Jeffrey A. Thompson, Ph.D.

Professional Background

Dr. Thompson is an Associate Professor of Biostatistics & Data Science, Senior Associate Vice Chancellor for Research Technology & AI for the University of Kansas, and joint Chief Research Informatics Officer for the University of Kansas Medical Center (KUMC) and the University of Kansas Health System. He earned his PhD in Quantitative Biomedical Science from Dartmouth College and is an expert in artificial intelligence and machine learning. Prior to working in academia, Dr. Thompson spent over a decade running a personal health informatics company that provided intuitive data products to people with dietary restrictions (such as Celiac Disease). In 2017, he joined KUMC in the Department of Biostatistics and led the development of the data science curriculum.

After joining the Department, Dr. Thompson co-led the creation of the Curated Cancer Clinical Outcomes Database (C3OD) for KU Cancer Center. C3OD is a tool that allows researchers to easily identify cohorts of patients that might qualify for clinical trials. C3OD is now a required step for cancer clinical trials, leading to more successful accrual.

In 2021, Dr. Thompson became Chief Research Informatics Officer and is working to modernize the digital research infrastructure at KUMC. This includes the creation of a centralized cloud-based research data lakehouse; the provision of Databricks as a HIPAA compliant data analytics platform; and the integration of many research systems in this platform, including electronic data capture systems, biospecimen management, medical records, EKG systems, clinical imaging, and more. This digital research platform helps to position KUMC as a national leader in healthcare research and established a culture of continuous improvement, for example, with the upcoming rollout of an electronic lab notebook.

In 2026, Dr. Thompson was appointed Senior Associate Vice Chancellor of Research Technology & AI for the University of Kansas. In this role he provides strategic leadership for initiatives related to research technology, AI-enabled research, advanced computing, research data strategy and digital research infrastructure.

In addition to this other roles, Dr. Thompson serves as the co-lead for the Informatics Core of the Frontiers Clinical and Translational Science Institute, the Associate Director of the Quantitative Omics Core for the Kansas Institute of Precision Medicine, and the EHR and Clinical Informatics Leader for the All of Us Research Program Heartland Consortium.

• BS, Computer Science, University of Southern Maine, Portland, ME
• PhD, Quantitative Biomedical Science, Dartmouth College, Hanover, NH

• American Statistical Association, Member, 2017 - Present

Research

Overview

Dr. Thompson's research spans AI, machine learning, and informatics. His research includes developing methods for integrating multi-modal data to create more holistic models of disease etiology and progression, developing new tools to facilitate research, studying the impact of generative AI on healthcare delivery, and developing new approaches to leverage latent data structure in deep learning models. For example, his lab's deep learning method FORCE consistently outperforms models that do not incorporate latent structure, while simultaneously revealing hidden phenotypes in the data.

Furthermore, by applying machine learning methods to genomic data to identify the possible functional changes that influence disease, his group developed the AMEND algorithm that can analyze multiplex and heterogeneous networks of omics data to identify modules of interacting molecules.

In the informatics space, Dr. Thompson works on developing intuitive tools for researchers to use, such as C3OD, which is a tool that allows researchers to easily identify cohorts of patients that might qualify for clinical trials. A study of C3OD showed that it has significantly increased clinical trial accrual success for cancer clinical trials.

• Mudaranthakam DineshPal, Thompson Jeffrey, Hu Jinxiang, Pei Dong, Chintala ShanthanReddy, Park Michele, Fridley BrookeL, Gajewski Byron, Koestler DevinC, Mayo MatthewS. 2018. A Curated Cancer Clinical Outcomes Database (C3OD) for accelerating patient recruitment in cancer clinical trials. JAMIA Open, 1 (2), 166-171. https://doi.org/10.1093/jamiaopen/ooy023
• Thompson JeffreyA., Koestler DevinC.. 2020. Equivalent Change Enrichment Analysis: Assessing Equivalent and Inverse Change in Biological Pathways between Diverse Experiments. BMC Genomics, 21 (1), 180. https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-020-6589-x
• Boyd SamuelS, Slawson Chad, Thompson Jeffrey. 2025. AMEND 2.0: Module Identification and Multi-Omic Data Integration with Multiplex-Heterogeneous Graphs. BMC Bioinformatics, 26. https://doi.org/10.1186/s12859-025-06063-x
• Thompson Jeffrey, Chollet-Hinton Lynn, Keighley John, Chang Audrey, Streeter David, Hu Jinxiang, Park Michele, Gajewski Byron. 2021. The Need to Study Rural Cancer Outcome Disparities on the Local Level: a Case Study in Kansas and Missouri. BMC Public Health, 21 (1). https://bmcpublichealth.biomedcentral.com/articles/10.1186/s12889-021-12190-w
• Thompson JeffreyA, Hu Jinxiang, Mudaranthakam DineshPal, Streeter David, Neums Lisa, Park Michele, Koestler DevinC, Gajewski Byron, Jensen Roy, Mayo MatthewS. 2019. Relevant Word Order Vectorization for Improved Natural Language Processing in Electronic Health Records. Scientific Reports, 9 (1), 9253. https://doi.org/10.1038/s41598-019-45705-y
• Mukherjee R, Thompson JA. 2026. FORCE: Feature-Oriented Representation with Clustering and Explanation.. European journal of artificial intelligence and machine learning, 5 (1), 23-29
• Albrecht Michael, Shanks Denton, Shah Tina, Hudson Taina, Thompson Jeffrey, Filardi Tanya, Wright Kelli, Ator GregoryA, Smith TimothyRyan. 2025. Enhancing clinical documentation with ambient artificial intelligence: a quality improvement survey assessing clinician perspectives on work burden, burnout, and job satisfaction. JAMIA Open, 8 (1). https://doi.org/10.1093/jamiaopen/ooaf013
• Pittman StephenP, Patel Shachi, Thompson Jeffrey, Nangia AjayK. 2022. 18-Year Population Trends Determine Factors Associated With Future Access to Urologists. Urology Practice, 9 (1)
• Mahoney DianeE., Mukherjee Rishav, Thompson Jeffrey. 2024. Elucidating the influences of social determinants of health on perceived overall health among African American/Black and Hispanic ovarian cancer survivors using the NIH All of Us Research Program. Gynecologic Oncology, 189, 24-29. https://doi.org/10.1016/j.ygyno.2024.06.027
• Boyd SS, Slawson C, Thompson JA. 2023. AMEND: active module identification using experimental data and network diffusion.. BMC bioinformatics, 24 (1), 277