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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:

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0
Claudia Skok Gibbs, Christopher A. Jackson, Giuseppe-Antonio Saldi, et al.
Bioinformatics (2022) Vol. 38, Iss. 9, pp. 2519-2528
Open Access | Times Cited: 49

Showing 1-25 of 49 citing articles:

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
Network inference with Granger causality ensembles on single-cell transcriptomics
Atul Deshpande, Li‐Fang Chu, Ron Stewart, et al.
Cell Reports (2022) Vol. 38, Iss. 6, pp. 110333-110333
Open Access | Times Cited: 91
Charting plant gene functions in the multi-omics and single-cell era
Thomas Depuydt, Bert De Rybel, Klaas Vandepoele
Trends in Plant Science (2022) Vol. 28, Iss. 3, pp. 283-296
Open Access | Times Cited: 47
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data
Marco Stock, Corinna Losert, M Zambon, et al.
Molecular Systems Biology (2025)
Closed Access | Times Cited: 1
Stem cells tightly regulate dead cell clearance to maintain tissue fitness
Katherine Stewart, Merve Deniz Abdusselamoglu, Matthew Tierney, et al.
Nature (2024) Vol. 633, Iss. 8029, pp. 407-416
Open Access | Times Cited: 6
spliceJAC : transition genes and state‐specific gene regulation from single‐cell transcriptome data
Federico Bocci, Peijie Zhou, Qing Nie
Molecular Systems Biology (2022) Vol. 18, Iss. 11
Open Access | Times Cited: 28
Coordinated control of neuronal differentiation and wiring by sustained transcription factors
Mehmet Neset Özel, Claudia Skok Gibbs, Isabel Holguera, et al.
Science (2022) Vol. 378, Iss. 6626
Open Access | Times Cited: 26
From time-series transcriptomics to gene regulatory networks: A review on inference methods
Malvina Marku, Véra Pancaldi
PLoS Computational Biology (2023) Vol. 19, Iss. 8, pp. e1011254-e1011254
Open Access | Times Cited: 15
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization
Claudia Skok Gibbs, Omar Mahmood, Richard Bonneau, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 5
Network-based approaches for modeling disease regulation and progression
Gihanna Galindez, Sepideh Sadegh, Jan Baumbach, et al.
Computational and Structural Biotechnology Journal (2022) Vol. 21, pp. 780-795
Open Access | Times Cited: 22
Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration
Andrea Tóth, Paranthaman S. Kannan, John Snowball, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 11
SPREd: a simulation-supervised neural network tool for gene regulatory network reconstruction
Zijun Wu, Saurabh Sinha
Bioinformatics Advances (2024) Vol. 4, Iss. 1
Open Access | Times Cited: 4
Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord
Elena Kandror, Anqi Wang, Mathieu Carrière, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access
Single-cell technology for plant systems biology
Sahand Amini, Sandra Thibivilliers, Andrew Farmer, et al.
Elsevier eBooks (2025), pp. 133-156
Closed Access
Inferring fungal cis-regulatory networks from genome sequences
Alan M Moses, Jason Stajich, Audrey P. Gasch, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape
Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, et al.
Bioinformatics (2023) Vol. 39, Iss. 5
Open Access | Times Cited: 10
Single-cell and spatial sequencing application in pathology
Yoon‐Seob Kim, Jinyong Choi, Sug Hyung Lee
Journal of Pathology and Translational Medicine (2023) Vol. 57, Iss. 1, pp. 43-51
Open Access | Times Cited: 9
Computational tools for inferring transcription factor activity
Dennis Hecker, Michael Lauber, Fatemeh Behjati Ardakani, et al.
PROTEOMICS (2023) Vol. 23, Iss. 23-24
Open Access | Times Cited: 9
Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference
Andreas Tjärnberg, Maggie Beheler-Amass, Christopher A. Jackson, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 3
Flexible modeling of regulatory networks improves transcription factor activity estimation
Chen Chen, Megha Padi
npj Systems Biology and Applications (2024) Vol. 10, Iss. 1
Open Access | Times Cited: 3
Multi-objective context-guided consensus of a massive array of techniques for the inference of Gene Regulatory Networks
Adrián Segura-Ortiz, José García-Nieto, José F. Aldana‐Montes, et al.
Computers in Biology and Medicine (2024) Vol. 179, pp. 108850-108850
Open Access | Times Cited: 3
New horizons in the stormy sea of multimodal single-cell data integration
Christopher A. Jackson, Christine Vogel
Molecular Cell (2022) Vol. 82, Iss. 2, pp. 248-259
Open Access | Times Cited: 12
Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS
Rémi Trimbour, Ina Maria Deutschmann, Laura Cantini
Bioinformatics (2024) Vol. 40, Iss. 5
Open Access | Times Cited: 2
NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration
Dhoha Abid, Michael R. Brent
Bioinformatics (2023) Vol. 39, Iss. 2
Open Access | Times Cited: 4
Neural cell diversity in the light of single-cell transcriptomics
Sandra María Fernández-Moya, Akshay Jaya Ganesh, Mireya Plass
Transcription (2023) Vol. 14, Iss. 3-5, pp. 158-176
Open Access | Times Cited: 4
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