Research Topics
Genomes and GenesSpecies | Joshua C DennySummaryAffiliation: Vanderbilt University Country: USA Publications
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Publications
Chapter 13: Mining electronic health records in the genomics eraJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
PLoS Comput Biol 8:e1002823. 2012..This chapter reviews several examples of phenotype extraction and their application to genetic research, demonstrating a viable future for genomic discovery using EHR-linked data...- 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... - 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... - 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... - 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")... 
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...
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...- 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... - 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... - 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... - 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... - 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.... - Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia riskMarylyn D Ritchie
Professor of Medicine and Pharmacology, Director, Oates Institute for Experimental Therapeutics, Assistant Vice Chancellor for Personalized Medicine, Vanderbilt University School of Medicine, 1285 Medical Research Bldg IV, Nashville, TN 37232 0575
Circulation 127:1377-85. 2013..ECG QRS duration, a measure of cardiac intraventricular conduction, varies ≈2-fold in individuals without cardiac disease. Slow conduction may promote re-entrant arrhythmias... - 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... - 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 37232 8300, USA
Med Decis Making 32:188-97. 2012..Difficulty identifying patients in need of colorectal cancer (CRC) screening contributes to low screening rates... - 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... - Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical recordsMatthew T Oetjens
Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232 0700, USA
Pharmacogenomics 14:735-44. 2013..Original submitted 25 October 2012; Revision submitted 20 March 2013... - A comparative study of current Clinical Natural Language Processing systems on handling abbreviations in discharge summariesYonghui Wu
Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
AMIA Annu Symp Proc 2012:997-1003. 2012..This study suggested that accurate identification of clinical abbreviations is a challenging task and that more advanced abbreviation recognition modules might improve existing clinical NLP systems... - 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..To evaluate the performance of a system that extracts medication information and administration-related actions from patient short message service (SMS) messages... - 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... - 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... - 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... - A study of transportability of an existing smoking status detection module across institutionsMei Liu
Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
AMIA Annu Symp Proc 2012:577-86. 2012..Our results showed that the customized module achieved significantly higher F-measures at all levels of classification (i.e., sentence, document, patient) compared to the direct application of the cTAKES module to the Vanderbilt data... - 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... - 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.... - 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... - 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... - 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..Often, medical educators and students do not know where important concepts are taught and learned in medical school. Manual efforts to identify and track concepts covered across the curriculum are inaccurate and resource intensive... - 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... - "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... - Portability of an algorithm to identify rheumatoid arthritis in electronic health recordsRobert J Carroll
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
J Am Med Inform Assoc 19:e162-9. 2012..This study evaluated the portability of a published phenotype algorithm to identify rheumatoid arthritis (RA) patients from EHR records at three institutions with different EHR systems... - Naïve Electronic Health Record phenotype identification for Rheumatoid arthritisRobert J Carroll
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
AMIA Annu Symp Proc 2011:189-96. 2011..We show that with an expert defined feature set as few as 50-100 training samples are required. This study demonstrates that SVMs operating on non-curated sets of attributes can accurately identify cases from an EHR... - Enabling genomic-phenomic association discovery without sacrificing anonymityRaymond D Heatherly
Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
PLoS ONE 8:e53875. 2013..We demonstrate this strategy with a dataset of over one million medical records and show that 192 genotype-phenotype associations can be discovered with fidelity equivalent to non-anonymized clinical data... - 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... - Mapping the incidentalome: estimating incidental findings generated through clinical pharmacogenomics testingMatthew J Westbrook
Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, Tennessee, USA
Genet Med 15:325-31. 2013..Genet Med 2013:15(5):325-331... - The effect of reducing maximum shift lengths to 16 hours on internal medicine interns' educational opportunitiesCecelia N Theobald
Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee 37212, USA
Acad Med 88:512-8. 2013..To evaluate educational experiences of internal medicine interns before and after maximum shift lengths were decreased from 30 hours to 16 hours... - Detecting temporal expressions in medical narrativesRuth M Reeves
Geriatric Research Education and Clinical Center, Tennessee Valley Healthcare System, Department of Veterans Affairs, Nashville, TN, United States Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States Electronic address
Int J Med Inform 82:118-27. 2013..TTK was developed on newspaper articles. We extended TTK to support medical notes using veterans' affairs (VA) clinical notes and compared it to TTK... - 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...