Joshua C. Denny

ORCID

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 81

Top Venues

AMIA

J. Am. Medical Informatics Assoc.

J. Biomed. Informatics

CRI

Publications

Chenjie Zeng, David J. Schlueter, Tam C. Tran, Anav Babbar, Thomas Cassini, Lisa Bastarache, Joshua C. Denny
Research Program against the US general population and the UK Biobank. J. Am. Medical Informatics Assoc. 31 (4) (2024)
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, James A. Feinstein, Asiyah Y. Lin, Blake Martin, Nicolas A. Matentzoglu, Daniella Meeker, Justin T. Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingmin Aaron Zhang, Joshua C. Denny, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Melissa A. Haendel, Peter N. Robinson, Lawrence E. Hunter, Michael G. Kahn
Ontologizing health systems data at scale: making translational discovery a reality. npj Digit. Medicine 6 (2023)
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 Ramirez, Slavina Goleva, Joshua C. Denny
Research Program. J. Am. Medical Informatics Assoc. 31 (1) (2023)
Pascal S. Brandt, Abel N. Kho, Yuan Luo, Jennifer A. Pacheco, Theresa L. Walunas, Hakon Hakonarson, George Hripcsak, Cong Liu, Ning Shang, Chunhua Weng, Nephi Walton, David S. Carrell, Paul K. Crane, Eric B. Larson, Christopher G. Chute, Iftikhar J. Kullo, Robert J. Carroll, Joshua C. Denny, Andrea H. Ramirez, Wei-Qi Wei, Jyotishman Pathak, Laura K. Wiley, Rachel L. Richesson, Justin B. Starren, Luke V. Rasmussen
Characterizing variability of electronic health record-driven phenotype definitions. J. Am. Medical Informatics Assoc. 30 (3) (2023)
Huan Mo, Joshua C. Denny
The U.S. National Library of Medicine's impact on precision and genomic medicine. Inf. Serv. Use 42 (1) (2022)
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) (2022)
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, Abel N. Kho, Hua Xu, Consuelo H. Wilkins, Hoda Anton-Culver, Eric Boerwinkle, Mine Cicek, Cheryl R. Clark, Elizabeth Cohn, Lucila Ohno-Machado, Sheri D. Schully, Brian K. Ahmedani, Maria Argos, Robert M. Cronin, Christopher J. O'Donnell, Mona Fouad, David B. Goldstein, Philip Greenland, Scott J. Hebbring, Elizabeth W. Karlson, Parinda Khatri, Bruce Korf, Jordan W. Smoller, Stephen Sodeke, John Wilbanks, Justin Hentges, Stephen Mockrin, Christopher Lunt, Stephanie A. Devaney, Kelly Gebo, Joshua C. Denny, Robert J. Carroll, David Glazer, Paul A. Harris, George Hripcsak, Anthony Philippakis, Dan M. Roden
Research Program: Data quality, utility, and diversity. Patterns 3 (8) (2022)
Patrick Wu, Scott D. Nelson, Juan Zhao, Cosby A. Stone Jr., QiPing Feng, Qingxia Chen, Eric A. Larson, Bingshan Li, Nancy J. Cox, C. Michael Stein, Elizabeth Phillips, Dan M. Roden, Joshua C. Denny, Wei-Qi Wei
DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions. J. Am. Medical Informatics Assoc. 28 (7) (2021)
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)
David J. Schlueter, Lina M. Sulieman, Jacob 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)
Ning Shang, Atlas Khan, Fernanda Polubriaginof, Francesca Zanoni, Karla Mehl, David Fasel, Paul E. Drawz, Robert J. Carrol, Joshua C. Denny, Matthew A. Hathcock, Adelaide M. Arruda-Olson, Peggy L. Peissig, Richard A. Dart, Murray H. Brilliant, Eric B. Larson, David S. Carrell, Sarah A. Pendergrass, Shefali Setia Verma, Marylyn D. Ritchie, Barbara Benoit, Vivian S. Gainer, Elizabeth W. Karlson, Adam S. Gordon, Gail P. Jarvik, Ian B. Stanaway, David R. Crosslin, Sumit Mohan, Iuliana Ionita-Laza, Nicholas P. Tatonetti, Ali G. Gharavi, George Hripcsak, Chunhua Weng, Krzysztof Kiryluk
Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. npj Digit. Medicine 4 (2021)
Teresa Zayas-Cabán, Kevin J. Chaney, Courtney C. Rogers, Joshua C. Denny, P. Jon White
Meeting the challenge: Health information technology's essential role in achieving precision medicine. J. Am. Medical Informatics Assoc. 28 (6) (2021)
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, Joshua C. Denny
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. J. Am. Medical Informatics Assoc. 28 (1) (2021)
Nick Strayer, Jana K. Shirey-Rice, Yu Shyr, Joshua C. Denny, Jill M. Pulley, Yaomin Xu
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. Bioinform. 37 (12) (2021)
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, Joshua C. Denny
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. AMIA (2020)
Neil S. Zheng, QiPing Feng, Vern Eric Kerchberger, Juan Zhao, Todd L. Edwards, Nancy J. Cox, C. Michael Stein, Dan M. Roden, Joshua C. Denny, Wei-Qi Wei
PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. J. Am. Medical Informatics Assoc. 27 (11) (2020)
Hannah L. Weeks, Cole Beck, Elizabeth McNeer, Michael L. Williams, Cosmin Adrian Bejan, Joshua C. Denny, Leena Choi
medExtractR: A targeted, customizable approach to medication extraction from electronic health records. J. Am. Medical Informatics Assoc. 27 (3) (2020)
Leigh Anne Tang, Sarah DeLozier, Lisa Bastarache, Colin Walsh, Joshua C. Denny
Developing a Phenotype Risk Score for Opioid Adverse Events. AMIA (2020)
Patrick Wu, QiPing Feng, Joshua C. Denny, Wei-Qi Wei
Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs. AMIA (2019)
Xinyuan Zhang, Yogasudha Veturi, Shefali Setia Verma, William Bone, Anurag Verma, Anastasia Lucas, Scott J. Hebbring, Joshua C. Denny, Ian Stanaway, Gail P. Jarvik, David R. Crosslin, Eric B. Larson, Laura Rasmussen-Torvik, Sarah A. Pendergrass, Jordan W. Smoller, Hakon Hakonarson, Patrick Sleiman, Chunhua Weng, David Fasel, Wei-Qi Wei, Iftikhar J. Kullo, Daniel J. Schaid, Wendy K. Chung, Marylyn D. Ritchie
Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE network. PSB (2019)
George Hripcsak, Ning Shang, Peggy L. Peissig, Luke V. Rasmussen, Cong Liu, Barbara Benoit, Robert J. Carroll, David S. Carrell, Joshua C. Denny, Ozan Dikilitas, Vivian S. Gainer, Kayla Marie Howell, Jeffrey G. Klann, Iftikhar J. Kullo, Todd Lingren, Frank D. Mentch, Shawn N. Murphy, Karthik Natarajan, Chunhua Weng
Facilitating phenotype transfer using a common data model. J. Biomed. Informatics 96 (2019)
Juan Zhao, Yun Zhang, David J. Schlueter, Patrick Wu, Vern Eric Kerchberger, S. Trent Rosenbloom, Quinn S. Wells, QiPing Feng, Joshua C. Denny, Wei-Qi Wei
Detecting time-evolving phenotypic topics via tensor factorization on electronic health records: Cardiovascular disease case study. J. Biomed. Informatics 98 (2019)
Qiang Wei, Yukun Chen, Mandana Salimi, Joshua C. Denny, Qiaozhu Mei, Thomas A. Lasko, Qingxia Chen, Stephen Wu, Amy Franklin, Trevor Cohen, Hua Xu
Cost-aware active learning for named entity recognition in clinical text. J. Am. Medical Informatics Assoc. 26 (11) (2019)
Luwan Zhang, Yichi Zhang, Tianrun A. Cai, Yuri Ahuja, Zeling He, Yuk-Lam Ho, Andrew Beam, Kelly Cho, Robert Carroll, Joshua C. Denny, Isaac S. Kohane, Katherine P. Liao, Tianxi Cai
Automated grouping of medical codes via multiview banded spectral clustering. J. Biomed. Informatics 100 (2019)
Jette Henderson, Bradley A. Malin, Joshua C. Denny, Abel N. Kho, Jimeng Sun, Joydeep Ghosh, Joyce C. Ho
CP Tensor Decomposition with Cannot-Link Intermode Constraints. SDM (2019)
Ning Shang, Cong Liu, 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, Vivian S. Gainer, Iftikhar J. Kullo, Jennifer A. Pacheco, Hakon Hakonarson, Theresa L. Walunas, Joshua C. Denny, Chunhua Weng
Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. J. Biomed. Informatics 99 (2019)
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) (2019)
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
Quality Analysis of the All of Us Research Program Health Surveys. AMIA (2019)
Juan Zhao, QiPing Feng, Patrick Wu, Joshua C. Denny, Wei-Qi Wei
Deep Learning Using Electronic Health Records and Genetic Data to Predict Cardiovascular Diseases. AMIA (2019)
Andrea H. Ramirez, Yaping Shi, Elliot M. Fielstein, Jonathan S. Schildcrout, Henry H. Ong, Joshua C. Denny, Josh F. Peterson
Extracting Drug Exposure Epochs and Drug Response Outcomes from Electronic Health Records. AMIA (2019)
Hannah L. Weeks, Cole Beck, Elizabeth McNeer, Cosmin Adrian Bejan, Joshua C. Denny, Leena Choi
medExtractR: A medication extraction algorithm for electronic health records using the R programming language. AMIA (2019)
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
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. J. Am. Medical Informatics Assoc. 25 (1) (2018)
Leena Choi, Robert J. Carroll, Cole Beck, Jonathan D. Mosley, Dan M. Roden, Joshua C. Denny, Sara L. Van Driest
Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects. Bioinform. 34 (17) (2018)
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, Yuan Luo
Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. BIBM (2018)
Andrea H. Ramirez, Elliot M. Fielstein, QiPing Feng, Henry H. Ong, Jonathan S. Schildcrout, Yaping Shi, Joshua C. Denny, Josh F. Peterson
EHR Extraction of Longitudinal Exposure to Proton Pump Inhibitors. AMIA (2018)
Jette Henderson, Huan He, Bradley A. Malin, Joshua C. Denny, Abel N. Kho, Joydeep Ghosh, Joyce C. Ho
Phenotyping through Semi-Supervised Tensor Factorization (PSST). AMIA (2018)
Juan Zhao, QiPing Feng, Patrick Wu, Joshua C. Denny, Wei-Qi Wei
Using Topic Modeling to Identify Relationship between LPA Variant and Disease Phenotypes. AMIA (2018)
Joshua C. Smith, Qingxia Chen, Joshua C. Denny, Dan M. Roden, Kevin B. Johnson, Randolph A. Miller
Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions. Appl. Clin. Inform. 9 (02) (2018)
Mary Regina Boland, Pradipta Parhi, Li Li, Riccardo Miotto, Robert J. Carroll, Usman Iqbal, Phung-Anh (Alex) Nguyen, Martijn J. Schuemie, Seng Chan You, Donahue Smith, Sean Mooney, Patrick B. Ryan, Yu-Chuan (Jack) Li, Rae Woong Park, Joshua C. Denny, Joel T. Dudley, George Hripcsak, Pierre Gentine, Nicholas P. Tatonetti
Uncovering exposures responsible for birth season - disease effects: a global study. J. Am. Medical Informatics Assoc. 25 (3) (2018)
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, Ning Shang, Barbara Benoit, Vivian S. Gainer, Kenneth Borthwick, Kathryn L. Jackson, Ambrish Sharma, Andy Yizhou Wu, Abel N. Kho, Dan M. Roden, Jyotishman Pathak, Joshua C. Denny, William K. Thompson
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. J. Am. Medical Informatics Assoc. 25 (11) (2018)
Joshua C. Denny
Huge Cohorts, Genomics, and Clinical Data to Personalize Medicine. BCB (2018)
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, Yuan Luo
Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. CoRR (2018)
Joseph R. Coco, Cheng Ye, Chen Hajaj, Yevgeniy Vorobeychik, Joshua C. Denny, Laurie L. Novak, Bradley A. Malin, Thomas A. Lasko, Daniel Fabbri
Crowdsourcing Clinical Chart Reviews. AMIA (2018)
Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner
Session Introduction. PSB (2018)
Peter Speltz, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, William Thompson, Guoqian Jiang, Jyotishman Pathak, Joshua C. Denny
The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs. AMIA (2017)
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)
Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
Session Introduction. PSB (2017)
Robert J. Carroll, Joshua C. Mandel, Karthik Natarajan, Scott Sutherland, Joshua C. Denny
The Data and Research Center of the All of Us Research Program: Framework for a National Cohort Program and Research Opportunities. AMIA (2017)
Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Lulu Wang, Carmelo Blanquicett, Ergin Soysal, Jun Xu, Hua Xu
A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). J. Am. Medical Informatics Assoc. 24 (e1) (2017)
Kelsey R. Mayo, Robert J. Carroll, Jason Tan, Rebecca Johnston, Celecia M. Scott, Joshua C. Denny, Paul A. Harris
HealthPro: An integrated web application for essential health data and biological specimen collection in the Precision Medicine Initiative. AMIA (2017)
Jette Henderson, Joyce C. Ho, Abel N. Kho, Joshua C. Denny, Bradley A. Malin, Jimeng Sun, Joydeep Ghosh
Granite: Diversified, Sparse Tensor Factorization for Electronic Health Record-Based Phenotyping. ICHI (2017)
Richard C. Kiefer, Luke V. Rasmussen, Jennifer A. Pacheco, Peter Speltz, Joshua C. Denny, William K. Thompson, Jyotishman Pathak, Guoqian Jiang
Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository. AMIA (2017)
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)
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) (2017)
Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Qingxia Chen, Sungrim Moon, Jingqi Wang, Ky Nguyen, Tolulola Dawodu, Trevor Cohen, Joshua C. Denny, Hua Xu
An active learning-enabled annotation system for clinical named entity recognition. BMC Medical Informatics Decis. Mak. 17 (2) (2017)
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
Large-Scale Text Mining of Social Determinants from Electronic Health Records: Case Studies of Homelessness and Adverse Childhood Experiences. AMIA (2017)
Laura K. Wiley, Jacob P. VanHouten, David Samuels, Melinda Aldrich, Dan M. Roden, Josh F. Peterson, Joshua C. Denny
Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population. PSB (2017)
Patrick Wu, Joshua C. Denny, Wei-Qi Wei
A Phenome-Wide Association Study (PheWAS) of Iron Deficiency in a Large Electronic Health Record Database. AMIA (2017)
Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu
Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. CRI (2017)
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, Peter Speltz, Elliot M. Fielstein, Jill M. Pulley, Sunil Kripalani, David Schlundt, Joshua C. Denny
Development and Testing of Participant Provided Information Modules for the Precision Medicine Initiative. CRI (2017)
Robert M. Cronin, Daniel Fabbri, Joshua C. Denny, S. Trent Rosenbloom, Gretchen Purcell Jackson
A comparison of rule-based and machine learning approaches for classifying patient portal messages. Int. J. Medical Informatics 105 (2017)
Hee-Jin Lee, Min Jiang, Yonghui Wu, Christian Shaffer, John H. Cleator, Eitan Friedman, Joshua P. Lewis, Dan M. Roden, Joshua C. Denny, Hua Xu
A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. CRI (2017)
Cosmin Adrian Bejan, Joshua C. Denny
A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects. AMIA (2017)
Andrea H. Ramirez, Anthony Philippakis, Gonçalo R. Abecasis, Paul A. Harris, Joshua C. Denny
The All of Us Research Program Researcher Portal: Innovative access to Unprecendented Data. AMIA (2017)
Laura K. Wiley, Peter Tarczy-Hornoch, Joshua C. Denny, Robert R. Freimuth, Casey L. Overby, Nigam Shah, Ross D. Martin, Indra Neil Sarkar
Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. J. Am. Medical Informatics Assoc. 23 (2) (2016)
Guoqian Jiang, William K. Thompson, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, Huan Mo, Peter Speltz, Joshua C. Denny, Jyotishman Pathak
An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution. AMIA (2016)
Rui Duan, Ming Cao, Yonghui Wu, Jing Huang, Joshua C. Denny, Hua Xu, Yong Chen
An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. AMIA (2016)
Anthony E. Solomonides, Russ B. Altman, Joshua C. Denny, Larry Ozeran, Jessica D. Tenenbaum
The Many Meanings of Precision Medicine. CRI (2016)
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, Lisa Bailey-Davis, Marc S. Williams, Keith Marsolo, Imre Solti, Ingrid Holm, John Harley, Isaac S. Kohane, Guergana Savova, Nancy Crimmins, Todd Lingren, Vidhu Thaker
Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. Appl. Clin. Inform. 7 (03) (2016)
Rachel L. Richesson, Jimeng Sun, Jyotishman Pathak, Abel N. Kho, Joshua C. Denny
Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods. Artif. Intell. Medicine 71 (2016)
Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, S. Trent Rosenbloom, Ky Nguyen, Tolulola Dawodu, Hua Xu
Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time. AMIA (2016)
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, Brian H. Shirts, Elena M. Stoffel, Peter Tarczy-Hornoch, Carolyn Rohrer Vitek, Wendy A. Wolf, Justin Starren, Luke V. Rasmussen
Practical considerations for implementing genomic information resources. Appl. Clin. Inform. 7 (03) (2016)
Lewis J. Frey, Elmer V. Bernstam, Joshua C. Denny
Precision medicine informatics. J. Am. Medical Informatics Assoc. 23 (4) (2016)
Huan Mo, Guoqian Jiang, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William Thompson
A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. CRI (2016)
Jessica D. Tenenbaum, Subha Madhavan, Robert R. Freimuth, Joshua C. Denny, Lewis J. Frey
Translational Bioinformatics 101. PSB (2016)
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, William K. Thompson, Guergana Savova, Jonathan L. Haines, Dan M. Roden, Paul A. Harris, Joshua C. Denny
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J. Am. Medical Informatics Assoc. 23 (6) (2016)
Guoqian Jiang, Richard C. Kiefer, Luke V. Rasmussen, Harold R. Solbrig, Huan Mo, Jennifer A. Pacheco, Jie Xu, Enid N. H. Montague, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak
Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. J. Biomed. Informatics 62 (2016)
Wei-Qi Wei, Pedro L. Teixeira, Huan Mo, Robert M. Cronin, Jeremy L. Warner, Joshua C. Denny
Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. J. Am. Medical Informatics Assoc. 23 (e1) (2016)
Laura K. Wiley, Marc Beller, Julie Field, Josh F. Peterson, Joshua C. Denny
Evaluating Physician Response to Pharmacogenomic-Guided Warfarin Dosing in an Hospitalized Population. CRI (2016)
Raymond Heatherly, Luke V. Rasmussen, Peggy L. Peissig, Jennifer A. Pacheco, Paul A. Harris, Joshua C. Denny, Bradley A. Malin
A multi-institution evaluation of clinical profile anonymization. J. Am. Medical Informatics Assoc. 23 (e1) (2016)
Yang Huang, Hua Xu, Joshua C. Denny
Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations. AMIA (2016)
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)
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
A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution. MedInfo (2015)
Cosmin Adrian Bejan, Wei-Qi Wei, Joshua C. Denny
Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. J. Am. Medical Informatics Assoc. 22 (e1) (2015)
Guergana Savova, Rebecca S. Jacobson, Joshua C. Denny, Nicole L. Washington, Harry Hochheiser
Natural Language Processing for Phenotype Extraction: Challenges in Extraction and Representation. AMIA (2015)
Enid N. H. Montague, Jie Xu, Luke V. Rasmussen, Joshua C. Denny, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Peter Speltz, William K. Thompson, Jyotishman Pathak
Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools. AMIA (2015)
You Chen, Joydeep Ghosh, Cosmin Adrian Bejan, Carl A. Gunter, Siddharth Gupta, Abel N. Kho, David M. Liebovitz, Jimeng Sun, Joshua C. Denny, Bradley A. Malin
Building bridges across electronic health record systems through inferred phenotypic topics. J. Biomed. Informatics 55 (2015)
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, Abel N. Kho
A Genome- and Phenome- Wide Study of Diverticulosis. AMIA (2015)
Robert M. Cronin, Daniel Fabbri, Joshua C. Denny, Gretchen Purcell Jackson
Automated Classification of Consumer Health Information Needs in Patient Portal Messages. AMIA (2015)
Guoqian Jiang, Harold R. Solbrig, Richard C. Kiefer, Luke V. Rasmussen, Huan Mo, Jennifer A. Pacheco, Enid N. H. Montague, Jie Xu, Peter Speltz, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak
Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study. AMIA (2015)
Jie Xu, Luke V. Rasmussen, Pamela L. Shaw, Guoqian Jiang, Richard C. Kiefer, Huan Mo, Jennifer A. Pacheco, Peter Speltz, Qian Zhu, Joshua C. Denny, Jyotishman Pathak, William K. Thompson, Enid N. H. Montague
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Yichen Wang, Robert Chen, Joydeep Ghosh, Joshua C. Denny, Abel N. Kho, You Chen, Bradley A. Malin, Jimeng Sun
Rubik: Knowledge Guided Tensor Factorization and Completion for Health Data Analytics. KDD (2015)
Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu, Zhongming Zhao
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput. Biol. 11 (6) (2015)
Jessica D. Tenenbaum, Joshua C. Denny, David Flannery, Douglas B. Fridsma, Marc S. Williams
Building the Computational Workforce for Precision Medicine. AMIA (2015)
Travis Osterman, Wei-Qi Wei, Joshua C. Denny
Quantifying Tobacco Exposure Using Clinical Notes and Natural Language Processing to Enable Lung Cancer Screening. AMIA (2015)
Joshua C. Denny, Anderson Spickard III, Peter Speltz, Renee Porier, Donna E. Rosenstiel, James S. Powers
Using natural language processing to provide personalized learning opportunities from trainee clinical notes. J. Biomed. Informatics 56 (2015)
Jeremy L. Warner, Joshua C. Denny, David A. Kreda, Gil Alterovitz
Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization. J. Am. Medical Informatics Assoc. 22 (2) (2015)
Min Jiang, Yang Huang, Jung-Wei Fan, Buzhou Tang, Joshua C. Denny, Hua Xu
Parsing clinical text: how good are the state-of-the-art parsers? BMC Medical Informatics Decis. Mak. 15 (S-1) (2015)
Huan Mo, William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Guoqian Jiang, Richard C. Kiefer, Qian Zhu, Jie Xu, Enid N. H. Montague, David S. Carrell, Todd Lingren, Frank D. Mentch, Yizhao Ni, Firas H. Wehbe, Peggy L. Peissig, Gerard Tromp, Eric B. Larson, Christopher G. Chute, Jyotishman Pathak, Joshua C. Denny, Peter Speltz, Abel N. Kho, Gail P. Jarvik, Cosmin Adrian Bejan, Marc S. Williams, Kenneth Borthwick, Terrie E. Kitchner, Dan M. Roden, Paul A. Harris
Desiderata for computable representations of electronic health records-driven phenotype algorithms. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Huan Mo, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson
Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME. AMIA (2015)

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Joshua C. Denny