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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:

Large language models improve annotation of prokaryotic viral proteins
Zachary Flamholz, Steven J. Biller, Libusha Kelly
Nature Microbiology (2024) Vol. 9, Iss. 2, pp. 537-549
Open Access | Times Cited: 28

Showing 1-25 of 28 citing articles:

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 18
Multimodal Large Language Models in Healthcare: Applications, Challenges, and Future Outlook (Preprint)
Rawan AlSaad, Alaa Abd‐Alrazaq, Sabri Boughorbel, et al.
Journal of Medical Internet Research (2024) Vol. 26, pp. e59505-e59505
Open Access | Times Cited: 6
Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment
Alexandre Boulay, Audrey Leprince, François Enault, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2025)
Open Access
DPFunc: accurately predicting protein function via deep learning with domain-guided structure information
Wenkang Wang, Yunyan Shuai, Min Zeng, et al.
Nature Communications (2025) Vol. 16, Iss. 1
Open Access
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
Deep Learning for Antimicrobial Peptides: Computational Models and Databases
Xiangrun Zhou, Guixia Liu, Shuyuan Cao, et al.
Journal of Chemical Information and Modeling (2025)
Closed Access
DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models
Robby Concha-Eloko, Michiel Stock, Bernard De Baets, et al.
PLoS Computational Biology (2024) Vol. 20, Iss. 8, pp. e1011831-e1011831
Open Access | Times Cited: 3
Modern microbiology: Embracing complexity through integration across scales
A. Murat Eren, Jillian F. Banfield
Cell (2024) Vol. 187, Iss. 19, pp. 5151-5170
Open Access | Times Cited: 3
Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy
Susanna R. Grigson, Sarah K. Giles, Robert A. Edwards, et al.
Clinical Infectious Diseases (2023) Vol. 77, Iss. Supplement_5, pp. S352-S359
Open Access | Times Cited: 10
Beware of Data Leakage from Protein LLM Pretraining
Leon Hermann, Tobias Fiedler, Hoang An Nguyen, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 2
Adversarial Text Purification: A Large Language Model Approach for Defense
Raha Moraffah, Shubh Khandelwal, Amrita Bhattacharjee, et al.
Lecture notes in computer science (2024), pp. 65-77
Closed Access | Times Cited: 1
Ten computational challenges in human virome studies
Yifan Wu, Yousong Peng
Virologica Sinica (2024) Vol. 39, Iss. 6, pp. 845-850
Open Access | Times Cited: 1
Assessing parameter efficient methods for pre-trained language model in annotating scRNA-seq data
Yucheng Xia, Yuhang Liu, Tianhao Li, et al.
Methods (2024) Vol. 228, pp. 12-21
Closed Access | Times Cited: 1
Interpretably deep learning amyloid nucleation by massive experimental quantification of random sequences
Michael Thompson, Mariano Martín, Trinidad Sanmartín Olmo, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Closed Access | Times Cited: 1
GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data
Guomei Fan, Qinglan Sun, Yan Sun, et al.
Nucleic Acids Research (2024) Vol. 53, Iss. D1, pp. D763-D771
Open Access | Times Cited: 1
Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models
Wenhui Li, Xianyue Jiang, Wuke Wang, et al.
Nature Communications (2024) Vol. 15, Iss. 1
Open Access | Times Cited: 1
Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models
Wenhui Li, Xianyue Jiang, Wuke Wang, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access
Hugging Face's impact on medical applications of artificial intelligence
Matteo Marco Riva, Tommaso Lorenzo Parigi, Federica Ungaro, et al.
Deleted Journal (2024) Vol. 1, pp. 100003-100003
Open Access
Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats
Steven J. Biller, Matthew J. Ryan, Jasmine Li, et al.
Research Square (Research Square) (2024)
Closed Access
Protein Set Transformer: A protein-based genome language model to power high diversity viromics
Cody Martin, Anthony Gitter, Karthik Anantharaman
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access
Protein Set Transformer: A protein-based genome language model to power high diversity viromics
Karthik Anantharaman, Cody Martin, Anthony Gitter
Research Square (Research Square) (2024)
Closed Access
Hyena architecture enables fast and efficient protein language modeling
Y. T. Zhang, Bian Bian, Manabu Okumura
iMetaOmics. (2024)
Closed Access
Advancements and Applications of Generative AI in Healthcare
Sandeep Chataut, Sandesh Bhatta, Bishwambhar Dahal, et al.
European Journal of Theoretical and Applied Sciences (2024) Vol. 2, Iss. 6, pp. 873-895
Closed Access
Deep functional profiling of gene sets using Large Language Models: A blueprint for tailored, context-aware functional annotation
Taushif Khan, Marina Yurieva, Basirudeen Syed Ahamed Kabeer, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Closed Access
An unsupervised framework for comparing SARS-CoV-2 protein sequences using LLMs
Sayantani B. Littlefield, Roy H. Campbell
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access
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