The Programmable Biology Group

We develop generative algorithms and experimental protein design platforms

for genome, proteome, and cell engineering.

Our Research

Home: Research

Programmable Proteome Editing

We are developing peptide-guided protein therapeutics to target disordered and "undruggable" proteins. To accomplish this goal, we train generative 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 specific targeting of dysregulated isoforms with PTM-Mamba, FusOn-pLM, and moPPIt!

Copy of Copy of Copy of Copy of Copy of Copy of Untitled recovered (3).png

Home: Our Team

Our Team

We program biology to do what we want.

Pranam Chatterjee

Assistant Professor of Biomedical Engineering

Assistant Professor of Computer Science

Assistant Professor of Biostatistics and Bioinformatics

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

Co-Founder of Gameto, Inc.

Co-Founder of UbiquiTx, Inc.

Lin Zhao

Postdoctoral Fellow

PhD (Fudan '20)

405290000_385500213809287_86966841138566

Fred Peng

PhD Student

BS (ECJTU '23)

Yinuo Zhang

PhD Student - Duke NUS

BS (UC Davis '20)

Howard Liu

Masters Student

BS (Emory '24)

Lauren Hong

PhD Student

BS (Georgia Tech '22)

Tian Wang

PhD Student

BS (UNC '24)

Tong Chen

Incoming PhD Student

BS (Fudan '25)

Shrey Goel

Undergraduate

Duke '27

Sophie Vincoff

PhD Student

BS (Duke '23)

Zachary Quinn

PhD Student

BS (SUNY Binghamton '20)

Rio Watson

Research Associate

MS (Kyoto '25)

Divya Srijay

Undergraduate

Duke '27

Sophia Tang

Undergraduate

Penn '27

Vatsal Parikh

Undergraduate

Princeton '27

Vishrut Thoutam

Undergraduate

Princeton '29

Our Alumni

Masters Students

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

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 Updates and Progress

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.