A New Tool to Identify Key Biomedical Concepts in Text Documents, with Special Application to Curriculum Content. - Joshua C. Denny; Jeffrey D. Smithers; Anderson Spickard III; Randolph A. Miller (AMIA, 2002)

Using Concept Markers to Find Genetics Content in a Medical School Curriculum. - Jeffrey D. Smithers; Joshua C. Denny; Anderson Spickard III; Randolph A. Miller (AMIA, 2002)

The KnowledgeMap Project: Development of a Concept-Based Medical School Curriculum Database. - Joshua C. Denny; Plomarz R. Irani; Firas H. Wehbe; Jeffrey D. Smithers; Anderson Spickard III (AMIA, 2003)

Formative Evaluation to Guide Early Deployment of an Online Content Management Tool for Medical Curriculum. - Firas H. Wehbe; Brian Armstrong; Matthew R. Peachey; Joshua C. Denny; Anderson Spickard III (AMIA, 2003)

Research Paper: "Understanding" Medical School Curriculum Content Using KnowledgeMap. - Joshua C. Denny; Jeffrey D. Smithers; Randolph A. Miller; Anderson Spickard III (J. Am. Medical Informatics Assoc., 2003)

Identifying UMLS concepts from ECG Impressions using Knowledge Map. - Joshua C. Denny; Anderson Spickard III; Randolph A. Miller; Jonathan S. Schildcrout; Dawood Darbar; S. Trent Rosenbloom; Josh F. Peterson (AMIA, 2005)

Can Users Estimate Their Usage of a Web-Based Application? Validating a Self-Report Usage Questionnaire. - Firas H. Wehbe; Joshua C. Denny; Anderson Spickard III (AMIA, 2005)

Analysis of Medical Student Content Searches that Resulted in Unidentified UMLS Concepts. - Benjamin P. Rosenbaum; Joshua C. Denny; Anderson Spickard III (AMIA, 2006)

Analysis of a Computerized Sign-out Tool: Identification of Unanticipated Uses and Contradictory Content. - Thomas R. Campion Jr.; Joshua C. Denny; Stuart T. Weinberg; Nancy M. Lorenzi; L. Russell Waitman (AMIA, 2007)

Identifying QT prolongation from ECG impressions using Natural Language Processing and Negation Detection. - Joshua C. Denny; Josh F. Peterson (MedInfo, 2007)

Development and Evaluation of a Clinical Note Section Header Terminology. - Joshua C. Denny; Randolph A. Miller; Kevin B. Johnson; Anderson Spickard III (AMIA, 2008)

Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. - Joshua C. Denny; Josh F. Peterson; Neesha N. Choma; Hua Xu 001; Randolph A. Miller; Lisa Bastarache; Neeraja B. Peterson (AMIA, 2009)

Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor. - Joshua C. Denny; Randolph A. Miller; Lemuel R. Waitman; Mark Arrieta; Josh F. Peterson (Int. J. Medical Informatics, 2009)

Research Paper: Evaluation of a Method to Identify and Categorize Section Headers in Clinical Documents. - Joshua C. Denny; Anderson Spickard III; Kevin B. Johnson; Neeraja B. Peterson; Josh F. Peterson; Randolph A. Miller (J. Am. Medical Informatics Assoc., 2009)

Tracking medical students' clinical experiences using natural language processing. - Joshua C. Denny; Lisa Bastarache; Elizabeth Ann Sastre; Anderson Spickard III (J. Biomed. Informatics, 2009)

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. - Joshua C. Denny; Marylyn D. Ritchie; Melissa A. Basford; Jill M. Pulley; Lisa Bastarache; Kristin Brown-Gentry; Deede Wang; Daniel R. Masys; Dan M. Roden; Dana C. Crawford (Bioinform., 2010)

Identifying potential drugs that induce QT prolongation using electronic medical records. - Mei Liu; Joshua C. Denny; Subramani Mani; Yukun Chen 001; Yong Hu 002; Hua Xu 001 (BMC Bioinform., 2010)

Extracting timing and status descriptors for colonoscopy testing from electronic medical records. - Joshua C. Denny; Josh F. Peterson; Neesha N. Choma; Hua Xu 001; Randolph A. Miller; Lisa Bastarache; Neeraja B. Peterson (J. Am. Medical Informatics Assoc., 2010)

Integrating existing natural language processing tools for medication extraction from discharge summaries. - Son Doan; Lisa Bastarache; Sergio Klimkowski; Joshua C. Denny; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2010)

The disclosure of diagnosis codes can breach research participants' privacy. - Grigorios Loukides; Joshua C. Denny; Bradley A. Malin (J. Am. Medical Informatics Assoc., 2010)

Application of information technology: MedEx: a medication information extraction system for clinical narratives. - Hua Xu 001; Shane P. Stenner; Son Doan; Kevin B. Johnson; Lemuel R. Waitman; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2010)

An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records. - Jonathan S. Schildcrout; Melissa A. Basford; Jill M. Pulley; Daniel R. Masys; Dan M. Roden; Deede Wang; Christopher G. Chute; Iftikhar J. Kullo; David Carrell; Peggy L. Peissig; Abel N. Kho; Joshua C. Denny (J. Biomed. Informatics, 2010)

A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. - Min Jiang 007; Yukun Chen 001; Mei Liu; S. Trent Rosenbloom; Subramani Mani; Joshua C. Denny; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2011)

Data from clinical notes: a perspective on the tension between structure and flexible documentation. - S. Trent Rosenbloom; Joshua C. Denny; Hua Xu 001; Nancy M. Lorenzi; William W. Stead; Kevin B. Johnson (J. Am. Medical Informatics Assoc., 2011)

Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. - Hua Xu 001; Min Jiang 007; Matthew Oetjens; Erica A. Bowton; Andrea H. Ramirez; Janina M. Jeff; Melissa A. Basford; Jill M. Pulley; James D. Cowan; Xiaoming Wang; Marylyn D. Ritchie; Daniel R. Masys; et al. (J. Am. Medical Informatics Assoc., 2011)

Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences. - Hua Xu 001; Samir AbdelRahman; Yanxin Lu; Joshua C. Denny; Son Doan (J. Biomed. Informatics, 2011)

Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR. - Lisa Bastarache; Wei-Qi Wei; Joshua C. Denny (AMIA, 2012)

Establishing Drug Treatment discovery rate of MedEx. - Haresh Bhatia; Eugenia R. McPeek Hinz; Joshua C. Denny (AMIA, 2012)

Extracting Semantic Lexicons from Discharge Summaries using Machine Learning and the C-Value Method. - Min Jiang 007; Joshua C. Denny; Buzhou Tang; Hongxin Cao; Hua Xu 001 (AMIA, 2012)

A Study of Transportability of an Existing Smoking Status Detection Module across Institutions. - Mei Liu; Anushi Shah; Min Jiang 007; Neeraja B. Peterson; Qi Dai; Melinda Aldrich; Qingxia Chen; Erica A. Bowton; Hongfang Liu; Joshua C. Denny; Hua Xu 001 (AMIA, 2012)

Type 2 Diabetes Risk Forecasting from EMR Data using Machine Learning. - Subramani Mani; Yukun Chen 001; Tom Elasy; Warren Clayton; Joshua C. Denny (AMIA, 2012)

Using Electronic Health Records to Identify Patient Cohorts for Drug-Induced Thrombocytopenia, Neutropenia and Liver Injury. - Jyotishman Pathak; Aref Al-Kali; Jayant Talwalkar; Abel N. Kho; Joshua C. Denny; Sean P. Murphy; Kevin Bruce; Matthew J. Durski; Christopher G. Chute (AMIA, 2012)

PheKB.org: An Online Collaboration Tool for Phenotype Algorithm Research. - Joshua Pruitt; Peter Speltz; Jacqueline Kirby; Melissa A. Basford; Jonathan L. Haines; Joshua C. Denny (AMIA, 2012)

MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text. - Anushi Shah; Min Jiang 007; Yonghui Wu; Joshua C. Denny; Hua Xu 001 (AMIA, 2012)

Understanding Patient-Provider Communication via a Patient Portal. - Si Sun; Xiaomu Zhou; Hua Xu 001; Joshua C. Denny (AMIA, 2012)

An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms. - William K. Thompson; Luke V. Rasmussen; Jennifer A. Pacheco; Peggy L. Peissig; Joshua C. Denny; Abel N. Kho; Aaron W. Miller; Jyotishman Pathak (AMIA, 2012)

Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes. - Wei-Qi Wei; Lisa Bastarache; Joshua C. Denny (AMIA, 2012)

A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. - Yonghui Wu; Joshua C. Denny; Samuel Rosenbloom; Randolph A. Miller; Dario A. Giuse; Hua Xu 001 (AMIA, 2012)

Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies. - Hua Xu 001; Melinda Aldrich; Qingxia Chen; Neeraja B. Peterson; Qi Dai; Mia A. Levy; Anushi Shah; Han Xue; Ying Li; Carol Friedman; Hongfang Liu; Joshua C. Denny (AMIA, 2012)

Understanding patient-provider communication entered via a patient portal system. - Si Sun; Xiaomu Zhou; Joshua C. Denny; S. Trent Rosenbloom; Hua Xu 001 (ASIST, 2012)

A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing. - Eugenia R. McPeek Hinz; Lisa Bastarache; Joshua C. Denny (HISB, 2012)

Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data. - Mei Liu; Michael E. Matheny; Yonghui Wu; Eugenia R. McPeek Hinz; Joshua C. Denny; Jonathan S. Schildcrout; Randolph A. Miller; Hua Xu 001 (HISB, 2012)

Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches. - Yanxin Lu; Hua Xu 001; Neeraja B. Peterson; Qi Dai; Min Jiang 007; Joshua C. Denny; Mei Liu (Int. J. Data Min. Bioinform., 2012)

Portability of an algorithm to identify rheumatoid arthritis in electronic health records. - Robert J. Carroll; William K. Thompson; Anne E. Eyler; Arthur M. Mandelin; Tianxi Cai; Raquel M. Zink; Jennifer A. Pacheco; Chad S. Boomershine; Thomas A. Lasko; Hua Xu 001; Elizabeth W. Karlson; Raúl G. Pérez; et al. (J. Am. Medical Informatics Assoc., 2012)

Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study. - Abel N. Kho; M. Geoffrey Hayes; Laura Rasmussen-Torvik; Jennifer A. Pacheco; William K. Thompson; Loren L. Armstrong; Joshua C. Denny; Peggy L. Peissig; Aaron W. Miller; Wei-Qi Wei; Suzette J. Bielinski; Christopher G. Chute; et al. (J. Am. Medical Informatics Assoc., 2012)

Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. - Peggy L. Peissig; Luke V. Rasmussen; Richard L. Berg; James G. Linneman; Catherine A. McCarty; Carol Waudby; Lin Chen; Joshua C. Denny; Russell A. Wilke; Jyotishman Pathak; David Carrell; Abel N. Kho; et al. (J. Am. Medical Informatics Assoc., 2012)

Focus on health information technology, electronic health records and their financial impact: PASTE: patient-centered SMS text tagging in a medication management system. - Shane P. Stenner; Kevin B. Johnson; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2012)

Chapter 13: Mining Electronic Health Records in the Genomics Era. - Joshua C. Denny (PLoS Comput. Biol., 2012)

Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems. - Lisa Bastarache; Wei-Qi Wei; Joshua C. Denny (AMIA, 2013)

Open Source R Implementation of the PheWAS Methodology. - Robert J. Carroll; Lisa Bastarache; Joshua C. Denny (AMIA, 2013)

A Study of Active Learning Methods for Clinical Entities Recognition. - Yukun Chen 001; Thomas A. Lasko; Qiaozhu Mei; Joshua C. Denny; Hua Xu 001 (AMIA, 2013)

Automated Identification of Drug and Food Allergies Entered in EHRs Using Non-Standard Terminology. - Richard H. Epstein; Jesse M. Ehrenfeld; Michael Stockin; Paul St. Jacques; Brian Rothman; Joshua C. Denny (AMIA, 2013)

A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype. - Eugenia R. McPeek Hinz; Joshua C. Denny; Lisa Bastarache (AMIA, 2013)

Using PheWAS and Natural Language Processing to Discover Clinical Associations for Congenital Chest Deformities. - Christine M. McEvoy; Robert J. Carroll; Lisa Bastarache; Wei-Qi Wei; Joshua C. Denny (AMIA, 2013)

Sharing of Genomic Information: Perspectives from Stakeholders. - Jeremy L. Warner; Gil Alterovitz; Joshua C. Denny; Robert Fassett; Kevin S. Hughes (AMIA, 2013)

Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information. - Jeremy L. Warner; Quan Ding; David A. Kreda; Zi'ou Zheng; Keshav Gupta; Joshua C. Denny; Gil Alterovitz (AMIA, 2013)

Validation and Enhancement of a Computable Medication Indication Resource (MEDI) Using a Large Practice-based Dataset. - Wei-Qi Wei; Jonathan D. Mosley; Lisa Bastarache; Joshua C. Denny (AMIA, 2013)

Establishing the Need for Personalized Medicine: Simvastatin Exposure Among a SLCO1B1 Variant Population. - Laura K. Wiley; Josh F. Peterson; Joshua C. Denny; William S. Bush (AMIA, 2013)

Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries. - Yonghui Wu; S. Trent Rosenbloom; Joshua C. Denny; Randolph A. Miller; Dario A. Giuse; Hua Xu 001 (AMIA, 2013)

Messaging to your doctors: understanding patient-provider communications via a portal system. - Si Sun; Xiaomu Zhou; Joshua C. Denny; S. Trent Rosenbloom; Hua Xu 001 (CHI, 2013)

A prototype application for real-time recognition and disambiguation of clinical abbreviations. - Yonghui Wu; Joshua C. Denny; S. Trent Rosenbloom; Randolph A. Miller; Dario A. Giuse; Min Song 001; Hua Xu 001 (DTMBIO, 2013)

Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model. - Buzhou Tang; Yonghui Wu; Min Jiang 007; Joshua C. Denny; Hua Xu 001 (CLEF (Working Notes), 2013)

Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. - Yonghui Wu; Buzhou Tang; Min Jiang 007; Sungrim Moon; Joshua C. Denny; Hua Xu 001 (CLEF (Working Notes), 2013)

Analytic Approaches to Phenotypic Complexity. - Jeremy L. Warner; Joshua C. Denny; David A. Kreda; Gil Alterovitz (MedInfo, 2013)

Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages. - Yonghui Wu; Jianbo Lei; Wei-Qi Wei; Buzhou Tang; Joshua C. Denny; S. Trent Rosenbloom; Randolph A. Miller; Dario A. Giuse; Kai Zheng 002; Hua Xu 001 (MedInfo, 2013)

Detecting temporal expressions in medical narratives. - Ruth M. Reeves; Ferdo R. Ong; Michael E. Matheny; Joshua C. Denny; Dominik Aronsky; Glenn T. Gobbel; Diane Montella; Theodore Speroff; Steven H. Brown (Int. J. Medical Informatics, 2013)

Automated identification of drug and food allergies entered using non-standard terminology. - Richard H. Epstein; Paul St. Jacques; Michael Stockin; Brian Rothman; Jesse M. Ehrenfeld; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2013)

Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. - Jungwei Fan 001; Elly W. Yang; Min Jiang 007; Rashmi Prasad; Richard M. Loomis; Daniel Zisook; Joshua C. Denny; Hua Xu 001; Yang Huang 008 (J. Am. Medical Informatics Assoc., 2013)

Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records. - Mei Liu; Eugenia Renne McPeek Hinz; Michael Edwin Matheny; Joshua C. Denny; Jonathan Scott Schildcrout; Randolph A. Miller; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2013)

A hybrid system for temporal information extraction from clinical text. - Buzhou Tang; Yonghui Wu; Min Jiang 007; Yukun Chen 001; Joshua C. Denny; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2013)

Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al. - Nicholas P. Tatonetti; Joshua C. Denny; Russ B. Altman (J. Am. Medical Informatics Assoc., 2013)

Development and evaluation of an ensemble resource linking medications to their indications. - Wei-Qi Wei; Robert M. Cronin; Hua Xu 001; Thomas A. Lasko; Lisa Bastarache; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2013)

Learning to Identify Treatment Relations in Clinical Text. - Cosmin Adrian Bejan; Joshua C. Denny (AMIA, 2014)

PheWAS and Genetics Define Subphenotypes in Drug Response. - Robert J. Carroll; Jeremy L. Warner; Anne E. Eyler; Charles Moore; Jayanth Doss; Katherine P. Liao; Robert M. Plenge; Joshua C. Denny (AMIA, 2014)

Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies. - Yukun Chen 001; Jesse O. Wrenn; Hua Xu 001; Anderson Spickard III; Ralf Habermann; James S. Powers; Joshua C. Denny (AMIA, 2014)

A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions. - Yukun Chen 001; Yaoyun Zhang; Qiaozhu Mei; Dead Account; Joshua C. Denny; Hua Xu 001 (AMIA, 2014)

Applying Active Learning to Word Sense Disambiguation in a Real-Time Setting. - Sungrim Moon; Yukun Chen 001; Jingqi Wang; Joshua C. Denny; Hua Xu 001 (AMIA, 2014)

A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project. - Casey L. Overby; Luke V. Rasmussen; Andrea L. Hartzler; John J. Connolly; Josh F. Peterson; RoseMary Hedberg; Robert R. Freimuth; Brian H. Shirts; Joshua C. Denny; Eric B. Larson; Christopher G. Chute; Gail P. Jarvik; et al. (AMIA, 2014)

Evaluation of Existing Phenotype Authoring Tools for Clinical Research. - Luke V. Rasmussen; Jie Xu 011; Ruijue Liu; Qian Zhu 003; Jennifer A. Pacheco; Jyotishman Pathak; William K. Thompson; Joshua C. Denny; Huan Mo; Richard C. Kiefer; Peter Speltz; Enid N. H. Montague (AMIA, 2014)

Identifying Metastases from Pathology Reports in Lung Cancer Patients. - Ergin Soysal; Jeremy L. Warner; Joshua C. Denny; Hua Xu 001 (AMIA, 2014)

Phenome-Wide Association Studies Using NLP-Derived Concepts. - Pedro L. Teixeira; Robert J. Carroll; Lisa Bastarache; Peter Speltz; Joshua C. Smith; Joshua C. Denny (AMIA, 2014)

Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype. - Wei-Qi Wei; Pedro L. Teixeira; Huan Mo; Robert M. Cronin; Jeremy L. Warner; Joshua C. Denny (AMIA, 2014)

Mining electronic health record data to detect drug-repurposing signals for cancers. - Hua Xu 001; Qingxia Chen; Jeremy L. Warner; Han Xue; Min Jiang 007; Anushi Shah; Melinda Aldrich; Qi Dai; Joshua C. Denny (AMIA, 2014)

Qualitative evaluation of three phenotype information models to find methotrexate liver injury. - Qian Zhu 003; Huan Mo; Luke V. Rasmussen; Andrew R. Post; Jennifer A. Pacheco; Jie Xu 011; Richard C. Kiefer; Peter Speltz; Enid N. H. Montague; William K. Thompson; Joshua C. Denny; Jyotishman Pathak (AMIA, 2014)

Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies. - Janina M. Jeff; Kristin Brown-Gentry; Robert J. Goodloe; Marylyn D. Ritchie; Joshua C. Denny; Abel N. Kho; Loren L. Armstrong; Bob McClellan Jr.; Ping Mayo; Melissa Allen; Hailing Jin; Niloufar B. Gillani; et al. (EvoApplications, 2014)

Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients. - Matthew Oetjens; William S. Bush; Kelly A. Birdwell; Holli H. Dilks; Erica A. Bowton; Joshua C. Denny; Russell A. Wilke; Dan M. Roden; Dana C. Crawford (Pacific Symposium on Biocomputing, 2014)

R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. - Robert J. Carroll; Lisa Bastarache; Joshua C. Denny (Bioinform., 2014)

SecureMA: protecting participant privacy in genetic association meta-analysis. - Wei Xie 002; Murat Kantarcioglu; William S. Bush; Dana C. Crawford; Joshua C. Denny; Raymond Heatherly; Bradley A. Malin (Bioinform., 2014)

Predicting changes in hypertension control using electronic health records from a chronic disease management program. - Jimeng Sun 001; Candace D. McNaughton; Ping Zhang 016; Adam Perer; Aris Gkoulalas-Divanis; Joshua C. Denny; Jacqueline Kirby; Thomas A. Lasko; Alexander Saip; Bradley A. Malin (J. Am. Medical Informatics Assoc., 2014)

Size matters: How population size influences genotype-phenotype association studies in anonymized data. - Raymond Heatherly; Joshua C. Denny; Jonathan L. Haines; Dan M. Roden; Bradley A. Malin (J. Biomed. Informatics, 2014)

Limestone: High-throughput candidate phenotype generation via tensor factorization. - Joyce C. Ho; Joydeep Ghosh; Steven R. Steinhubl; Walter F. Stewart; Joshua C. Denny; Bradley A. Malin; Jimeng Sun 001 (J. Biomed. Informatics, 2014)

Design patterns for the development of electronic health record-driven phenotype extraction algorithms. - Luke V. Rasmussen; William K. Thompson; Jennifer A. Pacheco; Abel N. Kho; David Carrell; Jyotishman Pathak; Peggy L. Peissig; Gerard Tromp; Joshua C. Denny; Justin B. Starren (J. Biomed. Informatics, 2014)

Real Time Active Learning Study for Clinical Named Entity Recognition. - Yukun Chen 001; Sungrim Moon; Thomas A. Lasko; Qiaozhu Mei; Jingqi Wang; Trevor Cohen; Qingxia Chen; Joshua C. Denny; Hua Xu 001 (AMIA, 2015)

Predicting Clinical Laboratory Turnaround Time. - Alex C. Cheng; Marc Beller; Joshua C. Denny (AMIA, 2015)

Automated Classification of Consumer Health Information Needs in Patient Portal Messages. - Robert M. Cronin; Daniel Fabbri; Joshua C. Denny; Gretchen Purcell Jackson (AMIA, 2015)

Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study. - Guoqian Jiang; Harold R. Solbrig; Richard C. Kiefer; Luke V. Rasmussen; Huan Mo; Jennifer A. Pacheco; Enid N. H. Montague; Jie Xu 011; Peter Speltz; William K. Thompson; Joshua C. Denny; Christopher G. Chute; et al. (AMIA, 2015)

A Genome- and Phenome- Wide Study of Diverticulosis. - Yoonjung Y. Joo; Jennifer A. Pacheco; Loren L. Armstrong; William K. Thompson; Robert J. Carroll; Joshua C. Denny; Peggy L. Peissig; James G. Linneman; Jyotishman Pathak; Girish N. Nadkarni; Laura Rasmussen-Torvik; M. Geoffrey Hayes; et al. (AMIA, 2015)

Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME. - Huan Mo; Jennifer A. Pacheco; Richard C. Kiefer; Luke V. Rasmussen; Jyotishman Pathak; Joshua C. Denny; William K. Thompson (AMIA, 2015)

Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools. - Enid N. H. Montague; Jie Xu 011; Luke V. Rasmussen; Joshua C. Denny; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Peter Speltz; William K. Thompson; Jyotishman Pathak (AMIA, 2015)

Quantifying Tobacco Exposure Using Clinical Notes and Natural Language Processing to Enable Lung Cancer Screening. - Travis Osterman; Wei-Qi Wei; Joshua C. Denny (AMIA, 2015)

(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping. - Jennifer A. Pacheco; Abel N. Kho; Jyotishman Pathak; Joshua C. Denny; Shawn N. Murphy (AMIA, 2015)

PhEMA: Phenotype Modeling, Sharing and Execution Architecture. - Jyotishman Pathak; Joshua C. Denny; William K. Thompson; Luke V. Rasmussen (AMIA, 2015)

Natural Language Processing for Phenotype Extraction: Challenges in Extraction and Representation. - Guergana Savova; Rebecca S. Jacobson; Joshua C. Denny; Nicole L. Washington; Harry Hochheiser (AMIA, 2015)

Building the Computational Workforce for Precision Medicine. - Jessica D. Tenenbaum; Joshua C. Denny; David Flannery; Douglas B. Fridsma; Marc S. Williams (AMIA, 2015)

PheWAS Network Analysis and Visualization. - Yaomin Xu; Todd L. Edwards; Lisa Bastarache; Rebecca N. Jerome; Shilin Zho; Eric Torstenson; Wei-Qi Wei; Jana Shirey-Rice; Erica A. Bowton; Yu Shyr; Jill M. Pulley; Joshua C. Denny (AMIA, 2015)

Rubik: Knowledge Guided Tensor Factorization and Completion for Health Data Analytics. - Yichen Wang 001; Robert Chen 001; Joydeep Ghosh; Joshua C. Denny; Abel N. Kho; You Chen 001; Bradley A. Malin; Jimeng Sun 001 (KDD, 2015)

A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution. - Guoqian Jiang; Harold R. Solbrig; Richard C. Kiefer; Luke V. Rasmussen; Huan Mo; Peter Speltz; William K. Thompson; Joshua C. Denny; Christopher G. Chute; Jyotishman Pathak (MedInfo, 2015)

Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. - Cosmin Adrian Bejan; Wei-Qi Wei; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2015)

Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. - Chen Lin 002; Elizabeth W. Karlson; Dmitriy Dligach; Monica P. Ramirez; Timothy A. Miller; Huan Mo; Natalie S. Braggs; Andrew Cagan; Vivian S. Gainer; Joshua C. Denny; Guergana K. Savova (J. Am. Medical Informatics Assoc., 2015)

Desiderata for computable representations of electronic health records-driven phenotype algorithms. - Huan Mo; William K. Thompson; Luke V. Rasmussen; Jennifer A. Pacheco; Guoqian Jiang; Richard C. Kiefer; Qian Zhu 003; Jie Xu 011; Enid N. H. Montague; David S. Carrell; Todd Lingren; Frank D. Mentch; et al. (J. Am. Medical Informatics Assoc., 2015)

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization. - Jeremy L. Warner; Joshua C. Denny; David A. Kreda; Gil Alterovitz (J. Am. Medical Informatics Assoc., 2015)

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. - Hua Xu 001; Melinda C. Aldrich; Qingxia Chen; Hongfang Liu; Neeraja B. Peterson; Qi Dai; Mia A. Levy; Anushi Shah; Han Xue; Xiaoyang Ruan; Min Jiang 007; Ying Li; et al. (J. Am. Medical Informatics Assoc., 2015)

Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. - Jie Xu 011; Luke V. Rasmussen; Pamela L. Shaw; Guoqian Jiang; Richard C. Kiefer; Huan Mo; Jennifer A. Pacheco; Peter Speltz; Qian Zhu 003; Joshua C. Denny; Jyotishman Pathak; William K. Thompson; et al. (J. Am. Medical Informatics Assoc., 2015)

Building bridges across electronic health record systems through inferred phenotypic topics. - You Chen 001; Joydeep Ghosh; Cosmin Adrian Bejan; Carl A. Gunter; Siddharth Gupta 005; Abel N. Kho; David M. Liebovitz; Jimeng Sun 001; Joshua C. Denny; Bradley A. Malin (J. Biomed. Informatics, 2015)

A study of active learning methods for named entity recognition in clinical text. - Yukun Chen 001; Thomas A. Lasko; Qiaozhu Mei; Joshua C. Denny; Hua Xu 001 (J. Biomed. Informatics, 2015)

Using natural language processing to provide personalized learning opportunities from trainee clinical notes. - Joshua C. Denny; Anderson Spickard III; Peter Speltz; Renee Porier; Donna E. Rosenstiel; James S. Powers (J. Biomed. Informatics, 2015)

Parsing clinical text: how good are the state-of-the-art parsers? - Min Jiang 007; Yang Huang 008; Jungwei Fan 001; Buzhou Tang; Joshua C. Denny; Hua Xu 001 (BMC Medical Informatics Decis. Mak., 2015)

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. - Jingchun Sun; Min Zhao 006; Peilin Jia; Lily Wang 001; Yonghui Wu; Carissa Iverson; Yubo Zhou; Erica A. Bowton; Dan M. Roden; Joshua C. Denny; Melinda C. Aldrich; Hua Xu 001; et al. (PLoS Comput. Biol., 2015)

An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. - Rui Duan 004; Ming Cao 005; Yonghui Wu; Jing Huang 021; Joshua C. Denny; Hua Xu 001; Yong Chen 016 (AMIA, 2016)

Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations. - Yang Huang 008; Hua Xu 001; Joshua C. Denny (AMIA, 2016)

An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution. - Guoqian Jiang; William K. Thompson; Luke V. Rasmussen; Richard C. Kiefer; Jennifer A. Pacheco; Huan Mo; Peter Speltz; Joshua C. Denny; Jyotishman Pathak (AMIA, 2016)

Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time. - Sungrim Moon; Yukun Chen 001; Jingqi Wang; Joshua C. Denny; S. Trent Rosenbloom; Ky Nguyen; Tolulola Dawodu; Hua Xu 001 (AMIA, 2016)

A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. - Huan Mo; Guoqian Jiang; Jennifer A. Pacheco; Richard C. Kiefer; Luke V. Rasmussen; Jyotishman Pathak; Joshua C. Denny; William K. Thompson (CRI, 2016)

The Many Meanings of Precision Medicine. - Anthony E. Solomonides; Russ B. Altman; Joshua C. Denny; Larry Ozeran; Jessica D. Tenenbaum (CRI, 2016)

Evaluating Physician Response to Pharmacogenomic-Guided Warfarin Dosing in an Hospitalized Population. - Laura K. Wiley; Marc Beller; Julie Field; Josh F. Peterson; Joshua C. Denny (CRI, 2016)

Translational Bioinformatics 101. - Jessica D. Tenenbaum; Subha Madhavan; Robert R. Freimuth; Joshua C. Denny; Lewis J. Frey (PSB, 2016)

Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. - Cassandra Brady; Bahram Namjou; Stephanie Kennebeck; Jonathan Bickel; Nandan Patibandla; Yizhao Ni; Sara Van Driest; Lixin Chen; Ashton Roach; Beth Cobb; Jacqueline Kirby; Joshua C. Denny; et al. (Appl. Clin. Inform., 2016)

Practical considerations for implementing genomic information resources. - Casey L. Overby; John J. Connolly; Christopher G. Chute; Joshua C. Denny; Robert R. Freimuth; Andrea L. Hartzler; Ingrid A. Holm; Shannon F. Manzi; Jyotishman Pathak; Peggy L. Peissig; Maureen E. Smith; Marc S. Williams; et al. (Appl. Clin. Inform., 2016)

Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods. - Rachel L. Richesson; Jimeng Sun 001; Jyotishman Pathak; Abel N. Kho; Joshua C. Denny (Artif. Intell. Medicine, 2016)

Precision medicine informatics. - Lewis J. Frey; Elmer V. Bernstam; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2016)

A multi-institution evaluation of clinical profile anonymization. - Raymond Heatherly; Luke V. Rasmussen; Peggy L. Peissig; Jennifer A. Pacheco; Paul A. Harris; Joshua C. Denny; Bradley A. Malin (J. Am. Medical Informatics Assoc., 2016)

PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. - Jacqueline Kirby; Peter Speltz; Luke V. Rasmussen; Melissa A. Basford; Omri Gottesman; Peggy L. Peissig; Jennifer A. Pacheco; Gerard Tromp; Jyotishman Pathak; David S. Carrell; Stephen B. Ellis; Todd Lingren; et al. (J. Am. Medical Informatics Assoc., 2016)

Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. - Wei-Qi Wei; Pedro L. Teixeira; Huan Mo; Robert M. Cronin; Jeremy L. Warner; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2016)

Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. - Laura K. Wiley; Peter Tarczy-Hornoch; Joshua C. Denny; Robert R. Freimuth; Casey L. Overby; Nigam Shah; Ross D. Martin; Indra Neil Sarkar (J. Am. Medical Informatics Assoc., 2016)

Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. - Guoqian Jiang; Richard C. Kiefer; Luke V. Rasmussen; Harold R. Solbrig; Huan Mo; Jennifer A. Pacheco; Jie Xu 011; Enid N. H. Montague; William K. Thompson; Joshua C. Denny; Christopher G. Chute; Jyotishman Pathak (J. Biomed. Informatics, 2016)

Large-Scale Text Mining of Social Determinants from Electronic Health Records: Case Studies of Homelessness and Adverse Childhood Experiences. - Cosmin Adrian Bejan; John Angiolillo; Douglas Conway; Robertson Nash; Jana Shirey-Rice; Loren Lipworth-Elliot; Robert M. Cronin; Jill M. Pulley; Sunil Kripalani; Shari Barkin; Kevin B. Johnson; Joshua C. Denny (AMIA, 2017)

A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects. - Cosmin Adrian Bejan; Joshua C. Denny (AMIA, 2017)

The Data and Research Center of the All of Us Research Program: Framework for a National Cohort Program and Research Opportunities. - Robert J. Carroll; Joshua C. Mandel; Karthik Natarajan; Scott Sutherland; Joshua C. Denny (AMIA, 2017)

Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository. - Richard C. Kiefer; Luke V. Rasmussen; Jennifer A. Pacheco; Peter Speltz; Joshua C. Denny; William K. Thompson; Jyotishman Pathak; Guoqian Jiang (AMIA, 2017)

HealthPro: An integrated web application for essential health data and biological specimen collection in the Precision Medicine Initiative. - Kelsey R. Mayo; Robert J. Carroll; Jason Tan; Rebecca Johnston; Celecia M. Scott; Joshua C. Denny; Paul A. Harris (AMIA, 2017)

The All of Us Research Program Researcher Portal: Innovative access to Unprecendented Data. - Andrea H. Ramirez; Anthony A. Philippakis; Gonçalo R. Abecasis; Paul A. Harris; Joshua C. Denny (AMIA, 2017)

Sub-Phenotyping of Crohn's Disease Using a Large Electronic Record Cohort. - Jamie R. Robinson; Lisa Bastarache; Robert J. Carroll; Elizabeth A. Scoville; David A. Schwartz; Joshua C. Denny (AMIA, 2017)

Association of BMI and Obesity Genetic Risk Score with Surgical Procedures Through a Procedure-wide Association Study. - Jamie R. Robinson; Zongyang Mou; Lisa Bastarache; Wei-Qi Wei; Robert J. Carroll; Joshua C. Denny (AMIA, 2017)

The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs. - Peter Speltz; Luke V. Rasmussen; Richard C. Kiefer; Jennifer A. Pacheco; William K. Thompson; Guoqian Jiang; Jyotishman Pathak; Joshua C. Denny (AMIA, 2017)

A Phenome-Wide Association Study (PheWAS) of Iron Deficiency in a Large Electronic Health Record Database. - Patrick Wu; Joshua C. Denny; Wei-Qi Wei (AMIA, 2017)

Development and Testing of Participant Provided Information Modules for the Precision Medicine Initiative. - Robert M. Cronin; Rebecca N. Jerome; Brandy Mapes; Kathryn Goggins; Ken Wallston; Katharine Donato; Mick P. Couper; Michael R. Elliott; Charles P. Mouton; Kemberlee Bonnet; Ezer Benaim; Jordan Sinclair; et al. (CRI, 2017)

A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. - Hee-Jin Lee; Min Jiang 007; Yonghui Wu; Christian Shaffer; John H. Cleator; Eitan Friedman; Joshua P. Lewis; Dan M. Roden; Joshua C. Denny; Hua Xu 001 (CRI, 2017)

Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. - Ergin Soysal; Jeremy L. Warner; Joshua C. Denny; Hua Xu 001 (CRI, 2017)

Granite: Diversified, Sparse Tensor Factorization for Electronic Health Record-Based Phenotyping. - Jette Henderson; Joyce C. Ho; Abel N. Kho; Joshua C. Denny; Bradley A. Malin; Jimeng Sun 001; Joydeep Ghosh (ICHI, 2017)

Session Introduction. - Alexander A. Morgan; Dana C. Crawford; Joshua C. Denny; Sean D. Mooney; Bruce J. Aronow; Steven E. Brenner (PSB, 2017)

Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population. - Laura K. Wiley; Jacob P. VanHouten; David Samuels; Melinda Aldrich; Dan M. Roden; Josh F. Peterson; Joshua C. Denny (PSB, 2017)

A comparison of rule-based and machine learning approaches for classifying patient portal messages. - Robert M. Cronin; Daniel Fabbri; Joshua C. Denny; S. Trent Rosenbloom; Gretchen Purcell Jackson (Int. J. Medical Informatics, 2017)

Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. - Pedro L. Teixeira; Wei-Qi Wei; Robert M. Cronin; Huan Mo; Jacob P. VanHouten; Robert J. Carroll; Eric LaRose; Lisa Bastarache; S. Trent Rosenbloom; Todd L. Edwards; Dan M. Roden; Thomas A. Lasko; et al. (J. Am. Medical Informatics Assoc., 2017)

A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). - Yonghui Wu; Joshua C. Denny; S. Trent Rosenbloom; Randolph A. Miller; Dario A. Giuse; Lulu Wang; Carmelo Blanquicett; Ergin Soysal; Jun Xu 007; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2017)

An active learning-enabled annotation system for clinical named entity recognition. - Yukun Chen 001; Thomas A. Lasko; Qiaozhu Mei; Qingxia Chen; Sungrim Moon; Jingqi Wang; Ky Nguyen; Tolulola Dawodu; Trevor Cohen; Joshua C. Denny; Hua Xu 001 (BMC Medical Informatics Decis. Mak., 2017)

Crowdsourcing Clinical Chart Reviews. - Joseph R. Coco; Cheng Ye 001; Chen Hajaj; Yevgeniy Vorobeychik; Joshua C. Denny; Laurie L. Novak; Bradley A. Malin; Thomas A. Lasko; Daniel Fabbri (AMIA, 2018)

Phenotyping through Semi-Supervised Tensor Factorization (PSST). - Jette Henderson; Huan He; Bradley A. Malin; Joshua C. Denny; Abel N. Kho; Joydeep Ghosh; Joyce C. Ho (AMIA, 2018)

EHR Extraction of Longitudinal Exposure to Proton Pump Inhibitors. - Andrea H. Ramirez; Elliot M. Fielstein; QiPing Feng; Henry H. Ong; Jonathan S. Schildcrout; Yaping Shi; Joshua C. Denny; Josh F. Peterson (AMIA, 2018)

Using Topic Modeling to Identify Relationship between LPA Variant and Disease Phenotypes. - Juan Zhao 003; QiPing Feng; Patrick Wu; Joshua C. Denny; Wei-Qi Wei (AMIA, 2018)

Huge Cohorts, Genomics, and Clinical Data to Personalize Medicine. - Joshua C. Denny (BCB, 2018)

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. - Yizhen Zhong; Luke V. Rasmussen; Yu Deng; Jennifer A. Pacheco; Maureen E. Smith; Justin Starren; Wei-Qi Wei; Peter Speltz; Joshua C. Denny; Nephi Walton; George Hripcsak; Christopher G. Chute; et al. (BIBM, 2018)

Session Introduction. - Dana C. Crawford; Alexander A. Morgan; Joshua C. Denny; Bruce J. Aronow; Steven E. Brenner (PSB, 2018)

Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions. - Joshua C. Smith; Qingxia Chen; Joshua C. Denny; Dan M. Roden; Kevin B. Johnson; Randolph A. Miller (Appl. Clin. Inform., 2018)

Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects. - Leena Choi; Robert J. Carroll; Cole Beck; Jonathan D. Mosley; Dan M. Roden; Joshua C. Denny; Sara L. Van Driest (Bioinform., 2018)

Mining 100 million notes to find homelessness and adverse childhood experiences: 2 case studies of rare and severe social determinants of health in electronic health records. - Cosmin Adrian Bejan; John Angiolillo; Douglas Conway; Robertson Nash; Jana Shirey-Rice; Loren Lipworth-Elliot; Robert M. Cronin; Jill M. Pulley; Sunil Kripalani; Shari Barkin; Kevin B. Johnson; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2018)

Uncovering exposures responsible for birth season - disease effects: a global study. - Mary Regina Boland; Pradipta Parhi; Li Li 062; Riccardo Miotto; Robert J. Carroll; Usman Iqbal; Phung-Anh (Alex) Nguyen; Martijn J. Schuemie; Seng Chan You; Donahue Smith; Sean D. Mooney; Patrick B. Ryan; et al. (J. Am. Medical Informatics Assoc., 2018)

A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. - Jennifer A. Pacheco; Luke V. Rasmussen; Richard C. Kiefer; Thomas R. Campion Jr.; Peter Speltz; Robert J. Carroll; Sarah C. Stallings; Huan Mo; Monika Ahuja; Guoqian Jiang; Eric R. LaRose; Peggy L. Peissig; et al. (J. Am. Medical Informatics Assoc., 2018)

Quality Analysis of the All of Us Research Program Health Surveys. - Robert M. Cronin; Sarah Feng; Brandy Mapes; Roxana Loperena-Cortes; Regina Andrade; David Schlundt; Ken A. Wallston; Mick P. Couper; Scott Sutherland; Cindy Chen; Joshua C. Denny (AMIA, 2019)

Extracting Drug Exposure Epochs and Drug Response Outcomes from Electronic Health Records. - Andrea H. Ramirez; Yaping Shi; Elliot M. Fielstein; Jonathan S. Schildcrout; Henry H. Ong; Joshua C. Denny; Josh F. Peterson (AMIA, 2019)

medExtractR: A medication extraction algorithm for electronic health records using the R programming language. - Hannah L. Weeks; Cole Beck; Elizabeth McNeer; Cosmin Adrian Bejan; Joshua C. Denny; Leena Choi (AMIA, 2019)

Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs. - Patrick Wu; QiPing Feng; Joshua C. Denny; Wei-Qi Wei (AMIA, 2019)

Deep Learning Using Electronic Health Records and Genetic Data to Predict Cardiovascular Diseases. - Juan Zhao 003; QiPing Feng; Patrick Wu; Joshua C. Denny; Wei-Qi Wei (AMIA, 2019)

Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. - Ergin Soysal; Jeremy L. Warner; Jingqi Wang; Min Jiang 007; Krysten Harvey; Sandeep Kumar Jain; Xiao Dong; Hsing-yi Song; Harish Siddhanamatha; Liwei Wang 010; Qi Dai; Qingxia Chen; et al. (MedInfo, 2019)

Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE network. - Xinyuan Zhang 003; Yogasudha Veturi; Shefali Setia Verma; William Bone; Anurag Verma; Anastasia Lucas; Scott J. Hebbring; Joshua C. Denny; Ian B. Stanaway; Gail P. Jarvik; David R. Crosslin; Eric B. Larson; et al. (PSB, 2019)

CP Tensor Decomposition with Cannot-Link Intermode Constraints. - Jette Henderson; Bradley A. Malin; Joshua C. Denny; Abel N. Kho; Jimeng Sun 001; Joydeep Ghosh; Joyce C. Ho (SDM, 2019)

Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease. - Lisa Bastarache; Jacob J. Hughey; Jeffery A. Goldstein; Julie A. Bastraache; Satya Das; Neil Charles Zaki; Chenjie Zeng; Leigh Anne Tang; Dan M. Roden; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2019)

Cost-aware active learning for named entity recognition in clinical text. - Qiang Wei 002; Yukun Chen 001; Mandana Salimi; Joshua C. Denny; Qiaozhu Mei; Thomas A. Lasko; Qingxia Chen; Stephen Wu 004; Amy Franklin; Trevor Cohen; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2019)

Facilitating phenotype transfer using a common data model. - George Hripcsak; Ning Shang; Peggy L. Peissig; Luke V. Rasmussen; Cong Liu 020; Barbara Benoit; Robert J. Carroll; David S. Carrell; Joshua C. Denny; Ozan Dikilitas; Vivian S. Gainer; Kayla Marie Howell; et al. (J. Biomed. Informatics, 2019)

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. - Ning Shang; Cong Liu 020; Luke V. Rasmussen; Casey N. Ta; Robert J. Carroll; Barbara Benoit; Todd Lingren; Ozan Dikilitas; Frank D. Mentch; David S. Carrell; Wei-Qi Wei; Yuan Luo 001; et al. (J. Biomed. Informatics, 2019)

Automated grouping of medical codes via multiview banded spectral clustering. - Luwan Zhang; Yichi Zhang; Tianrun A. Cai; Yuri Ahuja; Zeling He; Yuk-Lam Ho; Andrew Beam; Kelly Cho; Robert J. Carroll; Joshua C. Denny; Isaac S. Kohane; Katherine P. Liao; et al. (J. Biomed. Informatics, 2019)

Detecting time-evolving phenotypic topics via tensor factorization on electronic health records: Cardiovascular disease case study. - Juan Zhao 003; Yun Zhang; David J. Schlueter; Patrick Wu; Vern Eric Kerchberger; S. Trent Rosenbloom; Quinn Stanton Wells; QiPing Feng; Joshua C. Denny; Wei-Qi Wei (J. Biomed. Informatics, 2019)

Real-time Clinical Note Monitoring to Detect Conditions for Follow-up: a Case Study of Clinical Trial Enrollment in Drug-induced Torsades de Pointes and Stevens-Johnson Syndrome. - Sarah DeLozier; Peter Speltz; Jason Brito; Leigh Anne Tang; Janey Wang; Joshua C. Smith; Dario A. Giuse; Elizabeth Phillips; Kristina Williams; Teresa Strickland; Giovanni Davogustto; Dan M. Roden; et al. (AMIA, 2020)

Developing a Phenotype Risk Score for Opioid Adverse Events. - Leigh Anne Tang; Sarah DeLozier; Lisa Bastarache; Colin Walsh; Joshua C. Denny (AMIA, 2020)

medExtractR: A targeted, customizable approach to medication extraction from electronic health records. - Hannah L. Weeks; Cole Beck; Elizabeth McNeer; Michael L. Williams; Cosmin Adrian Bejan; Joshua C. Denny; Leena Choi (J. Am. Medical Informatics Assoc., 2020)

PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. - Neil S. Zheng; QiPing Feng; Vern Eric Kerchberger; Juan Zhao 003; Todd L. Edwards; Nancy J. Cox; C. Michael Stein; Dan M. Roden; Joshua C. Denny; Wei-Qi Wei (J. Am. Medical Informatics Assoc., 2020)

Using Genomic Association Replication Rates as an EHR Quality Measure via the Phenotype-Genotype Reference Map (PGRM). - Sarah DeLozier; Josh F. Peterson; Joshua C. Denny; Lisa Bastarache (AMIA, 2021)

Systematic replication of smoking disease associations in the All of Us Research Program. - David J. Schlueter; Lina M. Sulieman; Jacob M. Keaton; Tracey Ferrara; Kyle Webb; Ariel Williams; Francis Ratsimbazafy; Jun Qian; Lisa Bastarache; Andrea H. Ramirez; Joshua C. Denny (AMIA, 2021)

PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. - Nick Strayer; Jana K. Shirey-Rice; Yu Shyr; Joshua C. Denny; Jill M. Pulley; Yaomin Xu (Bioinform., 2021)

Real-time clinical note monitoring to detect conditions for rapid follow-up: A case study of clinical trial enrollment in drug-induced torsades de pointes and Stevens-Johnson syndrome. - Sarah DeLozier; Peter Speltz; Jason Brito; Leigh Anne Tang; Janey Wang; Joshua C. Smith; Dario A. Giuse; Elizabeth Phillips; Kristina Williams; T. Stephen Strickland; Giovanni Davogustto; Dan M. Roden; et al. (J. Am. Medical Informatics Assoc., 2021)

DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions. - Patrick Wu; Scott D. Nelson; Juan Zhao 003; Cosby A. Stone Jr.; QiPing Feng; Qingxia Chen; Eric A. Larson; Bingshan Li; Nancy J. Cox; C. Michael Stein; Elizabeth Phillips; Dan M. Roden; et al. (J. Am. Medical Informatics Assoc., 2021)

Meeting the challenge: Health information technology's essential role in achieving precision medicine. - Teresa Zayas-Cabán; Kevin J. Chaney; Courtney C. Rogers; Joshua C. Denny; P. Jon White (J. Am. Medical Informatics Assoc., 2021)

Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. - Ning Shang; Atlas Khan; Fernanda Polubriaginof; Francesca Zanoni; Karla Mehl; David Fasel; Paul E. Drawz; Robert J. Carroll; Joshua C. Denny; Matthew A. Hathcock; Adelaide M. Arruda-Olson; Peggy L. Peissig; et al. (npj Digit. Medicine, 2021)

Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS. - Rebecca Irlmeier; Jacob J. Hughey; Lisa Bastarache; Joshua C. Denny; Qingxia Chen (Bioinform., 2022)

The U.S. National Library of Medicine's impact on precision and genomic medicine. - Huan Mo; Joshua C. Denny (Inf. Serv. Use, 2022)

The All of Us Research Program: Data quality, utility, and diversity. - Andrea H. Ramirez; Lina M. Sulieman; David J. Schlueter; Alese E. Halvorson; Jun Qian; Francis Ratsimbazafy; Roxana Loperena-Cortes; Kelsey R. Mayo; Melissa A. Basford; Nicole Deflaux; Karthik Muthuraman; Karthik Natarajan; et al. (Patterns, 2022)

Ontologizing health systems data at scale: making translational discovery a reality. - Tiffany J. Callahan; Adrianne L. Stefanski; Jordan M. Wyrwa; Chenjie Zeng; Anna Ostropolets; Juan M. Banda; William A. Baumgartner Jr.; Richard D. Boyce; Elena Casiraghi; Ben D. Coleman; Janine H. Collins; Sara J. Deakyne Davies; et al. (npj Digit. Medicine, 2023)

Characterizing variability of electronic health record-driven phenotype definitions. - Pascal S. Brandt; Abel N. Kho; Yuan Luo 001; Jennifer A. Pacheco; Theresa L. Walunas; Hakon Hakonarson; George Hripcsak; Cong Liu 020; Ning Shang; Chunhua Weng; Nephi Walton; David S. Carrell; et al. (J. Am. Medical Informatics Assoc., 2023)

Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research Program. - David J. Schlueter; Lina M. Sulieman; Huan Mo; Jacob M. Keaton; Tracey M. Ferrara; Ariel Williams; Jun Qian; Onajia J. Stubblefield; Chenjie Zeng; Tam C. Tran; Lisa Bastarache; Jian Dai; et al. (J. Am. Medical Informatics Assoc., 2023)

Informatics innovation to provide return of value to participant communities in the All of Us Research Program. - Brandy Mapes; Rachele S. Peterson; Karriem Watson; Melissa A. Basford; Elizabeth Cohn; Paul A. Harris; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2024)

Comparison of phenomic profiles in the All of Us Research Program against the US general population and the UK Biobank. - Chenjie Zeng; David J. Schlueter; Tam C. Tran; Anav Babbar; Thomas Cassini; Lisa Bastarache; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2024)

Beyond Phecodes: leveraging PheMAP to identify patients lacking diagnosis codes in electronic health records. - Chao Yan 004; Monika E. Grabowska; Rut Thakkar; Alyson L. Dickson; Peter J. Embí; QiPing Feng; Joshua C. Denny; Vern Eric Kerchberger; Bradley A. Malin; Wei-Qi Wei (J. Am. Medical Informatics Assoc., 2025)