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Cell Systems|October 20, 2022
Ultrafast and interpretable single-cell 3D genome analysis with Fast-HigashiRuochi Zhang, Tianming Zhou, Jian MaNature Biotechnology|October 12, 2021
Multiscale and integrative single-cell Hi-C analysis with HigashiRuochi Zhang, Tianming Zhou, Jian MaAnnual Review of Biomedical Data Science|September 1, 2021
The 3D Genome Structure of Single CellsTianming Zhou, Ruochi Zhang, Jian MaCell Systems|June 19, 2020
MATCHA: Probing multi-way chromatin interaction with hypergraph representation learningRuochi Zhang, Jian MaNature Methods|April 8, 2024
scGHOST: identifying single-cell 3D genome subcompartmentsKyle Xiong, Ruochi Zhang, Jian MaBiorxiv : the Preprint Server for Biology|June 9, 2023
scGHOST: Identifying single-cell 3D genome subcompartmentsKyle Xiong, Ruochi Zhang, Jian MaBioinformatics (Oxford, England)|September 9, 2017
Exploiting sequence-based features for predicting enhancer-promoter interactionsYang Yang, Ruochi Zhang, Shashank Singh, et al.Cell Systems|April 25, 2026
Dango: Predicting higher-order genetic interactionsRuochi Zhang, Mihir Bafna, Jianzhu Ma, et al.Biorxiv : the Preprint Server for Biology|August 7, 2023
Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cellsTianming Zhou, Ruochi Zhang, Deyong Jia, et al.Nature Genetics|May 14, 2024
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cellsTianming Zhou, Ruochi Zhang, Deyong Jia, et al.Pageof 175