Journal Articles
- Qimin Zhang and Mingfu Shao, 2023, "Transcript assembly and annotations: Bias and adjustment", PLOS Computational Biology, 19, (12), pp. e1011734
- Ke Chen and Mingfu Shao, 2023, "Locality-sensitive bucketing functions for the edit distance", Algorithms for Molecular Biology, 18, (7)
- Qimin Zhang, Qian Shi and Mingfu Shao, 2022, "Accurate assembly of multi-end RNA-seq data with Scallop2", Nature Computational Science, 2, pp. 148--152
- Hongyi Xin, Mingfu Shao and Carl Kingsford, 2020, "Context-aware seeds for read mapping", Algorithms for Molecular Biology, 15, pp. 1--12
- Laura H Tung, Mingfu Shao and Carl Kingsford, 2019, "Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads", Genome Biology, 20, (1), pp. 1--18
- Mingfu Shao and Carl Kingsford, 2019, "Efficient heuristic for decomposing a flow with minimum number of paths", IEEE-ACM Transactions on Computational Biology and Bioinformatics, 16, (2), pp. 658--670
- Cong Ma, Mingfu Shao and Carl Kingsford, 2018, "SQUID: transcriptomic structural variation detection from RNA-seq", Genome Biology, 19, (1), pp. 52
- Mingfu Shao and Carl Kingsford, 2017, "Accurate assembly of transcripts through phase-preserving graph decomposition", Nature Biotechnology, 35, (12), pp. 1167--1169
- Mingfu Shao and Bernard M.E. Moret, 2017, "On computing breakpoint distances for genomes with duplicate genes", Journal of Computational Biology, 26, (6), pp. 571--580
- Mingfu Shao and Bernard M.E. Moret, 2016, "A fast and exact algorithm for the exemplar breakpoint distance", Journal of Computational Biology, 23, (5), pp. 337--346
- Nishanth U. Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher and Bernard M.E. Moret, 2016, "A maximum-likelihood approach for building cell-type trees by lifting", BMC Genomics, 17, (Suppl 1), pp. 14
- Mingfu Shao, Yu Lin and Bernard M.E. Moret, 2015, "An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes", Journal of Computational Biology, 22, (5), pp. 425--435
Conference Proceedings
- Xiang Li, Qian Shi, Ke Chen and Mingfu Shao, 2023, "Seeding with minimized subsequence", 39, (Supplement_1), pp. i232–i241
- Ke Chen and Mingfu Shao, 2022, "Locality-sensitive bucketing functions for the edit distance", 242, pp. 22:1--22:14
- Hongyi Xin, Mingfu Shao and Carl Kingsford, 2019, "Context-aware seeds for read mapping", 143, pp. 15:1--15:13
- Mingfu Shao, Jianzhu Ma and Sheng Wang, 2017, "DeepBound: Accurate identification of transcript boundaries via deep convolutional neural fields", 33, (14), pp. i267--i273
- Mingfu Shao and Bernard M.E. Moret, 2016, "On computing breakpoint distances for genomes with duplicate genes", 9649, pp. 189--203
- Mingfu Shao and Bernard M.E. Moret, 2015, "Comparing genomes with rearrangements and segmental duplications", 31, (12), pp. i329--i338
- Mingfu Shao and Bernard M.E. Moret, 2015, "A fast and exact algorithm for the exemplar breakpoint distance", 9029, pp. 309--322
- Mingfu Shao, Yu Lin and Bernard M.E. Moret, 2014, "An exact algorithm to compute the DCJ distance for genomes with duplicate genes", 8394, pp. 280--292
- Mingfu Shao and Bernard M.E. Moret, 2014, "On the DCJ median problem", 8486, pp. 273--282
- Mingfu Shao, Yu Lin and Bernard M.E. Moret, 2013, "Sorting genomes with rearrangements and segmental duplications through trajectory graphs", 14, (Suppl 15), pp. S9
- Mingfu Shao and Yu Lin, 2012, "Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion", 13, (Suppl 19), pp. S13
- Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai-Cheng Li, Wei-Mou Zheng and Dongbo Bu, 2011, "Incorporating ab initio energy into threading approaches for protein structure prediction", 12, (Suppl 1), pp. S54
- Yi Wei, Mingfu Shao, Jishuang Yang, Chao Wang, Shuai-Cheng Li and Dongbo Bu, 2010, "Approximating conserved regions of protein structures", 9, pp. 204--212
- Leran Ma, Ke Chen and Mingfu Shao, , "On the maximal independent sets of k-mers with the edit distance"
- Xiang Li and Mingfu Shao, , "On de novo bridging paired-end RNA-seq data"
