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, TR2-D2, and A2D2, 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, via our state-of-the-art peptide property predictors from PeptiVerse. Our multi-objective discrete flows enable motif- and isoform specific peptide design with moPPIt and SOAPIA, as well as the ability to shrink proteins (pCoMole), construct peptide-drug conjugates (CupOFMoCA), and design future-proof antivirals (PROPHET). Finally, we're now pioneered new Schrödinger Bridge frameworks (BranchSBM and EntangledSBM) that control stochastic transport between biological states.

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@upenn.edu

Postdoctoral Fellows

PhD Students

BS (UNC '24)

BS (Baylor '21)

Masters Students

Lab Manager

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
Yesol Kim, MS (Penn '26) → Research Scientist at Broad Institute
Howard Liu, MS (Duke '26) → Research Assistant at Duke
Zachary Quinn, PhD (Duke '26) → TBD in NYC

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 Anthropic
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
Kimberly Liang, BS, MS (Penn '26) → Quantitative Trader at Citadel
Julia Vizza (Cornell '27) → Undergraduate Researcher at Cornell

Check out our publications here!

Our Publications

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Our News and Highlights

A big NeurIPS 2026, with 6 main conference acceptances!

We have 6 main conference acceptances to NeurIPS 2026: AlloGen, EntangledSBM, CupOFMoCA, pCoMole, Expanding Flow Maps, and ActFlow!

This is in addition to 9 brand-new papers accepted at workshops: TreeSBM (STODY, GEM), LOOPY (AI4DD, GEM), NimblDrift (GEM), DiFfER (SimBioChem, GEM), uAb HTS (GEM), FORGE (GEM), COMPOSE (STODY, AI4DD), AlloShift (SimBioChem), and StapleBridge (AI4DD)!