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Selected Publications ∣ comparative genomics and sequence analysis

  • Zhang Y, Xiao Y, Yang M, and Ma J.
    Cancer mutational signatures representation by large-scale context embedding.
    ISMB, 2020.
    Bioinformatics, 36(Supplement_1):i309-i316, 2020.
  • Yang Y, Zhang Y, Ren B, Dixon J, and Ma J.
    Comparing 3D genome organization in multiple species using Phylo-HMRF.
    Cell Systems, 8(6):494-505.e14, 2019.
    RECOMB, 2019.
  • Yang Y, Gu Q, Zhang Y, Sasaki T, Crivello J, O'Neill R, Gilbert DM, and Ma J.
    Continuous-trait probabilistic model for comparing multi-species functional genomic data.
    Cell Systems, 7(2):208-218.e11, 2018.
    RECOMB, 2018.
  • Kim J, Farre MB, Auvil L, Capitanu B, Larkin D*, Ma J*, and Lewin HA*.
    Reconstruction and evolutionary history of eutherian chromosomes.
    PNAS, 114(27) E5379-E5388, 2017.
  • Rajaraman A and Ma J.
    Towards recovering allele-specific cancer genome graphs.
    RECOMB, 2017.
  • Li Y, Zhou S, Schwartz DC, and Ma J.
    Allele-specific quantification of structural variations in cancer genomes.
    Cell Systems, 3(1):21-34, 2016.
    RECOMB, 2016.
  • Yokoyama KD, Zhang Y, and Ma J.
    Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.
    PLOS Computational Biology, 10(8): e1003771, 2014.
  • Kim J and Ma J.
    PSAR-Align: improving multiple sequence alignment using probabilistic sampling.
    Bioinformatics, 30(7):1010-2, 2014.
  • Heo Y, Wu X-L, Chen D, Ma J, and Hwu W-M.
    BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads.
    Bioinformatics, 30(10):1354-62, 2014.
  • Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge RL, Auvil L, Capitanu B, Zhang G, Lewin HA*, and Ma J*.
    Reference-assisted chromosome assembly.
    PNAS, 110(5):1785-90, 2013.
  • Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KA, Elsik C, Wickline SA, Jacobsen SE, Ma J, and Robinson GE.
    RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee.
    PNAS, 110(31):12750-5, 2013.
  • Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, and Ma J.
    TrueSight: a new algorithm for splice junction detection using RNA-seq.
    Nucleic Acids Research, 41(4):e51, 2013.
    RECOMB, 2012.
  • Kim J and Ma J.
    PSAR: Measuring multiple sequence alignment reliability by probabilistic sampling.
    Nucleic Acids Research, 39(15):6359-68, 2011.
    RECOMB, 2011.
  • Orangutan Genome Sequencing and Analysis Consortium.
    Comparative and demographic analysis of orangutan genomes.
    Nature, 469(7331):529-33, 2011.
  • Ma J, Ratan A, Raney BJ, Suh BB, Miller W, and Haussler D.
    The infinite sites model of genome evolution.
    PNAS, 105(38):14254-14261, 2008.
  • Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, and Haussler D.
    DUPCAR: Reconstructing contiguous ancestral regions with duplications.
    Journal of Computational Biology, 15(8):1007-1027, Oct 2008.
  • Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, and Miller W.
    Reconstructing contiguous regions of an ancestral genome.
    Genome Research, 16(12):1557-1565, 2006.