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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:

MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells
Allen W. Lynch, Christina V. Theodoris, Henry W. Long, et al.
Nature Methods (2022) Vol. 19, Iss. 9, pp. 1097-1108
Open Access | Times Cited: 48

Showing 1-25 of 48 citing articles:

Best practices for single-cell analysis across modalities
Lukas Heumos, Anna C. Schaar, Christopher Lance, et al.
Nature Reviews Genetics (2023) Vol. 24, Iss. 8, pp. 550-572
Open Access | Times Cited: 486
The technological landscape and applications of single-cell multi-omics
Alev Baysoy, Zhiliang Bai, Rahul Satija, et al.
Nature Reviews Molecular Cell Biology (2023) Vol. 24, Iss. 10, pp. 695-713
Open Access | Times Cited: 414
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
Cooperative integration of spatially resolved multi-omics data with COSMOS
Yuansheng Zhou, Xue Xiao, Lei Dong, et al.
Nature Communications (2025) Vol. 16, Iss. 1
Open Access | Times Cited: 1
Single-cell immune aging clocks reveal inter-individual heterogeneity during infection and vaccination
Wenchao Li, Zhenhua Zhang, Saumya Kumar, et al.
Nature Aging (2025)
Open Access | Times Cited: 1
Multimodal deep learning approaches for single-cell multi-omics data integration
Tasbiraha Athaya, Rony Chowdhury Ripan, Xiaoman Li, et al.
Briefings in Bioinformatics (2023) Vol. 24, Iss. 5
Open Access | Times Cited: 33
An exhausted-like microglial population accumulates in aged and APOE4 genotype Alzheimer’s brains
Alon Millet, José Henrique Ledo, Sohail F. Tavazoie
Immunity (2023) Vol. 57, Iss. 1, pp. 153-170.e6
Open Access | Times Cited: 26
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis
Kathryn Weinand, Saori Sakaue, Aparna Nathan, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 11
Single-cell omics: experimental workflow, data analyses and applications
Fengying Sun, Haoyan Li, Dongqing Sun, et al.
Science China Life Sciences (2024)
Closed Access | Times Cited: 10
Gene networks and systems biology in Alzheimer's disease: Insights from multi‐omics approaches
Negin Rahimzadeh, Shushrruth Sai Srinivasan, Jing Zhang, et al.
Alzheimer s & Dementia (2024) Vol. 20, Iss. 5, pp. 3587-3605
Open Access | Times Cited: 8
Benchmarking algorithms for single-cell multi-omics prediction and integration
Yinlei Hu, Siyuan Wan, Yuanhanyu Luo, et al.
Nature Methods (2024)
Closed Access | Times Cited: 8
Single-Cell Multiomics
Emily Flynn, Ana Almonte-Loya, Gabriela K. Fragiadakis
Annual Review of Biomedical Data Science (2023) Vol. 6, Iss. 1, pp. 313-337
Open Access | Times Cited: 19
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: 7
scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration
Xiuhui Yang, Koren K. Mann, Hao Wu, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 7
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation
Pratik Singh, Wei Yong Gu, Shariq Madha, et al.
Cell stem cell (2024) Vol. 31, Iss. 7, pp. 1038-1057.e11
Open Access | Times Cited: 5
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
Yang Li, Anjun Ma, Yizhong Wang, et al.
Briefings in Bioinformatics (2024) Vol. 25, Iss. 5
Open Access | Times Cited: 5
AI learns from chromatin data to uncover gene interactions
Alicja Brożek, Christina V. Theodoris
Nature (2025)
Closed Access
Multi-modal Diffusion Model with Dual-Cross-Attention for Multi-Omics Data Generation and Translation
Erpai Luo, Qiao Liu, Minsheng Hao, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation
Pratik Singh, Wei Yong Gu, Shariq Madha, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 4
A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions
Xi Xi, Jiaqi Li, Jinmeng Jia, et al.
Nature Communications (2025) Vol. 16, Iss. 1
Open Access
Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system
Igor Adameyko, Trygve E. Bakken, Aparna Bhaduri, et al.
Nature Neuroscience (2024) Vol. 27, Iss. 12, pp. 2278-2291
Closed Access | Times Cited: 3
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery
Boyan Bonev, Gonçalo Castelo‐Branco, Fei Chen, et al.
Nature Neuroscience (2024) Vol. 27, Iss. 12, pp. 2292-2309
Closed Access | Times Cited: 3
The performance of deep generative models for learning joint embeddings of single-cell multi-omics data
Eva Brombacher, Maren Hackenberg, Clemens Kreutz, et al.
Frontiers in Molecular Biosciences (2022) Vol. 9
Open Access | Times Cited: 15
Multi-batch single-cell comparative atlas construction by deep learning disentanglement
Allen W. Lynch, Myles Brown, Clifford A. Meyer
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 7
Single-cell multi-omics topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures
Manqi Zhou, Hao Zhang, Zilong Bai, et al.
Cell Reports Methods (2023) Vol. 3, Iss. 8, pp. 100563-100563
Open Access | Times Cited: 7
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