Publications
Browser my recent articles.
Photo taken at Tsinghua Univerisity, credit to my friend: Haodong Zhou
2021
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
SPIN reveals genome-wide landscape of nuclear compartmentalization
Genome Biology, 22:36, 2021
Paper
2020

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
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
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