Author

Ruyi Chen

The University of QueenslandORCID 0000-0002-8657-267XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1 Research Focus:phylogenetics / evolution· 1 Assay:protein sequence· 1 Approach:statistical model· 1 Approach:transformer / foundation model· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Gabriel FoleyiD· 2 shared Mikael Bodén AiD· 2 shared Nathan J. PalpantiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

3 top collaborators · 3 mutual co-author links

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2 shared papersBioinformatics

Gabriel FoleyORCID

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2 papers

Recent·Most cited

Learning the Language of Phylogeny with MSA Transformer

Ruyi Chen, Gabriel Foley, Mikael Bodén A

This study evaluates how MSA Transformer captures evolutionary distance and epistasis in protein sequences, showing it can reconstruct phylogenetic trees consistent with maximum likelihood methods.

Cell Systems · Nov 17, 2025Peer-reviewedBioinformatics

Codon language model scores provide information beyond protein language models for missense variant interpretation

Ruyi Chen, Nathan J. Palpant, Gabriel Foley, Mikael Bodén A

The paper shows that codon-level scores from the CaLM model provide additional information for missense variant interpretation beyond protein-level representations.

bioRxiv · Mar 12, 2025 · PreprintBioinformatics