Group Members


Join Us
<a href=Marinka Zitnik" />

Marinka Zitnik

Assistant Professor

<a href=Kevin Li" />

Kevin Li

PhD Student
Harvard-MIT HST

<a href=Ada Fang" />

Ada Fang

PhD Student
Harvard CCB

<a href=Robert Calef" />

Robert Calef

PhD Student
MIT EECS

<a href=Yasha Ektefaie" />

Yasha Ektefaie

PhD Student
Harvard BIG

<a href=Valentina Giunchiglia" />

Valentina Giunchiglia

PhD Student
Imperial College London

<a href=Yepeng Huang" />

Yepeng Huang

PhD Student
Harvard BBS

<a href=Zhenglun Kong" />

Zhenglun Kong

Postdoctoral Fellow

<a href=Grey Kuling" />

Grey Kuling

Postdoctoral Fellow
Curriculum Fellow

<a href=Intae Moon" />

Intae Moon

Postdoctoral Fellow

<a href=Jason Poulos" />

Jason Poulos

Postdoctoral Fellow
Brigham and Women's Hospital

<a href=Michelle M. Li" />

Michelle M. Li

Postdoctoral Fellow
Harvard Berkowitz Fellow

<a href=Ruth Johnson" />

Ruth Johnson

Postdoctoral Fellow
Harvard Berkowitz Fellow

<a href=Shanghua Gao" />

Shanghua Gao

Postdoctoral Fellow

<a href=Wanxiang Shen" />

Wanxiang Shen

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=Pengwei Sui" />

Pengwei Sui

Research Associate

<a href=Alejandro Velez Arce" />

Alejandro Velez Arce

Research Associate

<a href=Michelle Dai" />

Michelle Dai

Research Associate

<a href=Andrew Shen" />

Andrew Shen

Graduate Researcher

<a href=Richard Zhu" />

Richard Zhu

Undergraduate Researcher
Harvard

<a href=Ayush Noori" />

Ayush Noori

Undergraduate Researcher
Harvard

Lab alumni

2024:
  • Zaixi Zhang (Visiting PhD Student → Postdoctoral Fellow, Princeton University)
  • Owen Queen (Research Associate → Computer Science PhD Student, Stanford University)
  • Varun Ullanat (HMS)
  • 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

Oct 2024:   Activity Cliffs in Molecular Property Prediction

Oct 2024:   Knowledge Graph Agent for Medical Reasoning

Sep 2024:   Three Papers Accepted to NeurIPS

Exciting projects include a unified multi-task time series model, a flow-matching approach for generating protein pockets using geometric priors, and a tokenization method that produces invariant molecular representations for integration into large language models.

Sep 2024:   TxGNN Published in Nature Medicine

Graph foundation model for drug repurposing published in Nature Medicine. [Harvard Gazette] [Harvard Medicine News] [Forbes] [NVIDIA]

Aug 2024:   Graph AI in Medicine

Excited to share a new perspective on Graph Artificial Intelligence in Medicine in Annual Reviews.

Aug 2024:   How Proteins Behave in Context

Harvard Medicine News on our new AI tool that captures how proteins behave in context. Kempner Institute on how context matters for foundation models in biology.

Jul 2024:   PINNACLE in Nature Methods

PINNACLE contextual AI model is published in Nature Methods. Paper. Research Briefing. Project website.

Jul 2024:   Digital Twins as Global Health and Disease Models of Individuals

Paper on digitial twins outlining strategies to leverage molecular and computational techniques to construct dynamic digital twins on the scale of populations to individuals.

Jul 2024:   Three Papers: TrialBench, 3D Structure Design, LLM Editing

Jun 2024:   TDC-2: Multimodal Foundation for Therapeutics

The Commons 2.0 (TDC-2) is an overhaul of Therapeutic Data Commons to catalyze research in multimodal models for drug discovery by unifying single-cell biology of diseases, biochemistry of molecules, and effects of drugs through multimodal datasets, AI-powered API endpoints, new tasks and benchmarks. Our paper.

May 2024:   Broad MIA: Protein Language Models

Apr 2024:   Biomedical AI Agents

Mar 2024:   Efficient ML Seminar Series

We started a Harvard University Efficient ML Seminar Series. Congrats to Jonathan for spearheading this initiative. Harvard Magazine covered the first meeting focusing on LLMs.

Mar 2024:   UniTS - Unified Time Series Model

UniTS is a unified time series model that can process classification, forecasting, anomaly detection and imputation tasks within a single model with no task-specific modules. UniTS has zero-shot, few-shot, and prompt learning capabilities. Project website.

Mar 2024:   Weintraub Graduate Student Award

Michelle receives the 2024 Harold M. Weintraub Graduate Student Award. The award recognizes exceptional achievement in graduate studies in biological sciences. News Story. Congratulations!

Mar 2024:   PocketGen - Generating Full-Atom Ligand-Binding Protein Pockets

PocketGen is a deep generative model that generates residue sequence and full-atom structure of protein pockets, maximizing binding to ligands. Project website.

Feb 2024:   SPECTRA - Generalizability of Molecular AI

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