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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:

The scverse project provides a computational ecosystem for single-cell omics data analysis
Isaac Virshup, Danila Bredikhin, Lukas Heumos, et al.
Nature Biotechnology (2023) Vol. 41, Iss. 5, pp. 604-606
Closed Access | Times Cited: 141

Showing 1-25 of 141 citing articles:

PyDESeq2: a python package for bulk RNA-seq differential expression analysis
Boris Muzellec, Maria Teleńczuk, Vincent Cabeli, et al.
Bioinformatics (2023) Vol. 39, Iss. 9
Open Access | Times Cited: 109
CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data
Shibla Abdulla, Brian D. Aevermann, Pedro Assis, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 62
Mapping cells through time and space with moscot
Dominik Klein, Giovanni Palla, Marius Lange, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 51
SpatialData: an open and universal data framework for spatial omics
Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, et al.
Nature Methods (2024)
Open Access | Times Cited: 51
CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity
Marco Varrone, Daniele Tavernari, Albert Santamaria‐Martínez, et al.
Nature Genetics (2023) Vol. 56, Iss. 1, pp. 74-84
Open Access | Times Cited: 44
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: 44
Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging
Florian Schueder, Felix Rivera‐Molina, Maohan Su, et al.
Cell (2024) Vol. 187, Iss. 7, pp. 1769-1784.e18
Closed Access | Times Cited: 30
CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data
Shibla Abdulla, Brian D. Aevermann, Pedro Assis, et al.
Nucleic Acids Research (2024) Vol. 53, Iss. D1, pp. D886-D900
Open Access | Times Cited: 28
Bento: a toolkit for subcellular analysis of spatial transcriptomics data
Clarence K. Mah, Noorsher Ahmed, Nicole A. Lopez, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 25
LIANA+ provides an all-in-one framework for cell–cell communication inference
Daniel Dimitrov, Philipp Schäfer, Elias Farr, et al.
Nature Cell Biology (2024) Vol. 26, Iss. 9, pp. 1613-1622
Open Access | Times Cited: 23
An integrated transcriptomic cell atlas of human neural organoids
Zhisong He, Leander Dony, Jonas Simon Fleck, et al.
Nature (2024) Vol. 635, Iss. 8039, pp. 690-698
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
Mapping cells through time and space with moscot
Dominik Klein, Giovanni Palla, Marius Lange, et al.
Nature (2025)
Open Access | Times Cited: 2
Recirculating regulatory T cells mediate thymic regeneration through amphiregulin following damage
Andri L. Lemarquis, Anastasia I. Kousa, Kimon V. Argyropoulos, et al.
Immunity (2025) Vol. 58, Iss. 2, pp. 397-411.e6
Open Access | Times Cited: 1
LIANA+: an all-in-one cell-cell communication framework
Daniel Dimitrov, Philipp Schäfer, Elias Farr, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 24
SpatialData: an open and universal data framework for spatial omics
Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 23
Mapping human tissues with highly multiplexed RNA in situ hybridization
Kian Kalhor, Chien-Ju Chen, Ho Suk Lee, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 12
OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing
Zehua Zeng, Yuqing Ma, Lei Hu, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 12
Vitessce: integrative visualization of multimodal and spatially resolved single-cell data
Mark S. Keller, Ilan Gold, Chuck McCallum, et al.
Nature Methods (2024)
Open Access | Times Cited: 12
Single-cell immune repertoire analysis
Sergio Erdal Irac, Megan Sioe Fei Soon, Nicholas Borcherding, et al.
Nature Methods (2024) Vol. 21, Iss. 5, pp. 777-792
Closed Access | Times Cited: 10
Single-cell spatiotemporal analysis of the lungs reveals Slamf9+ macrophages involved in viral clearance and inflammation resolution
Boyi Cong, Xuan Dong, Zongheng Yang, et al.
Cell Discovery (2024) Vol. 10, Iss. 1
Open Access | Times Cited: 10
Batch correction methods used in single cell RNA-sequencing analyses are often poorly calibrated
Sindri Emmanúel Antonsson, Páll Melsted
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 9
Sopa: a technology-invariant pipeline for analyses of image-based spatial omics
Quentin Blampey, Kevin Mulder, Margaux Gardet, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 9
Spatial transcriptomic characterization of pathologic niches in IPF
Christoph H. Mayr, Diana Santacruz, Sebastian Jarosch, et al.
Science Advances (2024) Vol. 10, Iss. 32
Open Access | Times Cited: 8
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
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