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Lujia Chen, PhD
- Assistant Professor of Biomedical Informatics
Department of Biomedical Informatics (DBMI) | University of Pittsburgh School of Medicine
Biography
Dr. Lujia Chen is an Assistant Professor in the Department of Biomedical Informatics at the University of Pittsburgh. She completed her PhD in Biomedical Informatics and postdoctoral training at the University of Pittsburgh and also earned an MBA in Business Management. Her research focuses on developing machine learning and deep learning methods to study cancer cell signaling systems, cell-cell communication in the tumor microenvironment, disease heterogeneity, and cancer pharmacogenomics. She integrates causal inference with AI models to identify molecular signatures and biomarkers and to predict clinical outcomes such as drug sensitivity and patient survival. Her work advances tumor-specific precision medicine and precision oncology.
Research Interests
Dr. Chen’s research focuses on developing machine learning methods, especially deep learning models, to study cancer cell signaling systems, cell-cell communication in the tumor microenvironment, disease heterogeneity, disease mechanisms, and cancer pharmacogenomics. She uses representations learned from deep learning models together with causal inference to identify molecular signatures and biomarkers. Her work also predicts clinical outcomes, including drug sensitivity and patient survival. Drawing on her background in bioinformatics, biomedical informatics, biology, and machine learning, she develops AI models that represent signaling states in cancer cells and support precision oncology.
Specialties
- Cancer Informatics
- Machine Learning in Biomedicine
- Deep Learning
- Precision Oncology
- Tumor Microenvironment
- Cancer Pharmacogenomics
Websites & Links
Education & Training
- BS, BiotechnologyUniversity of Science and Technology Beijing, Beijing, China2005-2009
- MS, Biomedical InformaticsUniversity of Pittsburgh, Pittsburgh, PA2010-2012
- Ph.D, Biomedical InformaticsUniversity of Pittsburgh, Pittsburgh, PA2012-2016
- MBA, Business ManagementUniversity of Pittsburgh, Pittsburgh, PA
- Postdoctoral Training, Department of Biomedical InformaticsUniversity of Pittsburgh, Pittsburgh, PA2016-2022
Awards & Distinctions
- 1st Place Prize, SBV Improver Challenge 42014
- 2nd Place Prize, DREAM 8 Challenge2013
- JCO Breakthrough Award2024
- ICIBM Award2023
Representative Publications
Chen L, et al. (2024). Machine learning predicts oxaliplatin benefit in early colon cancer. Journal of Clinical Oncology.
Ren S, Cooper GF, Chen L, Lu X. (2024). An interpretable deep learning framework for genome-informed precision oncology. Nature Machine Intelligence, 6, 864–875.
Chen X*, Chen L*, et al. (2022). An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors. PLoS Computational Biology, 18(12), e1010761.
Chen L, Lu X. (2018). Discovering functional impacts of miRNAs in cancers using a causal deep learning model. BMC Medical Genomics, 11, 116.
Zhang H, Lu X, Chen L. (2023). scGEM: unveiling the nested tree-structured gene co-expressing modules in single cell transcriptome data. Cancers, 15(17), 4277.
Research Grants
| Grant / Funding Agency | Role | Grant Number | Years |
|---|---|---|---|
| NIH R01 Grant NIH | PI | 1R01HG014023 | 2025–2030 |
| NLM | Co-I | 2R01LM012011 | 2024–2028 |
Trainees
| Trainee | Degree Program / Role & Years |
|---|---|
| Han Zhang, PhD | Alumni |
| Laizhi Zhang | M.S. Internship |
| Sanyukta Adap | M.S. Internship |
| Eduardo Ramirez | Undergraduate Internship |
| Amanda Zeng | High School Summer Student |
| Kevin Lu | High School Summer Student |