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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:

Codon language embeddings provide strong signals for use in protein engineering
Carlos Outeiral, Charlotte M. Deane
Nature Machine Intelligence (2024) Vol. 6, Iss. 2, pp. 170-179
Open Access | Times Cited: 24

Showing 24 citing articles:

Sequence modeling and design from molecular to genome scale with Evo
Eric Nguyen, Michael Poli, Matthew G. Durrant, et al.
Science (2024) Vol. 386, Iss. 6723
Open Access | Times Cited: 55
Nucleotide Transformer: building and evaluating robust foundation models for human genomics
Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza‐Revilla, et al.
Nature Methods (2024)
Open Access | Times Cited: 36
Genomic language model predicts protein co-regulation and function
Yunha Hwang, Andre Cornman, Elizabeth H. Kellogg, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 32
Leveraging mRNA technology for antigen based immuno-oncology therapies
Charalampos S. Floudas, Siranush Sarkizova, Michele Ceccarelli, et al.
Journal for ImmunoTherapy of Cancer (2025) Vol. 13, Iss. 1, pp. e010569-e010569
Open Access | Times Cited: 2
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: 12
CodonTransformer: a multispecies codon optimizer using context-aware neural networks
Adibvafa Fallahpour, Vincent Gureghian, Guillaume J. Filion, et al.
Nature Communications (2025) Vol. 16, Iss. 1
Open Access | Times Cited: 1
Interrogating nucleotide sequences with AI to understand codon usage patterns
Assaf Elazar, Steve Mathew, M. Madan Babu
Proceedings of the National Academy of Sciences (2025) Vol. 122, Iss. 7
Open Access
Enzyme functional classification using artificial intelligence
Hyung Kyu Kim, H. Ji, Gi Bae Kim, et al.
Trends in biotechnology (2025)
Closed Access
Paying attention to the SARS-CoV-2 dialect : a deep neural network approach to predicting novel protein mutations
Magdalyn E. Elkin, Xingquan Zhu
Communications Biology (2025) Vol. 8, Iss. 1
Open Access
Discovery of antimicrobial peptides from Bacillus genomes against phytopathogens with deep learning models
Huan Su, Mengli Gu, Zechao Qu, et al.
Chemical and Biological Technologies in Agriculture (2025) Vol. 12, Iss. 1
Open Access
Non-Viral RNA Therapies for Non-Small Cell Lung Cancer and Their Corresponding Clinical Trials
Palas Balakdas Tiwade, Vincent Fung, Rachel VanKeulen-Miller, et al.
Molecular Pharmaceutics (2025)
Closed Access
DeepSeMS: a large language model reveals hidden biosynthetic potential of the global ocean microbiome
Na Jiao, Tingjun Xu, Yuwei Yang, et al.
(2025)
Closed Access
TEMPRO: nanobody melting temperature estimation model using protein embeddings
Jerome Anthony E. Alvarez, Scott N. Dean
Scientific Reports (2024) Vol. 14, Iss. 1
Open Access | Times Cited: 2
ML-driven design of 3' UTRs for mRNA stability
Alyssa Morrow, Ashley Thornal, Elise D. Flynn, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 2
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
Yongxin Ji, Jiayu Shang, Jiaojiao Guan, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Closed Access | Times Cited: 1
CaLMPhosKAN: Prediction of General Phosphorylation Sites in Proteins via Fusion of Codon-Aware Embeddings with Amino Acid-Aware Embeddings and Wavelet-based Kolmogorov–Arnold Network
Pawel Pratyush, C. Carrier, Suresh Pokharel, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 1
Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder
Aashutosh Girish Boob, Shih‐I Tan, A. A. Zaidi, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 1
A Large-Scale Foundation Model for RNA Function and Structure Prediction
S. Zou, Tianhua Tao, Parvez Mahbub, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 1
RNAGenesis: Foundation Model for Enhanced RNA Sequence Generation and Structural Insights
Zaixi Zhang, Chao Liu, Ruofan Jin, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 1
Predicting gene sequences with AI to study codon usage patterns
Tomer Sidi, Shir Bahiri-Elitzur, Tamir Tuller, et al.
Proceedings of the National Academy of Sciences (2024) Vol. 122, Iss. 1
Open Access | Times Cited: 1
Integration of protein and coding sequences enables mutual augmentation of the language model
Heng-Rui Zhao, Meng‐Ting Cheng, Zhu Jinhua, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access
Are Genomic Language Models All You Need? Exploring Genomic Language Models on Protein Downstream Tasks
Sam Boshar, Evan Trop, Bernardo P. de Almeida, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access
HaloClass: Salt-Tolerant Protein Classification with Protein Language Models
Kush Narang, Abhigyan Nath, William Hemstrom, et al.
The Protein Journal (2024) Vol. 43, Iss. 6, pp. 1035-1044
Open Access
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
Yongxin Ji, Jiayu Shang, Jiaojiao Guan, et al.
GigaScience (2024) Vol. 13
Open Access
GOPhage: protein function annotation for bacteriophages by integrating the genomic context
Jiaojiao Guan, Jiayu Shang, Cheng Peng, et al.
Briefings in Bioinformatics (2024) Vol. 26, Iss. 1
Open Access
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