Ruochi Zhang

I am currently an Eric and Wendy Schmidt Center Postdoctoral Fellow at the Broad Institute.

Before joining the Broad, I received Ph.D. in Computational Biology from Carnegie Mellon University, advised by Prof. Jian Ma (2022). I received my Bachelor’s degree in Tsinghua University (2017).

I have broad interests in machine learning and computational biology, with a focus on developing and applying graph representation learning techniques for the study of the 3D genome organization.

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

Ruochi Zhang, Tianming Zhou, Jian Ma.
Paper

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

CMU CPCB Outstanding research accomplishment award 2020

Teaching

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

Contact Info

Email: zhangruo@broadinstitute.org

Twitter: @RuochiZhang

Linkedin: Ruochi Zhang