Publications

  • Ma, C., Shao, M., and Kingsford, C.
    “SQUID: transcriptomic structural variation detection from RNA-seq”.
    Genome Biology, (accpted, to appear, 2018).
  • Shao, M., and Kingsford, C.
    “Efficient heuristic for decomposing a flow with minimum number of paths”.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, (accepted, to appear, 2017).
  • 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).