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OpenAlex Citation Counts

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OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!

If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.

Requested Article:

Modeling gene regulation from paired expression and chromatin accessibility data
Zhana Duren, Xi Chen, Rui Jiang, et al.
Proceedings of the National Academy of Sciences (2017) Vol. 114, Iss. 25
Open Access | Times Cited: 199

Showing 1-25 of 199 citing articles:

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Feng Yan, David Powell, David J. Curtis, et al.
Genome biology (2020) Vol. 21, Iss. 1
Open Access | Times Cited: 374
Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks
Vikram Agarwal, Jay Shendure
Cell Reports (2020) Vol. 31, Iss. 7, pp. 107663-107663
Open Access | Times Cited: 206
Gene regulatory network inference in the era of single-cell multi-omics
Pau Badia-i-Mompel, Lorna Wessels, Sophia Müller‐Dott, et al.
Nature Reviews Genetics (2023) Vol. 24, Iss. 11, pp. 739-754
Closed Access | Times Cited: 189
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
Zhana Duren, Xi Chen, Mahdi Zamanighomi, et al.
Proceedings of the National Academy of Sciences (2018) Vol. 115, Iss. 30, pp. 7723-7728
Open Access | Times Cited: 165
Prediction of Gene Expression Patterns With Generalized Linear Regression Model
Shuai Liu, Mengye Lu, Hanshuang Li, et al.
Frontiers in Genetics (2019) Vol. 10
Open Access | Times Cited: 156
scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles
Suoqin Jin, Lihua Zhang, Qing Nie
Genome biology (2020) Vol. 21, Iss. 1
Open Access | Times Cited: 153
Prenatal immune stress blunts microglia reactivity, impairing neurocircuitry
Lindsay N. Hayes, Kyongman An, Elisa Carloni, et al.
Nature (2022) Vol. 610, Iss. 7931, pp. 327-334
Closed Access | Times Cited: 83
Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
Qiuyue Yuan, Zhana Duren
Nature Biotechnology (2024)
Open Access | Times Cited: 28
H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation
Naoki Kubo, Poshen B. Chen, Rong Hu, et al.
Molecular Cell (2024) Vol. 84, Iss. 9, pp. 1742-1752.e5
Open Access | Times Cited: 25
Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses
Xuelei Lin, Yongxin Xu, Dongzhi Wang, et al.
Molecular Plant (2024) Vol. 17, Iss. 3, pp. 438-459
Closed Access | Times Cited: 19
Unsupervised clustering and epigenetic classification of single cells
Mahdi Zamanighomi, Zhixiang Lin, Timothy Daley, et al.
Nature Communications (2018) Vol. 9, Iss. 1
Open Access | Times Cited: 124
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning
Wenran Li, Wing Hung Wong, Rui Jiang
Nucleic Acids Research (2019) Vol. 47, Iss. 10, pp. e60-e60
Open Access | Times Cited: 123
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
Emily R. Miraldi, Maria Pokrovskii, Aaron Watters, et al.
Genome Research (2019) Vol. 29, Iss. 3, pp. 449-463
Open Access | Times Cited: 108
Identification of crucial genes in abdominal aortic aneurysm by WGCNA
Siliang Chen, Dan Yang, Chuxiang Lei, et al.
PeerJ (2019) Vol. 7, pp. e7873-e7873
Open Access | Times Cited: 96
TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment
Lingjie Li, Yong Wang, Jessica L. Torkelson, et al.
Cell stem cell (2019) Vol. 24, Iss. 2, pp. 271-284.e8
Open Access | Times Cited: 92
Prediction of enhancer-promoter interactions via natural language processing
Wanwen Zeng, Mengmeng Wu, Rui Jiang
BMC Genomics (2018) Vol. 19, Iss. S2
Open Access | Times Cited: 89
Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis
Qi-Gang Li, Keyan Zhao, Carlos D. Bustamante, et al.
Genetics in Medicine (2019) Vol. 21, Iss. 9, pp. 2126-2134
Open Access | Times Cited: 88
Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage
Xianglong Zhang, David S. Hong, Shining Ma, et al.
Proceedings of the National Academy of Sciences (2020) Vol. 117, Iss. 9, pp. 4864-4873
Open Access | Times Cited: 86
Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates
Ittai Eres, Kaixuan Luo, Chiaowen Joyce Hsiao, et al.
PLoS Genetics (2019) Vol. 15, Iss. 7, pp. e1008278-e1008278
Open Access | Times Cited: 78
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation
Jingxue Xin, Hui Zhang, Yaoxi He, et al.
Nature Communications (2020) Vol. 11, Iss. 1
Open Access | Times Cited: 77
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data
Daniel Kim, Andy Tran, Hani Jieun Kim, et al.
npj Systems Biology and Applications (2023) Vol. 9, Iss. 1
Open Access | Times Cited: 38
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
Tareian Cazares, Faiz W. Rizvi, Balaji Iyer, et al.
PLoS Computational Biology (2023) Vol. 19, Iss. 1, pp. e1010863-e1010863
Open Access | Times Cited: 27
Human microglia maturation is underpinned by specific gene regulatory networks
Claudia Z. Han, Rick Z. Li, Emily A. Hansen, et al.
Immunity (2023) Vol. 56, Iss. 9, pp. 2152-2171.e13
Open Access | Times Cited: 27
Mapping the developmental trajectory of human astrocytes reveals divergence in glioblastoma
Caitlin Sojka, Hsiao‐Lin V. Wang, Tarun N. Bhatia, et al.
Nature Cell Biology (2025)
Closed Access | Times Cited: 1
Integrating ChIP-seq with other functional genomics data
Shan Jiang, A Mortazavi
Briefings in Functional Genomics (2018) Vol. 17, Iss. 2, pp. 104-115
Open Access | Times Cited: 80
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