The Programmable Biology Group
We develop novel generative algorithms and experimental modalities
to design molecules for therapeutics and bioremediation.
Our Research
Programmable Proteome Editing
We are developing peptide-guided protein therapeutics to target disordered and "undruggable" proteins. To accomplish this goal, we train language models, such as SaLT&PepPr, PepPrCLIP, and PepMLM, to de novo design peptide binders to any pathogenic protein without needing its structure, and subsequently link these binders to post-translational modification domains to edit the protein. Our current peptide-E3 ubiquitin ligase (uAbs) and peptide-deubiquitinase fusions (duAbs) represent a CRISPR-like approach for targeted protein degradation and stabilization. We are now extending this to multi-objective-guided generation of therapeutic peptides with PepTune and MOG-DFM, as well as specific targeting of dysregulated isoforms with PTM-Mamba, FusOn-pLM, and moPPIt!
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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)
PhD Students
BS (Georgia Tech '22)
BS (SUNY Binghamton '20)
BS (Duke '23)
BS (UNC '24)
BS (UC Davis '20)
BS (Fudan '25)
Masters Students
BS (Emory '24)
BS (Fudan '25)
Undergraduates
Penn '27
Duke '27
Duke '27
Princeton '27
Yale '26
Our Alumni
Graduate Students
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Tianlai (Leo) Chen, MS (Duke '24) → PhD Student at Harvard
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Zhangzhi (Fred) Peng, BS (ECJTU '24) → PhD Student at Duke
Research Associates
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Rio Watson, MS (KyotoU '23) → PhD Student at NTU Singapore
Undergraduate Students​
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Sabrina Koseki, BA (Wellesley '22) → PhD Student at Penn
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Kalyan Palepu, AB (Harvard '23) → ML Engineer at D.E. Shaw Research
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Garyk Brixi, AB (Harvard '23) → PhD Student at Stanford (NSF GRFP)
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Emma Tysinger, SB (MIT '23) → Data Science Engineer at :probabl.
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Teodora Stan, SB (MIT '24) → Software Engineer at Codex Health
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Suhaas Bhat, AB (Harvard '24) → PhD Student at Oxford (Rhodes Scholar)
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Benji Schussheim, BS (Duke '24) → Software Engineer at Microsoft
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Leyao Wang, BS (Vanderbilt '25) → MS Student at Yale
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Kseniia Kholina, BS (Duke '25) → ML Engineer at Ormoni Biosciences
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Pranay Vure, BS (Duke '25) → PhD Student at Penn (NSF GRFP)
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Rishab Pulugurta, BS (Duke '25) → Research Associate at NYU
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Srikar Kavirayuni, BS (Duke '25) → 4+1 MS Student at Duke
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Shubhika Munot, BS (Duke '25) → Research Scientist at BillionToOne
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Ishaan Mehrotra, BS (Duke '25) → 4+1 MS Student at Duke
High School Students
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Vishrut Thoutam → Undergraduate at Princeton
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Our Publications
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Check out our publications here!
Our News and Highlights
PepMLM is out at Nature Biotechnology!
One of our lab's flagship models, PepMLM, a purely target sequence-conditioned generator of peptides, has finally been published! Check out the press release here, a great news article here, and feel free to try out our model on Hugging Face and at Tamarind Bio!
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Center for Precision Engineering for Health
University of Pennsylvania
One uCity Square, Room 1012
25 North 38th Street
Philadelphia, PA 19104