Phenotyping
- Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC, Nicolae DL, Cox NJ, Im HK. A gene-based association method for mapping traits using reference transcriptome data. Nature genetics. 2015 Sep;47(9). 1091-8. NIHMSID: NIHMS706045.
- Wei WQ, Teixeira PL, Mo H, Cronin RM, Warner JL, Denny JC. Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. Journal of the American Medical Informatics Association : JAMIA. 2015 Sep 2.
- Mo H, Thompson WK, Rasmussen LV, Pacheco JA, Jiang G, Kiefer R, Zhu Q, Xu J, Montague E, Carrell DS, Lingren T, Mentch FD, Ni Y, Wehbe FH, Peissig PL, Tromp G, Larson EB, Chute CG, Pathak J, Denny JC, Speltz P, Kho AN, Jarvik GP, Bejan CA, Williams MS, Borthwick K, Kitchner TE, Roden DM, Harris PA. Desiderata for computable representations of electronic health records-driven phenotype algorithms. Journal of the American Medical Informatics Association : JAMIA. 2015 Nov;22(6). 1220-30.
- Barnado A, Casey C, Carroll RJ, Wheless L, Denny JC, Crofford LJ. Developing Electronic Health Record Algorithms That Accurately Identify Patients With Systemic Lupus Erythematosus. Arthritis care & research. 2017 May;69(5). 687-693. NIHMSID: NIHMS801960.
- Denny JC, Miller RA, Waitman LR, Arrieta MA, Peterson JF. Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor. International journal of medical informatics. 2009 Apr;78 Suppl 1. S34-42. NIHMSID: NIHMS104832.
- Denny JC, Peterson JF. Identifying QT prolongation from ECG impressions using natural language processing and negation detection. Studies in health technology and informatics. 129(Pt 2). 1283-8.
- Denny JC, Spickard A, Miller RA, Schildcrout J, Darbar D, Rosenbloom ST, Peterson JF. Identifying UMLS concepts from ECG Impressions using KnowledgeMap. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 196-200.
- Denny JC, Arndt FV, Dupont WD, Neilson EG. Increased hospital mortality in patients with bedside hippus. The American journal of medicine. 2008 Mar;121(3). 239-45.
- Roden DM, Denny JC. Integrating electronic health record genotype and phenotype datasets to transform patient care. Clinical pharmacology and therapeutics. 2015 Dec 14.
- Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA. The phenotypic legacy of admixture between modern humans and Neandertals. Science (New York, N.Y.). 2016 Feb 12;351(6274). 737-41.