Curriculum Vitae

Kun-Mao Chao (趙坤茂)

 

Work Address:

Department of Computer Science and Information Engineering

National Taiwan University

Taipei 106, Taiwan

Tel: 886-2-23625336 ext. 423

Fax: 886-2-23628167

Email: email

Homepage: http://www.csie.ntu.edu.tw/~kmchao

 

Education:

Ph.D. in Computer Science (August 1993), The Pennsylvania State University, University Park, PA, USA.

M.S. in Computer Engineering (June 1987), National Chiao Tung University, Hsinchu, Taiwan.

B.S. in Computer Engineering (June 1985), National Chiao Tung University, Hsinchu, Taiwan.

 

Employment:

Professor, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan, August 2006 – present.

Adjunct Professor, Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei, Taiwan, August 2004 – present.

Professor, Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, August 2002 – present.

Chair, Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, August 2014 – July 2017.

Director, System Design Division, Computer and Information Networking Center, National Taiwan University, Taipei, Taiwan, February 2009 – July 2009.

Director, E-Learning Division, Computer and Information Networking Center, National Taiwan University, Taipei, Taiwan, August 2006 – July 2009.

Adjunct Professor, Graduate Program for Bioinformatics, National Yang-Ming University, Taipei, Taiwan, August 2000 – July 2002.

Adjunct Professor, Institute of Biochemistry, National Yang-Ming University, Taipei, Taiwan, October 1999 – July 2002.

Professor, Department of Life Science, National Yang-Ming University, Taipei, Taiwan, August 1999 – July 2002.

Professor, Department of Computer Science and Information Management, Providence University, January 1999 – July 1999.

Associate Professor, Department of Computer Science and Information Management, Providence University, August 1994 – December 1998.

Visiting Scholar, NCBI, National Institutes of Health, January 1994 – July 1994.

Postdoctoral Fellow, Department of Computer Science and Engineering, The Pennsylvania State University, June 1993 – July 1994.

Teaching/Research Assistant, Department of Computer Science, The Pennsylvania State University, August 1989 – May 1993.

Second Lieutenant Engineer: Chinese Air Force Headquarter, July 1987 – May 1989.

Teaching/Research Assistant, Department of Computer Engineering, National Chiao Tung University, July 1985 – June 1987.

Programmer: Microtek Ltd., July 1984 – September 1984.

  

Research Interests: (ABC'S)

  • Algorithms

  • Bioinformatics

  • Computational Molecular Biology

  • Software Tools

 

Publications:

(A) Journal papers:

[1] Chang, R.-C. and Chao, K.-M., 1990, Parallel Operator-Precedence Parsing, Journal of Information Science and Engineering, 6: 51-62.

[2] Chao, K.-M., Pearson, W. R. and Miller, W., 1992, Aligning Two Sequences within a Specified Diagonal Band, Computer Applications in the Biosciences (CABIOS, now Bioinformatics), 8: 481-487. (PostScript version)

[3] Chao, K.-M., Hardison, R. C. and Miller, W., 1993, Constrained Sequence Alignment, Bulletin of Mathematical Biology, 55: 503-524. (PostScript version)

[4] Chao, K.-M., Hardison, R. C. and Miller, W., 1993, Locating Well-Conserved Regions within a Pairwise Alignment, Computer Applications in the Biosciences (CABIOS, now Bioinformatics), 9: 387-396. (PostScript version)

[5] Hardison, R. C., Chao, K.-M., Adamkiewicz, M., Price, D., Jackson, J., Zeigler, T., Stojanovic, N. and Miller, W., 1993, Positive and Negative Regulatory Elements of the Rabbit Embryonic e-Globin Gene Revealed by an Improved Multiple Alignment Program and Functional Analysis, DNA Sequence, 4: 163-176.

[6] Hardison, R. C., Chao, K.-M., Schwartz, S., Stojanovic, N., Ganetsky, M. and Miller, W., 1994, Globin Gene Server: A Prototype E-Mail Database Server Featuring Extensive Multiple Alignments and Data Compilation for Electronic Genetic Analysis, Genomics,  21: 344-353.

[7] Chao, K.-M., Hardison R. C. and Miller, W., 1994, Recent Developments in Linear-Space Alignment Methods: a Survey, Journal of Computational Biology, 1: 271-291. (PostScript version)

[8] Chao, K.-M. and Miller, W., 1995, Linear-Space Algorithms that Build Local Alignments from Fragments, Algorithmica, 13: 106-134.

[9] Chao, K.-M., Zhang, J., Ostell, J. and Miller, W., 1995, A Local Alignment Tool for Very Long DNA Sequences, Computer Applications in the Biosciences (CABIOS, now Bioinformatics),  11: 147-153. (PostScript version)

[10] Chao, K.-M., Zhang, J., Ostell, J. and Miller, W., 1997, A Tool for Aligning Very Similar DNA sequences, Computer Applications in the Biosciences (CABIOS, now Bioinformatics),  13: 75-80.

[11] Chao, K.-M., 1998, “On Computing all Suboptimal Alignments,” Information Sciences, 105: 189-207.

[12] Wu, Q. S., Chao, K.-M. and Lee, R. C. T., 1998, “The NPO-Completeness of the Longest Hamiltonian Cycle Problem,” Information Processing Letters, 65: 119-123.

[13] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 1999, “Efficient Algorithms for the Length-Constrained Heaviest Path Problems on a Tree,” Information Processing Letters, 69: 63-67.

[14] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 1999, “Exact and Approximation Algorithms for Constructing Ultrametric Trees from Distance Matrices,” Journal of Combinatorial Optimization, 3: 199-211.

[15] Chao, K.-M., 1999, “Calign: Aligning Sequences with Restricted Affine Gap Penalties,” Bioinformatics, 15: 298-304.

[16] Wu, B. Y., Chao, K.-M. and Tang, C. Y. , 2000, “Approximation Algorithms for some Optimum Communication Spanning Tree Problems,” Discrete Applied Mathematics, 102: 245-266.

[17] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 2000, “A Polynomial Time Approximation Scheme for Optimal Product-Requirement Communication Spanning Trees,” Journal of Algorithms, 36: 182-204.

[18] Wu, B. Y., Lancia, G., Bafna, V., Chao, K.-M., Ravi, R. and Tang, C. Y., 2000, A Polynomial-Time Approximation Scheme for Minimum Routing Cost Spanning Trees, SIAM Journal on Computing, 29: 761-778.

[19] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 2000, “Approximation Algorithms for the Shortest Total Path Length Spanning Tree Problem,” Discrete Applied Mathematics, 105: 273-289.

[20] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 2002, “Light Graph with Small Routing Cost,” Networks, 39: 130-138.

[21] 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.

[22] 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.

[23] Huang, X. and Chao, K.-M., 2003, “A Generalized Global Alignment Algorithm,” Bioinformatics, 19: 228-233.

[24] Tang, C. Y., Lu, C. L., Chang, M. D.-T., Tsai Y.-T, Sun, Y.-J., Chao, K.-M., Chang, J.-M., Chiou, Y.-H., Wu, C.-M., Chang, H.-T. and Chou, W.-I., 2003, “A Constrained Multiple Sequence Alignment Tool Development and its Application to RNase Family Alignment,” Journal of Bioinformatics and Computational Biology, 1: 267-287.

[25] Liu, H.-F., Chang, Y.-H. and Chao, K.-M., 2004, “An Optimal Algorithm for Querying Tree Structures and its Applications in Bioinformatics,” ACM SIGMOD Record, 33: 21-26.

[26] 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.

[27] Yang, I.-H., Huang, C.-P. and Chao, K.-M., 2005, “A Fast Algorithm for Computing a Longest Common Increasing Subsequence,” Information Processing Letters, 93: 249-253.

[28] Lin, R.-R., Kuo, W.-H. and Chao, K.-M., 2005, “Finding a Length-Constrained Maximum-Density Path in a Tree,” Journal of Combinatorial Optimization, 9: 147-156.

[29] Chen, K.-Y. and Chao, K.-M.,  2005, “Optimal Algorithms for Locating the Longest and Shortest Segments Satisfying a Sum or an Average Constraint,” Information Processing Letters, 96: 197-201.

[30] 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.

[31] 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.

[32] Chang, C.-J., Huang, Y.-T., and Chao, K.-M., 2006, “A Greedier Approach for Finding Tag SNPs,” Bioinformatics, 22: 685-691.

[33] Su, J.-S, Tsai, T.-F., Chang, H.-M., Chao, K.-M., Su, T.-S., and Tsai, S.-F., 2006, “Distant HNF1 Site as a Master Control for the Human Class I Alcohol Dehydrogenase Gene Expression,” The Journal of Biological Chemistry, 281(29): 19809-19821.

[34] Cheng, C.-H., Chen, K.-Y., Tien, W.-C., and Chao, K.-M., 2006, “Improved Algorithms for the k Maximum-Sums Problems,” Theoretical Computer Science, 362: 162-170.

[35] Wu, B.Y., Wang, H.-L., Kuan, S.T. and Chao, K.-M., 2007, “On the Uniform Edge-Partition of a Tree,” Discrete Applied Mathematics, 155: 1213-1223.

[36] Chen, K.-Y. and Chao, K.-M.,  2007, “On the Range Maximum-Sum Segment Query Problem,” Discrete Applied Mathematics, 155: 2043-2052.

[37] Liu, H.-F. and Chao, K.-M, 2007, “A Tight Analysis of the Katriel-Bodlaender Algorithm for Online Topological Ordering,” Theoretical Computer Science, 389: 182-189.

[38] Wu, B.Y., Hsiao, C.Y., and Chao, K.-M., 2008, “The Swap Edges of a Multiple-Sources Routing Tree,” Algorithmica, 50: 299-311.

[39] 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.

[40] Yang, C.-Y., Chang, C.-H., Lin, T.-C., Yu, Y.-L., Lee, S.-A., Yen, C.-C., Yang, J.-M., Lai, J.-M., Hong, Y.-R., Tseng, T.-L., Chao, K.-M., and Huang, C.-Y., 2008,  “PhosphoPOINT: a Comprehensive Human Kinase Interactome and Phospho-Protein Database,” Bioinformatics, 24: i14-i20. (ECCB'08 paper)

[41] Liu, H.-F. and Chao, K.-M, 2008, “Algorithms for Finding the Weight-Constrained k Longest Paths in a Tree and the Length-Constrained k Maximum-Sum Segments of a Sequence,” Theoretical Computer Science, 407: 349-358.

[42] Wang, H.-L. and Chao, K.-M., 2008, “The 2-radius and 2-radiian Problems on Trees,” Theoretical Computer Science, 407: 524-531.

[43] Chen, P.-A., Liu, H.-F., and Chao, K.-M., 2008, “CNVDetector: Locating Copy Number Variations Using Array CGH Data,” Bioinformatics, 24: 2773-2775.

[44] Wang, H.-L., Wu, B.Y., and Chao, K.-M., 2009, “The Backup 2-Center and Backup 2-Median Problems on Trees,” Networks, 53(1): 39-49.

[45] Cheng, C.-H., Liu, H.-F., and Chao, K.-M, 2009, “Optimal Algorithms for the Average-Constrained Maximum-Sum Segment Problem,” Information Processing Letters, 109(3): 171-174.

[46] Shyu, S.J., Chen, M.-C., and Chao, K.-M, 2009, “Securing Information Display for Multiple Secrets,” Optical Engineering, 48: 57005.

[47] Liu, H.-F. and Chao, K.-M, 2009, “On Locating Disjoint Segments with Maximum Sum of Densities,” Algorithmica, 54(1): 107-117.

[48] Chu, A.-C., Wu, B.Y., Wang, H.-L., and Chao, K.-M., 2010, “A Tight Bound on the Min-Ratio Edge-Partitioning Problem of a Tree,” Discrete Applied Mathematics, 158(14): 1471-1478.

[49] Hsu, P.-H., Chen, K.-Y., and Chao, K.-M., 2010, “Finding All Approximate Gapped Palindromes,” International Journal of Foundations of Computer Science, 21(6): 925-939. (An invited paper for the special issue of IJFCS for ISAAC 2009)

[50] Chen, K.-Y., Hsu, P.-H., and Chao, K.-M., 2010, “Hardness of Comparing Two Run-Length Encoded Strings,” Journal of Complexity, 26(4): 364-374.

[51] Bernt, M., Chen, K.-Y., Chen, M.-C., Chu, A.-C., Merkle, D., Wang, H.-L., Chao, K.-M., and Middendorf, M.,  2011, “Finding All Sorting Tandem Duplication Random Loss Operations,” Journal of Discrete Algorithms, 9(1): 32-48.

[52] Chen, Y.-C. and Chao, K.-M, 2011, “On the Generalized Constrained Longest Common Subsequence Problems,” Journal of Combinatorial Optimizations, 21(3): 383-392.

[53] Luo, C.-W., Chen, M.-C., Chen, Y.-C., Yang, R.W.-L., Liu, H.-F., and Chao, K.-M, 2011, “Linear-Time Algorithms for the Multiple Gene Duplication Problems,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1): 260-265.

[54] Luo, C.-W., Liu, H.-F., Chen, P.-A., and Chao, K.-M, 2011, “Minkowski Sum Selection and Finding,” International Journal of Computational Geometry and Applications, 21(3): 283-311. (An invited paper for the special issue of IJCGA for ISAAC 2008)

[55] Lin, R.-R., Chang, Y.-H. and Chao, K.-M., 2011, “Improving the Performance of Identifying Contributors for XML Keyword Search,” ACM SIGMOD Record, 40(1): 5-10.

[56] Lee, C.-H., Wu, Y.-K., Wang, J.-Y., Lan, C.-C., Lee, C.-Y., Hsu, K.-Y., Chao, K.-M., Chang, H., 2011, “Influence of Pressure Control Levels on the Pulse Pressure Variations,” Shock, 36(6): 628-632.

[57] Chen, M.-H., Yang, W.-L. R., Lin, K.-T., Liu, C.-H., Liu, Y.-W., Huang, K.-W., Chang, M.-H., Lai, J.-M., Chun-Nan Hsu, C.-N., Chao, K.-M., Kao, C.-Y, and Huang, C.-Y. F., 2011, “Gene Expression-Based Chemical Genomics Identifies Potential Therapeutic Drugs in Hepatocellular Carcinoma,” PLoS ONE, 6(11): e27186.

[58] Huang, Y.-T., Chang, C.-J., and Chao, K.-M., 2011, “The Extent of Linkage Disequilibrium and Computational Challenges of Single Nucleotide Polymorphisms in Genome-Wide Association Studies,” Current Drug Metabolism, 12(5): 498-506.

[59] Chang, C.-J. and Chao, K.-M., 2012, “Efficient Algorithms for Local Ranking,” Information Processing Letters, 112(13): 517-522.

[60] Chen, K.-Y., Hsu, P.-H., and Chao, K.-M., 2012, “Efficient Retrieval of Approximate Palindromes in a Run-Length Encoded String,” Theoretical Computer Science, 432: 28-37.

[61] Lee, C.-H., Lee, M.-C., Lin, H.-H., Shu, C.-C., Wang, J.-Y., Lee, L.-N., and Chao, K.-M., 2012, “Pulmonary Tuberculosis and Delay in Anti-tuberculous Treatment are Important Risk Factors for Chronic Obstructive Pulmonary Disease” PLoS ONE,  7(5): e37978.

[62] Chen, K.-Y. and Chao, K.-M., 2013, “A Fully Compressed Algorithm for Computing the Edit Distance of Run-Length Encoded Strings,” Algorithmica, 65(2): 354-370.

[63] Chu, A.-C., Wu, B.Y., and Chao, K.-M., 2013, “A Linear-time Algorithm for Finding an Edge-partition with Max-min Ratio at Most Two,” Discrete Applied Mathematics, 161(7-8): 932-943.

[64] Lee, C.-H., Lee, M.-C., Shu, C.-C., Lim, C.-S., Wang, J.-Y., Lee, L.-N., and Chao, K.-M., 2013, “Risk Factors for Pulmonary Tuberculosis in Patients with Chronic Obstructive Airway Disease in Taiwan: A Nationwide Cohort Study,” BMC Infectious Diseases, 13:194.

[65] Yang, W.-L. R.,Lee,  Y.-E., Chen, M.-H., Chao, K.-M., and Huang, C.-Y. F., 2013, “In-silico Drug Screening and Potential Target Identification for Hepatocellular Carcinoma Using Support Vector Machine Based on Drug Screening Result,” Gene, 518(1): 201-208.

[66] Lien, Y.-c., Wang, J.-Y., Lee, M.-C., Shu, C.-C., Chen, H.-Y., Hsieh, C.-H., Lee, C.-H., Lee, L.-N., and Chao, K.-M., 2013, “Urinary Tuberculosis Is Associated with the Development of Urothelial Carcinoma but Not Renal Cell Carcinoma: A Nationwide Cohort Study in Taiwan,” British Journal of Cancer, 26;109(11): 2933-2940.

[67] Lin, R.-R., Chang, Y.-H. and Chao, K.-M., 2014, “Locating Valid SLCAs for XML Keyword Search with NOT Semantics,” ACM SIGMOD Record, 43(2): 29-34.

[68] 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.

[69] Chang, C.-J., Tamura, T., Chao, K.-M., and T. Akutsu, 2015, “A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth Date of Evaluation,” IEICE Transactions on Fundamentals, 98-A(1): 384-390.

[70] Wang, J.-Y., Lee, M.-C., Shu, C.-C., Lee, C.-H., Lee, L.-N., Chao, K.-M., and Chang, F.-Y., 2015, “Optimal Duration of Anti-tuberculosis Treatment in Diabetic Patients: Nine or Six months?,” CHEST, 147(2):520-528.

[71] Wang, J.-Y., Lee, M.-C., Chang, J.-H., Yu, M.-C., Wu, V.-C., Huang, K.-L., Su, C.-P., Chao, K.-M., Lee, C.-H., 2015, “Mycobacterium tuberculosis nucleic acid amplification tests reduce nosocomial tuberculosis exposure in intensive care units: A nationwide cohort study,” Respirology; 20(8):1233-1240.

[72] 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.

[73] Ho, B.-S., and Chao, K.-M., 2017, “Data-driven Interdisciplinary Mathematical Modelling Quantitatively Unveils Competition Dynamics of Co-circulating Influenza Strains,” Journal of Translational Medicine, 15(1):163.

[74] Ho, B.-S., and Chao, K.-M., 2020, “On the Influenza Vaccination Policy through Mathematical Modeling,” International Journal of Infectious Diseases, 98: 71-79.

[75] Chiang, C.-W., Hsiao, Y.-C., Jheng, P.-R., Chen, C.-H., Manga, Y. B., Lekha, R., Chao, K.-M., Ho, Y.-C., Chuang, E.-Y., 2021, “Strontium Ranelate-laden Near-infrared Photothermal-inspired Methylcellulose Hydrogel for Arthritis Treatment,” Materials Science and Engineering: C, Vol. 123, 111980.

[76] Chiang, C.-W., Chen, C.-H, Manga, Y. B, Huang, S.-C., Chao, K.-M., Jheng, P.-R., Wong, P.-C., Nyambat, B., Satapathy, M.-K., Chuang, E.-Y., 2021, “Facilitated and Controlled Strontium Ranelate Delivery Using GCS-HA Nanocarriers Embedded into PEGDA Coupled with Decortication Driven Spinal Regeneration,” International Journal of Nanomedicine, Vol. 16, 4209-4224.

[77] Chen, M.-J., and Chao, K.-M., 2022, “Proof of a Conjecture About Minimum Spanning Tree Cycle Intersection,” Discrete Applied Mathematics, 321: 19-23.

(B) Conference papers:
 (Note: Polished forms of many of the following papers have appeared or will appear in journals listed above.)

[1] Shaw, J.-R., Suen, J.-S., Chao, K.-M., Chen, S.-H. and Du, M.-W. , 1986, A Syntax-Directed Editor for C Language, Proceedings of the Sixth Workshop on Computer System Technology, 407-416, Taiwan.

[2] Chao, K.-M. and Chang, R.-C. , 1987, Parallel Operator-Precedence Parsing, Proceedings of National Computer Symposium, 889-894, Taiwan.

[3] Chao, K.-M. and Chang, R.-C. , 1987, Incremental Operator-Precedence Parsing, Proceedings of National Computer Symposium, 145-151, Taiwan.

[4] Chao, K.-M., 1994, Computing All Suboptimal Alignments in Linear Space, Combinatorial Pattern Matching '94, Lecture Notes in Computer Science 807, 31-42, California, USA.

[5] Chao, K.-M., 1994,  An O(MN)-Time, O()-Space Algorithm for Computing All Suboptimal Grid Points, Proceedings of the 10th Workshop on Combinatorial Mathematics and Computational Theory,.48-51, Taiwan.

[6] Chao, K.-M., 1994, Flexible Space-Saving Strategies for Computing All Suboptimal Alignments, Proceedings of International Computer Symposium, 414-419, Taiwan.

[7] Chao, K.-M., 1995, Multi-Pattern String Matching with Spacers and Ambiguity, Proceedings of the 12th Workshop on Combinatorial Mathematics and Computational Theory, 131-134, Taiwan.

[8] Chao, K.-M., 1996, Aligning Genomic DNA Sequences, The First Symposium on Genome Research and Analysis, 15, Taiwan.

[9] Chao, K.-M., 1996, On Building an Interactive Alignment Tool,” International Symposium on Combinatorics and Applications (SOCA '96), 84-93, Mainland China.

[10] Hsu, W. L., Chao, K.-M., 1996, Searching Patterns in DNA Sequences, International Computer Symposium (poster session, 5 pages), Taiwan.

[11] Zhang, J., Chao, K.-M., Florea, L., Miller, W., 1997, Alignment Requirements for NCBI's Genomes Division, First Annual International Conference on Computational Molecular Biology (RECOMB 97) (poster session, 15 pages), New Mexico, USA.

[12] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 1997, Approximation Algorithms for the Shortest Total Path Length Spanning Tree Problem,” Proceedings of the 14th Workshop on Combinatorial Mathematics and Computational Theory,  10-15, Taiwan.

[13] Chao, K.-M., 1997, “Fast Algorithms for Aligning Sequences with Restricted Affine Gap Penalties,” Third Annual International Computing and Combinatorics Conference (COCOON 97), Lecture Notes in Computer Science 1276, 264-273, Shanghai, Mainland China.

[14] Wu, B. Y., Chao, K.-M., and Tang, C. Y., 1997,  Algorithms for Finding the Shortest Total Path Length 2-stars, National Computer Symposium, E73-76, Taiwan.

[15] Wu, Q. S., Chao, K.-M. and Lee, R. C. T., 1997, “Approximation Algorithms,” International Symposium on Parallel Architectures, Algorithms and Networks (ISPAN ’97), Taiwan.

[16] Wu, B. Y., Lancia, G., Bafna, V., Chao, K.-M., Ravi, R. and Tang, C. Y., 1998, A Polynomial-Time Approximation Scheme for Minimum Routing Cost Spanning Trees, Ninth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 98), California, USA, 21-32.

[17] Chao, K.-M., 1998  A Whirlwind Tour of Computational Molecular Biology,” Proceedings of the 15th Workshop on Combinatorial Mathematics and Computational Theory, 31-35, Taiwan.

[18] Chao, K.-M., 1998 “Recent Developments in Linear-Space Alignment Methods,” Fourth Symposium on Recent Advances in Biophysics, S37, Taiwan.

[19] Wu, B. Y., Chao, K.-M., and Tang, C. Y, 1998 “Approximation and Exact Algorithms for Constructing Minimum Ultrametric Trees from Distance Matrices,” Fourth Annual International Computing and Combinatorics Conference (COCOON 98), Lecture Notes in Computer Science 1449, 299-308, Taiwan.

[20] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 1998, “Approximation Algorithms for some Optimum Communication Spanning Tree Problems,” Ninth Annual International Symposium on Algorithm and Computation (ISAAC ’98), Lecture Notes in Computer Science, 1533, 107-416, Taejon, Korea.

[21] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 1999, “Constructing Light Spanning Trees with Small Routing Cost,” 16th International Symposium on Theoretical Aspects of Computer Science (STACS ’99), Lecture Notes in Computer Science, 1563, 334-344, Trier, Germany.

[22] 蔡永恆, 林明信, 陳智賢, 柯建全, 王孝熙, 林敏惠, 趙坤茂, 1999, “電子商城的經營型態分析,” 邁向二十一世紀亞太管理學術研討會, 成功大學, Taiwan.

[23] 申永德, 李進成, 周文光, 王讚彬, 趙坤茂, 1999, “無線網路、商機無限,” 邁向二十一世紀亞太管理學術研討會, 成功大學, Taiwan.

[24] Wu, Q. S., Lee, R. C. T. and Chao, K.-M., 2000, “Linear Time Algorithm for the Hamiltonian Path Problem on a Series-Paralle Graph,” Fifth International Conference on Computer Science and Informatics (CS&I'2000), Atlantic City, USA.

[25] Chen, C.-Y., Su, J.-S., Chang, H.-M., Chao, K.-M., Hsiao, K.-J. and Tsai, S.-F., 2000, “The Complete Genome Sequence of the Human ADH Gene Family,” HGM 2000 Gene Mapping and Large Scale Sequencing, (poster session), Vancouver, BC, Canada.

[26] Chao, K.-M., 2002, “Dynamic-Programming Strategies for Biomolecular Sequence Analysis,” Workshop on Sequence and Gene Expression Analysis, 1-40, Singapore. (Invited Tutorial Speaker)

[27] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 2002, “On the Optimum Requirement Graph Problem,” The 19th Workshop on Combinatorial Mathematics and Computational Theory.

[28] Lin, Y.-L., Jiang, T. and Chao, K.-M., 2002, “Efficient Algorithm for Locating the Length-Constrained Heaviest Segments, with Applications to Biomolecular Sequence Analysis,” The 27th International Symposium on Mathematical Foundations of Computer Science (MFCS 2002), Lecture Notes in Computer Science, Poland.

[29] Tang, C. Y., Lu, C. L., Chang, M. D.-T., Tsai Y.-T, Sun, Y.-J., Chao, K.-M., Chang, J.-M., Chiou, Y.-H., Wu, C.-M., Chang, H.-T., Chou, and W.-I., 2002, “A Constrained Multiple Sequence Alignment Tool Development and its Application to RNase Family Alignment,” The First IEEE Computer Society Bioinformatics Conference (CSB 2002), Stanford University, Palo Alto, CA, USA.

[30] Yang, I.-H., Huang, C.-P. and Chao, K.-M., 2003, “A Fast Algorithm for Computing a Longest Common Increasing Subsequence,” The 20th Workshop on Combinatorial Mathematics and Computational Theory, 93-97, Taiwan.

[31] Lin, R.-R., Kuo, W.-H. and Chao, K.-M., 2003, “Finding a Length-Constrained Maximum-Density Path in a Tree,” The 14th Annual International Symposium on Algorithms and Computation (ISAAC 2003), Lecture Notes in Computer Science 2906, 78-87, Kyoto, Japan.

[32] Yang, I. -H., Wang, S. -H., Chen, Y. -H., Huang, P. -H., Ye, L., Huang, X. and Chao, K.-M., 2004, “Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds,” IEEE Fourth Symposium on  Bioinformatics and Bioengineering (IEEE BIBE 2004), 411-418, Taiwan.

[33] Huang, Y.-T. and Chao, K.-M., 2004, “On the Selection of Robust Tag SNPs,” The 21th Workshop on Combinatorial Math and Computation Theory, 241-248, Taiwan.

[34] Wu, B. Y., Wang, H.-L., Kuan, S. T. and Chao, K.-M., 2004, “On the Uniform Edge-Partition of a Tree,” The 21th Workshop on Combinatorial Math and Computation Theory, 132-140, Taiwan.

[35] Chen, K.-Y. and Chao, K.-M., 2004, “An Optimal Algorithm for the Range Maximum-Sum Segment Query Problem,” The 21th Workshop on Combinatorial Math and Computation Theory, 257-265, Taiwan.

[36] Cheng, C. H., Huang, C. C., Hu, S. Y. and Chao, K.-M., 2004, “Efficient Algorithms for Some Variants of the Farthest String Problem,” The 21th Workshop on Combinatorial Math and Computation Theory, 266-272, Taiwan.

[37] Huang, X., Ye, L., Yang, I-H. and Chao, K.-M., 2004, “A Sensitive Sequence Comparison Method,” The 5th International Conference on Software Engineering, Artificial Intelligence, Networking, and Parallel/Distributed Computing, 77-80, Beijing, China.

[38] Huang, Y.-T., Zhang, K., Chen, T. and Chao, K.-M., 2004, “Approximation Algorithms for the Selection of Robust Tag SNPs,” The 4th Workshop on Algorithms in Bioinformatics (WABI 2004), Lecture Notes in Computer Science / Lecture Notes in Bioinformatics, 278-289, Bergen, Norway.

[39] Chen, K.-Y. and Chao, K.-M.,  2004, “On the Range Maximum-Sum Segment Query Problem,” The 15th Annual Symposium on Algorithms and Computation (ISAAC 2004) Lecture Notes in Computer Science, 294-305, Hong Kong.

[40] Huang, Y.-T., Chao, K.-M., and Chen, T., 2005, “An Approximation Algorithm for Haplotype Inference by Maximum Parsimony,” The 20th Annual ACM Symposium on Applied Computing (SAC 2005), 146-150, New Mexico, USA.

[41] Wu, B.Y., Hsiao, C.Y., and Chao, K.-M., 2005, “The Swap Edges of a Multiple Source Routing Tree,” The 22th Workshop on Combinatorial Math and Computation Theory, Taiwan.

[42] Cheng, C.-H., Chen, K.-Y., Tien, W.-C., Chao, K.-M., 2005, “Improved Algorithms for the k Maximum-Sums Problems,” The 16th Annual Symposium on Algorithms and Computation (ISAAC 2005), Lecture Notes in Computer Science 3827, 799-808, Sanya, China.

[43] Liu, H.-F. and Chao, K.-M., 2006, “On Locating Disjoint Segments with Maximum Sum of Densities,” The 17th Annual Symposium on Algorithms and Computation (ISAAC 2006), Lecture Notes in Computer Science, India.

[44] Wang, H.-L., Wu, B. Y. and Chao, K.-M., 2007, “A Linear Time Algorithm for the Backup 2-Center Problem on a Tree,” The 24th Workshop on Combinatorial Math and Computation Theory, 189-195, Taiwan.

[45] Liu, H.-F., Chen, P.-A.  and Chao, K.-M., 2007, “Algorithms for Computing the Length-Constrained Max-Score Segments with Applications to DNA Copy Number Data Analysis,” The 18th Annual Symposium on Algorithms and Computation (ISAAC 2007), Lecture Notes in Computer Science, Japan.

[46] Yang, C.-Y., Chang, C.-H., Lin, T.-C., Yu, Y.-L., Lee, S.-A., Yen, C.-C., Yang, J.-M., Lai, J.-M., Hong, Y.-R., Tseng, T.-L., Chao, K.-M., and Huang, C.-Y., 2008,  “PhosphoPOINT: a Comprehensive Human Kinase Interactome and Phospho-Protein Database,” European Conference on Computational Biology (ECCB 2008), Italy.

[47] Luo, C.-W., Liu, H.-F., Chen, P.-A., and Chao, K.-M., 2008, “Minkowski Sum Selection and Finding,” The 19th Annual Symposium on Algorithms and Computation (ISAAC 2008), Lecture Notes in Computer Science, Australia.

[48] Bernt, M., Chen, M.-C., Merkle, D., Wang, H.-L., Chao, K.-M., and Middendorf, M., 2009, “Finding All Sorting Tandem Duplication Random Loss Operations,” The 20th Annual Symposium on Combinatorial Pattern Matching (CPM'09), Lecture Notes in Computer Science, France.

[49] Chen, K.-Y., Hsu, P.-H., and Chao, K.-M., 2009, “Approximate Matching for Run-Length Encoded Strings is 3Sum-Hard,” The 20th Annual Symposium on Combinatorial Pattern Matching (CPM'09), Lecture Notes in Computer Science, France.

[50] Hsu, P.-H., Chen, K.-Y., and Chao, K.-M., 2009, “Finding All Approximate Gapped Palindromes,” The 20th Annual Symposium on Algorithms and Computation (ISAAC 2009), Lecture Notes in Computer Science, Hawaii, USA.

[51] Lin, R.-R., Chang, Y.-H. and Chao, K.-M., 2010, “Faster Algorithms for Searching Relevant Matches in XML Databases,” The 21st International Conference on Database and Expert Systems Applications (DEXA 2010), Lecture Notes in Computer Science, Bilbao, Spain.

[52] Chen, K.-Y. and Chao, K.-M., 2010, “A Fully Compressed Algorithm for Computing the Edit Distance of Run-Length Encoded Strings,” The 18th Annual European Symposium on Algorithms (ESA 2010), Lecture Notes in Computer Science, Liverpool, United Kingdom.

[53] Chen, K.-Y., Hsu, P.-H., and Chao, K.-M., 2010, “Identifying Approximate Palindromes in Run-Length Encoded Strings,” The 21th Annual Symposium on Algorithms and Computation (ISAAC 2010), Lecture Notes in Computer Science, Korea.

[54] Lin, R.-R., Chang, Y.-H. and Chao, K.-M., 2011, “Identifying Relevant Matches with NOT Semantics over XML Documents,” The 16th International Conference on Database Systems for Advanced Applications (DASFAA 2011), Lecture Notes in Computer Science, Hong Kong.

[55] Chao, K.-M., Chu, A.-C., Jansson, J., Lemence, R., and Mancheron, A., 2012, “Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics,” The 9th Annual Conference on Theory and Applications of Models of Computation (TAMC 2012), Lecture Notes in Computer Science, Beijing, China.

[56] Bernt, M., Chao, K.-M., Kao, J.-W., Middendorf, M., and Tannier, E., 2012, “Preserving Inversion Phylogeny Reconstruction,” The 12th Workshop on Algorithms in Bioinformatics (WABI 2012), Lecture Notes in Bioinformatics, Ljubljana, Slovenia.

[57] Yang, W.-L. R.,Lee,  Y.-E., Chen, M.-H., Chao, K.-M., and Huang, C.-Y. F., 2012, “In-silico Drug Screening and Potential Target Identification for Hepatocellular Carcinoma Using Support Vector Machine Based on Prior Screening Result,” The 23rd International Conference on Genome Informatics (GIW 2012), Taiwan.

[58] Lin, R.-R., Chang, Y.-H. and Chao, K.-M., 2013, “A Compact and Efficient Labeling Scheme for XML Documents,” The 18th International Conference on Database Systems for Advanced Applications (DASFAA 2013), Lecture Notes in Computer Science, China.

[59] Wu, Y.-W., Lin, W.-Y., Wang, H.-L., and Chao, K.-M., 2013, “An Optimal Algorithm for the Popular Condensation Problem,” International Workshop on Combinatorial Algorithms (IWOCA 2013), Lecture Notes in Computer Science, France.

[60] Wu, Y.-W., Lin, W.-Y., Wang, H.-L., and Chao, K.-M., 2013, “Computing Plurality Points and Condorcet Points in Euclidean Space,” The 24th Annual Symposium on Algorithms and Computation (ISAAC 2013), Lecture Notes in Computer Science, Hong Kong.

[61] Wu, Y.-W., Lin, W.-Y., Wang, H.-L., and Chao, K.-M., 2014, “The Generalized Popular Condensation Problem,” The 25th Annual Symposium on Algorithms and Computation (ISAAC 2014), Lecture Notes in Computer Science, Korea.

[62] Lin, W.-Y., Wu, Y.-W., Wang, H.-L., and Chao, K.-M., 2015, “Forming Plurality at Minimum Cost,” The 9th International Workshop on Algorithms and Computation (WALCOM 2015), Lecture Notes in Computer Science, Bangladesh.

[63] Huang, A., Wang, H.-L., and Chao, K.-M., 2016, “Computing the line-constrained $k$-center in the plane for small k,” The Eleventh International Conference on Algorithmic Aspects in Information and Management (AAIM 2016), Lecture Notes in Computer Science, Italy.

[64] Ling, P.-T., Wang, H.-L., and Chao, K.-M., 2018, “Determining a social choice with respect to linear preferences,” The Seventh International Workshop on Computational Social Choice (COMSOC-2018), USA.

 (C) Books and others:

  (C1) Books:

[1] 與王孝熙等合著(1997, 1998, 2000, 2002 & 2003)「計算機概論」，東華書局。(ISBN 957-483-143-4) 本書第六版(2004年)，改由碁峯出版社發行。(ISBN 986-421-565-5)

[2] Wu, B. Y. and Chao, K.-M. (2004) “Spanning Trees and Optimization Problems,” Chapman & Hall / CRC Press, USA. (200 pages; ISBN 1-58488-436-3) (website)

[3] 趙坤茂, 張雅惠, 黃寶萱, 黃俊穎 (2004年初版；2024年修訂第十九版)「計算機概論 -- AI與科技的共舞」，全華科技圖書公司。(ISBN 978-626-328-906-2) (website)

[4] Chao, K.-M. and Zhang, L. (2009) “Sequence Comparison: Theory and Methods,” Springer. (210 pages; ISBN 978-1848003194)

[5] Chao, K.-M., Hsu, T.-s., and Lee, D.-T. (Eds.) (2012)  “Algorithms and Computation,” Lecture Notes in Computer Science 7676, Springer. (702 pages; ISBN 978-3-642-35260-7) (see I, II, III, IV, and IV)

[6] 張雅惠,黃俊穎,趙坤茂 (2014年初版；2016年修訂第二版)「計算機概論 -- 與資訊接軌」，全華科技圖書公司。

  (C2) Book chapters:

[1] Chao, K.-M. (2004) “Dynamic-Programming Strategies for Biomolecular Sequence Analysis ,” Chapter 1 of the book “Selected Topics in Post-Genome Knowledge Discovery,” edited by L. Wong and L. Zhang, IMS Lecture Notes Series, Imperial College Press, UK. (ISBN 981-238-780-3)

[2] Wu, B.Y., Tang, C.Y., and Chao, K.-M. (2007) “Optimum Communication Spanning Trees,” Chapter 59 of the book “Handbook of Approximation Algorithms and Metaheuristics,” edited by Teofilo F. Gonzalez, Chapman & Hall/CRC Press, USA. (ISBN 1-58488-550-5)

[3] Huang, Y.-T., Zhang, K., Chen, T., and Chao, K. -M. (2007) “Approximation Algorithms for the Selection of Robust Tag SNPs,” Chapter 77 of the book “Handbook of Approximation Algorithms and Metaheuristics,” edited by Teofilo F. Gonzalez, Chapman & Hall/CRC Press, USA. (ISBN 1-58488-550-5)

[4] Chao, K.-M. (2007) “Genomic Sequence Analysis: A Case Study in Constrained Heaviest Segments,” Chapter 4 of the book “Computational Genomics: Current Methods," edited by Nikola Stojanovic,  Horizon Press, UK. (ISBN 978-1-904933-30-4)

[5] Chao, K.-M. and Jiang, T. (2008) “Computational Methods for Biomolecular Sequence Comparison,” A chapter in the book “Frontiers in Biostatistics and Bioinformatics,” edited by S. Ma and Y. Wang, USTC Press.

[6] Chao, K.-M. (2011) “Pattern Identification in a Haplotype Block,” Chapter 2 of the book “Bioinformatics for Biologists,” edited by Pavel Pevzner and Ron Shamir, Cambridge University Press, UK.

[7] Chao, K.-M. (2016) “Maximum-Average Segments,” in “Encyclopedia of Algorithms,” edited by Ming-Yang Kao, Springer.

[8] Chao, K.-M. (2016) “Maximum-Sum Segments,” in “Encyclopedia of Algorithms,” edited by Ming-Yang Kao, Springer.

  (C3) Translations:

[1] 趙坤茂及孫嶠聖譯(1987)「PC AT使用手冊」，松崗書局。

[2] 陳佩華及趙坤茂譯(1989)「計算機概論」，松崗書局。

[3] 趙坤茂譯(1989)「作業系統導論」，松崗書局。

Professional Activities:

[a]       Academic community service:

-        Editor, Information Processing Letters (IPL; Feb., 2017 -- 2019)

-        Board member, the Asian Association for Algorithms and Computation (AAAC) (Sept., 2016 -- Oct., 2021)

-        Guest editor: Algorithmica, International Journal of Computational Geometry and Applications, Theoretical Computer Science

-        PC co-chair: IEEE BIBE 2011; ISAAC 2012

-        Special-Track Workshop chair: MSE 2003; BIBE 2004; NCS 2007; NCS 2009; ICS 2016

-        Advisory Committee member, BIBE 2016

-        PC member, APBC (2005, 2006, 2011, 2012, 2014 -- 2017)

-        PC member, BIBE (2004, 2009, 2018)

-        PC member, BIBM (2010, 2012, 2013, 2014, 2016 -- 2024)

-        PC member, BICOB (2009 -- 2012, 2015 -- 2025)

-        PC member, BIOINFORMATICS (2010 -- 2015)

-        PC member, BIOT (2006 -- 2009)

-        PC member, GIW (2014 -- 2016)

-        PC member, ICS (2000, 2002, 2012)

-        PC member, ISAAC (2011, 2012, 2017)

-        PC member, ITBAM (2010 -- 2014)

-        PC member, IWBBIO (2022 -- 2025)

-        PC member, RECOMB (2003, 2008, 2013)

-        PC member, Workshop on Combinatorial Mathematics and Computational Theory (2003 -- 2015)

-        PC member, DMBIO 2005; MIST 2007; TANET 2007; IWOCA 2007; BIRD 2008; ICCABS 2011, 2013;

-        PC member, BioMedCom 2012; RECOMB-Seq/CCB-2015; WABI 2015; COCOA 2016, 2017, 2020; WALCOM 2017; AIME 2024

-        Organizing Chair, AWNE 2006

-        Deputy Director, 2008 ACM ICPC Asia Taipei Regional Contest

-        國科會工程處大學生創意比賽評審委員

-        教育部大專生軟體創思競賽評審委員

-        國科會工程處資訊學門、智慧計算學門複審委員

-        國科會生物處生物資訊臨時學門複審委員

-        高等教育評鑑中心評鑑委員、國內多所大學之自評委員及諮議委員

-        法國Ecole Polytechnique及紐西蘭University of Canterbury等的博士論文外審委員

-        美國多所大學的終身職及升等申請案的外審委員

　

[b]       Reviewer for the following journals:

-         Algorithmica

-         Bioinformatics

-         BMC Bioinformatics

-         Computational Statistics and Data Analysis

-         Computer Applications in the Biosciences

-         The Computer Journal

-         Discrete Applied Mathematics

-         IEEE Transactions on Computational Biology and Bioinformatics

-         IEEE Transactions on Knowledge and Data Engineering

-         Information and Computation

-         Information Processing Letters

-         Information Sciences

-         International Journal of Foundation of Computer Science

-         Journal of the ACM (JACM)

-         Journal of Algorithms

-         Journal of Bioinformatics and Computational Biology

-         Journal of Combinatorial Optimizations

-         Journal of Computational Biology

-         Journal of Computer and System Sciences

-         Journal of Information Science and Engineering

-         Nucleic Acids Research

-         SIAM Journal on Computing

　

[c]      Reviewer for the following conferences:

-         APBC

-         COCOON

-         CPM

-         ICALP

-         ICONIP

-         ICS

-         IEEE BIBE

-         IEEE MSE

-         ISAAC

-         NCS

-         RECOMB

-         STOC