Algorithms and Computational Biology Laboratory
Dept. of Computer Science and Information Engineering
National Taiwan University, Taiwan

PI: Prof. Kun-Mao Chao

Software Tools for Bioinformatics and Medical Informatics:

• Pairwise Sequence Alignment
  • Huang, X. and Chao, K.-M., 2003, “A Generalized Global Alignment Algorithm,” Bioinformatics, 19: 228-233.
  • Huang, X., Ye, L., Chou, H. -H., Yang, I. -H and Chao, K.-M., 2004, “Efficient Combination of Multiple Word Models for Improved Sequence Comparison,” Bioinformatics, 20: 2529-2533.
• Finding CpG Islands
  • Lin, Y.-L., Jiang, T. and Chao, K.-M., 2002, “Efficient Algorithms for Locating the Length-Constrained Heaviest Segments, with Applications to Biomolecular Sequence Analysis,” Journal of Computer and System Sciences (JCSS), 65: 570-586.
  • Lin, Y.-L., Huang, X., Jiang, T. and Chao, K.-M., 2003, “MAVG: Locating Non-Overlapping Maximum Average Segments in a Given Sequence,” Bioinformatics, 19: 151-152.
• Robust Tag SNPs
  • Huang, Y.-T., Zhang, K., Chen, T. and Chao, K.-M., 2005, “Selecting Additional Tag SNPs for Tolerating Missing Data in Genotyping,” BMC Bioinformatics, 6: 263.
  • Chang, C.-J., Huang, Y.-T., and Chao, K.-M., 2006, “A Greedier Approach for Finding Tag SNPs,” Bioinformatics, 22: 685-691.
• Haplotype Inference
  • Huang, Y.-T., Chao, K.-M., and Chen, T., 2005, “An Approximation Algorithm for Haplotype Inference by Maximum Parsimony,” Journal of Computational Biology, 12: 1261-1274.
• HapTagger
  • Huang, Y.-T. and Chao, K.-M., 2008, “A New Framework for the Selection of Tag SNPs by Multimarker Haplotypes” Journal of Biomedical Informatics, 6: 953-961.
• CNVDetector
  • Chen, P.-A., Liu, H.-F., Chao, K.-M., 2008, "CNVDetector: Locating Copy Number Variations Using Array CGH Data", Bioinformatics, 24: 2773-2775.
• SimHLA
  • Chang, C.-J., Chen, P.-L., Yang, W.-S., and Chao, K.-M., 2014, “A Fault-tolerant Method for HLA Typing with PacBio Data,” BMC Bioinformatics, 15: 296.
• SMART
  • Liang, Y.-J., Lin, Y.-T., Chen, C.-W., Lin, C.-W., Chao, K.-M., Pan, W.-H., and Yang, H.-C., 2016, “SMART: Statistical Metabolomics Analysis – An R Tool,” Analytical Chemistry, 88(12):6334-6341.
• Advance_Vaccine_Distribution
  • Ho, B.-S., and Chao, K.-M., Manuscript under review.
• Other Software

This site was last updated 12/14/19