Author

William Harrigan

University of Hawaiʻi at MānoaORCID 0000-0003-2935-6863Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Organism:virus· 2 Research Focus:benchmarking· 1 Approach:machine learning (classical)· 1 Research Focus:protein design· 1 Research Focus:protein structure prediction· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Barbra D. FerrelliD· 2 shared K. Eric WommackiD· 2 shared Mahdi BelcaidiD· 2 shared Rajan SawhneyiD· 2 shared Shawn W. PolsoniD· 2 shared Thibaut DejeaniD· 2 shared Zachary D. SchreiberiD· 2 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

7 top collaborators · 21 mutual co-author links

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2 shared papersBioinformatics

Barbra D. FerrellORCID

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2 papers

Recent·Most cited

BioinformaticsGigaSciencePeer-reviewedJan 1, 2026

EXTENDING PROTEIN LANGUAGE MODELS TO A VIRAL GENOMIC SCALE USING BIOLOGICALLY INDUCED SPARSE ATTENTION

Thibaut Dejean, Barbra D. Ferrell, William Harrigan…·Mahdi Belcaid

This paper extends protein language models to a viral genomic scale using sparse attention, improving embeddings for long-range interprotein interactions.

1 citation

virusprotein sequence

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BioinformaticsPeerJPeer-reviewedSep 18, 2025

Fine-Tuning Protein Language Models Unlocks the Potential of Underrepresented Viral Proteomes

Rajan Sawhney, Barbra D. Ferrell, Thibaut Dejean…·Mahdi Belcaid

This study fine-tunes pre-trained protein language models on viral protein sequences to improve their performance on downstream tasks and representation quality.

14 citationstop 4%

virusprotein sequence

𝕏 PostBluesky