Author

Sarthak Jain

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Synthetic Biology· 2

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Assay:protein sequence· 2 Organism:E. coli· 1 Approach:experimental assay· 1 Approach:large language model· 1 Organism:multiple species· 1 Research Focus:protein design· 1 Assay:protein structure· 1

Frequent Co-Authors

Aadyot Bhatnagar· 2 shared Ali MadaniiD· 2 shared Jeffrey A. RuffoloiD· 2 shared Joel Beazer· 2 shared Alexander M. HoffnagleiD· 1 shared Kyle Ching· 1 shared Michael Martyn· 1 shared Samuel C. Curran· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

9 top collaborators · 36 mutual co-author links

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2 shared papersSynthetic Biology

Aadyot Bhatnagar

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2 papers

Recent·Most cited

E1: Retrieval-Augmented Protein Encoder Models

Sarthak Jain, Joel Beazer, Jeffrey A. Ruffolo, Aadyot Bhatnagar, Ali Madani

The paper introduces Profluent-E1, retrieval-augmented protein language models that improve performance by conditioning on homologous sequences, achieving state-of-the-art results in fitness prediction and contact-map prediction.

bioRxiv · Nov 12, 2025 · PreprintSynthetic Biology

Scaling unlocks broader generation and deeper functional understanding of proteins

Aadyot Bhatnagar, Sarthak Jain, Joel Beazer, Samuel C. Curran, Alexander M. Hoffnagle, Kyle Ching, Michael Martyn, Stephen Nayfach, Jeffrey A. Ruffolo, Ali Madani

Scaling sparse Mixture-of-Experts protein language models up to 46B parameters on 1.5T curated tokens broadens viable protein generation across families and amplifies gains from laboratory preference alignment.

neural information processing systems · Jan 1, 2025Peer-reviewedSynthetic Biology✦ In-depth digest