Group Members


Join Us
<a href=Marinka Zitnik" />

Marinka Zitnik

Associate Professor

<a href=Shvat Messica" />

Shvat Messica

PhD Student
Harvard AIM

<a href=Yepeng Huang" />

Yepeng Huang

PhD Student
Harvard BBS

<a href=Walker Rickord " />

Walker Rickord

PhD Student
Harvard-MIT HST

<a href=Ada Fang" />

Ada Fang

PhD Student
Harvard CCB

<a href=Kevin Li" />

Kevin Li

PhD Student
Harvard-MIT HST

<a href=Lukas Fesser" />

Lukas Fesser

PhD Student
Harvard Applied Mathematics

<a href=Michael Sun" />

Michael Sun

PhD Student
MIT EECS

<a href=Robert Calef" />

Robert Calef

PhD Student
MIT EECS

<a href=Valentina Giunchiglia" />

Valentina Giunchiglia

PhD Student
Imperial College London

<a href=Zhenglun Kong" />

Zhenglun Kong

Postdoctoral Fellow

<a href=Boyang Fu" />

Boyang Fu

Postdoctoral Fellow

<a href=Grey Kuling" />

Grey Kuling

Postdoctoral Fellow
Curriculum Fellow

<a href=Intae Moon" />

Intae Moon

Postdoctoral Fellow

<a href=Michelle M. Li" />

Michelle M. Li

Postdoctoral Fellow
Harvard Berkowitz Fellow

<a href=Minsheng Hao" />

Minsheng Hao

Postdoctoral Fellow

<a href=Ruth Johnson" />

Ruth Johnson

Postdoctoral Fellow
Harvard Berkowitz Fellow

<a href=Shanghua Gao" />

Shanghua Gao

Postdoctoral Fellow

<a href=Xiang Lin" />

Xiang Lin

Postdoctoral Fellow

<a href=Xiaorui Su" />

Xiaorui Su

Postdoctoral Fellow

<a href=Ying Jin" />

Ying Jin

Postdoctoral Fellow
Harvard Data Science Fellow

<a href=Aarthi Venkat" />

Aarthi Venkat

Postdoctoral Fellow
Eric and Wendy Schmidt Fellow

<a href=Pengwei Sui" />

Pengwei Sui

Research Associate

<a href=Michelle Dai" />

Michelle Dai

Research Associate

<a href=Ayush Noori" />

Ayush Noori

Undergraduate Researcher
Harvard

<a href=Richard Zhu" />

Richard Zhu

Undergraduate Researcher
Harvard

<a href=Iñaki Arango" />

Iñaki Arango

Undergraduate Researcher
Harvard

<a href=Lucas Vittor" />

Lucas Vittor

Researcher

<a href=Joaquín Polonuer" />

Joaquín Polonuer

Visiting Student

<a href=Kexin Chen" />

Kexin Chen

Visiting PhD Student

Lab alumni

2025:
  • Wanxiang Shen (Postdoctoral Fellow → Assistant Professor, Zhejiang University)
  • Andrew Shen (Associate → Biomedical Data Science PhD Student, Stanford University)
  • Yasha Ektefaie (PhD Student → Eric and Wendy Schmidt Fellow, Broad Institute)
2024:
  • Zaixi Zhang (Visiting PhD Student → Postdoctoral Fellow, Princeton University)
  • Owen Queen (Associate → Computer Science PhD Student, Stanford University)
  • Varun Ullanat (Associate → Computer Science PhD Student, MIT)
  • Ivy Liang (Harvard College)
  • Tianlong Chen (Postdoctoral Fellow → Assistant Professor, University of North Carolina at Chapel Hill)
2023:
  • Guadalupe Gonzalez (Visiting PhD Student → Research Scientist, Prescient Design, Genentech, Roche)
  • Tom Cobley (Undergraduate Researcher → Machine Learning Engineer, Google DeepMind)
  • Ziyuan Zhao (Undergraduate Researcher → Systems Biology PhD Student, Harvard Medical School)
  • Nicholas Ho (Undergraduate Researcher → Computer Science PhD Student, Carnegie Mellon University)
  • Yepeng Huang (Graduate Researcher at Harvard Chan → Biological and Medical Sciences PhD Student, Harvard Medical School)
  • Marissa Sumathipala (Undergraduate Researcher at Harvard College; Gates Cambridge Scholarship; Churchill Scholarship; Cambridge University → Neuroscience PhD Student, Harvard University)
  • Julia Balla (Undergraduate Researcher at MIT → Computer Science PhD Student, MIT)
  • Jiali Cheng (Undergraduate Researcher → Computer Science PhD Student, UMass Lowell)
  • Isuru Herath (Undergraduate Researcher → Data Scientist, Merck)
  • Jean-Guillaume Brasier (Harvard IACS Graduate Student → Data Scientist, Moderna)
2022:
  • Marie Zhang (HMS)
  • Man Qing Liang (HMS → Data Scientist, Dandelion)
  • Payal Chandak (Undergraduate Researcher → Harvard-MIT HST PhD Student, Harvard University & MIT)
  • Xiang Zhang (Postdoctoral Fellow → Assistant Professor, UNC Charlotte)
  • Chirag Agarwal (Postdoctoral Fellow, HMS → Assistant Professor, University of Virginia)
  • Josh Pan (Postdoctoral Fellow, Broad Institute → Research Scientist, DeepMind)
  • Michelle Lu (Harvard College)
  • Raunak Chowdhuri (MIT)
  • Marie Zhang (HMS)
  • Satvik Tripathi (Undergraduate Researcher, Drexel University)
  • Varun Tekur (Undergraduate Researcher)
  • Lydia Fozo (Undergraduate Researcher, Johns Hopkins University)
2021:
  • Kexin Huang (Harvard Chan → Computer Science PhD Student, Stanford University)
  • Haoxin Li (Harvard Chan)
  • Yucong Lin (Harvard Chan → Beijing Institute of Technology)
  • Mert Erden (Tufts University)
  • Jingyi Liu (HMS)
2020:
  • Yujie Shao (HMS)
  • Stone Chen (HMS)
  • Kathleen Sucipto (HMS)
  • Min Jean Cho (Undergraduate Researcher, Brown University)

Latest News

Jun 2025:   One Patient, Many Contexts: Scaling Medical AI

Jun 2025:   ToolUniverse - 211+ Tools for "AI Scientist" Agents

ToolUniverse now offers access to over 211 cutting-edge biological and medical tools, all integrated with Model Context Protocol (MCP). Any “AI Scientist” agent can tap into these tools for biomedical research. [Tutorial] [ToolUniverse] [TxAgent]

May 2025:   What Perturbation Can Reverse Disease Effects?

In press at Nature Biomedical Engineering: PDGrapher AI predicts chemicals to reverse disease phenotypic effects — with applications to drug target identification.

May 2025:   Decision Transformers for Cell Reprogramming

New preprint: Decision transformers for generating reach-avoid policies in sequential decision making — with applications from robotics to cell reprogramming.

May 2025:   COMPASS: Immunotherapy Outcome Prediction

Apr 2025:   ATOMICA and TxAgent on the Kempner Blog

Check out the Kempner Deeper Learning posts describing our latest ATOMICA and TxAgent AI models.

Apr 2025:   ATOMICA - A Universal Model of Molecular Interactions

Mar 2025:   On Biomedical AI in Harvard Gazette

Read about AI in medicine in the latest Harvard Gazette and New York Times.

Mar 2025:   TxAgent: AI Agent for Therapeutic Reasoning

TxAgent is an AI agent for therapeutic reasoning that consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights. [Project website] [TxAgent] [ToolUniverse]

Mar 2025:   Multimodal AI predicts clinical outcomes of drug combinations from preclinical data

Mar 2025:   KGARevion: AI Agent for Knowledge-Intensive Biomedical QA

KGARevion is an AI agent designed for complex biomedical QA that integrates the non-codified knowledge of LLMs with the structured, codified knowledge found in knowledge graphs. [ICLR 2025 publication]

Feb 2025:   MedTok: Unlocking Medical Codes for GenAI

Meet MedTok, a multimodal medical code tokenizer that transforms how AI understands structured medical data. By integrating textual descriptions and relational contexts, MedTok enhances tokenization for transformer-based models—powering everything from EHR foundation models to medical QA. [Project website]

Feb 2025:   What If You Could Rewrite Biology? Meet CLEF

What if we could anticipate molecular and medical changes before they happen? Introducing CLEF, an approach for counterfactual generation in biological and medical sequence models. [Project website]

Feb 2025:   Digital Twins as Global Health and Disease Models

Jan 2025:   LLM and KG+LLM agent papers at ICLR

Jan 2025:   Artificial Intelligence in Medicine 2

Excited to share our new graduate course on Artificial Intelligence in Medicine 2.

Jan 2025:   ProCyon AI Highlighted by Kempner

Thanks to Kempner Institute for highlighting our latest research, ProCyon, our protein-text foundation model for modeling protein functions.

Jan 2025:   AI Design of Proteins for Therapeutics

Dec 2024:   Unified Clinical Vocabulary Embeddings

New paper: A unified resource provides a new representation of clinical knowledge by unifying medical vocabularies. (1) Phenotype risk score analysis across 4.57 million patients, (2) Inter-institutional clinician panels evaluate alignment with clinical knowledge across 90 diseases and 3,000 clinical codes.

Zitnik Lab  ·  Artificial Intelligence in Medicine and Science  ·  Harvard  ·  Department of Biomedical Informatics