Open Access Helper

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:

Universal Cell Embeddings: A Foundation Model for Cell Biology
Yanay Rosen, Yusuf Roohani, Ayush Agrawal, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 39

Showing 1-25 of 39 citing articles:

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: 24
Establishing a conceptual framework for holistic cell states and state transitions
Susanne M. Rafelski, Julie A. Theriot
Cell (2024) Vol. 187, Iss. 11, pp. 2633-2651
Open Access | Times Cited: 21
Transformers in single-cell omics: a review and new perspectives
Artur Szałata, Karin Hrovatin, Sören Becker, et al.
Nature Methods (2024) Vol. 21, Iss. 8, pp. 1430-1443
Closed Access | Times Cited: 17
scTab: Scaling cross-tissue single-cell annotation models
Felix Fischer, David S. Fischer, R. S. Mukhin, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 12
GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model
Xiaodong Yang, Guole Liu, Guihai Feng, et al.
Cell Research (2024)
Open Access | Times Cited: 10
How to build the virtual cell with artificial intelligence: Priorities and opportunities
Charlotte Bunne, Yusuf Roohani, Yanay Rosen, et al.
Cell (2024) Vol. 187, Iss. 25, pp. 7045-7063
Open Access | Times Cited: 10
Nicheformer: A Foundation Model for Single-Cell and Spatial Omics
Anna C. Schaar, Alejandro Tejada-Lapuerta, Giovanni Palla, et al.
(2024)
Open Access | Times Cited: 7
Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods
Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 7
Evaluating the Utilities of Foundation Models in Single-cell Data Analysis
Tianyu Liu, Kexing Li, Yuge Wang, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 16
Nicheformer: a foundation model for single-cell and spatial omics
Anna C. Schaar, Alejandro Tejada-Lapuerta, Giovanni Palla, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 6
AI learns from chromatin data to uncover gene interactions
Alicja Brożek, Christina V. Theodoris
Nature (2025)
Closed Access
Benchmarking cross-species single-cell RNA-seq data integration methods: towards a cell type tree of life
Zhong Hua-wen, Wenkai Han, David Gómez-Cabrero, et al.
Nucleic Acids Research (2025) Vol. 53, Iss. 1
Open Access
Addressing Wide-Data Studies of Gene Expression Microarrays with the Relevance Feature and Vector Machine
Albert Belenguer-Llorens, Carlos Sevilla salcedo, Emilio Parrado Hernández, et al.
(2025)
Closed Access
Harnessing artificial intelligence to fill global shortfalls in biodiversity knowledge
Laura J. Pollock, Justin Kitzes, Sara Beery, et al.
(2025)
Closed Access
Application of Deep Learning for Single Cell Multi-Omics: A State-of-the-Art Review
Shahid Ahmad Wani, Sumeer Ahmad Khan, S. M. K. Quadri
Archives of Computational Methods in Engineering (2025)
Closed Access
Metric Mirages in Cell Embeddings
Hanchen Wang, Jure Leskovec, Aviv Regev
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 4
Optimal transport for single-cell and spatial omics
Charlotte Bunne, Geoffrey Schiebinger, Andreas Krause, et al.
Nature Reviews Methods Primers (2024) Vol. 4, Iss. 1
Closed Access | Times Cited: 4
CpGPT: a Foundation Model for DNA Methylation
Lucas Paulo de Lima Camillo, Raghav Sehgal, Judith Armstrong, et al.
(2024)
Open Access | Times Cited: 4
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: 3
85 million cells — and counting — at your fingertips
Jeffrey M. Perkel
Nature (2024) Vol. 629, Iss. 8010, pp. 248-249
Open Access | Times Cited: 2
Understanding liver repair through space and time
Lenka Belicová, Noémi Van Hul, Emma Andersson
Nature Genetics (2024) Vol. 56, Iss. 5, pp. 740-742
Closed Access | Times Cited: 2
A thousand and one tumors: the promise of AI for cancer biology
Joy Linyue Fan, Achille Nazaret, Elham Azizi
Nature Methods (2024) Vol. 21, Iss. 8, pp. 1403-1406
Closed Access | Times Cited: 2
Genomic evolution reshapes cell type diversification in the amniote brain
Duoyuan Chen, Zhenkun Zhuang, Maolin Huang, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Closed Access | Times Cited: 1
scPRINT: pre-training on 50 million cells allows robust gene network predictions
Jérémie Kalfon, Jules Samaran, Gabriel Peyré, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 1
Cell-to-cell distance that combines gene expression and gene embeddings
Fangfang Guo, Dailin Gan, Jun Li
Computational and Structural Biotechnology Journal (2024) Vol. 23, pp. 3929-3937
Open Access | Times Cited: 1
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