Author

Ada Y. Shaw

Harvard UniversityORCID 0000-0002-5283-9559Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Organism:multiple species· 1 Research Focus:protein design· 1 Assay:protein structure· 1

Frequent Co-Authors

Debora S. MarksiD· 2 shared Hansen Spinner· 2 shared Nathan J. RollinsiD· 2 shared Aaron W. KollaschiD· 1 shared Daniel RitteriD· 1 shared Dinko Franceschi· 1 shared Jonathan FrazeriD· 1 shared June ShiniD· 1 shared

Activity by Year

2023-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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2 shared papersSynthetic Biology

Debora S. MarksORCID

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2 papers

Recent·Most cited

ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction

Pascal Notin, Aaron W. Kollasch, Daniel Ritter, Lood van Niekerk, Steffan B. Paul, Hansen Spinner, Nathan J. Rollins, Ada Y. Shaw, Ruben Weitzman, Jonathan Frazer, Mafalda Dias, Dinko Franceschi, Rose Orenbuch, Yarin Gal, Debora S. Marks

ProteinGym unifies over 250 deep mutational scans and ~65k clinical variants to benchmark over 70 models in zero-shot and supervised settings; TranceptEVE ranks best overall.

bioRxiv · Dec 7, 2023 · PreprintSynthetic Biology✦ In-depth digest

Removing bias in sequence models of protein fitness

Ada Y. Shaw, Hansen Spinner, June Shin, Sarah F. Gurev, Nathan J. Rollins, Debora S. Marks

This paper introduces a de-biasing method for sequence models of protein fitness to improve predictions of functional variants far from natural sequences.

bioRxiv · Sep 28, 2023 · PreprintBioinformatics