Chidester B, Zhou T, Ma J. SpiceMix: Integrative single-cell spatial modeling for inferring cell identity. bioRxiv [Preprint]. 2020 November 30. DOI: https://doi.org/https://doi.org/10.1101/2020.11.29.383067.

Zhang R, Zhou T, Ma J. Multiscale and integrative single-cell Hi-C analysis with Higashi. bioRxiv [Preprint]. 2020 December 15. DOI: https://doi.org/https://doi.org/10.1101/2020.12.13.422537.

Zhang R, Ma J, Ma J. DANGO: Predicting higher-order genetic interactions. bioRxiv [Preprint]. 2020 November 27. DOI: https://doi.org/https://doi.org/10.1101/2020.11.26.400739.

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, Ma J. SPIN reveals genome-wide landscape of nuclear compartmentalization. Genome biology. 2021 January 14;22(1):36. PubMed PMID: 33446254; PubMed Central PMCID: PMC7809771; DOI: 10.1186/s13059-020-02253-3.