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Selected Publications ∣ 3D genome and epigenomics


  • Tian D, Zhang R, Zhang Y, Zhu X, and Ma J.
    MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome.
    Genome Research, 30(2):227-238, 2020.
    [Cover Article]
  • Zhang R and Ma J.
    Probing multi-way chromatin interaction with hypergraph representation learning.
    RECOMB, 2020.
    bioRxiv, doi: https://doi.org/10.1101/2020.01.22.916171
  • Xiong K and Ma J.
    Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions.
    Nature Communications, 10, 5069, 2019.
  • 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.
  • Ma J and Duan Z.
    Replication timing becomes intertwined with 3D genome organization.
    Cell, 176(4):681-684, 2019 (Preview).
  • 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.
  • Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, and Belmont AS.
    Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.
    Journal of Cell Biology, 217(11):4025-4048, 2018.
  • Zhang R, Wang Y, Yang Y, Zhang Y, and Ma J.
    Predicting CTCF-mediated chromatin loops using CTCF-MP.
    ISMB, 2018.
    Bioinformatics, 34(13):i133–i141, 2018.
  • Yang Y, Zhang R, Singh S, and Ma J.
    Exploiting sequence-based features for predicting enhancer-promoter interactions.
    ISMB, 2017.
    Bioinformatics, 33(14): i252-i260, 2017.
  • Kim Y-C, Byun S, Zhang Y, Seok S, Kemper BW, Ma J*, and Kemper JK*.
    Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2.
    Genome Biology, 16:268, 2015.