Publications

The 3D Genome Structure of Single Cells
Tianming Zhou*, Ruochi Zhang*(co-first author), Jian Ma.
Annual Review of Biomedical Data Science, doi: https://doi.org/10.1146/annurev-biodatasci-020121-084709

Multiscale and integrative single-cell Hi-C analysis with Higashi
Ruochi Zhang, Tianming Zhou, Jian Ma.
bioRxiv, doi: https://doi.org/10.1101/2020.12.13.422537

DANGO: Predicting higher-order genetic interactions
Ruochi Zhang, Jianzhu Ma*, Jian Ma*.
RECOMB 2021, 25th Annual Conference on Research in Computational Molecular Biology, 2021.

SPIN reveals genome-wide landscape of nuclear compartmentalization
Yuchuan Wang, Yang Zhang, Ruochi Zhang, Tom van Schaik, Liguo Zhang, Takayo Sasaki, Daniel Peric-Hupkes, Yu Chen, David M Gilbert, Bas van Steensel, Andrew S. Belmont, Jian Ma.
Genome Biology, doi: 10.1186/s13059-020-02253-3, 2021.

Large-scale CHANGE-seq CRISPR-Cas9 profiling reveals genetic and epigenetic determinants of genome-wide nuclease activity
Cicera R. Lazzarotto , Nikolay L. Malinin , Yichao Li , Ruochi Zhang , Yang Yang , Yanghua He , Xin Lan , Kasey Jividen , Varun Katta , Natalia G. Kolmakova , Christopher T. Petersen , Qian Qi , Evgheni Strelcov , Samantha Maragh , Giedre Krenciute , Jian Ma , Yong Cheng , Shengdar Q. Tsai.
Nature Biotechnology, 10.1038/s41587-020-0555-7, 2020.

Probing multi-way chromatin interaction with hypergraph representation learning
Ruochi Zhang, Jian Ma.
RECOMB 2020, 24th Annual Conference on Research in Computational Molecular Biology, 2020.
Cell Systems, doi: 10.1016/j.cels.2020.04.004, 2020.

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome
Dechao Tian*, Ruochi Zhang*(co-first author), Yang Zhang, Xiaopeng Zhu, Jian Ma.
Genome Research, doi: 10.1101/gr.250316.119, 2020.

Hyper-SAGNN: a self-attention based graph neural network for hypergraphs
Ruochi Zhang, Yuesong Zou, Jian Ma.
ICLR 2020, 8th International Conference on Learning Representations.
arXiv, arXiv:1911.02613 [cs.LG]

Predicting CTCF-mediated chromatin loops using CTCF-MP
Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma.
ISMB 2018. in Proceedings of the 26th Conference on Intelligent Systems for Molecular Biology.
Bioinformatics, 34(13):i133–i141, 2018.

Exploiting sequence-based features for predicting enhancer-promoter interactions
Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma.
ISMB 2017. in Proceedings of the 25th Conference on Intelligent Systems for Molecular Biology.
Bioinformatics, 33(14): i252-i260, 2017.