The Programmable Biology Group

We develop novel generative algorithms and experimental modalities

to design molecules for therapeutics and bioremediation.

Our Research

Home: Research

Discrete Generative Algorithms

We are establishing new theoretical frameworks for the generative design of molecules. We've developed discrete diffusion frameworks, such as PepTune and TR2-D2, as well as discrete flow matching methods, MOG-DFM and AReUReDi, to design Pareto-optimal therapeutic peptides across key properties, including target binding affinity, half-life, membrane permeability, and non-toxicity, all of which are supported by our state-of-the-art peptide property predictors from PeptiVerse. We’ve also pioneered new Schrödinger Bridge frameworks, including BranchSBM, EntangledSBM, and ScooBDoob, that learn controlled stochastic transport between biological states. As such, we’re now moving toward a unified design framework for cellular state and molecular dynamics control that respects branching, coupling, and metastable transitions in sequence or conformational space.

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

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

Co-Founder of Gameto, Inc.

Co-Founder of UbiquiTx, Inc.

Co-Founder of AtomBioworks, Inc.

pranam@seas.upenn.edu

Postdoctoral Fellows

PhD Students

BS (UC Davis '20)

Masters Students

Undergraduates

Our Alumni

Graduate Students

Tianlai (Leo) Chen, MS (Duke '24) → PhD Student at Harvard
Zhangzhi (Fred) Peng, BS (ECJTU '24) → PhD Student at Duke

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 Publications

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Check out our publications here!

Our News and Highlights

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15 Workshop Paper Acceptances at NeurIPS 2025!

Check out our papers accepted at NeurIPS 2025, including MemDLM (Oral at AI4Science, FPI, SPIGM, FM4LS), moPPIt-v3 (FPI, SPIGM, AI4Science), NOSIE (FPI, AI4Science, SPIGM), EntangledSBM (FPI, SPIGM), ScooBDoob (FPI, SPIGM), and uAb Screening (AI4D3)!