
Papers
(†=co-first author; *=co-corresponding author)
2022
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.
RECOMB 2022, 26th Annual Conference on Research in Computational Molecular Biology, 2022
Ruochi Zhang†,*, Tianming Zhou†, Jian Ma*
2021
Multiscale and integrative single-cell Hi-C analysis with Higashi
Nature Biotechnology, https://doi.org/10.1038/s41587-021-01034-y, 2021
The 3D Genome Structure of Single Cells
Annual Review of Biomedical Data Science, Vol. 4, 2021
Tianming Zhou†, Ruochi Zhang†, 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*.
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.
Paper
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome
Genome Research, 30(2):227-238, 2020.
Dechao Tian†, Ruochi Zhang†, Yang Zhang, Xiaopeng Zhu, Jian Ma.
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.
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.
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
Awards
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CMU CPCB Outstanding research accomplishment award 2020
Teaching
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Teaching Assistant for Computational Genomics: School of Computer Science, Carnegie Mellon University. 01/2018 — 05/2018
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Teaching Assistant for Algorithms & Advanced Data Structures: School of Computer Science, Carnegie Mellon University. 08/2018 — 12/2018
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Teaching Assistant for Bioinformatics: Dragon Star Program 2017, Harbin, China. 08/2017 — 08/2017