Publications

Accurate reconstruction of circular RNAs from complex rolling circular long reads with CircPlex [preprint] [code]
Tasfia Zahin, Irtesam Mahmud Khan, Mingfu Shao
bioarxiv, Nov 2025

Accurate detection of tandem repeats from error-prone sequences with EquiRep [paper] [code]
Zhezheng Song^*, Tasfia Zahin^*, Xiang Li, Mingfu Shao
Genome Research, December 2025 35: 2714-2721

Accurate detection of tandem repeats from error-prone sequences with EquiRep [paper] [preprint] [slide]
Zhezheng Song^*, Tasfia Zahin^*, Xiang Li, Mingfu Shao
Proceedings of 29th International Conference on Computational Molecular Biology (RECOMB 2025)
Lecture Notes in Computer Science, vol 15647, pp. 390–394. Springer, Cham, 2025

Accurate assembly of circular RNAs with TERRACE [paper] [code]
Tasfia Zahin, Qian Shi^*, Carl Zang^*, Mingfu Shao
Genome Research, September 2024 34: 1365-1370

Accurate assembly of circular RNAs with TERRACE [paper] [preprint] [slide]
Tasfia Zahin, Qian Shi^*, Carl Zang^*, Mingfu Shao
Proceedings of 28th International Conference on Computational Molecular Biology (RECOMB 2024)
Lecture Notes in Computer Science, vol 14758, pp. 444–447. Springer, Cham, 2024

Amaranth: enhanced single-cell transcript assembly via discriminative modeling of UMI reads and internal reads [preprint] [code]
Xiaofei Carl Zang, Tasfia Zahin, Irtesam Mahmud Khan, Qian Shi, Yi Xing, Mingfu Shao
bioarxiv, Nov 2025

Boosting transcript assembly via delineating transcript start and end sites [preprint] [code]
Irtesam Mahmud Khan, Xiaofei Carl Zang, Ange Teng, Tasfia Zahin, Mingfu Shao
bioarxiv, Oct 2025

An alignment-free method for phylogeny estimation using maximum likelihood [paper] [code]
Tasfia Zahin^*, Md Hasin Abrar^*, Mizanur Rahman Jewel, Tahrina Tasnim, Md. Shamsuzzoha Bayzid, Atif Rahman
BMC Bioinformatics, 2025 Mar 7;26(1):77