Author

James Nichols

Australian National UniversityORCID 0000-0001-9486-3648Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Approach:experimental assay· 1 Research Focus:protein design· 1 Research Focus:protein folding & dynamics· 1 Assay:protein sequence· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1 Research Focus:sequence-to-function modeling· 1

Frequent Co-Authors

Colin J. JacksoniD· 2 shared Dana S. MatthewsiD· 2 shared Mahakaran Sandhu· 2 shared Matthew A. SpenceiD· 2 shared Adam C. MateriD· 1 shared Charlotte M. MitoniD· 1 shared Eric A. StoneiD· 1 shared Joe A. KaczmarskiiD· 1 shared

Activity by Year

2024-2025 · peak 1/yr

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10 top collaborators · 40 mutual co-author links

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2 shared papersEvolutionary Biology

Colin J. JacksonORCID

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2 papers

Recent·Most cited

Evolutionary BiologybioRxivPreprintApr 12, 2025

The composition of biophysical constraints generates complex, rugged regions of protein fitness landscapes

Matthew A. Spence, Mahakaran Sandhu, Dana S. Matthews…·Colin J. Jackson

The paper introduces a graph-based measure of protein fitness landscape ruggedness and shows it concentrates at regions where dominant constraints change.

DOI 10.1101/2025.04.12.648556

protein structurestatistical model

𝕏 PostBluesky

BioinformaticsNature Machine IntelligencePeer-reviewedDec 18, 2024

Leveraging ancestral sequence reconstruction for protein representation learning

Dana S. Matthews, Matthew A. Spence, Adam C. Mater…·Colin J. Jackson

This paper introduces LASE, a method using ancestral sequence reconstruction to train protein language models with higher accuracy and faster computation than large models.

21 citations

protein sequencestatistical model

𝕏 PostBluesky