
selected publications
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academic article
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Zhang, M., Cui, Y., Liu, Y., Xu, W., Sze, S., Murray, S. C., Xu, S., & Zhang, H.
(2020).
Accurate prediction of maize grain yield using its contributing genes for gene-based breeding. Genomics.
112(1), 225-236.
-
Pimsler, M. L., Sze, S., Saenz, S., Fu, S., Tomberlin, J. K., & Tarone, A. M.
(2019).
Gene expression correlates of facultative predation in the blow fly Chrysomya rufifacies (Diptera: Calliphoridae). Ecology and Evolution.
9(15), 8690-8701.
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Zhu, Z., Rehman, K. U., Yu, Y., Liu, X., Wang, H., Tomberlin, J. K., ... Zheng, L.
(2019).
De novo transcriptome sequencing and analysis revealed the molecular basis of rapid fat accumulation by black soldier fly (Hermetia illucens, L.) for development of insectival biodiesel. Biotechnology for Biofuels.
12(1), 194.
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Zhang, Y. u., Pechal, J. L., Schmidt, C. J., Jordan, H. R., Wang, W. W., Benbow, M. E., Sze, S., & Tarone, A. M.
(2019).
Machine learning performance in a microbial molecular autopsy context: A cross-sectional postmortem human population study. PLoS ONE.
14(4), e0213829-e0213829.
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Song, J., Arif, M., Zhang, M., Sze, S., & Zhang, H.
(2019).
Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection. Food Chemistry.
284, 312-322.
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Pandey, A., Ding, S. L., Qin, Q., Gupta, R., Gomez, G., Lin, F., ... de Figueiredo, P.
(2017).
Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection. Cell Host and Microbe.
21(5), 637-649.e6.
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Yuan, Y. e., Zhang, Y. u., Fu, S., Crippen, T. L., Visi, D. K., Benbow, M. E., ... Tarone, A. M.
(2017).
Genome Sequence of a Providencia stuartii Strain Isolated from Luciliasericata Salivary Glands. Genome Announcements.
5(17), e00250-e00217.
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Sze, S., Pimsler, M. L., Tomberlin, J. K., Jones, C. D., & Tarone, A. M.
(2017).
A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC GENOMICS.
18(Suppl 4), 387.
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Qiu, C., Erinne, O. C., Dave, J. M., Cui, P., Jin, H., Muthukrishnan, N., ... Kaplan, C. D.
(2016).
High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLOS Genetics.
12(11), e1006321-e1006321.
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Yuan, Y. e., Zhang, Y. u., Fu, S., Crippen, T. L., Visi, D. K., Benbow, M. E., ... Tarone, A. M.
(2016).
Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata. Genome Announcements.
4(4), e00672-e00616.
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Fu, S., Tarone, A. M., & Sze, S.
(2015).
Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. 16 Suppl 11(Suppl 11), S5.
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Edman, R. M., Linger, R. J., Belikoff, E. J., Li, F., Sze, S., Tarone, A. M., & Scott, M. J.
(2015).
Functional characterization of calliphorid cell death genes and cellularization gene promoters for controlling gene expression and cell viability in early embryos. INSECT MOLECULAR BIOLOGY.
24(1), 58-70.
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Chen, J., Fan, J., & Sze, S.
(2015).
Parameterized and approximation algorithms for maximum agreement forest in multifurcating trees. Theoretical Computer Science.
562(C), 496-512.
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Sze, S., & Tarone, A. M.
(2014).
A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data. BMC GENOMICS.
15 Suppl 5(Suppl 5), S6.
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International Glossina Genome Initiative.
(2014).
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science.
344(6182), 380-386.
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Hsieh, M., & Sze, S.
(2014).
Finding alignments of conserved graphlets in protein interaction networks. Journal of Computational Biology.
21(3), 234-246.
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Radulovi, ., Kim, T. K., Porter, L. M., Sze, S., Lewis, L., & Mulenga, A.
(2014).
A 24-48 h fed Amblyomma americanum tick saliva immuno-proteome. BMC GENOMICS.
15(1), 518.
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Sze, S., Dunham, J. P., Carey, B., Chang, P. L., Li, F., Edman, R. M., ... 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(2), 205-221.
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Fan, J., Chen, J., & Sze, S.
(2012).
Identifying complexes from protein interaction networks according to different types of neighborhood density. Journal of Computational Biology.
19(12), 1284-1294.
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Yi, G., Thon, M. R., & Sze, S.
(2012).
Supervised protein family classification and new family construction. Journal of Computational Biology.
19(8), 957-967.
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Madina, B. R., Kuppan, G., Vashisht, A. A., Liang, Y., Downey, K. M., Wohlschlegel, J. A., ... Cruz-Reyes, J.
(2011).
Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei. RNA.
17(10), 1821-1830.
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Zhu, H., Hu, F., Wang, R., Zhou, X., Sze, S., Liou, L. W., ... Zhang, X.
(2011).
Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell.
145(2), 242-256.
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Zhao, X., & Sze, S.
(2011).
Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains. Journal of Computational Biology.
18(5), 759-770.
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Yang, Q., Yi, G., Zhang, F., Thon, M. R., & Sze, S.
(2010).
Identifying gene clusters within localized regions in multiple genomes. Journal of Computational Biology.
17(5), 657-668.
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Qian, X., Sze, S., & Yoon, B.
(2009).
Querying pathways in protein interaction networks based on hidden Markov models. Journal of Computational Biology.
16(2), 145-157.
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Lu, Y., & Sze, S.
(2009).
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Research (NAR).
37(2), 463-472.
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Chen, J., Kneis, J., Lu, S., Moelle, D., Richter, S., Rossmanith, P., Sze, S., & Zhang, F.
(2009).
RANDOMIZED DIVIDE-AND-CONQUER: IMPROVED PATH, MATCHING, AND PACKING ALGORITHMS. SIAM Journal on Computing.
38(6), 2526-2547.
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Yang, Q., & Sze, S.
(2008).
Large-scale analysis of gene clustering in bacteria. Genome Research.
18(6), 949-956.
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Yang, Q., & Sze, S.
(2008).
Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. BMC Bioinformatics.
9(1), 320.
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Lu, S., Zhang, F., Chen, J., & Sze, S.
(2007).
Finding pathway structures in protein interaction networks. Algorithmica: an international journal in computer science.
48(4), 363-374.
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Yi, G., Sze, S., & Thon, M. R.
(2007).
Identifying clusters of functionally related genes in genomes. Bioinformatics.
23(9), 1053-1060.
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Yang, Q., & Sze, S.
(2007).
Path matching and graph matching in biological networks. Journal of Computational Biology.
14(1), 56-67.
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Samuel Yang, S., Cheung, F., Lee, J. J., Ha, M., Wei, N. E., Sze, S., ... Jeffrey Chen, Z.
(2006).
Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. 47(5), 761-775.
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Lee, J. J., Hassan, O., Gao, W., Wei, N. E., Kohel, R. J., Chen, X., ... Chen, Z. J.
(2006).
Developmental and gene expression analyses of a cotton naked seed mutant. Planta: an international journal of plant biology.
223(3), 418-432.
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Wang, N., Lu, S., Yang, Q., Sze, S., & 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(1), 160-168.
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Wang, J., Adelson, D. L., Yilmaz, A., Sze, S. H., Jin, Y., & 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.
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Wang, J., Adelson, D. L., Yilmaz, A., Sze, S., Jin, Y., & 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(1), 45.
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Sze, S. H., Lu, S. J., & Chen, J. E.
(2004).
Integrating sample-driven and pattern-driven approaches in motif finding. Lecture Notes in Artificial Intelligence.
3240, 438-449.
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Lunyak, V. V., Burgess, R., Prefontaine, G. G., Nelson, C., Sze, S., Chenoweth, J., ... Rosenfeld, M. G.
(2002).
Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science.
298(5599), 1747-1752.
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Sze, S. H., Gelfand, M. S., & Pevzner, P. A.
(2002).
Finding weak motifs in DNA sequences. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
235-246.
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Heber, S., Alekseyev, M., Sze, S., Tang, H., & Pevzner, P. A.
(2002).
Splicing graphs and EST assembly problem. Bioinformatics.
18 Suppl 1(suppl_1), S181-S188.
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Pevzner, P. A., & Sze, S. H.
(2000).
Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology.
8, 269-278.
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Sze, S. H., Roytberg, M. A., Gelfand, M. S., Mironov, A. A., Astakhova, T. V., & Pevzner, P. A.
(1998).
Algorithms and software for support of gene identification experiments. Bioinformatics.
14(1), 14-19.
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Xu, G., Sze, S. H., Liu, C. P., Pevzner, P. A., & Arnheim, N.
(1998).
Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs. Genomics.
47(2), 171-179.
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Zhang, M., Cui, Y., Liu, Y., Xu, W., Sze, S., Murray, S. C., Xu, S., & Zhang, H.
(2020).
Accurate prediction of maize grain yield using its contributing genes for gene-based breeding. Genomics.
112(1), 225-236.
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chapter
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Sze, S.
(2016).
Computational Approaches for Studying Alternative Splicing in Nonmodel Organisms from RNASEQ Data. Computational Methods for Next Generation Sequencing Data Analysis.
(pp. 287-299).
Wiley.
-
Sze, S.
(2008).
Recent Developments in Alignment and Motif Finding for Sequences and Networks. Bioinformatics Algorithms.
(pp. 259-276).
Wiley.
-
Sze, S.
(2016).
Computational Approaches for Studying Alternative Splicing in Nonmodel Organisms from RNASEQ Data. Computational Methods for Next Generation Sequencing Data Analysis.
(pp. 287-299).
Wiley.
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conference paper
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Fu, S., Chang, P. L., Friesen, M. L., Teakle, N. L., Tarone, A. M., & Sze, S.
(2019).
Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus. BMC GENOMICS.
425-1.
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Sze, S., Parrott, J. J., & Tarone, A. M.
(2017).
A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms. BMC GENOMICS.
895.
-
Sze, S., & Tarone, A. M.
(2013).
A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de bruijn graphs of RNA-seq data. 1-1.
-
Chen, J., Fan, J., & Sze, S.
(2013).
Parameterized and Approximation Algorithms for the MAF Problem in Multifurcating Trees. Lecture Notes in Artificial Intelligence.
152-164.
-
Chen, J., Liu, Y., Lu, S., Sze, S., & Zhang, F.
(2012).
Iterative Expansion and Color Coding: An Improved Algorithm for 3D-Matching. ACM Transactions on Algorithms.
1-22.
-
Hsieh, M., & Sze, S.
(2010).
GRAPHLET ALIGNMENT IN PROTEIN INTERACTION NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
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Lu, Y., & Sze, S.
(2008).
Multiple sequence alignment based on profile alignment of intermediate sequences. Journal of Computational Biology.
767-777.
-
Sze, S., & Zhao, X.
(2007).
Improved pattern-driven algorithms for motif finding in DNA sequences. Lecture Notes in Artificial Intelligence.
198-+.
-
Lu, Y., & Sze, S.
(2007).
Multiple sequence alignment based on profile alignment of intermediate sequences. Lecture Notes in Artificial Intelligence.
283-+.
-
Chen, J., Lu, S., Sze, S., & Zhang, F.
(2007).
Improved Algorithms for Path, Matching, and Packing Problems. 298-307.
-
Sze, S., Lu, Y., & Yang, Q.
(2006).
A polynomial time solvable formulation of multiple sequence alignment. Journal of Computational Biology.
309-319.
-
Liu, Y., Lu, S., Chen, J., & Sze, S.
(2006).
Greedy localization and color-coding: Improved matching and packing algorithms. Lecture Notes in Artificial Intelligence.
84-95.
-
Sze, S. H., Lu, Y., & Yang, Q. W.
(2005).
A polynomial time solvable formulation of multiple sequence alignment. Lecture Notes in Artificial Intelligence.
204-216.
-
Sze, S. H., & Pevzner, P. A.
(1997).
Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. Journal of Computational Biology.
297-309.
-
Sze, S. H., & Pevzner, P. A.
(1997).
Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. 300-309.
-
Fu, S., Chang, P. L., Friesen, M. L., Teakle, N. L., Tarone, A. M., & Sze, S.
(2019).
Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus. BMC GENOMICS.
425-1.
Research
Teaching
teaching activities
- BICH419 Cmptl Tech Evol Analy Instructor
- BICH491 Hnr-research Instructor
- BICH628 Computational Biology Instructor
- BICH685 Directed Studies Instructor
- BICH691 Research Instructor
- CSCE222 Discrete Struc Computing Instructor
- CSCE222 Discrete Struc Computing Instructor
- CSCE411 Design Analy Algorithms Instructor
- CSCE433 Formal Languages Autom Instructor
- CSCE491 Hnr-research Instructor
- CSCE627 Th Of Computability Instructor
- CSCE628 Computational Biology Instructor
- CSCE629 Analysis Of Algorithms Instructor
- CSCE684 Professional Internship Instructor
- CSCE685 Directed Studies Instructor
- CSCE691 Research Instructor
- GENE419 Cmptl Tech Evol Analy Instructor
- GENE491 Hnr-research Instructor
Works By Students
chaired theses and dissertations
-
Chin, See Loong (2004-09). Incomplete gene structure prediction with almost 100% specificity.
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Fan, Jia-Hao (2013-07). Cuts and Partitions in Graphs/Trees with Applications.
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Fu, Shuhua (2015-05). Genomic and Transcriptomic Studies on Non-Model Organisms.
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Lu, Songjian (2010-07). Randomized and Deterministic Parameterized Algorithms and Their Applications in Bioinformatics.
-
Lu, Yue (2009-05). Improving the quality of multiple sequence alignment.
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Yang, Qingwu (2009-05). Finding conserved patterns in biological sequences, networks and genomes.
-
Yi, Gang Man (2009-05). An algorithm for identifying clusters of functionally related genes in genomes.
-
Yi, Gang Man (2012-07). Algorithms for Gene Clustering Analysis on Genomes.
-
Zhao, Xiaoyan (2012-02). Improved Algorithms for Discovery of Transcription Factor Binding Sites in DNA Sequences.
Background
education and training
- Ph.D. in Computer Science, University of Southern California - (Los Angeles, California, United States) 2000
- M.S. in Computer Science, Pennsylvania State University - (State College, Pennsylvania, United States) 1995
- B.S. in Computer Science, Chinese University of Hong Kong - (Shatin, Hong Kong, China) 1990
Contact
first name
- Sing-Hoi
has last name
- Sze
mailing address
-
Texas A&M University
Computer Science & Engineering
3112 TAMU
College Station, TX 77843-3112
USA
Other
- shsze@tamu.edu