Precision-medicine AI Lab · PAI Lab

Jun Wen 文俊

Assistant Professor, Department of Computational Biology @ MBZUAI

Building network-based, knowledge-guided, and foundation-model-powered AI systems for computational genetics, pharmacogenomics, electronic health records, and AI-driven drug discovery.

Mohamed bin Zayed University of Artificial Intelligence 1B Building, Masdar City, Abu Dhabi, UAE jun.wen@mbzuai.ac.ae / jungel2star@gmail.com
Portrait of Jun Wen

About Me

I am an Assistant Professor in the Department of Computational Biology at Mohamed bin Zayed University of Artificial Intelligence (MBZUAI), and a Visiting Scholar at Harvard Medical School. I lead the Precision-medicine AI Lab (PAI Lab), where we develop next-generation AI systems for computational genetics, pharmacogenomics, and AI-driven drug discovery.

Our mission is to advance AI for precision medicine by integrating multi-scale biomedical data — including genomics, transcriptomics, electronic health records, biomedical knowledge graphs, foundation models, and large-scale biobank data — to improve disease diagnosis, treatment optimization, and therapeutic discovery.

Previously, I was a Postdoctoral Research Fellow working with Professor Tianxi Cai at Harvard Medical School, and served as a data scientist at the Veterans Affairs Boston Healthcare System. I received my Ph.D. in Computer Science from Zhejiang University in 2020.

🚀 I am looking for postdoctoral fellows, Ph.D. students, master’s students, and visiting researchers working at the intersection of AI and precision medicine. Interested candidates are warmly welcome to send me their CV and research statement.

♠️ Outside research, I enjoy playing poker and ultimate frisbee (飞盘).

Research Interest

Our research focuses on developing AI-driven frameworks, particularly network-based, knowledge-guided, and foundation-model-powered AI models, to advance precision medicine by integrating multimodal biomedical data, including biomedical knowledge graphs, electronic health records (EHRs), genomics, transcriptomics, protein and molecule foundation models, and large-scale biobank data. We aim to understand the complex interplays among medications, genetic variants, molecular profiles, and diseases or phenotypes.

Research overview

Research overview summarizing Jun Wen's work in precision medicine AI

A unifying view of my research: integrating biological networks, transcriptomics, biobank data, and clinical evidence to study variant-to-phenotype interpretation, drug development and repurposing, pharmacogenomics, and EHR-based translational research.

PheMART · variant → phenotype INTERLACE / HERMES · drug–gene–disease SynCell · drug synergy HyperADRs · drug–gene–ADR LATTE / SeDDLeR / DOME · EHR translation
🧬

Precision-medicine questions

  • Variant-to-phenotype interpretationMissense / non-coding variants, pharmacogenomics, therapeutic and adverse drug effects.
  • Drug discovery, repurposing & safetyDrug–gene–disease relations, drug synergy, rare disease treatment, ADR prediction.
  • EHR-based translational researchIncident phenotyping, risk prediction, rare disease diagnosis, recurrence estimation.

Method contributions

Biologically aligned architecture Multimodal representation learning High-order relation inference Uncertainty modeling AI interpretability Generalization

Long-term vision

Create robust, interpretable, and generalizable AI methodologies that bridge basic biomedical research and clinical practice.

DiagnosisTreatment optimizationTherapeutic discovery

Variant-to-phenotype interpretation and pharmacogenomics

Understand the clinical phenotypic consequences of genetic variants and their therapeutic or adverse effects on medications.

PheMART

Multi-omics informed biomedicine discovery

Leverage bulk and single-cell transcriptomic signatures with biomedical knowledge graphs and EHR-derived evidence to discover drug–gene–disease/ADR relationships, predict context-specific drug synergy, and support drug development, repurposing, and safety assessment.

SynCellHERMESHyperADRsINTERLACECaSBRE

EHR-based translational research

Develop robust models for incident phenotyping, disease risk prediction, rare disease diagnosis, cancer recurrence estimation, and data-driven medical knowledge graphs.

LATTESeDDLeRDOME

Selected Publications

Full publications: Google Scholar

Journal impact factors use the latest available JCR / publisher metrics where available. * indicates equal contribution; † indicates corresponding or senior contribution where applicable.

AI for Precision Medicine, Genetics, and Drug Discovery

2025
Integrating Knowledge Graph and Electronic Health Records for Drug Repurposing
J. Wen, N. Zhou, S. Cai, ..., T. Cai
Under submission, 2025

EHR-based Translational Research

Machine Learning & Representation Learning

Neuroscience & Systems Biology

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