Ruochi Zhang

Also affiliated with Massachusetts Institute of Technology, Carnegie Mellon University

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 17 papers. Top paper: “Multiscale footprints reveal the organization of cis-regulatory elements”.

Multiscale footprints reveal the organization of cis-regulatory elements

Nature(2025)10.1038/s41586-024-08443-4

N/A

0.928DataRank · unranked

52 citations

Max A. Horlbeck, Ruochi Zhang, Sai Ma, Rojesh Shrestha, Vinay K. Kartha +17 more

Degradation of IKZF1 prevents epigenetic progression of T cell exhaustion in an antigen-specific assay

Cell Reports Medicine(2024)10.1016/j.xcrm.2024.101804

N/A

0.500DataRank · unranked

12 citations

Gayathri Bommakanti, Elizabeth Jaensch, Aparna Gorthi, Iswarya Karapa Reddy, Yan Hu +11 more

Multiscale and integrative single-cell Hi-C analysis with Higashi

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.13.422537

N/A

0.416DataRank · unranked

15 citations

Tianming Zhou, Jian Ma, Ruochi Zhang

Engineered histones reshape chromatin in human cells

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.10.674980

N/A

0.104DataRank · unranked

1 citations

Surya Nagaraja, Andrew Earl, Amalia Rose Driller-Colangelo, Michael A. Quezada, Ena Oreskovic +5 more

Multiscale and integrative single-cell Hi-C analysis with Higashi

Nature Biotechnology(2021)10.1038/s41587-021-01034-y

N/A

0DataRank · unranked

188 citations

Tianming Zhou, Jian Ma, Ruochi Zhang

SPIN reveals genome-wide landscape of nuclear compartmentalization

Genome biology(2021)10.1186/s13059-020-02253-3

N/A

0DataRank · unranked

134 citations

Yang Zhang, Ruochi Zhang, Tom van Schaik, Liguo Zhang, Takayo Sasaki +7 more

Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi

Cell Systems(2022)10.1016/j.cels.2022.09.004

N/A

0DataRank · unranked

47 citations

Tianming Zhou, Jian Ma, Ruochi Zhang

MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning

Cell Systems(2020)10.1016/j.cels.2020.04.004

N/A

0DataRank · unranked

28 citations

Jian Ma, Ruochi Zhang

Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.20.549578

N/A

0DataRank · unranked

12 citations

Ruochi Zhang, Deyong Jia, Raymond T. Doty, Adam D. Munday, Daniel Gao +5 more

scGHOST: Identifying single-cell 3D genome subcompartments

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.24.542032

N/A

0DataRank · unranked

7 citations

Ruochi Zhang, Jian Ma, Kyle Xiong

PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.01.560404

N/A

0DataRank · unranked

2 citations

Ruochi Zhang, Pan Xu, Jian Ma, Quanquan Gu, Yihe Deng

GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells

Nature Genetics(2024)10.1038/s41588-024-01745-3

N/A

0DataRank · unranked

58 citations

Ruochi Zhang, Deyong Jia, Raymond T. Doty, Adam D. Munday, Daniel Gao +5 more

scGHOST: identifying single-cell 3D genome subcompartments

Nature Methods(2024)10.1038/s41592-024-02230-9

N/A

0DataRank · unranked

18 citations

Ruochi Zhang, Jian Ma, Kyle Xiong

Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.18.488683

N/A

0DataRank · unranked

4 citations

Tianming Zhou, Jian Ma, Ruochi Zhang

SPIN reveals genome-wide landscape of nuclear compartmentalization

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.09.982967

N/A

0DataRank · unranked

19 citations

Yang Zhang, Ruochi Zhang, Tom van Schaik, Liguo Zhang, Takayo Sasaki +7 more

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

Genome Research(2020)10.1101/gr.250316.119

N/A

0DataRank · unranked

18 citations

Ruochi Zhang, Yang Zhang, Xiaopeng Zhu, Jian Ma, Dechao Tian

Probing multi-way chromatin interaction with hypergraph representation learning

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.22.916171

N/A

0DataRank · unranked

3 citations

Jian Ma, Ruochi Zhang