| 2016 | AAIM | Computing the Line-Constrained k-center in the Plane for Small k. | Albert Jhih-Heng Huang, Hung-Lung Wang, Kun-Mao Chao |
| 2015 | WALCOM | Forming Plurality at Minimum Cost. | Wei-Yin Lin, Yen-Wei Wu, Hung-Lung Wang, Kun-Mao Chao |
| 2014 | ISAAC | The Generalized Popular Condensation Problem. | Yen-Wei Wu, Wei-Yin Lin, Hung-Lung Wang, Kun-Mao Chao |
| 2013 | DASFAA | A Compact and Efficient Labeling Scheme for XML Documents. | Rung-Ren Lin, Ya-Hui Chang, Kun-Mao Chao |
| 2013 | ISAAC | Computing Plurality Points and Condorcet Points in Euclidean Space. | Yen-Wei Wu, Wei-Yin Lin, Hung-Lung Wang, Kun-Mao Chao |
| 2013 | IWOCA | An Optimal Algorithm for the Popular Condensation Problem. | Yen-Wei Wu, Wei-Yin Lin, Hung-Lung Wang, Kun-Mao Chao |
| 2012 | TAMC | Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. | Kun-Mao Chao, An-Chiang Chu, Jesper Jansson, Richard S. Lemence, Alban Mancheron |
| 2012 | WABI | Preserving Inversion Phylogeny Reconstruction. | Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier |
| 2011 | DASFAA | Identifying Relevant Matches with NOT Semantics over XML Documents. | Rung-Ren Lin, Ya-Hui Chang, Kun-Mao Chao |
| 2010 | DEXA | Faster Algorithms for Searching Relevant Matches in XML Databases. | Rung-Ren Lin, Ya-Hui Chang, Kun-Mao Chao |
| 2010 | ESA | A Fully Compressed Algorithm for Computing the Edit Distance of Run-Length Encoded Strings. | Kuan-Yu Chen, Kun-Mao Chao |
| 2010 | ISAAC | Identifying Approximate Palindromes in Run-Length Encoded Strings. | Kuan-Yu Chen, Ping-Hui Hsu, Kun-Mao Chao |
| 2009 | CPM | Finding All Sorting Tandem Duplication Random Loss Operations. | Matthias Bernt, Ming-Chiang Chen, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf |
| 2009 | CPM | Approximate Matching for Run-Length Encoded Strings Is 3sum-Hard. | Kuan-Yu Chen, Ping-Hui Hsu, Kun-Mao Chao |
| 2009 | ISAAC | Finding All Approximate Gapped Palindromes. | Ping-Hui Hsu, Kuan-Yu Chen, Kun-Mao Chao |
| 2008 | ECCB | PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. | Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, Tsu-Chun Emma Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao, Chi-Ying F. Huang |
| 2008 | ISAAC | Minkowski Sum Selection and Finding. | Cheng-Wei Luo, Hsiao-Fei Liu, Peng-An Chen, Kun-Mao Chao |
| 2007 | ISAAC | Algorithms for Computing the Length-Constrained Max-Score Segments with Applications to DNA Copy Number Data Analysis. | Hsiao-Fei Liu, Peng-An Chen, Kun-Mao Chao |
| 2006 | ISAAC | On Locating Disjoint Segments with Maximum Sum of Densities. | Hsiao-Fei Liu, Kun-Mao Chao |
| 2005 | ISAAC | Improved Algorithms for the | Chih-Huai Cheng, Kuan-Yu Chen, Wen-Chin Tien, Kun-Mao Chao |
| 2005 | SAC | An approximation algorithm for haplotype inference by maximum parsimony. | Yao-Ting Huang, Kun-Mao Chao, Ting Chen |
| 2004 | BIBE | Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds. | I-Hsuan Yang, Sheng-Ho Wang, Yang-Ho Chen, Pao-Hsian Huang, Liang Ye, Xiaoqiu Huang, Kun-Mao Chao |
| 2004 | ISAAC | On the Range Maximum-Sum Segment Query Problem. | Kuan-Yu Chen, Kun-Mao Chao |
| 2004 | SNPD | A Sensitive Sequence Comparison Method. | Xiaoqiu Huang, Liang Ye, I-Hsuan Yang, Kun-Mao Chao |
| 2004 | WABI | Approximation Algorithms for the Selection of Robust Tag SNPs. | Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao |
| 2003 | ISAAC | Finding a Length-Constrained Maximum-Density Path in a Tree. | Rung-Ren Lin, Wen-Hsiung Kuo, Kun-Mao Chao |
| 2002 | MFCS | Efficient Algorithms for Locating the Length-Constrained Heaviest Segments, with Applications to Biomolecular Sequence Analysis. | Yaw-Ling Lin, Tao Jiang, Kun-Mao Chao |
| 1999 | STACS | Constructing Light Spanning Trees with Small Routing Cost. | Bang Ye Wu, Kun-Mao Chao, Chuan Yi Tang |
| 1998 | COCOON | Approximation and Exact Algorithms for Constructing Minimum Ultrametric Trees from Distance Matrices. | Bang Ye Wu, Kun-Mao Chao, Chuan Yi Tang |
| 1998 | ISAAC | Approximation Algorithms for Some Optimum Communication Spanning Tree Problems. | Bang Ye Wu, Kun-Mao Chao, Chuan Yi Tang |
| 1998 | SODA | A Polynomial Time Approximation Scheme for Minimum Routing Cost Spanning Trees. | Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, Kun-Mao Chao, R. Ravi, Chuan Yi Tang |
| 1997 | COCOON | Fast Algorithms for Aligning Sequences with Restricted Affine Gap Penalties. | Kun-Mao Chao |
| 1994 | CPM | Computing all Suboptimal Alignments in Linear Space. | Kun-Mao Chao |