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The Programmable Biology Group

We integrate generative algorithms and experimental protein design to create programmable platforms for genome, proteome, and cell engineering.

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Our Research

Home: Research

Programmable Proteome Editing

We are developing peptide-guided protein therapeutics to target disordered and "undruggable" proteins. To accomplish this goal, we train generative language models, such as SaLT&PepPrPepPrCLIPPepMLM, and moPPIt to de novo design "guide" peptide binders to any pathogenic protein without needing its structure, and subsequently link these binders to post-translational modification domains to edit the protein. Our current peptide-E3 ubiquitin ligase fusions represent a CRISPR-like approach for targeted protein degradation. But why stop there? Our goal is to define the engineering and delivery principles for truly programmable proteome editing outcomes, including degradation, phosphorylation, glycosylation, acetylation, and beyond.

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Home: Our Team

Our Team

We program biology to do what we want.

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Assistant Professor of Biomedical Engineering

Assistant Professor of Computer Science

Assistant Professor of Biostatistics and Bioinformatics

MIT (SB '16, SM '18, PhD '20)

Co-Founder of Gameto, Inc.

Co-Founder of UbiquiTx, Inc.

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Postdoctoral Fellow

PhD (Fudan '20)

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PhD Student

BS (ECJTU '23)

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PhD Student - Duke NUS

BS (UC Davis '20)

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Undergraduate

Duke '25

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Undergraduate

Duke '25

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Undergraduate

Duke '27

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Visiting Undergraduate

Vanderbilt '25

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PhD Student

BS (Georgia Tech '22)

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PhD Student

BS (UNC '24)

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Masters Student

BS (Duke Kunshan '23)

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Undergraduate

Duke '25

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Undergraduate

Duke '25

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Undergraduate

Duke '27

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Visiting Undergraduate

Penn '27

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PhD Student

BS (Duke '23)

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PhD Student

BS (SUNY Binghamton '20)

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Research Associate 
MS (Kyoto U '23)

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Undergraduate

Duke '25

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Undergraduate

Duke '25

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Visiting Undergraduate

Fudan '25

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Visiting High School Student

High Technology HS '25

Our Alumni
 

  • Sabrina Koseki, BA (Wellesley '22) → Microbiologist at Mass Dept of Health

  • Kalyan Palepu, AB (Harvard '23) → ML Engineer at D.E. Shaw Research 

  • Garyk Brixi, AB (Harvard '23) → PhD Student at Stanford (NSF GRFP) 

  • Emma Tysinger, SB (MIT '23) → M.Eng. Student at MIT

  • Teodora Stan, SB (MIT '24) → Software Engineer at Codex Health

  • Suhaas Bhat, AB (Harvard '24) → PhD Student at Oxford (Rhodes Scholar)

  • Benji Schussheim, BS (Duke '24)  → Software Engineer at Microsoft

Our Updates and Progress

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Read our new summer preprints!

We've been hard at work over the summer, with new papers describing motif-specific peptide binder generation with moPPIt, metal binding prediction with MetaLATTE, a protein language model for fusion oncoproteins (FusOn-pLM), and a new duAb system for protein stabilization!

Check out our publications here!

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Contact Us!

Feel free to reach out and

learn more about our work!

Center for Advanced Genomic Technologies
Fitzpatrick Center (CIEMAS), Room 2339A
101 Science Drive
Duke University
Durham, NC 27705

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