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· 2 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:drug response / drug discovery· 2 Assay:protein sequence· 2 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Approach:genetic perturbation / CRISPR· 1 Approach:graph neural network· 1

Frequent Co-Authors

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

Activity by Year

2019-2025 · peak 1/yr

Co-Author Collaboration Network

7 top collaborators · 10 mutual co-author links

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2 shared papersBioengineering

Manvitha R. Ponnapati

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3 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

𝕏 PostBluesky

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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BioengineeringbioRxivPreprintApr 26, 2019

Robust Genome Editing of Single-Base PAM Targets with Engineered ScCas9 Variants

Pranam Chatterjee, Noah Jakimo, Joseph M. Jacobson

This study engineers ScCas9 variants to enable robust genome editing at single-base PAM targets with improved activity and fidelity.

DOI 10.1101/620351

experimental assaygenetic perturbation / CRISPR

𝕏 PostBluesky