• Jonathan Badger PharmD, MS

  • Research Project Pharmacist

    • Center for Precision Medicine Research
    • 1000 North Oak Ave. ML8 Marshfield, WI 54449


2016 to 2018:
M.S., Biomedical Data Science, UW-Madison, Madison, WI
2006 to 2010:
PharmD, Pharmacy, UW-Madison School of Pharmacy, Madison, WI
2001 to 2006:
B.S., Chemistry/Biology, UW-Stevens Point, Stevens Point, WI

Work Experience

2011 to 2017:
Relief Pharmacist, JAT Veterinary Pharmacy, Sun Prairie, WI
2008 to 2016:
Staff Pharmacist, Wal-Mart, various


Jon has a passion for the life sciences and a love of programming and technology that have led to a career involving research, biomedical informatics, and the application of technology to improve patient care. Recent projects have included: using self-controlled case series to determine if there are differences in the incidence of adverse drug events (ADEs) of brand and generic drugs, mining the text of PubMed for ADEs, and utilizing machine learning to detect ADEs in electronic health record (EHR). Currently, Jon is focused on research related to the opioid epidemic where he is using machine learning to better characterize overdose events and develop novel algorithms for risk prediction. Jon is also involved in a project to implement pharmacogenetic drug alerts in the MCHS EHR to inform physicians of drug-gene interactions with the potential to cause harm and/or treatment failure.

Research Interests

Jon is interested in the application of machine learning to patient phenotyping, drug-drug interactions, adverse drug event discovery, and for disease and risk prediction modeling. Neural networks and their applications in the medical domain are of particular interest right now as their success has made them ubiquitous in smart phone apps for voice recognition and text translation.

Select Publications

  • Kleiman RS, LaRose ER, Badger JC, Page D, Caldwell MD, Clay JA, Peissig PL. Using Machine Learning Algorithms to Predict Risk for Development of Calciphylaxis in Patients with Chronic Kidney Disease. [published online ahead of print 2018 May 18]. AMIA Jt Summits Transl Sci Proc.. 2017 :139-146.
    PubMed ID: 29888059
  • Bashiri FS, LaRose E, Badger JC, D’Souza RM, Yu Z, Peissig P. Object Detection to Assist Visually Impaired People: A Deep Neural Network Adventure. Advances in Visual Computing. 2018 November 10; 11241
  • Tafti AP, Assefi M, LaRose E, Badger J, Ye Z, Shimpi N,...Peissig P [including Bashiri FS, Sagheb E, McLean H.] Big data deep neural network to analyze adverse vaccine reactions. AMIA 2018 Informatics Summit. 2018 March;
  • Tafti AP, Badger J, LaRose E, Shirzadi E, Mahnke M, Mayer J,...Peissig PL [including Ye Z.] (2017 Nov). Adverse Drug event Discovery using Biomedical Literature: a Big Data Neural Network Adventure. JMIR Med Inform.
  • Ahmad P. Tafti, Ehsun Behravesh, Mehdi Assefi, Eric LaRose, Jonathan Badger, John Mayer,...Peggy Peissig. (2017 Dec). bigNN: An open-source big data toolkit focused on biomedical sentence classification. 2017 IEEE International Conference on Big Data (Big Data).