Author

Varun R. Shanker

Stanford UniversityORCID 0000-0003-4443-9229Unclaimed 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:drug response / drug discovery· 3 Approach:deep learning· 2 Approach:experimental assay· 2 Assay:protein sequence· 2 Organism:human· 1 Approach:large language model· 1 Organism:multiple species· 1 Assay:perturbation screen· 1

Frequent Co-Authors

Brian HieiD· 2 shared Peter S. KimiD· 2 shared Theodora U. J. BruuniD· 2 shared Bingchen YuiD· 1 shared Duo XuiD· 1 shared Franco F. FaucheriD· 1 shared Heeyoung KimiD· 1 shared John E. PakiD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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2 shared papersSynthetic Biology

Brian HieORCID

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3 papers

Recent·Most cited

MicrobiologyJournal of the American Chemical SocietyPeer-reviewedFeb 24, 2025

Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein-Protein Interactions Using Phage Display

Sijie Wang, Franco F. Faucher, Matilde Bertolini…·Matthew S. Bogyo

This paper identifies covalent cyclic peptide inhibitors targeting protein-protein interactions using phage display, demonstrating antiviral activity against SARS-CoV-2.

37 citationstop 1%

proteomicsexperimental assay

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Synthetic BiologybioRxivPreprintDec 19, 2023

Inverse folding of protein complexes with a structure-informed language model enables unsupervised antibody evolution

Varun R. Shanker, Theodora U. J. Bruun, Brian Hie, Peter S. Kim

This paper uses a structure-informed language model for unsupervised antibody evolution, achieving significant improvements in neutralization and affinity against viral variants.

18 citations

protein sequencedeep learning

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Synthetic BiologyNature BiotechnologyPeer-reviewedApr 24, 2023

✦ In-depth digest

Efficient evolution of human antibodies from general protein language models and sequence information alone

Brian Hie, Varun R. Shanker, Duo Xu…·Peter S. Kim

Consensus likelihoods from general, unsupervised protein language models evolve seven human antibodies using only a wildtype sequence and <=20 tested variants, improving binding affinity up to 160-fold.

458 citationstop 1%

humanvirus

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