Hyper-SAGNN: a self-attention based graph neural network for hypergraphs R Zhang, Y Zou, J Ma International Conference on Learning Representations (ICLR 2020), 2020 | 205 | 2020 |
CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity CR Lazzarotto, NL Malinin, Y Li, R Zhang, Y Yang, GH Lee, E Cowley, ... Nature biotechnology 38 (11), 1317-1327, 2020 | 190 | 2020 |
Multiscale and integrative single-cell Hi-C analysis with Higashi R Zhang, T Zhou, J Ma Nature biotechnology 40 (2), 254-261, 2022 | 116 | 2022 |
Exploiting sequence-based features for predicting enhancer–promoter interactions Y Yang, R Zhang, S Singh, J Ma Bioinformatics 33 (14), i252-i260, 2017 | 97 | 2017 |
SPIN reveals genome-wide landscape of nuclear compartmentalization Y Wang, Y Zhang, R Zhang, T van Schaik, L Zhang, T Sasaki, ... Genome biology 22, 1-23, 2021 | 77 | 2021 |
Predicting CTCF-mediated chromatin loops using CTCF-MP R Zhang, Y Wang, Y Yang, Y Zhang, J Ma Bioinformatics 34 (13), i133-i141, 2018 | 58 | 2018 |
The 3D genome structure of single cells T Zhou, R Zhang, J Ma Annual review of biomedical data science 4 (1), 21-41, 2021 | 45 | 2021 |
MATCHA: probing multi-way chromatin interaction with hypergraph representation learning R Zhang, J Ma Cell systems 10 (5), 397-407. e5, 2020 | 26 | 2020 |
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi R Zhang, T Zhou, J Ma Cell systems 13 (10), 798-807. e6, 2022 | 22 | 2022 |
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome D Tian, R Zhang, Y Zhang, X Zhu, J Ma Genome research 30 (2), 227-238, 2020 | 12 | 2020 |
Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements Y Hu, S Ma, VK Kartha, FM Duarte, M Horlbeck, R Zhang, R Shrestha, ... bioRxiv, 2023 | 9 | 2023 |
scGHOST: Identifying single-cell 3D genome subcompartments K Xiong, R Zhang, J Ma Nature methods, 1-9, 2024 | 7 | 2024 |
Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells T Zhou, R Zhang, D Jia, RT Doty, AD Munday, D Gao, L Xin, JL Abkowitz, ... bioRxiv, 2023 | 6 | 2023 |
DiffRNAFold: Generating RNA Tertiary Structures with Latent Space Diffusion M Bafna, V Keerthipati, SC Kanaparthi, R Zhang Deep Generative Models for Health Workshop NeurIPS 2023, 2023 | 1 | 2023 |
DANGO: Predicting higher-order genetic interactions R Zhang, J Ma, J Ma bioRxiv, 2020.11. 26.400739, 2020 | 1 | 2020 |
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells T Zhou, R Zhang, D Jia, RT Doty, AD Munday, D Gao, L Xin, JL Abkowitz, ... Nature Genetics, 1-11, 2024 | | 2024 |
Abstract LB234: Identifying cancer vulnerabilities associated with changes in chromatin accessibility by simultaneously profiling hundreds of cancer cell lines with ATAC-seq P Borck, K Wienand, F Duarte, A Qin, R Zhang, J Babu, S Zhang, S Maffa, ... Cancer Research 84 (7_Supplement), LB234-LB234, 2024 | | 2024 |
Degradation of IKAROS prevents epigenetic progression of T cell exhaustion in a novel antigen-specific assay T Tay, G Bommakanti, E Jaensch, A Gorthi, I Reddy, Y Hu, R Zhang, ... bioRxiv, 2024.02. 22.581548, 2024 | | 2024 |
PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning Y Deng, R Zhang, P Xu, J Ma, Q Gu bioRxiv, 2023 | | 2023 |
Author Correction: Multiscale and integrative single-cell Hi-C analysis with Higashi R Zhang, T Zhou, J Ma Nature Biotechnology 40 (3), 432-432, 2022 | | 2022 |