Research Topics
Genomes and GenesSpecies | Joshua C DennySummaryAffiliation: Vanderbilt University Country: USA Publications
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Publications
Tracking medical students' clinical experiences using natural language processingJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University Medical Center, Eskind Biomedical Library, Room 442, 2209 Garland Ave, Nashville, TN 37232, USA
J Biomed Inform 42:781-9. 2009..The coupling of section header identification and concept identification holds promise for other natural language processing tasks, such as clinical research or phenotype identification...- Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studiesJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
Am J Hum Genet 89:529-42. 2011..Our findings indicate that EMR-linked genomic data could allow discovery of genes associated with many diseases without additional genotyping cost... - Extracting timing and status descriptors for colonoscopy testing from electronic medical recordsJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
J Am Med Inform Assoc 17:383-8. 2010..Further investigations must validate extension of NLP approaches for other types of CRC screening applications... - Identifying QT prolongation from ECG impressions using natural language processing and negation detectionJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Stud Health Technol Inform 129:1283-8. 2007..We conclude that a natural language processing system can effectively identify QT prolongation and other cardiac diagnoses from ECG impressions for potential decision support and clinical research... - PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associationsJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
Bioinformatics 26:1205-10. 2010..The primary outcome of this study was replication of seven previously known SNP-disease associations for these SNPs... - Identifying QT prolongation from ECG impressions using a general-purpose Natural Language ProcessorJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
Int J Med Inform 78:S34-42. 2009..We investigated the accuracy of natural language processing (NLP) for identifying QT prolongation from cardiologist-generated, free-text ECG impressions compared to corrected QT (QTc) thresholds reported by ECG machines... - Evaluation of a method to identify and categorize section headers in clinical documentsJoshua C Denny
Department of Biomedical Informatics, Vanderbilt UniversitySchool of Medicine, Eskind Biomedical Library, Room 442, 2209 Garland Ave, Nashville TN 37232, USA
J Am Med Inform Assoc 16:806-15. 2009..quot; The authors designed and evaluated an algorithm ("SecTag") to identify both labeled and unlabeled (implied) note section headers in "history and physical examination" documents ("H&P notes")... - Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical recordMarylyn D Ritchie
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Am J Hum Genet 86:560-72. 2010.... - Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome scienceJoshua C Denny
Office of Personalized Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232 0575, USA
Circulation 122:2016-21. 2010..The extent to which this can be demonstrated in cohorts derived from electronic medical records is unknown... - Assessing the accuracy of observer-reported ancestry in a biorepository linked to electronic medical recordsLogan Dumitrescu
Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
Genet Med 12:648-50. 2010.... - Development of a natural language processing system to identify timing and status of colonoscopy testing in electronic medical recordsJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
AMIA Annu Symp Proc 2009:141. 2009..The system detected completed colonoscopies with recall and precision of 0.93 and 0.92. The system was superior to a query of colonoscopy billing codes to determine screening status... - Analyses of longitudinal, hospital clinical laboratory data with application to blood glucose concentrationsJonathan S Schildcrout
Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
Stat Med 30:3208-20. 2011..To illustrate these points, we present a detailed analysis of the relationship between blood glucose levels and insulin doses on the basis of data from an intensive care unit... - Modulators of normal electrocardiographic intervals identified in a large electronic medical recordAndrea H Ramirez
Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
Heart Rhythm 8:271-7. 2011..Traditional electrocardiographic (ECG) reference ranges were derived from studies in communities or clinical trial populations. The distribution of ECG parameters in a large population presenting to a healthcare system has not been studied... - An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical recordsJonathan S Schildcrout
Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232 2156, USA
J Biomed Inform 43:914-23. 2010..The phenotypes studied include type II diabetes and type II diabetes controls, peripheral arterial disease and peripheral arterial disease controls, normal cardiac conduction as measured by electrocardiography, and senile cataracts... - Integrating existing natural language processing tools for medication extraction from discharge summariesSon Doan
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
J Am Med Inform Assoc 17:528-31. 2010..This task required accurate recognition of medication name, dosage, mode, frequency, duration, and reason for drug administration... - Natural language processing improves identification of colorectal cancer testing in the electronic medical recordJoshua C Denny
Division of General Internal Medicine and Public Health, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee JCD, NNC, JFP, NBP
Med Decis Making 32:188-97. 2012..Difficulty identifying patients in need of colorectal cancer (CRC) screening contributes to low screening rates... - A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summariesMin Jiang
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 18:601-6. 2011..This project was part of the 2010 Center of Informatics for Integrating Biology and the Bedside/Veterans Affairs (VA) natural-language-processing challenge... - Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarinHua Xu
Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 18:387-91. 2011..This study sought to develop natural-language-processing algorithms to extract drug-dose information from clinical text, and to assess the capabilities of such tools to automate the data-extraction process for pharmacogenetic studies... - Data from clinical notes: a perspective on the tension between structure and flexible documentationS Trent Rosenbloom
Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
J Am Med Inform Assoc 18:181-6. 2011..When reusable data are needed from notes, providers can use structured documentation or rely on post-hoc text processing to produce structured data, as appropriate... - Applying semantic-based probabilistic context-free grammar to medical language processing--a preliminary study on parsing medication sentencesHua Xu
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
J Biomed Inform 44:1068-75. 2011..Our evaluation using a 10-fold cross validation showed that the PCFG parser dramatically improved parsing performance when compared to the CFG parser... - Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health recordAndrea H Ramirez
Department of Medicine, Vanderbilt University in Nashville, TN 37232, USA
Pharmacogenomics 13:407-18. 2012..Electronic health record (EHR) systems linked to biobanks may allow for pharmacogenomic analysis, but they have not yet been used for this purpose... - Detecting abbreviations in discharge summaries using machine learning methodsYonghui Wu
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
AMIA Annu Symp Proc 2011:1541-9. 2011..8% (precision 98.8% and recall of 91.2%). When a voting scheme was used to combine output from various ML classifiers, the system achieved the highest F-measure of 95.7%... - Modeling drug exposure data in electronic medical records: an application to warfarinMei Liu
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
AMIA Annu Symp Proc 2011:815-23. 2011..We applied the framework to determine patient warfarin exposure at hospital admissions and achieved 87% precision, 79% recall, and an area under the receiver-operator characteristic curve of 0.93... - Development of inpatient risk stratification models of acute kidney injury for use in electronic health recordsMichael E Matheny
Geriatric Research Education Clinical Center, Tennessee Valley Health System, Veterans Health Administration, Nashville, TN, USA
Med Decis Making 30:639-50. 2010.... - Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanksStephen D Turner
Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
PLoS ONE 6:e19586. 2011..These results demonstrate that gene-gene interactions modulate complex human traits, including HDL cholesterol... - Teaching evidence-based medicine: Impact on students' literature use and inpatient clinical documentationElizabeth Ann Sastre
Vanderbilt University Medical Center, Nashville, TN 37232, USA
Med Teach 33:e306-12. 2011..Effective teaching of evidence-based medicine (EBM) to medical students is important for lifelong self-directed learning... - The disclosure of diagnosis codes can breach research participants' privacyGrigorios Loukides
Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, Tennessee 37203, USA
J Am Med Inform Assoc 17:322-7. 2010.... - "Where do we teach what?" Finding broad concepts in the medical school curriculumJoshua C Denny
Department of Medicine, Vanderbilt School of Medicine, Nashville, TN 37232, USA
J Gen Intern Med 20:943-6. 2005..Use of KM or similar tools may prove useful for other medical schools to identify broad concepts in their curricula... - "Understanding" medical school curriculum content using KnowledgeMapJoshua C Denny
Department of Biomedical Informatics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 10:351-62. 2003..In addition, the ability of KM to meet specific, personal information needs should be assessed... - MedEx: a medication information extraction system for clinical narrativesHua Xu
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 17:19-24. 2010..5%, 93.9%, and 96.0% respectively. We then applied MedEx unchanged to outpatient clinic visit notes. It performed similarly with F-measures over 90% on a set of 25 clinic visit notes... - Comparing content coverage in medical curriculum to trainee-authored clinical notesJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
AMIA Annu Symp Proc 2010:157-61. 2010..Such methods may prove useful for future curriculum evaluations and revisions... - PASTE: patient-centered SMS text tagging in a medication management systemShane P Stenner
Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee, USA
J Am Med Inform Assoc 19:368-74. 2012..This evaluation demonstrates the feasibility of extracting medication information from patient-generated medication messages... - Automatic capture of student notes to augment mentor feedback and student performance on patient write-upsAnderson Spickard
Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
J Gen Intern Med 23:979-84. 2008..To determine whether the integration of an automated electronic clinical portfolio into clinical clerkships can improve the quality of feedback given to students on their patient write-ups and the quality of students' write-ups... - Portal venous hyperinsulinemia does not stimulate gut glucose absorption in the conscious dogRaul C Camacho
Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashille, TN 37232, USA
Metabolism 53:1290-5. 2004..This study shows that under physiological conditions, a portal vein insulin infusion that results in circulating hyperinsulinemia does not increase either transporter-mediated or passive absorption of an intraduodenal glucose load...