Author

Joseph M. Jacobson

Massachusetts Institute of TechnologyORCID 0000-0002-1332-3197Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioengineering· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Approach:graph neural network· 1 Organism:human· 1 Approach:large language model· 1 Approach:optimal transport· 1 Research Focus:protein design· 1

Frequent Co-Authors

Manvitha R. Ponnapati· 2 shared Allan dos Santos CostaiD· 1 shared Brian LynchiD· 1 shared Edward S. BoydeniD· 1 shared Pranam ChatterjeeiD· 1 shared Sapna SinhaiD· 1 shared

Activity by Year

2021-2025 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 9 mutual co-author links

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2 shared papersBioengineering

Manvitha R. Ponnapati

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2 papers

Recent·Most cited

BioengineeringbioRxivPreprintSep 27, 2025

Designing proteins with reduced T-cell epitopes through policy optimization

Manvitha R. Ponnapati, Sapna Sinha, Brian Lynch…·Joseph M. Jacobson

The paper designs proteins with reduced T-cell epitopes using deep generative models and policy optimization to improve immune compatibility across MHC Class I alleles.

DOI 10.1101/2025.09.27.678937

humanprotein sequence

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Synthetic BiologybioRxivPreprintJun 2, 2021

Distillation of MSA Embeddings to Folded Protein Structures with Graph Transformers

Allan dos Santos Costa, Manvitha R. Ponnapati, Joseph M. Jacobson, Pranam Chatterjee

The paper introduces a graph transformer architecture that uses MSA embeddings to predict protein structures directly from sequences.

5 citations

protein sequencegraph neural network

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