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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:

ProGen2: Exploring the boundaries of protein language models
Erik Nijkamp, Jeffrey A. Ruffolo, Eli N. Weinstein, et al.
Cell Systems (2023) Vol. 14, Iss. 11, pp. 968-978.e3
Open Access | Times Cited: 183

Showing 1-25 of 183 citing articles:

ProtGPT2 is a deep unsupervised language model for protein design
Noelia Ferruz, Steffen Schmidt, Birte Höcker
Nature Communications (2022) Vol. 13, Iss. 1
Open Access | Times Cited: 414
Genome-wide prediction of disease variant effects with a deep protein language model
Nadav Brandes, Grant Goldman, Charlotte H. Wang, et al.
Nature Genetics (2023) Vol. 55, Iss. 9, pp. 1512-1522
Open Access | Times Cited: 209
ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction
Pascal Notin, Aaron W. Kollasch, Daniel P. Ritter, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 90
Machine Learning-Guided Protein Engineering
Petr Kouba, Pavel Kohout, Faraneh Haddadi, et al.
ACS Catalysis (2023) Vol. 13, Iss. 21, pp. 13863-13895
Open Access | Times Cited: 86
Simulating 500 million years of evolution with a language model
Thomas Hayes, Roshan Rao, Halil Akin, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Closed Access | Times Cited: 86
Machine learning for functional protein design
Pascal Notin, Nathan Rollins, Yarin Gal, et al.
Nature Biotechnology (2024) Vol. 42, Iss. 2, pp. 216-228
Closed Access | Times Cited: 83
From sequence to function through structure: Deep learning for protein design
Noelia Ferruz, Michael Heinzinger, Mehmet Akdel, et al.
Computational and Structural Biotechnology Journal (2022) Vol. 21, pp. 238-250
Open Access | Times Cited: 75
Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides
Amir Pandi, David Adam, Amir Zare, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 70
Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering
Jason Yang, Francesca-Zhoufan Li, Frances H. Arnold
ACS Central Science (2024) Vol. 10, Iss. 2, pp. 226-241
Open Access | Times Cited: 64
xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein
Bo Chen, Xingyi Cheng, Li Pan, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 59
IgLM: Infilling language modeling for antibody sequence design
Richard W. Shuai, Jeffrey A. Ruffolo, Jeffrey J. Gray
Cell Systems (2023) Vol. 14, Iss. 11, pp. 979-989.e4
Open Access | Times Cited: 56
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
Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences
Jeffrey A. Ruffolo, Stephen Nayfach, Joseph P. Gallagher, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 35
Sparks of function by de novo protein design
Alexander E. Chu, Tianyu Lu, Po‐Ssu Huang
Nature Biotechnology (2024) Vol. 42, Iss. 2, pp. 203-215
Closed Access | Times Cited: 30
Simulating 500 million years of evolution with a language model
Thomas Hayes, Roshan Rao, Halil Akin, et al.
Science (2025)
Open Access | Times Cited: 28
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology
Wei Liu, Ziye Wang, Ronghui You, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 25
Computational scoring and experimental evaluation of enzymes generated by neural networks
Sean R. Johnson, Xiaozhi Fu, Sandra Viknander, et al.
Nature Biotechnology (2024)
Open Access | Times Cited: 25
Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations
Daniel J. Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 23
Protein language models are biased by unequal sequence sampling across the tree of life
Frances Ding, Jacob Steinhardt
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 22
Enhancing efficiency of protein language models with minimal wet-lab data through few-shot learning
Ziyi Zhou, Liang Zhang, Yuanxi Yu, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 22
Fine-tuning protein language models boosts predictions across diverse tasks
Robert Schmirler, Michael Heinzinger, Burkhard Rost
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 22
Addressing the antibody germline bias and its effect on language models for improved antibody design
Tobias Hegelund Olsen, Iain H. Moal, Charlotte M. Deane
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 17
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN
Robbert J. de Haas, Natalie Brunette, Alex Goodson, et al.
Proceedings of the National Academy of Sciences (2024) Vol. 121, Iss. 13
Open Access | Times Cited: 17
Democratizing protein language models with parameter-efficient fine-tuning
Samuel Sledzieski, Meghana Kshirsagar, Minkyung Baek, et al.
Proceedings of the National Academy of Sciences (2024) Vol. 121, Iss. 26
Open Access | Times Cited: 16
Recent advances in deep learning and language models for studying the microbiome
Binghao Yan, Yunbi Nam, Lingyao Li, et al.
Frontiers in Genetics (2025) Vol. 15
Open Access | Times Cited: 2
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