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The Programmable Biology Group

We develop generative algorithms and experimental platforms 

for the design of next-generation biologics.

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Our Research

Home: Research

Generative Algorithms for Sequence Design

We are developing new theoretical frameworks for generative design of biologics, with the goal of enabling design directly from sequence. PepTune and MOG-DFM introduce multi-objective-guided discrete generation to design therapeutic peptides optimized across key properties like binding, half-life, membrane permeability, and non-toxicity. P2 redefines how discrete diffusion models sample sequences through planner-guided unmasking; Gumbel-Softmax brings flow matching into the categorical space for smooth generation of DNA, peptides, and proteins; finally, BranchSBM models functional perturbations as branching Schrödinger bridges, capturing how interventions induce divergent cell state transitions from a common starting point. Together, these tools expand generative modeling for next-generation therapeutic design.

Home: Our Team

Our Team

We program biology to do what we want.

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Assistant Professor of Bioengineering

Assistant Professor of Computer and Information Science

University of Pennsylvania

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 (UNC '24)

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PhD Student

BS (Fudan '25)

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Undergraduate

Penn '27

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Undergraduate

Yale '26

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PhD Student

BS (Georgia Tech '22)

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PhD Student - Duke

BS (SUNY Binghamton '20)

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Visiting PhD Student - Duke

BS (ECJTU '23)

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Undergraduate

Duke '27

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Undergraduate

Princeton '27

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PhD Student

BS (Duke '23)

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PhD Student - Duke NUS

BS (UC Davis '20)

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Visting Masters Student - Duke

BS (Emory '24)

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Undergraduate

Duke '27

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Undergraduate

Princeton '29

Our Alumni
 

Masters Students

Research Associates

  • Rio Watson, MS (KyotoU '23) → PhD Student at NTU Singapore

Undergraduate Students​

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Our News and Highlights

Thomas Wagner, not a scientist or doctor (just a dad to Max), suggested that we can use SaLT&PepPr, PepPrCLIP, and PepMLM, to design peptides to bind and degrade GFAP, the driver of AxD. With the support of Thomas and the EndAxD Foundation, that's exactly what we've been doing. 

Check out our publications here!

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Contact Us!

Center for Precision Engineering for Health

University of Pennsylvania

One uCity Square, 10th Floor
25 North 38th Street

Philadelphia, PA 19104

Home: Contact
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