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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:

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation
Johannes Linder, Divyanshi Srivastava, Han Yuan, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 50

Showing 1-25 of 50 citing articles:

Cell-type-directed design of synthetic enhancers
Ibrahim Ihsan Taskiran, Katina I. Spanier, Hannah Dickmänken, et al.
Nature (2023) Vol. 626, Iss. 7997, pp. 212-220
Open Access | Times Cited: 73
Machine-guided design of cell-type-targeting cis-regulatory elements
Sager J. Gosai, Rodrigo Castro, Natalia Fuentes, et al.
Nature (2024) Vol. 634, Iss. 8036, pp. 1211-1220
Open Access | Times Cited: 26
Genomic language models: opportunities and challenges
Gonzalo Benegas, Chengzhong Ye, Carlos Albors, et al.
Trends in Genetics (2025)
Open Access | Times Cited: 5
Evaluating the representational power of pre-trained DNA language models for regulatory genomics
Ziqi Tang, Nikunj V. Somia, Yiyang Yu, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 14
Multiplexed single-cell characterization of alternative polyadenylation regulators
Madeline H. Kowalski, Hans‐Hermann Wessels, Johannes Linder, et al.
Cell (2024) Vol. 187, Iss. 16, pp. 4408-4425.e23
Closed Access | Times Cited: 14
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Anusri Pampari, Anna Shcherbina, Evgeny Z. Kvon, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 11
Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models
E. Seitz, David M. McCandlish, Justin B. Kinney, et al.
Nature Machine Intelligence (2024) Vol. 6, Iss. 6, pp. 701-713
Closed Access | Times Cited: 9
Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation
Adam He, Charles G. Danko
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 8
SegmentNT: annotating the genome at single-nucleotide resolution with DNA foundation models
Bernardo P. de Almeida, Hugo Dalla-Torre, Guillaume Richard, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 8
Dissecting the cis-regulatory syntax of transcription initiation with deep learning
Kelly Cochran, Melody Yin, Anika Mantripragada, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 8
Interpreting cis-regulatory interactions from large-scale deep neural networks
Shushan Toneyan, Peter K. Koo
Nature Genetics (2024) Vol. 56, Iss. 11, pp. 2517-2527
Closed Access | Times Cited: 7
Rewriting regulatory DNA to dissect and reprogram gene expression
Gabriella E. Martyn, Michael T. Montgomery, H. Spencer Jones, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 14
Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity
C Cameron Yin, Sebastian M. Castillo-Hair, Gun Woo Byeon, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 6
Machine learning integrative approaches to advance computational immunology
Fabiola Curion, Fabian J. Theis
Genome Medicine (2024) Vol. 16, Iss. 1
Open Access | Times Cited: 5
Deep-learning prediction of gene expression from personal genomes
Shiron Drusinsky, Sean Whalen, Katherine S. Pollard
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 5
Current genomic deep learning models display decreased performance in cell type-specific accessible regions
Pooja Kathail, Richard W. Shuai, Ryan Chung, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 5
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
Johannes Hingerl, Laura D. Martens, Alexander Karollus, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 5
Using machine learning to enhance and accelerate synthetic biology
Kshitij Rai, Yiduo Wang, Ronan W. O’Connell, et al.
Current Opinion in Biomedical Engineering (2024) Vol. 31, pp. 100553-100553
Closed Access | Times Cited: 4
From computational models of the splicing code to regulatory mechanisms and therapeutic implications
Charlotte Capitanchik, Oscar G. Wilkins, Nils Wagner, et al.
Nature Reviews Genetics (2024)
Closed Access | Times Cited: 4
A community effort to optimize sequence-based deep learning models of gene regulation
Abdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, et al.
Nature Biotechnology (2024)
Open Access | Times Cited: 4
GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies
Zhihan Zhou, Robert Riley, Satria A. Kautsar, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access
Polygraph: a software framework for the systematic assessment of synthetic regulatory DNA elements
Avantika Lal, Laura Gunsalus, Anay Gupta, et al.
Genome biology (2025) Vol. 26, Iss. 1
Open Access
GENA-Web - GENomic Annotations Web Inference using DNA language models
Alexey Shmelev, Maxim Petrov, Dmitry Penzar, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 3
AI approaches for the discovery and validation of drug targets
Aaron Wenteler, Claudia Cabrera, Wei Wei, et al.
Cambridge Prisms Precision Medicine (2024) Vol. 2
Open Access | Times Cited: 3
Predicting cell type-specific epigenomic profiles accounting for distal genetic effects
Alan E Murphy, William Beardall, Marek Rei, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Closed Access | Times Cited: 3
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