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Photo taken at Tsinghua Univerisity, credit to my friend: Haodong Zhou

2021

Multiscale and integrative single-cell Hi-C analysis with Higashi

Nature Biotechnology, in press, 2021

Ruochi Zhang, Tianming Zhou, Jian Ma.
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The 3D Genome Structure of Single Cells

Annual Review of Biomedical Data Science, Vol. 4, 2021

Tianming Zhou*, Ruochi Zhang*(co-first author), Jian Ma.
Paper

Towards the prediction of higher-order genetic interactions

RECOMB 2021, 25th Annual Conference on Research in Computational Molecular Biology, 2021.

Ruochi Zhang, Jianzhu Ma*, Jian Ma*.
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SPIN reveals genome-wide landscape of nuclear compartmentalization

Genome Biology, 22:36, 2021

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.
Paper

2020

MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning

Cell Systems, 10(5):397-407.E5, 2020.

RECOMB 2020, 24th Annual Conference on Research in Computational Molecular Biology, 2020.

Ruochi Zhang, Jian Ma.
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MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

Genome Research, 30(2):227-238, 2020.

Dechao Tian*, Ruochi Zhang*(co-first author), Yang Zhang, Xiaopeng Zhu, Jian Ma.
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Hyper-SAGNN: a self-attention based graph neural network for hypergraphs

ICLR, 8th International Conference on Learning Representations, 2020.

Ruochi Zhang, Yuesong Zou, Jian Ma.
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CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity

Nature Biotechnology, 38(11):1317-1327, 2020.

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.
Paper

2018

Predicting CTCF-mediated chromatin loops using CTCF-MP

Bioinformatics, 34(13):i133–i141, 2018.

ISMB 2018. in Proceedings of the 26th Conference on Intelligent Systems for Molecular Biology.

Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma.
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2017

Exploiting sequence-based features for predicting enhancer-promoter interactions

Bioinformatics, 33(14): i252-i260, 2017.

ISMB 2017. in Proceedings of the 25th Conference on Intelligent Systems for Molecular Biology.

Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma.
Paper F1000Prime Recommended