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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:

scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks
Han Yuan, David R. Kelley
Nature Methods (2022) Vol. 19, Iss. 9, pp. 1088-1096
Open Access | Times Cited: 79

Showing 1-25 of 79 citing articles:

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
Ieva Rauluševičiūtė, Rafael Riudavets Puig, Romain Blanc‐Mathieu, et al.
Nucleic Acids Research (2023) Vol. 52, Iss. D1, pp. D174-D182
Open Access | Times Cited: 312
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: 179
Cell-type-directed design of synthetic enhancers
Ibrahim Ihsan Taskiran, Katina I. Spanier, Hannah Dickmänken, et al.
Nature (2023) Vol. 626, Iss. 7997, pp. 212-220
Open Access | Times Cited: 68
Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings
Alexander Sasse, Bernard Ng, Anna Spiro, et al.
Nature Genetics (2023) Vol. 55, Iss. 12, pp. 2060-2064
Open Access | Times Cited: 47
A fast, scalable and versatile tool for analysis of single-cell omics data
Kai Zhang, Nathan R. Zemke, Ethan J. Armand, et al.
Nature Methods (2024) Vol. 21, Iss. 2, pp. 217-227
Open Access | Times Cited: 45
Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges
Manoj Kumar Goshisht
ACS Omega (2024) Vol. 9, Iss. 9, pp. 9921-9945
Open Access | Times Cited: 27
Deciphering the impact of genomic variation on function
J Engreitz, Heather A. Lawson, Harinder Singh, et al.
Nature (2024) Vol. 633, Iss. 8028, pp. 47-57
Closed Access | Times Cited: 20
Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis
Sneha Mitra, Rohan Malik, Wilfred Wong, et al.
Nature Genetics (2024) Vol. 56, Iss. 4, pp. 627-636
Open Access | Times Cited: 18
Challenges and best practices in omics benchmarking
Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela, et al.
Nature Reviews Genetics (2024) Vol. 25, Iss. 5, pp. 326-339
Closed Access | Times Cited: 16
Interpreting non-coding disease-associated human variants using single-cell epigenomics
Kyle J. Gaulton, Sebastian Preißl, Bing Ren
Nature Reviews Genetics (2023) Vol. 24, Iss. 8, pp. 516-534
Open Access | Times Cited: 39
Applications of deep learning in understanding gene regulation
Zhongxiao Li, Elva Gao, Juexiao Zhou, et al.
Cell Reports Methods (2023) Vol. 3, Iss. 1, pp. 100384-100384
Open Access | Times Cited: 29
Single-cell omics: experimental workflow, data analyses and applications
Fengying Sun, Haoyan Li, Dongqing Sun, et al.
Science China Life Sciences (2024)
Closed Access | Times Cited: 10
Benchmarking algorithms for single-cell multi-omics prediction and integration
Yinlei Hu, Siyuan Wan, Yuanhanyu Luo, et al.
Nature Methods (2024)
Closed Access | Times Cited: 9
Topological identification and interpretation for single-cell epigenetic regulation elucidation in multi-tasks using scAGDE
Guoqian Hao, Fan Yi, Zhuohan Yu, et al.
Nature Communications (2025) Vol. 16, Iss. 1
Open Access | Times Cited: 1
Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings
Alexander Sasse, Bernard Ng, Anna Spiro, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 21
scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data
Songming Tang, Xuejian Cui, Rongxiang Wang, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 7
Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets
Erfaneh Gharavi, Nathan J. LeRoy, Guangtao Zheng, et al.
Bioengineering (2024) Vol. 11, Iss. 3, pp. 263-263
Open Access | Times Cited: 6
Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace
Zakieh Tayyebi, Allison R. Pine, Christina Leslie
Nature Methods (2024) Vol. 21, Iss. 6, pp. 1014-1022
Open Access | Times Cited: 6
Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity
Xuejian Cui, Xiaoyang Chen, Zhen Li, et al.
Nature Computational Science (2024) Vol. 4, Iss. 5, pp. 346-359
Closed Access | Times Cited: 6
A survey on algorithms to characterize transcription factor binding sites
Manuel Tognon, Rosalba Giugno, Luca Pinello
Briefings in Bioinformatics (2023) Vol. 24, Iss. 3
Open Access | Times Cited: 14
Deciphering cell types by integrating scATAC-seq data with genome sequences
Yuansong Zeng, Mai Luo, Ningyuan Shangguan, et al.
Nature Computational Science (2024) Vol. 4, Iss. 4, pp. 285-298
Open Access | Times Cited: 5
Advances and applications in single-cell and spatial genomics
Jingjing Wang, Fang Ye, Haoxi Chai, et al.
Science China Life Sciences (2024)
Closed Access | Times Cited: 5
Toward a comprehensive catalog of regulatory elements
Kaili Fan, Edith L. Pfister, Zhiping Weng
Human Genetics (2023) Vol. 142, Iss. 8, pp. 1091-1111
Closed Access | Times Cited: 12
Genotype imputation methods for whole and complex genomic regions utilizing deep learning technology
Tatsuhiko Naito, Yukinori Okada
Journal of Human Genetics (2024)
Open Access | Times Cited: 4
Current genomic deep learning models display decreased performance in cell type-specific accessible regions
Pooja Kathail, Richard W. Shuai, Ryan Chung, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 4
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