| 2026 | WABI | Minimum Flow Decomposition Guided by Saturating Subflows (Extended Abstract). | Ke Chen, Abhishek Talesara, Sanchal Thakkar, Mingfu Shao |
| 2025 | RECOMB | An Exact and Fast SAT Formulation for the DCJ Distance. | Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao |
| 2025 | RECOMB | Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRep. | Zhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao |
| 2025 | WABI | Sequence Similarity Estimation by Random Subsequence Sketching. | Ke Chen, Vinamratha Pattar, Mingfu Shao |
| 2024 | RECOMB | Accurate Assembly of Circular RNAs with TERRACE. | Tasfia Zahin, Qian Shi, Xiaofei Carl Zang, Mingfu Shao |
| 2024 | WABI | Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. | Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, Mingfu Shao |
| 2022 | WABI | Locality-Sensitive Bucketing Functions for the Edit Distance. | Ke Chen, Mingfu Shao |
| 2019 | WABI | Context-Aware Seeds for Read Mapping. | Hongyi Xin, Mingfu Shao, Carl Kingsford |
| 2016 | RECOMB | On Computing Breakpoint Distances for Genomes with Duplicate Genes. | Mingfu Shao, Bernard M. E. Moret |
| 2015 | RECOMB | A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. | Mingfu Shao, Bernard M. E. Moret |
| 2014 | CPM | On the DCJ Median Problem. | Mingfu Shao, Bernard M. E. Moret |
| 2014 | RECOMB | An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. | Mingfu Shao, Yu Lin, Bernard M. E. Moret |