Pingjun Chen-陈平君 Principal Data Scientist Institute for Data Science in Oncology UT MD Anderson Cancer Center Email: pchen6 at mdanderson dot org

Introduction

Dr. Chen serves as Principal Data Scientist dedicated to Computational Pathology at The University of Texas MD Anderson Cancer Center . He received a B.S. degree in software engineering and an M.S. degree in medical image analysis from the Dalian University of Technology in 2012 and 2015, respectively. He received a Ph.D. degree in biomedical engineering from the University of Florida in 2020.

He concentrates on developing cutting-edge computational models and pipelines to advance cancer interception, diagnosis, and treatment. Three pillars of his research are 1) AI/ML-assisted pathology analysis to automate routine pathologic diagnosis, 2) data- and biology-driven approaches to identify novel pathological biomarkers, and 3) intelligent multimodal fusion to facilitate personalized cancer therapy. Dr. Chen aims to harmonize the perspectives of computer scientists, pathologists, oncologists, and biologists towards developing robust solutions to address critical unmet oncology needs.

Updates

• [2025/03/11] One first-authored journal paper was accepted by Cancer Cell (IF: 48.8).
• [2025/01/06] Four abstracts were accepted by AACR Annual Meeting 2025.
• [2025/01/02] One first-authored conference paper was accepted by ISBI 2025. Welcome to Houston Apr, 2025.
• [2024/10/23] Two abstracts were accepted by USCAP 114th Annual Meeting.
• [2024/06/17] One co-authored conference paper was accepted by MICCAI 2024.
• [2024/04/05] One co-authored conference paper was accepted by MIDL 2024.
• [2024/02/11] One co-authored journal paper was accepted by IEEE Transactions on Image Processing (IF: 10.6).
• [2024/01/25] One co-authored journal paper was accepted by Nature Communications (IF: 16.6).
• [2024/01/22] One co-authored journal paper was accepted by Cell Reports Medicine (IF: 14.3).
• [2023/12/04] Start as Principal Data Scientist at the UT MD Anderson Cancer Center in Houston, TX.
• [2023/08/31] One first-authored journal paper was accepted by Modern Pathology (IF: 7.5).
• [2023/04/04] One co-authored journal paper was accepted by The Lancet Digital Health (IF: 36.615).
• [2023/04/01] Start as Instructor at the UT MD Anderson Cancer Center in Houston, TX.
• [2023/02/02] Five abstracts were accepted by AACR Annual Meeting 2023.
• [2022/11/25] One co-authored journal paper was accepted by Nature Communications (IF: 17.694).
• [2022/10/20] Two abstracts were accepted by USCAP 112th Annual Meeting.
• [2022/08/27] Honored to be recognized as IEEE TMI Silver Distinguished Reviewer.
• [2022/08/01] Two first-authored conference papers were accepted by MICCAI-CMMCA2022.
• [2022/07/15] One co-authored journal paper was accepted by Cancers (IF: 6.575).
• [2022/05/25] One first-authored review paper was accepted by 21st Century Pathology.
• [2022/04/25] One first-authored journal paper was accepted by Cancers (IF: 6.639).
• [2022/04/01] Three abstracts were accepted by 2022 ASCO Annual Meeting.
• [2022/01/04] One first-authored journal paper was accepted by Modern Pathology (IF: 7.842).
• [2021/12/23] Two patents were published, as can be found at Google Patents.
• [2021/10/01] Two abstracts were accepted by The 63rd ASH Annual Meeting and Exposition.
• [2021/09/01] One first-authored journal paper was accepted by The Journal of Pathology (IF: 7.996).
• [2021/06/11] One first-authored conference paper was accepted by MICCAI 2021.
• [2020/12/16] One co-authored journal paper was accepted by IEEE Transactions on Image Processing (IF: 9.34).
• [2020/10/12] Start the postdoctoral training at the UT MD Anderson Cancer Center in Houston, TX.
• [2020/07/30] One first-authored conference paper was accepted by MICCAI-MLMI2020.
• [2020/06/23] One first-authored journal paper was accepted by Artificial Intelligence in Medicine (IF: 4.383).
• [2020/06/22] One first-authored journal paper was accepted by Computer Methods and Programs in Biomedicine (IF: 3.632).
• [2020/06/16] Successfully defended my dissertation at UF-BME, PHinally Done!
• [2020/05/02] One first-authored journal paper was accepted by Neurocomputing (IF: 4.438).
• [2020/05/01] Finish a fulfilling internship at UII America, Inc.
• [2020/04/10] One first-authored conference paper was accepted by EMBC 2020 for oral presentation.
• [2019/12/09] Start the internship at UII America, Inc. in Cambridge, MA.
• [2019/11/19] One co-authored journal paper was accepted by IEEE Transactions on Pattern Analysis and Machine Intelligence (IF: 17.861).
• [2019/08/13] One co-authored journal paper was accepted by BMC Bioinformatics (IF: 3.213).
• [2019/06/12] One first-authored journal paper was accepted by Computerized Medical Imaging and Graphics (IF: 3.75).
• [2019/04/15] One co-authored paper was jounral accepted by Nature Machine Intelligence (IF: 15.508).
• [2019/01/02] One first-authored software paper was accepted by Journal of Open Source Software.
• [2018/09/01] The homepage was launched.

Recent Publications

  *Equal Contribution

• Bo Zhu*, Pingjun Chen*, et al., Spatial and Single-Cell Profiling of Human and Murine Lung Adenocarcinoma Precursors Reveals TIM-3 as A Putative Target for Precancer Interception, in Cancer Cell, 2025.
• Pingjun Chen*, Frank Rojas*, et al., Pathomic Features Reveal Immune and Molecular Evolution from Lung Preneoplasia to Invasive Adenocarcinoma, in Modern Pathology, 2023. Presentation
• Siba El Hussein*, Pingjun Chen*, et al., Artificial Intelligence Strategy Integrating Morphologic and Architectural Biomarkers Provides Robust Diagnostic Accuracy for Disease Progression in Chronic Lymphocytic Leukemia, in The Journal of Pathology, 2021. Invited Commentary

Patents

• Joseph D. Khoury, Jia Wu, Siba EI Hussein & Pingjun Chen, Methods and Systems for Determining Leukemia or Lymphoma Levels using Lymphoid Images. 2025. US20250102509A1
• Shanhui Sun, Pingjun Chen, Xiao Chen, Zhang Chen & Terrence Chen, Systems and Methods for Image Segmentation, 2021. US20210397966A1
• Xiao Chen, Pingjun Chen, Zhang Chen, Terrence Chen & Shanhui Sun, Anatomy-Aware Motion Estimation, 2021. US20210397886A1

Software

• slide-deid: Pathology Whole Slide Imaging (WSI) De-Identification.
• pycontour: A Python Toolkit for 2D Contour Processing. [docs]
• tissueloc: Whole Slide Digital Pathology Image Tissue Localization. [docs]

Datasets

• Pingjun Chen, Frank Rojas, et al., Lung Adenocarcinoma Evolution H&E Pathomic Feature Analysis Dataset, 2023. Mendeley Data
• Pingjun Chen, Knee Osteoarthritis Severity Grading Dataset, 2018. Mendeley Data