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Chongle Pan

Chongle Pan

Chongle Pan

Professor of Computer Science and Biomedical Engineering

Email: cpan@ou.edu
Phone: (405) 325-2972
Office: Devon Energy Hall (DEH) 251

Lab Website

Education
Ph.D. Computer Science 
University of Tennessee, Knoxville
B.S. Computer Science 
East China Normal University, China

Research Focus

My research spans artificial intelligence, biomedical informatics, medical imaging, immunoengineering, and microbiome systems biology, with the overarching goal of developing computational technologies that advance biomedical discovery and improve human health.

In AI for health and biomedical informatics, I develop machine learning, large language models, multimodal AI, explainable AI, and high-performance computing methods for complex biomedical and clinical data. Applications include clinical decision support, patient–trial matching, digital health and behavioral interventions, and precision medicine.

In medical imaging, my research focuses on deep learning, computer vision, and multimodal foundation models for biomedical image analysis, including image classification, detection, segmentation, and quantitative characterization of disease.

In immunoengineering, I develop AI, bioinformatics, and multi-omics approaches to characterize immune responses and support the development and evaluation of new immunotherapies and other engineered interventions. This work integrates genomic, transcriptomic, proteomic, and other molecular data with advanced computational modeling.

My research in microbiome systems biology seeks to understand the metabolism and function of human and environmental microbial communities and their interactions with their hosts and environments. Our approaches include computational biology, proteomic stable isotope probing, integrated multi-omics, mechanistic modeling, and synthetic microbiomes.

Across these areas, my laboratory develops new computational and AI methodologies while applying them to fundamental and translational problems at the intersection of engineering, computing, and biomedicine.

Dr. Pan is a computational scientist whose research bridges artificial intelligence, biomedical engineering, and systems biology. His research program develops artificial intelligence and machine learning methods—including large language models, multimodal AI, computer vision, and explainable AI—for biomedical and healthcare applications. Major application areas include medical imaging, clinical and biomedical informatics, immunoengineering, digital health, and precision medicine. His laboratory also develops computational and high-performance computing methods for multi-omics and microbiome research, including proteomics, genomics, and proteomic stable isotope probing.

Dr. Pan has published more than 100 peer-reviewed articles and has led or contributed to interdisciplinary research supported by the National Institutes of Health, National Science Foundation, Department of Energy, Department of Defense, and other sponsors. He has extensive experience building multidisciplinary collaborations across computing, engineering, biology, and medicine and mentoring students, postdoctoral researchers, and junior faculty in computational and biomedical research.

  • P. Wang, D. Verma, Y. Chiu, J. Klier, C. Pan (2025) Luedeking-Piret Regression for Multi-Step-Ahead Forecasting and Clone Selection in mAb Biomanufacturing. Communication Engineering. 
  • A. Bates, R. Vavricka, S. Carleton, R. Shao, C. Pan. (2025) Unified modeling language code generation from diagram images using multimodal large language models. Machine Learning with Applications. 20:100660. doi: 10.1016/j.mlwa.2025.100660.
  • P. Calle, A. Bates, J.C. Reynolds, Y. Liu, H. Cui, S. Ly, C. Wang, Q. Zhang, A.J. de Armendi, S.S. Shettar, K.M. Fung, Q. Tang, C. Pan. (2025) Integration of nested cross-validation, automated hyperparameter optimization, high-performance computing to reduce and quantify the variance of test performance estimation of deep learning models.Computer Methods and Programs in Biomedicine. 10;272:109063. doi: 10.1016/j.cmpb.2025.109063.
  • Y. Xiong, R.S. Mueller, S. Feng, X. Guo, C. Pan (2024) Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins. Microbiome 12(1):148. doi:10.1186/s40168-024-01866-1.
  • A. Badré, C. Pan (2023) Explainable Multi-Task Learning Improves the Parallel Estimation of Polygenic Risk Scores for Many Diseases Through Shared Genetic Basis. PLoS Computational Biology 19(7):e1011211. doi: 10.1371/journal.pcbi.1011211.
  • L. Zhang, K.R. Jonscher, Z. Zhang, Y. Xiong, R.S. Mueller, J.E. Friedman, C. Pan (2022) Islet Autoantibody Seroconversion in Type-1 Diabetes is Associated with Metagenome-Assembled Genomes in Infant Gut Microbiomes.Nature Communication 13(1). 10.1038/s41467-022-31227-1.