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ORCIDJoshua C. Denny
- > Home > Persons > Joshua C. Denny
Publications
- 2024
[j83]Chenjie Zeng
, David J. Schlueter, Tam C. Tran, Anav Babbar, Thomas Cassini, Lisa Bastarache, Joshua C. Denny:
Comparison of phenomic profiles in the All of Us Research Program against the US general population and the UK Biobank. J. Am. Medical Informatics Assoc. 31(4): 846-854 (2024)- 2023
- [j81]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, Anav Babbar, Andrea H. Ramirez, Slavina Goleva, Joshua C. Denny:
Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research Program. J. Am. Medical Informatics Assoc. 31(1): 139-153 (2023) - 2022
- [j79]Rebecca Irlmeier, Jacob J. Hughey, Lisa Bastarache, Joshua C. Denny, Qingxia Chen:
Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS. Bioinform. 38(8): 2297-2306 (2022) - 2021
- [c118]Sarah DeLozier, Josh F. Peterson, Joshua C. Denny, Lisa Bastarache:
Using Genomic Association Replication Rates as an EHR Quality Measure via the Phenotype-Genotype Reference Map (PGRM). AMIA 2021 - [c117]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:
Systematic replication of smoking disease associations in the All of Us Research Program. AMIA 2021 - 2020
- [c115]Leigh Anne Tang, Sarah DeLozier, Lisa Bastarache, Colin Walsh, Joshua C. Denny:
Developing a Phenotype Risk Score for Opioid Adverse Events. AMIA 2020 - 2019
- [j68]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:
Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease. J. Am. Medical Informatics Assoc. 26(12): 1437-1447 (2019) - 2017
- [j57]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, Richard A. Dart, Anne M. Nikolai, Peggy L. Peissig, Joshua C. Denny:
Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. J. Am. Medical Informatics Assoc. 24(1): 162-171 (2017) - [c93]Jamie R. Robinson, Lisa Bastarache, Robert J. Carroll, Elizabeth A. Scoville, David A. Schwartz, Joshua C. Denny:
Sub-Phenotyping of Crohn's Disease Using a Large Electronic Record Cohort. AMIA 2017 - [c92]Jamie R. Robinson, Zongyang Mou, Lisa Bastarache, Wei-Qi Wei, Robert J. Carroll, Joshua C. Denny:
Association of BMI and Obesity Genetic Risk Score with Surgical Procedures Through a Procedure-wide Association Study. AMIA 2017 - 2015
- [c63]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:
PheWAS Network Analysis and Visualization. AMIA 2015 - 2014
- [j34]Robert J. Carroll, Lisa Bastarache, Joshua C. Denny:
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. Bioinform. 30(16): 2375-2376 (2014) - [c52]Pedro L. Teixeira, Robert J. Carroll, Lisa Bastarache, Peter Speltz, Joshua C. Smith, Joshua C. Denny:
Phenome-Wide Association Studies Using NLP-Derived Concepts. AMIA 2014 - 2013
- [j24]Wei-Qi Wei, Robert M. Cronin, Hua Xu, Thomas A. Lasko, Lisa Bastarache, Joshua C. Denny:
Development and evaluation of an ensemble resource linking medications to their indications. J. Am. Medical Informatics Assoc. 20(5): 954-961 (2013) - [c45]Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny:
Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems. AMIA 2013 - [c44]Robert J. Carroll, Lisa Bastarache, Joshua C. Denny:
Open Source R Implementation of the PheWAS Methodology. AMIA 2013 - [c41]Eugenia R. McPeek Hinz, Joshua C. Denny, Lisa Bastarache:
A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype. AMIA 2013 - [c40]Christine M. McEvoy, Robert J. Carroll, Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny:
Using PheWAS and Natural Language Processing to Discover Clinical Associations for Congenital Chest Deformities. AMIA 2013 - [c37]Wei-Qi Wei, Jonathan D. Mosley, Lisa Bastarache, Joshua C. Denny:
Validation and Enhancement of a Computable Medication Indication Resource (MEDI) Using a Large Practice-based Dataset. AMIA 2013 - 2012
- [c28]Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny:
Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR. AMIA 2012 - [c18]Wei-Qi Wei, Lisa Bastarache, Joshua C. Denny:
Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes. AMIA 2012 - [c12]Eugenia R. McPeek Hinz, Lisa Bastarache, Joshua C. Denny:
A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing. HISB 2012: 149 - 2010
- [j11]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:
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinform. 26(9): 1205-1210 (2010) - [j7]Joshua C. Denny, Josh F. Peterson, Neesha N. Choma, Hua Xu, Randolph A. Miller, Lisa Bastarache, Neeraja B. Peterson:
Extracting timing and status descriptors for colonoscopy testing from electronic medical records. J. Am. Medical Informatics Assoc. 17(4): 383-388 (2010) - [j6]Son Doan, Lisa Bastarache, Sergio Klimkowski, Joshua C. Denny, Hua Xu:
Integrating existing natural language processing tools for medication extraction from discharge summaries. J. Am. Medical Informatics Assoc. 17(5): 528-531 (2010) - 2009
- [j2]Joshua C. Denny, Lisa Bastarache, Elizabeth Ann Sastre, Anderson Spickard III:
Tracking medical students' clinical experiences using natural language processing. J. Biomed. Informatics 42(5): 781-789 (2009) - [c11]Joshua C. Denny, Josh F. Peterson, Neesha N. Choma, Hua Xu, Randolph A. Miller, Lisa Bastarache, Neeraja B. Peterson:
Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. AMIA 2009
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