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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:

Alignment of spatial genomics data using deep Gaussian processes
Andrew Jones, F. William Townes, Didong Li, et al.
Nature Methods (2023) Vol. 20, Iss. 9, pp. 1379-1387
Open Access | Times Cited: 40

Showing 1-25 of 40 citing articles:

BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies
Zheng Li, Xiang Zhou
Genome biology (2022) Vol. 23, Iss. 1
Open Access | Times Cited: 75
STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping
Kalen Clifton, Manjari Anant, Gohta Aihara, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 48
Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics
Gunsagar S. Gulati, Jeremy Philip D’Silva, Yunhe Liu, et al.
Nature Reviews Molecular Cell Biology (2024) Vol. 26, Iss. 1, pp. 11-31
Closed Access | Times Cited: 31
Mapping cells through time and space with moscot
Dominik Klein, Giovanni Palla, Marius Lange, et al.
Nature (2025)
Open Access | Times Cited: 2
Partial alignment of multislice spatially resolved transcriptomics data
Xinhao Liu, Ron Zeira, Benjamin J. Raphael
Genome Research (2023)
Closed Access | Times Cited: 29
Benchmarking clustering, alignment, and integration methods for spatial transcriptomics
Yunfei Hu, Manfei Xie, Yikang Li, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 10
Search and match across spatial omics samples at single-cell resolution
Zefang Tang, Shuchen Luo, Hu Zeng, et al.
Nature Methods (2024)
Closed Access | Times Cited: 8
Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data
Guanao Yan, Shuo Harper Hua, Jingyi Jessica Li
Nature Communications (2025) Vol. 16, Iss. 1
Open Access | Times Cited: 1
Computational methods for alignment and integration of spatially resolved transcriptomics data
Yuyao Liu, Can Yang
Computational and Structural Biotechnology Journal (2024) Vol. 23, pp. 1094-1105
Open Access | Times Cited: 5
Integrating Spatially‐Resolved Transcriptomics Data Across Tissues and Individuals: Challenges and Opportunities
Boyi Guo, Wodan Ling, Sang Ho Kwon, et al.
Small Methods (2025)
Open Access
DeST-OT: Alignment of spatiotemporal transcriptomics data
Peter Halmos, Xinhao Liu, Julian Gold, et al.
Cell Systems (2025)
Closed Access
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data
Xinhao Liu, Ron Zeira, Benjamin J. Raphael
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 12
Alignment of spatial transcriptomics data using diffeomorphic metric mapping
Kalen Clifton, Manjari Anant, Gohta Aihara, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 12
Computational modeling for deciphering tissue microenvironment heterogeneity from spatially resolved transcriptomics
Chuanchao Zhang, Lequn Wang, Qianqian Shi
Computational and Structural Biotechnology Journal (2024) Vol. 23, pp. 2109-2115
Open Access | Times Cited: 4
Spatial omics advances for in situ RNA biology
Jingyi Ren, Shuchen Luo, Hailing Shi, et al.
Molecular Cell (2024)
Closed Access | Times Cited: 4
Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access
Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning
Wei Tu, Lihua Zhang
PLoS Computational Biology (2025) Vol. 21, Iss. 4, pp. e1012948-e1012948
Open Access
Year in review 2023

Nature Methods (2024) Vol. 21, Iss. 1, pp. 1-2
Open Access | Times Cited: 3
Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections
Kaitlin Stouffer, Alain Trouvé, Laurent Younès, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 3
Mapping the topography of spatial gene expression with interpretable deep learning
Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 8
DeST-OT: Alignment of Spatiotemporal Transcriptomics Data
Peter Halmos, Xinhao Liu, Julian Gold, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 2
Integration of Multiple Spatial Omics Modalities Reveals Unique Insights into Molecular Heterogeneity of Prostate Cancer
Wanqiu Zhang, Xander Spotbeen, Sebastiaan Vanuytven, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 5
How to Design Reinforcement Learning Methods for the Edge: An Integrated Approach toward Intelligent Decision Making
Guanlin Wu, D. Zhang, Zhengyuan Miao, et al.
Electronics (2024) Vol. 13, Iss. 7, pp. 1281-1281
Open Access | Times Cited: 1
Optimizing the design of spatial genomic studies
Andrew Jones, Diana Cai, Didong Li, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 1
Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport
Zizhan Gao, Kai Cao, Lin Wan
Bioinformatics (2024) Vol. 40, Iss. Supplement_2, pp. ii137-ii145
Open Access | Times Cited: 1
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