Author

Deniz Oktay

ORCID 0000-0001-7104-0104Unclaimed 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

Approach:deep learning· 2 Research Focus:protein design· 2 Assay:protein sequence· 2 Research Focus:protein structure prediction· 2 Organism:E. coli· 1 Approach:large language model· 1 Organism:multiple species· 1 Research Focus:phylogenetics / evolution· 1

Frequent Co-Authors

Alexander DerryiD· 2 shared Alexander W. RivesiD· 2 shared Halil AkiniD· 2 shared Jonathan DeatoniD· 2 shared Marius WiggertiD· 2 shared Neil ThomasiD· 2 shared Nicholas SofroniewiD· 2 shared Robert VerkuiliD· 2 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 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 papersBioinformatics

Alexander DerryORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJun 4, 2026

Language Modeling Materializes a World Model of Protein Biology

Salvatore Candido, Thomas Hayes, Alexander Derry…·Alexander W. Rives

The paper uses language modeling to create a comprehensive representation of protein biology, enabling structure prediction and discovery of high-affinity protein interactions.

35 citations

protein sequencedeep learning

𝕏 PostBluesky

Synthetic BiologySciencePeer-reviewedJan 16, 2025

✦ In-depth digest

Simulating 500 million years of evolution with a language model

Thomas Hayes, Roshan Rao, Halil Akin…·Alexander W. Rives

ESM3, a 98-billion-parameter multimodal protein language model tokenized across sequence, structure, and function, designs a bright green fluorescent protein at 58% sequence identity to known fluorescent proteins.

941 citationstop 1%

multiple speciesE. coli

𝕏 PostBluesky