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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:

Quantifying the effect of experimental perturbations at single-cell resolution
Daniel B. Burkhardt, Jay S. Stanley, Alexander Tong, et al.
Nature Biotechnology (2021) Vol. 39, Iss. 5, pp. 619-629
Open Access | Times Cited: 159

Showing 26-50 of 159 citing articles:

Trellis tree-based analysis reveals stromal regulation of patient-derived organoid drug responses
María Ramos Zapatero, Alexander Tong, James W. Opzoomer, et al.
Cell (2023) Vol. 186, Iss. 25, pp. 5606-5619.e24
Open Access | Times Cited: 36
Causal identification of single-cell experimental perturbation effects with CINEMA-OT
Mingze Dong, Bao Wang, Jessica Wei, et al.
Nature Methods (2023) Vol. 20, Iss. 11, pp. 1769-1779
Open Access | Times Cited: 31
Microglial expression of CD83 governs cellular activation and restrains neuroinflammation in experimental autoimmune encephalomyelitis
Pia Sinner, Katrin Peckert-Maier, Hashem Mohammadian, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 29
Precise identification of cell states altered in disease using healthy single-cell references
Emma Dann, Ana-Maria Cujba, Amanda J. Oliver, et al.
Nature Genetics (2023) Vol. 55, Iss. 11, pp. 1998-2008
Open Access | Times Cited: 29
MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention
Bettina Weigel, Jana F. Tegethoff, Sarah D. Grieder, et al.
Molecular Psychiatry (2023) Vol. 28, Iss. 5, pp. 2122-2135
Open Access | Times Cited: 25
Trajectory inference across multiple conditions with condiments
Hector Roux de Bézieux, Koen Van den Berge, Kelly Street, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 15
Pertpy: an end-to-end framework for perturbation analysis
Lukas Heumos, Yuge Ji, L T May, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 12
Developmental origin of oligodendrocytes determines their function in the adult brain
Sarah Foerster, Elisa M. Floriddia, David van Bruggen, et al.
Nature Neuroscience (2024) Vol. 27, Iss. 8, pp. 1545-1554
Open Access | Times Cited: 11
A mini-review on perturbation modelling across single-cell omic modalities
George Gavriilidis, Vasileios Vasileiou, Aspasia Orfanou, et al.
Computational and Structural Biotechnology Journal (2024) Vol. 23, pp. 1886-1896
Open Access | Times Cited: 10
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets
Haidong Yi, Alec Plotkin, Natalie Stanley
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 9
A pharmacological toolkit for human microglia identifies Topoisomerase I inhibitors as immunomodulators for Alzheimer’s disease
Verena Haage, John F. Tuddenham, Natacha Comandante-Lou, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 9
Defining and benchmarking open problems in single-cell analysis
Malte D. Luecken, Scott Gigante, Daniel B. Burkhardt, et al.
Research Square (Research Square) (2024)
Open Access | Times Cited: 9
Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity
Elsa Brunet‐Ratnasingham, Sacha Morin, Haley E. Randolph, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 9
Transcriptomic Profiling Unveils EDN3+ Meningeal Fibroblasts as Key Players in Sturge‐Weber Syndrome Pathogenesis
Daosheng Ai, Tang Ming, Xiaoli Li, et al.
Advanced Science (2025)
Open Access | Times Cited: 1
Explainable modeling of single-cell perturbation data using attention and sparse dictionary learning
Yang Xu, Stephen M. Fleming, Matthew Tegtmeyer, et al.
Cell Systems (2025), pp. 101245-101245
Closed Access | Times Cited: 1
Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium
Neal G. Ravindra, Mia Madel Alfajaro, Victor Gasque, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2020)
Open Access | Times Cited: 63
Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics
Yakir Reshef, Laurie Rumker, Joyce B. Kang, et al.
Nature Biotechnology (2021) Vol. 40, Iss. 3, pp. 355-363
Open Access | Times Cited: 55
Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease
Travis S. Johnson, Christina Y. Yu, Zhi Huang, et al.
Genome Medicine (2022) Vol. 14, Iss. 1
Open Access | Times Cited: 33
Aortic Cellular Diversity and Quantitative Genome-Wide Association Study Trait Prioritization Through Single-Nuclear RNA Sequencing of the Aneurysmal Human Aorta
Elizabeth L. Chou, Mark Chaffin, Bridget Simonson, et al.
Arteriosclerosis Thrombosis and Vascular Biology (2022) Vol. 42, Iss. 11, pp. 1355-1374
Open Access | Times Cited: 33
Case-control analysis of single-cell RNA-seq studies
Viktor Petukhov, Anna A. Igolkina, Rasmus Rydbirk, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2022)
Open Access | Times Cited: 31
Best practices for multi-ancestry, meta-analytic transcriptome-wide association studies: Lessons from the Global Biobank Meta-analysis Initiative
Arjun Bhattacharya, Jibril Hirbo, Dan Zhou, et al.
Cell Genomics (2022) Vol. 2, Iss. 10, pp. 100180-100180
Open Access | Times Cited: 31
Immune cells and their inflammatory mediators modify β cells and cause checkpoint inhibitor–induced diabetes
Ana Luisa Perdigoto, Songyan Deng, Katherine Du, et al.
JCI Insight (2022) Vol. 7, Iss. 17
Open Access | Times Cited: 30
SOTIP is a versatile method for microenvironment modeling with spatial omics data
Zhiyuan Yuan, Yisi Li, Minglei Shi, et al.
Nature Communications (2022) Vol. 13, Iss. 1
Open Access | Times Cited: 29
A Wox3-patterning module organizes planar growth in grass leaves and ligules
James W. Satterlee, Lukas J Evans, Brianne R. Conlon, et al.
Nature Plants (2023) Vol. 9, Iss. 5, pp. 720-732
Open Access | Times Cited: 23
Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon
Dominik J. Otto, C. Diana Jordan, Brennan Dury, et al.
Nature Methods (2024) Vol. 21, Iss. 7, pp. 1185-1195
Closed Access | Times Cited: 8

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