Jian Ma

Also affiliated with Carnegie Mellon University

Biochemistry, Genetics and Molecular BiologyAgricultural and Biological Sciences

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 2%percentile

2.5Author DataRank

Indexed papers

5in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 5 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Complete sequencing of ape genomes

Nature(2025)10.1038/s41586-025-08816-3

Top 16%

1.3DataRank

Top 16%128 citations

Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar +123 more

Papers

Driven by 68 papers — median percentile 62. Top paper: “Fasting-induced FGF21 signaling activates hepatic autophagy and lipid degradation via JMJD3 histone demethylase”.

Fasting-induced FGF21 signaling activates hepatic autophagy and lipid degradation via JMJD3 histone demethylase

Nature Communications(2020)10.1038/s41467-020-14384-z

N/A

5.5DataRank · unranked

215 citations

Sunmi Seok, Young‐Chae Kim, Yang Zhang, Peter M. Yau, Naoki Iwamori +5 more

Reconstruction and evolutionary history of eutherian chromosomes

Proceedings of the National Academy of Sciences(2017)10.1073/pnas.1702012114

N/A

3.2DataRank · unranked

121 citations

Marta Farré, Loretta Auvil, Boris Capitanu, Denis M. Larkin, Jian Ma +2 more

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

Nature Aging(2022)10.1038/s43587-022-00326-5

N/A

2.1DataRank · unranked

128 citations

Patty J. Lee, Christopher C. Benz, Philip D. Blood, Katy Börner, Judith Campisi +93 more

ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins

Nucleic Acids Research(2017)10.1093/nar/gkw1304

N/A

2.0DataRank · unranked

50 citations

Vidisha Tripathi, Abid Khan, Je-Hyun Yoon, Deepak K. Singh, Omid Gholamalamdari +11 more

Intestinal FGF15/19 physiologically repress hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A

Nature Communications(2020)10.1038/s41467-020-19803-9

N/A

1.9DataRank · unranked

73 citations

Sunmi Seok, Yang Zhang, Jian Ma, Bo Kong, Grace L. Guo +3 more

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Molecular Cell(2023)10.1016/j.molcel.2023.06.018

N/A

1.7DataRank · unranked

97 citations

Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G. Bruneau, Andrew S. Belmont +30 more

Current and future directions in network biology

Bioinformatics Advances(2024)10.1093/bioadv/vbae099

N/A

1.6DataRank · unranked

100 citations

Michelle M. Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Krishnan, Arjun +32 more

Complete sequencing of ape genomes

Nature(2025)10.1038/s41586-025-08816-3

Top 16%

1.3DataRank

Top 16%128 citations

Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar +123 more

Deciphering the impact of genomic variation on function

Nature(2024)10.1038/s41586-024-07510-0

N/A

1.1DataRank · unranked

89 citations

Jesse M. Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon +95 more

Computational methods for analysing multiscale 3D genome organization

Nature Reviews Genetics(2023)10.1038/s41576-023-00638-1

N/A

0.683DataRank · unranked

94 citations

Lorenzo Boninsegna, Muyu Yang, Tom Misteli, Frank Alber, Jian Ma +1 more

Complete sequencing of ape genomes

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.31.605654

Top 34%

0.582DataRank

Top 34%26 citations

Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar +123 more

Major nuclear locales define nuclear genome organization and function beyond A and B compartments

eLife(2024)10.7554/elife.99116

N/A

0.491DataRank · unranked

14 citations

Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang +8 more

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.10.447969

Top 43%

0.435DataRank

Top 43%8 citations

Xingzhao Wen, John Lalith Charles Richard, Zhifei Luo, Tri C. Nguyen, Chien-Ju Chen +14 more

The IGVF catalog—from genetic variation to function

Nucleic Acids Research(2025)10.1093/nar/gkaf1341

Top 63%

0.219DataRank

Top 63%3 citations

Shane Liu, Pedro Assis, Mingjie Li, Shengcheng Dong, Ian Whaling +42 more

Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.23.590809

N/A

0.208DataRank · unranked

3 citations

Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang +8 more

DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks

Nature Communications(2025)10.1038/s41467-025-65077-4

N/A

0.165DataRank · unranked

2 citations

Zhenqiao Song, Yang Zhang, Shike Wang, Danqing Wang, Muyu Yang +3 more

Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.21.481225

N/A

0.104DataRank · unranked

1 citations

Yang Zhang, Yuchuan Wang, Dechao Tian, Andrew S. Belmont, Jason R. Swedlow +2 more

Distinct progenitor behavior underlying neocortical gliogenesis related to tumorigenesis

Cell Reports(2021)10.1016/j.celrep.2021.108853

N/A

0DataRank · unranked

64 citations

Yang Lin, Jiajun Yang, David J. Jörg, Yuwei Peng, Xiuli Zhang +6 more

Assessing the contribution of tumor mutational phenotypes to cancer progression risk

PLoS Computational Biology(2021)10.1371/journal.pcbi.1008777

N/A

0DataRank · unranked

7 citations

Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao +5 more

Genome Compartmentalization with Nuclear Landmarks: Random yet Precise

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.12.468401

N/A

0DataRank · unranked

8 citations

Yifeng Qi, Yuchuan Wang, Jian Ma, Bin Zhang, Kartik Kamat

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

Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function

Cell stem cell(2022)10.1016/j.stem.2022.02.010

N/A

0DataRank · unranked

38 citations

J. Philip Creamer, Sintra Stewart, Massiel Chavez Stolla, Yuchuan Wang, Jing Du +12 more

Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167666

N/A

0DataRank · unranked

29 citations

Jian Ma, Muyu Yang

Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome

Nature Methods(2022)10.1038/s41592-022-01559-3

N/A

0DataRank · unranked

28 citations

Yang Zhang, Yuchuan Wang, Dechao Tian, Andrew S. Belmont, Jason R. Swedlow +2 more

Feeding activates FGF15‐SHP‐TFEB‐mediated lipophagy in the gut

The EMBO Journal(2022)10.15252/embj.2021109997

N/A

0DataRank · unranked

19 citations

Young‐Chae Kim, Yang Zhang, Bo Kong, Grace L. Guo, Jian Ma +3 more

Best Practices for Interpretable Machine Learning in Computational Biology

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.28.513978

N/A

0DataRank · unranked

16 citations

Muyu Yang, Wenbo Cui, Joon Sik Kim, Ameet Talwalkar, Jian Ma +1 more

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

Concert: Genome-wide prediction of sequence elements that modulate DNA replication timing

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.21.488684

N/A

0DataRank · unranked

3 citations

Yuchuan Wang, Yang Zhang, Jian Ma, Yang Yang

SpiceMix enables integrative single-cell spatial modeling of cell identity

Nature Genetics(2023)10.1038/s41588-022-01256-z

N/A

0DataRank · unranked

104 citations

Tianming Zhou, Shahul Alam, Jian Ma, Benjamin Chidester

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

Nature Communications(2023)10.1038/s41467-023-42274-7

N/A

0DataRank · unranked

58 citations

Xingzhao Wen, John Lalith Charles Richard, Zhifei Luo, Tri C. Nguyen, Chien-Ju Chen +14 more

Compartmentalization with nuclear landmarks yields random, yet precise, genome organization

Biophysical Journal(2023)10.1016/j.bpj.2023.03.003

N/A

0DataRank · unranked

38 citations

Zhuohan Lao, Yifeng Qi, Yuchuan Wang, Jian Ma, Bin Zhang +1 more

Developmental neuronal origin regulates neocortical map formation

Cell Reports(2023)10.1016/j.celrep.2023.112170

N/A

0DataRank · unranked

10 citations

Xin‐Jun Zhang, Jiajun Yang, Shuo Li, Laura Li, Xiaohui Lv +3 more

UNADON: transformer-based model to predict genome-wide chromosome spatial position

Bioinformatics(2023)10.1093/bioinformatics/btad246

N/A

0DataRank · unranked

7 citations

Jian Ma, Muyu Yang

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

Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.29.564613

N/A

0DataRank · unranked

4 citations

Omid Gholamalamdari, Yang Zhang, Liguo Zhang, Anastassiia Vertii, Tom van Schaik +8 more

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

Applying interpretable machine learning in computational biology—pitfalls, recommendations and opportunities for new developments

Nature Methods(2024)10.1038/s41592-024-02359-7

N/A

0DataRank · unranked

96 citations

Muyu Yang, Wenbo Cui, Joon Sik Kim, Ameet Talwalkar, Jian Ma +1 more

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

L2G: Repurposing Language Models for Genomics Tasks

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.09.627422

N/A

0DataRank · unranked

1 citations

Jun-Hong Shen, Mikhail Khodak, Jian Ma, Ameet Talwalkar, Wenduo Cheng

Integrative analysis of clinical and epigenetic biomarkers of mortality

UNC Libraries(2024)10.17615/xaw2-3j65

N/A

0DataRank · unranked

0 citations

Jian Ma, James S. Pankow, M Waldenberger, Yao, C, Annette Peters +43 more

Major nuclear locales define nuclear genome organization and function beyond A and B compartments

eLife(2025)10.7554/elife.99116.4

N/A

0DataRank · unranked

11 citations

Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang +8 more

Steamboat: Attention-based multiscale delineation of cellular interactions in tissues

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.06.647437

N/A

0DataRank · unranked

4 citations

Junjie Tang, G.X. Wang, Jian Ma, Shaoheng Liang

DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.06.631595

N/A

0DataRank · unranked

6 citations

Zhenqiao Song, Yang Zhang, Shike Wang, Danqing Wang, Muyu Yang +3 more

Unified integration of spatial transcriptomics across platforms

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.03.31.646238

N/A

0DataRank · unranked

3 citations

Ajinkya Deshpande, Jian Ma, Spencer Krieger, Ellie Haber

HEIMDALL: Disentangling tokenizer design for robust transfer in single-cell foundation models

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.09.687403

N/A

0DataRank · unranked

2 citations

Shahul Alam, Nicholas Ho, Renming Liu, Evan Trop, Shaoheng Liang +4 more

Unified integration of spatial transcriptomics across platforms with LLOKI

Genome Research(2025)10.1101/gr.280803.125

N/A

0DataRank · unranked

1 citations

Ajinkya Deshpande, Jian Ma, Spencer Krieger, Ellie Haber

MIMYR: Generative modeling of missing tissue in spatial transcriptomics

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.24.690239

N/A

0DataRank · unranked

1 citations

Zhilei Bei, Jian Ma, Spencer Krieger, Ajinkya Deshpande

Author response: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function

(2025)10.7554/elife.99116.2.sa0

N/A

0DataRank · unranked

0 citations

Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang +8 more

EYKTHYR reveals transcriptional regulators of spatial gene programs

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.19.654884

N/A

0DataRank · unranked

0 citations

Ellie Haber, Jian Ma, Spencer Krieger

TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.24.690325

N/A

0DataRank · unranked

0 citations

Junjie Tang, Jian Ma, Shaoheng Liang, Sizhe Liu

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

Breastfeeding and childhood obesity: A 12‐country study

Maternal and Child Nutrition(2020)10.1111/mcn.12984

N/A

0DataRank · unranked

112 citations

Yijuan Qiao, Pei Zhao, Wei Li, Peter T. Katzmarzyk, Jean-Philippe Chaput +14 more

Behavior and lineage progression of neural progenitors in the mammalian cortex

Current Opinion in Neurobiology(2020)10.1016/j.conb.2020.10.017

N/A

0DataRank · unranked

65 citations

Jiajun Yang, Zhongfu Shen, Jian Ma, Benjamin D. Simons, Song‐Hai Shi +1 more

Antagonism between splicing and microprocessor complex dictates the serum-induced processing of lnc-MIRHG for efficient cell cycle reentry

RNA(2020)10.1261/rna.075309.120

N/A

0DataRank · unranked

18 citations

Qinyu Hao, Yo-Chuen Lin, You Jin Song, Sushant Bangru, Waqar Arif +12 more

COL2A1 Is a Novel Biomarker of Melanoma Tumor Repopulating Cells

Biomedicines(2020)10.3390/biomedicines8090360

N/A

0DataRank · unranked

14 citations

Kshitij Amar, Michael C. Saul, Tasnim Shireen, Vjollca Konjufca, Jian Ma +3 more

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

Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis

Bioinformatics(2020)10.1093/bioinformatics/btaa396

N/A

0DataRank · unranked

6 citations

Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz +1 more

Neural Network Deconvolution Method for Resolving Pathway-Level Progression of Tumor Clonal Expression Programs With Application to Breast Cancer Brain Metastases

Frontiers in Physiology(2020)10.3389/fphys.2020.01055

N/A

0DataRank · unranked

3 citations

Haoyun Lei, Adrian V. Lee, Jian Ma, Russell Schwartz, Yifeng Tao

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

Genome Research(2020)10.1101/gr.266239.120

N/A

0DataRank · unranked

152 citations

Yang Zhang, Yu Chen, Omid Gholamalamdari, Yuchuan Wang, Jian Ma +2 more

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

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

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

N/A

0DataRank · unranked

15 citations

Tianming Zhou, Jian Ma, Ruochi Zhang

Distinct progenitor behavior underlying neocortical gliogenesis related to tumorigenesis

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.13.338459

N/A

0DataRank · unranked

12 citations

Yang Lin, Jiajun Yang, David J. Jörg, Yuwei Peng, Xiuli Zhang +6 more

SPICEMIX: Integrative single-cell spatial modeling of cell identity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.29.383067

N/A

0DataRank · unranked

11 citations

Tianming Zhou, Shahul Alam, Jian Ma, Benjamin Chidester

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

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

Jian Ma

Indexed papers

Top data-sharing exemplar

Papers