Author

Ada Y. Shaw

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

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

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

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersSynthetic Biology

Debora S. MarksORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

Synthetic BiologybioRxivPreprintDec 7, 2023

✦ In-depth digest

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

Pascal Notin, Aaron W. Kollasch, Daniel Ritter…·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.

207 citations

multiple speciesprotein sequence

𝕏 PostBluesky

BioinformaticsbioRxivPreprintSep 28, 2023

Removing bias in sequence models of protein fitness

Ada Y. Shaw, Hansen Spinner, June Shin…·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.

11 citations

protein sequencestatistical model

𝕏 PostBluesky