| 2013 | ISAAC | Computing Minimum Tile Sets to Self-Assemble Color Patterns. | Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki |
| 2010 | DNA | Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-assembly Systems. | Ho-Lin Chen, Ming-Yang Kao |
| 2010 | TAMC | Deterministic Polynomial-Time Algorithms for Designing Short DNA Words. | Ming-Yang Kao, Henry C. M. Leung, He Sun, Yong Zhang |
| 2009 | COCOON | The Closest Pair Problem under the Hamming Metric. | Kerui Min, Ming-Yang Kao, Hong Zhu |
| 2009 | ISAAC | Two-Vertex Connectivity Augmentations for Graphs with a Partition Constraint (Extended Abstract). | Pei-Chi Huang, Hsin-Wen Wei, Yen-Chiu Chen, Ming-Yang Kao, Wei-Kuan Shih, Tsan-sheng Hsu |
| 2009 | TAMC | Discovering Almost Any Hidden Motif from Multiple Sequences in Polynomial Time with Low Sample Complexity and High Success Probability. | Bin Fu, Ming-Yang Kao, Lusheng Wang |
| 2008 | ICALP | Randomized Self-assembly for Approximate Shapes. | Ming-Yang Kao, Robert T. Schweller |
| 2008 | TAMC | Efficient Algorithms for Model-Based Motif Discovery from Multiple Sequences. | Bin Fu, Ming-Yang Kao, Lusheng Wang |
| 2007 | ISAAC | Using Nash Implementation to Achieve Better Frugality Ratios. | Chien-Chung Huang, Ming-Yang Kao, Xiang-Yang Li, Weizhao Wang |
| 2007 | IWQoS | Detecting Stealthy Spreaders Using Online Outdegree Histograms. | Yan Gao, Yao Zhao, Robert T. Schweller, Shobha Venkataraman, Yan Chen, Dawn Xiaodong Song, Ming-Yang Kao |
| 2006 | AAIM | Algorithmic DNA Self-assembly. | Ming-Yang Kao |
| 2006 | CIAC | An Approximation Algorithm for a Bottleneck Traveling Salesman Problem. | Ming-Yang Kao, Manan Sanghi |
| 2006 | INFOCOM | Reverse Hashing for High-Speed Network Monitoring: Algorithms, Evaluation, and Applications. | Robert T. Schweller, Zhichun Li, Yan Chen, Yan Gao, Ashish Gupta, Yin Zhang, Peter A. Dinda, Ming-Yang Kao, Gokhan Memik |
| 2006 | ISAAC | A 6-Approximation Algorithm for Computing Smallest Common AoN-Supertree with Application to the Reconstruction of Glycan Trees. | Kiyoko F. Aoki-Kinoshita, Minoru Kanehisa, Ming-Yang Kao, Xiang-Yang Li, Weizhao Wang |
| 2006 | ISAAC | Flexible Word Design and Graph Labeling. | Ming-Yang Kao, Manan Sanghi, Robert T. Schweller |
| 2006 | SODA | Reducing tile complexity for self-assembly through temperature programming. | Ming-Yang Kao, Robert T. Schweller |
| 2006 | SP | Hamsa: Fast Signature Generation for Zero-day PolymorphicWorms with Provable Attack Resilience. | Zhichun Li, Manan Sanghi, Yan Chen, Ming-Yang Kao, Brian Chavez |
| 2006 | WABI | Linear-Time Haplotype Inference on Pedigrees Without Recombinations. | Bethany Man-Yee Chan, Joseph Wun-Tat Chan, Francis Y. L. Chin, Stanley P. Y. Fung, Ming-Yang Kao |
| 2005 | ICALP | Randomized Fast Design of Short DNA Words. | Ming-Yang Kao, Manan Sanghi, Robert T. Schweller |
| 2005 | ISAAC | Average Case Analysis for Tree Labelling Schemes. | Ming-Yang Kao, Xiang-Yang Li, Weizhao Wang |
| 2004 | SODA | Complexities for generalized models of self-assembly. | Gagan Aggarwal, Michael H. Goldwasser, Ming-Yang Kao, Robert T. Schweller |
| 2002 | ICALP | Fast Universalization of Investment Strategies with Provably Good Relative Returns. | Karhan Akcoglu, Petros Drineas, Ming-Yang Kao |
| 2002 | WABI | Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. | Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder |
| 2002 | WABI | Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics. | Michael H. Goldwasser, Ming-Yang Kao, Hsueh-I Lu |
| 2001 | BIBE | Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs. | Samuel Ieong, Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Siu-Ming Yiu |
| 2001 | ESA | Fast Pricing of European Asian Options with Provable Accuracy: Single-Stock and Basket Options. | Karhan Akcoglu, Ming-Yang Kao, Shuba V. Raghavan |
| 2001 | ISAAC | A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model. | James Aspnes, Julia Hartling, Ming-Yang Kao, Junhyong Kim, Gauri Shah |
| 2001 | ISAAC | DNA Self-Assembly For Constructing 3D Boxes. | Ming-Yang Kao, Vijay Ramachandran |
| 2001 | SODA | Towards understanding the predictability of stock markets from the perspective of computational complexity. | James Aspnes, David F. Fischer, Michael J. Fischer, Ming-Yang Kao, Alok Kumar |
| 2000 | CPM | A Faster and Unifying Algorithm for Comparing Trees. | Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting |
| 2000 | ISAAC | Optimal Bid Sequences for Multiple-Object Auctions with Unequal Budgets. | Yuyu Chen, Ming-Yang Kao, Hsueh-I Lu |
| 2000 | ISAAC | Improved Phylogeny Comparisons: Non-shared Edges, Nearest Neighbor Interchanges, and Subtree Transfers. | Wing-Kai Hon, Ming-Yang Kao, Tak Wah Lam |
| 2000 | ISAAC | Unbalanced and Hierarchical Bipartite Matchings with Applications to Labeled Tree Comparison. | Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting |
| 2000 | SODA | A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. | Ting Chen, Ming-Yang Kao, Matthew Tepel, John Rush, George M. Church |
| 2000 | STOC | The risk profile problem for stock portfolio optimization (extended abstract). | Ming-Yang Kao, Andreas Nolte, Stephen R. Tate |
| 1999 | ESA | On the Informational Asymmetry between Upper and Lower Bounds for Ultrametric Evolutionary Trees. | Ting Chen, Ming-Yang Kao |
| 1999 | ESA | A Fast General Methodology for Information - Theoretically Optimal Encodings of Graphs. | Xin He, Ming-Yang Kao, Hsueh-I Lu |
| 1999 | ESA | A Decomposition Theorem for Maximum Weight Bipartite Matchings with Applications to Evolutionary Trees. | Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting |
| 1999 | SODA | Nonplanar Topological Inference and Political-Map Graphs. | Zhi-Zhong Chen, Xin He, Ming-Yang Kao |
| 1999 | SODA | Recovering Evolutionary Trees Through Harmonic Greedy Triplets. | Mikls Csrs, Ming-Yang Kao |
| 1999 | SODA | Designing Proxies for Stock Market Indices is Computationally Hard. | Ming-Yang Kao, Stephen R. Tate |
| 1999 | STOC | Optimal Buy-and-Hold Strategies for Financial Markets with Bounded Daily Returns. | Gen-Huey Chen, Ming-Yang Kao, Yuh-Dauh Lyuu, Hsing-Kuo Wong |
| 1999 | STACS | Balanced Randomized Tree Splitting with Applications to Evolutionary Tree Constructions. | Ming-Yang Kao, Andrzej Lingas, Anna stlin |
| 1998 | ICALP | Compact Encodings of Planar Graphs via Canonical Orderings and Multiple Parentheses. | Richie Chih-Nan Chuang, Ashim Garg, Xin He, Ming-Yang Kao, Hsueh-I Lu |
| 1998 | ICALP | Efficient Minimization of Numerical Summation Errors. | Ming-Yang Kao, Jie Wang |
| 1997 | CIAC | Tree Contractions and Evolutionary Trees. | Ming-Yang Kao |
| 1997 | COCOON | Optimal Bidding Algorithms Against Cheating in Multiple-Object Auctions. | Ming-Yang Kao, Junfeng Qi, Lei Tan |
| 1997 | ISAAC | All-Cavity Maximum Matchings. | Ming-Yang Kao, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting |
| 1997 | SODA | On-Line Difference Maximization. | Ming-Yang Kao, Stephen R. Tate |
| 1997 | STOC | Reducing Randomness via Irrational Numbers. | Zhi-Zhong Chen, Ming-Yang Kao |
| 1997 | STOC | General Techniques for Comparing Unrooted Evolutionary Trees. | Ming-Yang Kao, Tak Wah Lam, Teresa M. Przytycka, Wing-Kin Sung, Hing-Fung Ting |
| 1997 | SSDBM | Security Problems for Statistical Databases with General Cell Suppressions. | Tsan-sheng Hsu, Ming-Yang Kao |
| 1996 | COCOON | Optimal Bi-Level Augmentation for Selectivity Enhancing Graph Connectivity with Applications. | Tsan-sheng Hsu, Ming-Yang Kao |
| 1996 | ISAAC | Optimal Augmentation for Bipartite Componentwise Biconnectiviy in Linear Time (Extended Abstract). | Tsan-sheng Hsu, Ming-Yang Kao |
| 1995 | FOCS | Load Balancing in the L | Baruch Awerbuch, Yossi Azar, Edward F. Grove, Ming-Yang Kao, P. Krishnan, Jeffrey Scott Vitter |
| 1995 | WADS | Online Perfect Matching and Mobile Computing. | Edward F. Grove, Ming-Yang Kao, P. Krishnan, Jeffrey Scott Vitter |
| 1994 | DCC | Data Compression Techniques for Stock Market Prediction. | Salman Azhar, Greg J. Badros, Arman Glodjo, Ming-Yang Kao, John H. Reif |
| 1994 | GD | Regular Edge Labelings and Drawings of Planar Graphs. | Xin He, Ming-Yang Kao |
| 1994 | ICPP | Optimal Broadcast in All-Port Wormhole-Routed Hypercubes. | Ching-Tien Ho, Ming-Yang Kao |
| 1994 | ISAAC | Simple and Efficient Graph Compression Schemes for Dense and Complement Graphs. | Ming-Yang Kao, Shang-Hua Teng |
| 1994 | SODA | Optimal Constructions of Hybrid Algorithms. | Ming-Yang Kao, Yuan Ma, Michael Sipser, Yiqun Lisa Yin |
| 1994 | STACS | Total Protection of Analytic Invariant Information in Cross Tabulated Tables. | Ming-Yang Kao |
| 1993 | ISAAC | Parallel Construction of Canonical Ordering and Convex Drawing of Triconnected Planar Graphs. | Xin He, Ming-Yang Kao |
| 1993 | SODA | Searching in an Unknown Environment: An Optimal Randomized Algorithm for the Cow-Path Problem. | Ming-Yang Kao, John H. Reif, Stephen R. Tate |
| 1993 | STOC | Optimal online scheduling of parallel jobs with dependencies. | Anja Feldmann, Ming-Yang Kao, Jir Sgall, Shang-Hua Teng |
| 1993 | WADS | Improved Parallel Depth-First Search in Undirected Planar Graphs. | Ming-Yang Kao, Shang-Hua Teng, Kentaro Toyama |
| 1992 | SPAA | O(n log log n)-Work Parallel Algorithms for Straight-Line Grid Embeddings of Planar Graphs. | Martin Frer, Xin He, Ming-Yang Kao, Balaji Raghavachari |
| 1990 | STOC | Towards Overcoming the Transitive-Closure Bottleneck: Efficient Parallel Algorithms for Planar Digraphs | Ming-Yang Kao, Philip N. Klein |
| 1989 | STOC | Parallel Depth-First Search in General Directed Graphs (Preliminary Version) | Alok Aggarwal, Richard J. Anderson, Ming-Yang Kao |
| 1989 | STOC | Local Reorientation, Global Order, and Planar Topology (Preliminary Version) | Ming-Yang Kao, Gregory E. Shannon |