The Programmable Biology Group

We develop generative algorithms and experimental platforms

for the design of next-generation biologics.

Our Research

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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.

Pranam Chatterjee

Assistant Professor of Bioengineering

Assistant Professor of Computer and Information Science

University of Pennsylvania

Vishrut Thoutam

Undergraduate

Princeton '29

Our Alumni

Masters Students

Tianlai (Leo) Chen, MS (Duke '24) → PhD Student at Harvard

Research Associates

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

Undergraduate Students

Sabrina Koseki, BA (Wellesley '22) → PhD Student at Penn
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) → Data Science Engineer at :probabl.
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
Leyao Wang, BS (Vanderbilt '25) → MS Student at Yale
Kseniia Kholina, BS (Duke '25) → ML Engineer at Ormoni Biosciences
Pranay Vure, BS (Duke '25) → PhD Student at Penn (NSF GRFP)
Rishab Pulugurta, BS (Duke '25) → Research Associate at NYU
Srikar Kavirayuni, BS (Duke '25) → 4+1 MS Student at Duke
Shubhika Munot, BS (Duke '25) → Research Scientist at BillionToOne
Ishaan Mehrotra, BS (Duke '25) → 4+1 MS Student at Duke

Our News and Highlights

The TODAY Show shares our part in finding a cure for Alexander disease!

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

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