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Selected Publications ∣ 3D genome and epigenomics

  • Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z*, and Ma J*.
    Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells
    bioRxiv, doi:
  • Xiong K, Zhang R, and Ma J.
    scGHOST: Identifying single-cell 3D genome subcompartments.
    bioRxiv, doi:
  • Zhang Y, Boninsegna L, Yang M, Misteli T*, Alber F*, and Ma J*.
    Computational methods for analysing multiscale 3D genome organization.
    Nature Reviews Genetics,, 2023.
  • Yang M and Ma J.
    UNADON: Transformer-based model to predict genome-wide chromosome spatial position.
    ISMB, 2023.
    Bioinformatics, 39(39 Suppl 1):i553-i562, 2023.
  • Chidester B, Zhou T, Alam S, and Ma J.
    SPICEMIX enables integrative single-cell spatial modeling of cell identity.
    Nature Genetics, 55(1):78-88, 2023. [Cover Article]
    RECOMB, 2021.
  • Zhu X, Zhang Y, Wang Y, Tian D, Belmont AS, Swedlow JR, and Ma J.
    Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome.
    Nature Methods, 19(8):911-913, 2022.
  • Yang Y, Wang Y, Zhang Y, and Ma J.
    CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing.
    bioRxiv, doi:
    RECOMB, 2022.
  • Zhang R, Zhou T, and Ma J.
    Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.
    Cell Systems, 13(10):P798-807.E6, 2022. [Cover Article]
    RECOMB, 2022.
  • Zhang R, Zhou T, and Ma J.
    Multiscale and integrative single-cell Hi-C analysis with Higashi.
    Nature Biotechnology, 40:254–261, 2022.
  • Wang Y, Zhang Y, Zhang R, van Schaik T, Zhang L, Sasaki T, Peric-Hupkes D, Chen Y, Gilbert DM, van Steensel B, Belmont AS, and Ma J.
    SPIN reveals genome-wide landscape of nuclear compartmentalization.
    Genome Biology, 22:36, 2021.
  • Zhang L, Zhang Y, Chen Y, Gholamalamdari O, Wang Y, Ma J, and Belmont AS.
    TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes.
    Genome Research, 31(2):251-264, 2021.
  • Zhang R and Ma J.
    MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning.
    Cell Systems, 10(5):397-407.E5, 2020.
    RECOMB, 2020.
  • 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]
  • Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, and Tsai SQ.
    CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity.
    Nature Biotechnology, 38(11):1317-1327, 2020.
  • 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.
  • Seok S, Fu T, Choi SE, Li Y, Zhu R, Kumar S, Sun X, Yoon G, Kang Y, Zhong W, Ma J, Kemper B, and Kemper JK.
    Transcriptional regulation of autophagy by an FXR-CREB axis.
    Nature, 516(7529):108-11, 2014.