The Programmable Biology Group
We develop novel generative algorithms and experimental modalities
to design molecules for therapeutics and bioremediation.
Our 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, 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. 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.
Our Team
We program biology to do what we want.
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.
Postdoctoral Fellows
PhD (Fudan '20)
PhD (Cornell '23)
.jpeg)
MD, PhD (Yale '23)
PhD (Duke-NUS '26)
PhD Students
BS (Georgia Tech '22)
BS (Fudan '25)
BS (Duke '23)
MS (Boston U '23)
BS (UNC '24)
BS (Fudan '25)
Masters Students
BS (UC Davis '24)
BS (UC Santa Barbara '25)
Undergraduates
Penn '27
Cornell '28
Duke '27
Penn '28
Duke '27
Georgia Tech '29
Penn '28
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 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
-
Kimberly Liang, BS, MS (Penn '26) → Quantitative Trader at Citadel
​
​
Check out our publications here!
Our Publications
I'm a paragraph. Click here to add your own text and edit me. It's easy.
Our News and Highlights
More new papers at ICML 2026, including TD3B (Spotlight)!
In addition to our Main Conference Spotlight paper TD3B which design peptide agonists with discrete diffusion, we have 9 exciting new workshop papers to present in Korea: SF-Cluster (AI4Science Oral), PROPHET (GenBio Spotlight), SOAPIA (GenBio), SPROUT (GenBio), PIGEON (GenBio), CupOFLATTE (GenBio), EFlows (SPIGM), and ActFlow (SPIGM)! Please come by our posters!​
.jpg)
Center for Precision Engineering for Health
University of Pennsylvania
One uCity Square, Room 1012
25 North 38th Street
Philadelphia, PA 19104