Sing-Hoi Sze
Department of Computer Science and Engineering,
Department of Biochemistry & Biophysics,
Texas A&M University,
College Station, TX 77843.
Office: PETR 427
Phone: (979)845-5009
Email: shsze@cse.tamu.edu
Research
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.
Software
- NDComplex - Identifying complexes from a protein
interaction network by considering different types of complexes separately
- Post-Processing - Post-processing on the de Bruijn
graph from the Velvet assembler
- SClassify - Supervised protein family classification
- PosMotif - Finding DNA motifs based on skipping
positions in background Markov chains
- GCFinder - Finding conserved gene clusters on multiple
genomes
- GCQuery - Finding related gene clusters on a given
genome from a given query cluster
- ISPAlign - Intermediate sequence profile alignment
- MotifEnumerator - Improved pattern-driven
algorithms for motif finding in DNA sequences
- NRAlign - Neighboring residue alignment
- PathMatch and GraphMatch
- Path matching and graph matching in biological networks
- PSAlign - Preserving multiple sequence alignment
- SSFold - Predicting protein folding pathways at the
mesoscopic level based on native interactions between secondary structure
elements
Courses
- Fall 24, 23, Spring 14, 12: CSCE 433/627 Formal Languages and
Automata / Theory of Computability
- Fall 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 11, Spring 10, 09: BICH/GENE
419 Computational Techniques for Evolutionary Analysis
- Spring 24, 22, Fall 21, 20, Spring 20, 17, 16, 13, Fall 11, 10, 09, Spring 09: CSCE
222 Discrete Structures for Computing
- Spring 23, Fall 19, 18, 15: CSCE 411 Design and Analysis of Algorithms
- Fall 22, Spring 21, 15: CSCE/BICH 628 Computational Biology
- Spring 19, Fall 17, 16, Spring 16, Fall 14, 13, 12: Honor-CSCE
222 Discrete Structures for Computing
- Spring 18: CSCE 629 Analysis of Algorithms
- Fall 12, 10: BICH 689 Special Topics in Biological
Discovery through Computation
- Fall 10: CSCE 181 Introduction to Computing
- Fall 09, 08, 07, 06, 05, Spring 04: CSCE 433 Formal
Languages and Automata
- Spring 08, 07, 06, 05, 03: CPSC 627 Theory of
Computability
- Fall 04, 03 and 02: CPSC/BICH 689 Special Topics in
Computational Biology