Publications

Browser my recent articles.

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.
Read more Paper

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*.
Read more Paper

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.
Read more Paper

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.
Read more Paper Cover article CMU News

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.
Read more Paper

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.
Read more Paper

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