Author

Bowen Jing

Massachusetts Institute of Technology

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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Bioinformatics· 3 Biophysics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Assay:protein structure· 4 Approach:deep learning· 3 Research Focus:protein design· 3 Research Focus:benchmarking· 2 Assay:protein sequence· 2 Research Focus:protein structure prediction· 2 Approach:benchmark study· 1 Approach:diffusion model· 1

Frequent Co-Authors

Bonnie BergeriD· 4 shared Adam R. KlivansiD· 2 shared Daniel J. DiaziD· 2 shared Mihir BafnaiD· 2 shared Adrina Tang· 1 shared Ali ShaibiD· 1 shared Alina Heimbrodt· 1 shared Anna SappingtoniD· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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4 shared papersBioinformatics

Bonnie BergerORCID

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Author profile →

5 papers

Recent·Most cited

Thousandfold Expansion Microscopy

Helena Hu, Donatus Krah, Antonios Ntolkeras, Sushovan Chanda, Alina Heimbrodt, Milton Mondal, Jonas Altendorf, Bowen Jing, Bonnie Berger, Ali Shaib, Silvio O. Rizzoli, Edward S. Boyden

A four-network sodium acrylate/dimethylacrylamide hydrogel, cast ionic-within-ionic without neutral re-embedding, reaches about 1000-fold linear expansion and resolves individual peptide residues on standard confocal microscopes.

bioRxiv · Jul 21, 2026 · PreprintMolecular Biology✦ In-depth digest

Promera: a unified model for biomolecular structure prediction, filtering, and design

Bowen Jing, Mihir Bafna, Daniel J. Diaz, Adam R. Klivans, Bonnie Berger

Promera is a generative model for biomolecular structure prediction, filtering, and design that improves binder filtering and controllable design compared to existing methods.

bioRxiv · Jun 10, 2026 · PreprintBioinformatics

Learning the language of protein-protein interactions

Varun Ullanat, Bowen Jing, Samuel Sledzieski, Bonnie Berger

The paper introduces MINT, a protein language model designed to model protein-protein interactions, outperforming existing models in tasks like binding affinity prediction and mutational effect estimation.

Nature Communications · Jan 7, 2026Peer-reviewedBioinformatics

Advancing Protein Ensemble Predictions Across the Order-Disorder Continuum

Michele Invernizzi, Sandro Bottaro, Julian O. Streit, Bruno Trentini, Niccolò Alberto Elia Venanzi, Danny Reidenbach, Youhan Lee, Christian Dallago, Hassan Sirelkhatim, Bowen Jing, Fabio Airoldi, Kresten Lindorff‐Larsen, Carlo Fisicaro, Kamil Tamiola

The paper introduces a benchmark for evaluating protein ensemble generators across ordered and disordered proteins and presents a new model that improves performance on disordered regions.

bioRxiv · Oct 18, 2025 · PreprintBiophysics

Generating functional and multistate proteins with a multimodal diffusion transformer

Bowen Jing, Anna Sappington, Mihir Bafna, Ravi Shah, Adrina Tang, Rohith Krishna, Adam R. Klivans, Daniel J. Diaz, Bonnie Berger

This paper introduces ProDiT, a multimodal diffusion model for generating functional proteins with multiple states, demonstrating its ability to design proteins with specific molecular functions and allosteric regulation.

bioRxiv · Sep 3, 2025 · PreprintBioinformatics