Joshua Denny, MD, MS

2012 New Investigator Award

Joshua Denny, MD, MS, is an Assistant Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt School of Medicine in Nashville, Tenn. His primary research focuses on developing methods to identify phenotypes from electronic health records (EHR), performing genomic and pharmacogenomic analyses using EHR-linked genomic data, and creating the resources needed to translate this knowledge into clinical practice.Dr. Denny received his bachelors and medical degrees from Vanderbilt University, where he was elected into Alpha Omega Alpha. He then completed an internal medicine residency, followed by a Master of Science in Biomedical Informatics, both at Vanderbilt.During medical school, he began development of the KnowledgeMap natural language processing (NLP) system and associated web-based curriculum management system, which has since been installed by seven other medical schools. Dr. Denny currently leads development for Vanderbilt’s Synthetic Derivative, the de-identified version of the electronic health record that serves as the source of phenotypic data for BioVU, Vanderbilt’s DNA biobank, which now has more than 150,000 samples.He has applied structured terminologies and natural language processing systems for more than 30 phenotype extraction algorithms for clinical research projects, candidate gene analyses, and genome-wide association studies. He first described the phenome-wide association study (PheWAS) method, and has led or assisted in development of NLP algorithms to support clinical phenotyping. He leads HER phenotyping efforts for the Vanderbilt site of the NHGRI-funded Electronic Medical Records and Genomics (eMerge) Network, in addition to serving as co-chair of the eMERGE phenotype workgroup.Dr. Denny has been the lead of senior author on numerous manuscripts. His work has received Homer Warner awards (2008, 2009), AMIA Distinguished Paper (2009) and Poster (2010) awards, and IMIA Yearbook of Informatics citations (2010-2012).Dr. Denny has been committed to AMIA throughout his career. He served on the Clinical Research Informatics Scientific program committee for 2012 and is a track chair for the 2013 Translational Bioinformatics Summit. He has reviewed manuscript submissions to JAMIA since 2003, and served on the student editorial board 2006-7. He has also participated as a mentor for 25 pre- and post-doctor trainees since completing his fellowship.