Brett K. Beaulieu-Jones, Ph.D.
Brett K. Beaulieu-Jones, Ph.D.
Research Fellow in Biomedical Informatics
Biomedical Informatics Research Training Fellow, 2017-2019
Mentor: Zak Kohane, MD, PhD

Brett Beaulieu-Jones received his PhD from the Perelman School of Medicine at the University of Pennsylvania under the supervision of Dr. Jason Moore and Dr. Casey Greene. Beaulieu-Jones’ doctoral research focused on using machine learning-based methods to more precisely define phenotypes from large-scale biomedical data repositories, e.g. those contained in clinical records. At DBMI he is expanding this concentration to include large-scale data integration (genomic, therapeutic, imaging) to both better understand disease etiology as well as provide precise therapeutic recommendations. Initially, he is working to develop targeted models of drug selection for patients with refractory epilepsy and to further develop machine learning methods that model the way patients progress over time using longitudinal data.  

Learning Contextual Hierarchical Structure of Medical Concepts with Poincairé Embeddings to Clarify Phenotypes.
Authors: Beaulieu-Jones BK, Kohane IS, Beam AL.
Pac Symp Biocomput
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Opportunities and obstacles for deep learning in biology and medicine.
Authors: Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS.
J R Soc Interface
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Characterizing and Managing Missing Structured Data in Electronic Health Records: Data Analysis.
Authors: Beaulieu-Jones BK, Lavage DR, Snyder JW, Moore JH, Pendergrass SA, Bauer CR.
JMIR Med Inform
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Mapping Patient Trajectories using Longitudinal Extraction and Deep Learning in the MIMIC-III Critical Care Database.
Authors: Beaulieu-Jones BK, Orzechowski P, Moore JH.
Pac Symp Biocomput
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Reproducibility of computational workflows is automated using continuous analysis.
Authors: Beaulieu-Jones BK, Greene CS.
Nat Biotechnol
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MISSING DATA IMPUTATION IN THE ELECTRONIC HEALTH RECORD USING DEEPLY LEARNED AUTOENCODERS.
Authors: Beaulieu-Jones BK, Moore JH.
Pac Symp Biocomput
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Semi-supervised learning of the electronic health record for phenotype stratification.
Authors: Beaulieu-Jones BK, Greene CS.
J Biomed Inform
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