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Ruochi Zhang


(†=co-first author; *=co-corresponding author)


scGHOST: Identifying single-cell 3D genome subcompartments.

Nature Methods (accepted in principle)

Kyle Xiong, Ruochi Zhang, Jian Ma

Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells.

Nature Genetics (accepted in principle)

Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T. Doty, Adam D. Munday, Daniel Gao, Li Xin, Janis L. Abkowitz, Zhijun Duan*, Jian Ma*

DiffRNAFold: Generating RNA Tertiary Structures with Latent Space Diffusion

NeurIPS 2023, MLSB

Mihir Bafna, Vikranth Keerthipati, Subhash Kanaparthi, Ruochi Zhang

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements

bioRxiv, doi: 10.1101/2023.03.28.533945

Yan Hu, Sai Ma, Vinay K Kartha, Fabiana M Duarte, Max Horlbeck, Ruochi Zhang, Rojesh Shrestha, Ajay Labade, Heidi Kletzien, Alia Meliki, Andrew Castillo, Neva Durand, Eugenio Mattei, Lauren J Anderson, Tristan Tay, Andrew S Earl, Noam Shoresh, Charles B Epstein, Amy Wagers, Jason D Buenrostro*

PhyGCN: Pre-trained gypergraph convolutional neural networks with self-supervised learning.

bioRxiv, doi: 10.1101/2023.10.01.560404

Yihe Deng, Ruochi Zhang, Pan Xu, Jian Ma*, Quanquan Gu*


Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.

Cell Systems, 13(10):798-807.E6, 2022

RECOMB 2022, 26th Annual Conference on Research in Computational Molecular Biology, 2020.

Ruochi Zhang†,*, Tianming Zhou, Jian Ma*



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

Nature Biotechnology,, 2021

Ruochi Zhang, Tianming Zhou, Jian Ma.

The 3D Genome Structure of Single Cells

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

Tianming ZhouRuochi Zhang, Jian Ma.

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*.

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.


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.

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

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

Dechao TianRuochi 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.

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.


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.


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


  • CMU CPCB Outstanding research accomplishment award 2020


  • Teaching Assistant for Computational Genomics: School of Computer Science, Carnegie Mellon University. 01/2018 — 05/2018

  • Teaching Assistant for Algorithms & Advanced Data Structures: School of Computer Science, Carnegie Mellon University. 08/2018 — 12/2018

  • Teaching Assistant for Bioinformatics: Dragon Star Program 2017, Harbin, China. 08/2017 — 08/2017

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