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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:

IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data
Tiam Heydari, Matthew A. Langley, Cynthia L. Fisher, et al.
PLoS Computational Biology (2022) Vol. 18, Iss. 2, pp. e1009907-e1009907
Open Access | Times Cited: 22

Showing 22 citing articles:

Learning single-cell perturbation responses using neural optimal transport
Charlotte Bunne, Stefan G. Stark, Gabriele Gut, et al.
Nature Methods (2023) Vol. 20, Iss. 11, pp. 1759-1768
Open Access | Times Cited: 55
Attractor Landscape Analysis Reveals a Reversion Switch in the Transition of Colorectal Tumorigenesis
Dongkwan Shin, Jeong‐Ryeol Gong, Sang Kwon Jeong, et al.
Advanced Science (2025)
Open Access | Times Cited: 1
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
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: 5
scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model
Andy Tran, Pengyi Yang, Jean Yang, et al.
NAR Genomics and Bioinformatics (2022) Vol. 4, Iss. 1
Open Access | Times Cited: 13
Virtual cells in a virtual microenvironment recapitulate early development-like patterns in human pluripotent stem cell colonies
Himanshu Kaul, Nicolas Werschler, Ross D. Jones, et al.
Stem Cell Reports (2022) Vol. 18, Iss. 1, pp. 377-393
Open Access | Times Cited: 13
BoNesis: a Python-Based Declarative Environment for the Verification, Reprogramming, and Synthesis of Most Permissive Boolean Networks
Stéphanie Chevalier, Déborah Boyenval, Gustavo Magaña-López, et al.
Lecture notes in computer science (2024), pp. 71-79
Open Access | Times Cited: 2
Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector
Nicholas Ceglia, Zachary Sethna, Samuel S. Freeman, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 6
Transcriptional networks of transient cell states during human prefrontal cortex development
Aditi Singh, Vijay Tiwari
Frontiers in Molecular Neuroscience (2023) Vol. 16
Open Access | Times Cited: 3
Normalizing Input–Output Relationships of Cancer Networks for Reversion Therapy
Jae Il Joo, Hwa‐Jeong Park, Kwang‐Hyun Cho
Advanced Science (2023) Vol. 10, Iss. 24
Open Access | Times Cited: 3
GeneVector: Identification of transcriptional programs using dense vector representations defined by mutual information
Nicholas Ceglia, Zachary Sethna, Samuel S. Freeman, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2022)
Open Access | Times Cited: 5
Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL
Tiam Heydari, Peter W. Zandstra
Methods in molecular biology (2023), pp. 251-262
Closed Access | Times Cited: 2
Time- and lineage-resolved transcriptional profiling uncovers gene expression programs and clonal relationships that underlie human T lineage specification
Yale S. Michaels, Matthew C. Major, Becca Bonham-Carter, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 2
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era
Andy Tran, Pengyi Yang, Jean Yang, et al.
Briefings in Functional Genomics (2022) Vol. 21, Iss. 4, pp. 270-279
Open Access | Times Cited: 4
Network Activity Evaluation Reveals Significant Gene Regulatory Architectures During SARS-CoV-2 Viral Infection From Dynamic scRNA-seq Data
Chuan‐Yuan Wang, Zhi‐Ping Liu
IEEE Journal of Biomedical and Health Informatics (2024) Vol. 28, Iss. 4, pp. 2373-2384
Closed Access
OneSC: A computational platform for recapitulating cell state transitions
Da Peng, Patrick Cahan
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access
Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming
Stéphanie Chevalier, Julia C. Becker, Yujuan Gui, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access
OneSC: A computational platform for recapitulating cell state transitions
Da Peng, Patrick Cahan
Bioinformatics (2024) Vol. 40, Iss. 12
Open Access
Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells
Yale S. Michaels, Matthew C. Major, Becca Bonham-Carter, et al.
Cell Systems (2024)
Open Access
Control of Cellular Differentiation Trajectories for Cancer Reversion
Jeong‐Ryeol Gong, Chun‐Kyung Lee, Hoon‐Min Kim, et al.
Advanced Science (2024)
Open Access
Systems bioengineering approaches for developmental toxicology
Beatriz Xavier Soares, Cláudia C. Miranda, Tiago G. Fernandes
Computational and Structural Biotechnology Journal (2023) Vol. 21, pp. 3272-3279
Open Access | Times Cited: 1
Editorial: Transcription regulation — Brain development and homeostasis — A finely tuned and orchestrated scenario in physiology and pathology, volume II
Estela M. Muñoz, Verónica Martínez‐Cerdeño
Frontiers in Molecular Neuroscience (2023) Vol. 16
Open Access | Times Cited: 1
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