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Ruochi Zhang
Ruochi Zhang
Broad Institute
Verified email at broadinstitute.org - Homepage
Title
Cited by
Cited by
Year
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
1812020
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
1712020
Multiscale and integrative single-cell Hi-C analysis with Higashi
R Zhang, T Zhou, J Ma
Nature biotechnology 40 (2), 254-261, 2022
942022
Exploiting sequence-based features for predicting enhancer–promoter interactions
Y Yang, R Zhang, S Singh, J Ma
Bioinformatics 33 (14), i252-i260, 2017
942017
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
702021
Predicting CTCF-mediated chromatin loops using CTCF-MP
R Zhang, Y Wang, Y Yang, Y Zhang, J Ma
Bioinformatics 34 (13), i133-i141, 2018
552018
The 3D genome structure of single cells
T Zhou, R Zhang, J Ma
Annual review of biomedical data science 4, 21-41, 2021
372021
Matcha: probing multi-way chromatin interaction with hypergraph representation learning
R Zhang, J Ma
Cell systems 10 (5), 397-407. e5, 2020
252020
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
172022
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
112020
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
62023
scGHOST: Identifying single-cell 3D genome subcompartments
K Xiong, R Zhang, J Ma
bioRxiv, 2023
32023
DANGO: Predicting higher-order genetic interactions
R Zhang, J Ma, J Ma
bioRxiv, 2020.11. 26.400739, 2020
12020
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
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
2023
PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning
Y Deng, R Zhang, P Xu, J Ma, Q Gu
bioRxiv, 2023
2023
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
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
Predicting enhancer-promoter interaction using genomic sequence features
S Singh, Y Yang, R Zhang, B Póczos, J Ma
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Articles 1–19