(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. [SCI]

[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. [SCI] (PostScript version)

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

[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. [SCI]

[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. [SCI] (PostScript version)

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

[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. [SCI] (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. [SCI]

[11] Chao, K.-M., 1998, ¡§On Computing all Suboptimal Alignments,¡¨ Information Sciences, 105: 189-207. [SCI, EI]

[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. [SCI, EI]

[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. [SCI, EI]

[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. [SCI]

[15] Chao, K.-M., 1999, ¡§Calign: Aligning Sequences with Restricted Affine Gap Penalties,¡¨ Bioinformatics, 15: 298-304. [SCI]

[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. [SCI, EI]

[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. [SCI, EI]

[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. [SCI, EI]

[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. [SCI, EI]

[20] Wu, B. Y., Chao, K.-M. and Tang, C. Y., 2002, ¡§Light Graph with Small Routing Cost,¡¨ Networks, 39: 130-138. [SCI, EI]

[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. [SCI, EI]

[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. [SCI]

[23] Huang, X. and Chao, K.-M., 2003, ¡§A Generalized Global Alignment Algorithm,¡¨ Bioinformatics, 19: 228-233. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI, EI]

[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. [SCI]

[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. [SCI, EI]

[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. [SCI]

[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. [SCI]

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

[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. [SCI]

[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. [SCI]

[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. [SCI, EI]

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

[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. [SCI]

[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. [SCI, EI]

[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. [SCI]

[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) [SCI]

[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. [SCI]

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

[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. [SCI]

[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. [SCI, EI]

[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. [SCI]

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

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

[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. [SCI]

[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) [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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) [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

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

[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. [SCI]

[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. [SCI]

[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. [SCI, EI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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 ¡V An R Tool,¡¨ Analytical Chemistry, 88(12):6334-6341. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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. [SCI]

[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 10^th 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 12^th 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 14^th 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 15^th 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,¡¨ 16^th International Symposium on Theoretical Aspects of Computer Science (STACS ¡¦99), Lecture Notes in Computer Science, 1563, 334-344, Trier, Germany.

[22] ½²¥Ã«í, ªL©ú«H, ³¯´¼½å, ¬_«Ø¥þ, ¤ý§µº³, ªL±Ó´f, »¯©[­Z, 1999, ¡§¹q¤l°Ó«°ªº¸gÀ竬ºA¤ÀªR,¡¨ ÁÚ¦V¤G¤Q¤@¥@¬ö¨È¤ÓºÞ²z¾Ç³N¬ã°Q·|, ¦¨¥\¤j¾Ç, Taiwan.

[23] ¥Ó¥Ã¼w, §õ¶i¦¨, ©P¤å¥ú, ¤ýÆg±l, »¯©[­Z, 1999, ¡§µL½uºô¸ô¡B°Ó¾÷µL­­,¡¨ ÁÚ¦V¤G¤Q¤@¥@¬ö¨È¤ÓºÞ²z¾Ç³N¬ã°Q·|, ¦¨¥\¤j¾Ç, 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 19^th 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 27^th 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 20^th 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 14^th 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 21^st 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] »P¤ý§µº³µ¥¦XµÛ(1997, 1998, 2000, 2002 & 2003)¡u­pºâ¾÷·§½×¡v¡AªFµØ®Ñ§½¡C(ISBN 957-483-143-4) ¥»®Ñ²Ä¤»ª©(2004¦~)¡A§ï¥ÑùÖ峯¥Xª©ªÀµo¦æ¡C(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] »¯©[­Z, ±i¶®´f, ¶ÀÄ_¸©, ¶À«T¿o (2004¦~ªìª©¡F2024¦~­×­q²Ä¤Q¤Eª©)¡u­pºâ¾÷·§½× -- AI»P¬ì§Þªº¦@»R¡v¡A¥þµØ¬ì§Þ¹Ï®Ñ¤½¥q¡C(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] ±i¶®´f,¶À«T¿o,»¯©[­Z (2014¦~ªìª©¡F2016¦~­×­q²Ä¤Gª©)¡u­pºâ¾÷·§½× -- »P¸ê°T±µ­y¡v¡A¥þµØ¬ì§Þ¹Ï®Ñ¤½¥q¡C

  (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: