- Yuan, X., Chen, K., Li, X., Shi, Q., and Shao, M.
“Learning locality-sensitive bucketing functions”.
In Proc. 32nd Int’l Conf. Intelligent Systems Mol. Bio. (ISMB’24; accepted, to appear)
software - Shi, Q., Zhang, Q., and Shao, M.
“Accurate assembly of multiple RNA-seq samples with Aletsch”.
In Proc. 32nd Int’l Conf. Intelligent Systems Mol. Bio. (ISMB’24; accepted, to appear)
software - Zahin, T., Shi, Q., Zang, C., and Shao, M.
“Accurate assembly of circular RNAs with TERRACE”.
In Proc. 28th Int’l Conf. Comput. Mol. Biol. (RECOMB’24),
preprint, software - Zhang, Q. and Shao, M.
“Transcript assembly and annotations: Bias and adjustment”.
PLOS Computational Biology, 19(12):e1011734 (2023)
DOI, software - Li, X. and Shao, M.
“On de novo bridging paired-end RNA-seq data”.
In Proc. 14th Conf. Bioinfo., Comp. Biol., Health Informatics (ACM-BCB’23),
Article No. 41, Pages 1–5
proceeding, preprint, software - Ma, L., Chen, K., and Shao, M.
“On the maximal independent sets of k-mers with the edit distance”.
In Proc. 14th Conf. Bioinfo., Comp. Biol., Health Informatics (ACM-BCB’23),
Article No. 42, Pages 1–6
proceeding, preprint, software - Chen, K. and Shao, M.
“Locality-sensitive bucketing functions for the edit distance”.
Algorithms for Molecular Biology, 18, Article 7, (2023).
DOI, software - Li, X., Shi, Q., Chen, K., and Shao, M.
“Seeding with minimized subsequence”.
In Proc. 31st Int’l Conf. Intelligent Systems Mol. Bio. (ISMB/ECCB’23),
Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i232–i241
DOI, software - Chen, K., and Shao, M.
“Locality-sensitive bucketing functions for the edit distance”.
In Proc. 22th Int’l Workshop on Algorithms in Bioinformatics (WABI’22),
volume 242 of Leibniz Int’l Proc. Informatics (LIPIcs), 22:1–22:14, (2022)
DOI, software - Zhang, Q., Shi, Q., and Shao, M.
“Accurate assembly of multi-end RNA-seq data with Scallop2”.
Nature Computational Science, 2, 148-152 (2022)
DOI, free version, software - Xin, H., Shao, M., and Kingsford, C.
“Context-aware seeds for read mapping”.
Algorithms for Molecular Biology, 15, Article 10, (2020). - Tung, L.H., Shao, M., and Kingsford, C.
“Quantifying the benefit offered by transcript assembly on single-molecule long reads”.
Genome Biology, 20(1):1-18 (2019). - Shao, M., and Kingsford, C.
“Theory and a heuristic for the minimum path flow decomposition Problem”.
IEEE/ACM Trans. on Computational Biology and Bioinformatics, 16(2):658-670, (2019). - Xin, H., Shao, M., and Kingsford, C.
“Context-aware seeds for read mapping”.
In Proc. 19th Int’l Workshop on Algorithms in Bioinformatics (WABI’19),
volume 143 of Leibniz Int’l Proc. Informatics (LIPIcs), 15:1-15:13, (2019). - Ma, C., Shao, M., and Kingsford, C.
“SQUID: transcriptomic structural variation detection from RNA-seq”.
Genome Biology, 19(1):52 (2018). - Shao, M., and Kingsford, C.
“Accurate assembly of transcripts through phasing-preserving graph decomposition”.
Nature Biotechnology, 35(12):1167-1169 (2017) - Shao, M., Ma, J., and Wang, S.
“DeepBound: Accurate identification of transcript boundaries via deep convolutional neural fields”.
In Proc. 25rd Int’l Conf. Intelligent Systems Mol. Bio. (ISMB’17),
Bioinformatics, 33(14):i267-i273 (2017). - Shao, M., and Moret, B.M.E.
“On computing breakpoint distances for genomes with duplicate genes”.
J. Comput. Biol., 26(6):571-580 (2017). - Shao, M., and Moret, B.M.E.
“A fast and exact algorithm for the exemplar breakpoint distance”.
J. Comput. Biol., 23(5):337-346 (2016). - Shao, M., and Moret, B.M.E.
“On computing breakpoint distances for genomes with duplicate genes”.
In Proc. 20th Int’l Conf. Comput. Mol. Biol. (RECOMB’16),
volume 9649 of Lecture Notes in Comp. Sci., 189-203, (2016). - Nair, N.U., Hunter, L., Shao, M., Grnarova, P., Lin, Y., Bucher, P., and Moret, B.M.E.
“A maximum-likelihood approach for building cell-type trees by lifting”.
In Proc. 14th Asia Pacific Bioinf. Conf. (APBC’16),
BMC Genomics, 17(Suppl 1):14 (2016). - Shao, M., and Moret, B.M.E.
“Comparing genomes with rearrangements and segmental duplications”.
In Proc. 23rd Int’l Conf. Intelligent Systems Mol. Bio. (ISMB’15),
Bioinformatics, 31(12):i329-i338 (2015). - Shao, M., Lin, Y., and Moret, B.M.E.
“An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes”.
J. Comput. Biol., 22(5):425-435 (2015). - Shao, M., and Moret, B.M.E.
“A fast and exact algorithm for the exemplar breakpoint distance”.
In Proc. 19th Int’l Conf. Comput. Mol. Bio. (RECOMB’15),
volume 9029 of Lecture Notes in Comp. Sci., pages 309-322, (2015). - Shao, M., and Moret, B.M.E.
“On the DCJ median problem”.
In Proc. 25th Symp. on Combinatorial Pattern Matching (CPM’14),
volume 8486 of Lecture Notes in Comp. Sci., 273-282, (2014). - Shao, M., Lin, Y., and Moret, B.M.E.
“An exact algorithm to compute the DCJ distance for genomes with duplicate genes”.
In Proc. 18th Int’l Conf. Comput. Mol. Bio. (RECOMB’14),
volume 8394 of Lecture Notes in Comp. Sci., 282-290, (2014). - Shao, M., Lin, Y., and Moret, B.M.E.
“Sorting genomes with rearrangements and segmental duplications through trajectory graphs”.
In Proc. 11th RECOMB Workshop on Comparative Genomics (RECOMB-CG’13),
BMC Bioinformatics 14(Suppl. 15):S9 (2013). - Shao, M., and Lin, Y.
“Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion”.
In Proc. 10th RECOMB Workshop on Comparative Genomics (RECOMB-CG’12),
BMC Bioinformatics 13(Suppl. 19):S13 (2012). - Shao, M., Wang, S., Wang, C., Yuan, X., Li, S.-C., Zheng, W.-M., and Bu, D.
“Incorporating ab initio energy into threading approaches for protein structure prediction”.
In Proc. 9th Asia Pacific Bioinf. Conf. (APBC’11),
BMC Bioinformatics 12(Suppl. 1):S54 (2011). - Wei, Y., Shao, M., Yang, J., Wang, C., Li, S.-C., and Bu, D.
“Approximating conserved regions of protein structures”.
In Proc. 9th Ann. Int’l Comput. Systems Bioinf. Conf (CSB’10),
volume 9, pages 204-212 (2010).