Joshua C. Denny

209 papers A* 2A 1B 1Misc 96Journal 88Unranked 21

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A one-shot, lossless algorithm for cross-cohort learning in mixed-outcomes analysis. Patterns Ruowang Li, Luke Benz, Rui Duan, Joshua C. Denny, Hakon Hakonarson, Jonathan D. Mosley, Jordan W. Smoller, Wei-Qi Wei, Thomas Lumley, Marylyn D. Ritchie, Jason H. Moore, Yong Chen
2025	J	`jnl`	Beyond Phecodes: leveraging PheMAP to identify patients lacking diagnosis codes in electronic health records. J. Am. Medical Informatics Assoc. Chao Yan, 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
2025	J	`jnl`	PheWAS analysis on large-scale biobank data with PheTK. Bioinform. Tam C. Tran, David J. Schlueter, Chenjie Zeng, Huan Mo, Robert J. Carroll, Joshua C. Denny
2024	J	`jnl`	Comparison of phenomic profiles in the J. Am. Medical Informatics Assoc. Chenjie Zeng, David J. Schlueter, Tam C. Tran, Anav Babbar, Thomas Cassini, Lisa Bastarache, Joshua C. Denny
2024	J	`jnl`	Informatics innovation to provide return of value to participant communities in the J. Am. Medical Informatics Assoc. Brandy Mapes, Rachele S. Peterson, Karriem Watson, Melissa A. Basford, Elizabeth Cohn, Paul A. Harris, Joshua C. Denny
2023	J	`jnl`	Characterizing variability of electronic health record-driven phenotype definitions. J. Am. Medical Informatics Assoc. 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
2023	J	`jnl`	Ontologizing health systems data at scale: making translational discovery a reality. npj Digit. Medicine 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
2023	J	`jnl`	Systematic replication of smoking disease associations using survey responses and EHR data in the J. Am. Medical Informatics Assoc. 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
2022	Misc	`conf`	Comparing Effect Sizes in Covid Positive Phenomic Profiles. AMIA Ariel Williams, David J. Schlueter, Jacob Keaton, Tracey Ferrara, Onajia J. Stubblefield, Kyle Webb, Slavina Goleva, Jian Dai, Chenjie Zeng, Huan Mo, Thomas Cassini, Joshua C. Denny
2022	J	`jnl`	Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS. Bioinform. Rebecca Irlmeier, Jacob J. Hughey, Lisa Bastarache, Joshua C. Denny, Qingxia Chen
2022	Misc	`conf`	Impact of COVID-19 on mental health outcomes in the All of Us Research Program. AMIA Onajia J. Stubblefield, David J. Schlueter, Jacob Keaton, Ariel Williams, Slavina Goleva, Tracey Ferrara, Chenjie Zeng, Huan Mo, Joshua C. Denny
2022	J	`jnl`	The Patterns 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 A. Philippakis, Dan M. Roden
2022	J	`jnl`	The U.S. National Library of Medicine's impact on precision and genomic medicine. Inf. Serv. Use Huan Mo, Joshua C. Denny
2021	Misc	`conf`	Comparing the Phenomic Profile of All of Us Research Program and National COVID Cohort Collaborative. AMIA Kyle P. Webb, David J. Schlueter, Jacob Keaton, Tracey Ferrara, Ariel Williams, Joshua C. Denny
2021	J	`jnl`	DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions. J. Am. Medical Informatics Assoc. 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
2021	Misc	`conf`	Informatics-izing the National Institutes of Health. AMIA Clement J. McDonald, Patricia Flatley Brennan, Michael F. Chiang, Joshua C. Denny, Zhiyong Lu
2021	J	`jnl`	Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. npj Digit. Medicine 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, 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
2021	J	`jnl`	Meeting the challenge: Health information technology's essential role in achieving precision medicine. J. Am. Medical Informatics Assoc. Teresa Zayas-Cabán, Kevin J. Chaney, Courtney C. Rogers, Joshua C. Denny, P. Jon White
2021	J	`jnl`	PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. Bioinform. Nick Strayer, Jana K. Shirey-Rice, Yu Shyr, Joshua C. Denny, Jill M. Pulley, Yaomin Xu
2021	J	`jnl`	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. 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
2021	Misc	`conf`	Systematic replication of smoking disease associations in the All of Us Research Program. AMIA 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
2021	Misc	`conf`	Using Genomic Association Replication Rates as an EHR Quality Measure via the Phenotype-Genotype Reference Map (PGRM). AMIA Sarah DeLozier, Josh F. Peterson, Joshua C. Denny, Lisa Bastarache
2020	Misc	`conf`	Developing a Phenotype Risk Score for Opioid Adverse Events. AMIA Leigh Anne Tang, Sarah DeLozier, Lisa Bastarache, Colin Walsh, Joshua C. Denny
2020	J	`jnl`	PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. J. Am. Medical Informatics Assoc. 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
2020	Misc	`conf`	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 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
2020	J	`jnl`	medExtractR: A targeted, customizable approach to medication extraction from electronic health records. J. Am. Medical Informatics Assoc. Hannah L. Weeks, Cole Beck, Elizabeth McNeer, Michael L. Williams, Cosmin Adrian Bejan, Joshua C. Denny, Leena Choi
2019	J	`jnl`	Automated grouping of medical codes via multiview banded spectral clustering. J. Biomed. Informatics 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, Tianxi Cai
2019	A	`conf`	CP Tensor Decomposition with Cannot-Link Intermode Constraints. SDM Jette Henderson, Bradley A. Malin, Joshua C. Denny, Abel N. Kho, Jimeng Sun, Joydeep Ghosh, Joyce C. Ho
2019	Misc	`conf`	Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs. AMIA Patrick Wu, QiPing Feng, Joshua C. Denny, Wei-Qi Wei
2019	J	`jnl`	Cost-aware active learning for named entity recognition in clinical text. J. Am. Medical Informatics Assoc. Qiang Wei, Yukun Chen, Mandana Salimi, Joshua C. Denny, Qiaozhu Mei, Thomas A. Lasko, Qingxia Chen, Stephen Wu, Amy Franklin, Trevor Cohen, Hua Xu
2019	Misc	`conf`	Deep Learning Using Electronic Health Records and Genetic Data to Predict Cardiovascular Diseases. AMIA Juan Zhao, QiPing Feng, Patrick Wu, Joshua C. Denny, Wei-Qi Wei
2019	Misc	`conf`	Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE network. PSB Xinyuan Zhang, 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, 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
2019	J	`jnl`	Detecting time-evolving phenotypic topics via tensor factorization on electronic health records: Cardiovascular disease case study. J. Biomed. Informatics Juan Zhao, Yun Zhang, David J. Schlueter, Patrick Wu, Vern Eric Kerchberger, S. Trent Rosenbloom, Quinn Stanton Wells, QiPing Feng, Joshua C. Denny, Wei-Qi Wei
2019	Misc	`conf`	Extracting Drug Exposure Epochs and Drug Response Outcomes from Electronic Health Records. AMIA Andrea H. Ramirez, Yaping Shi, Elliot M. Fielstein, Jonathan S. Schildcrout, Henry H. Ong, Joshua C. Denny, Josh F. Peterson
2019	J	`jnl`	Facilitating phenotype transfer using a common data model. J. Biomed. Informatics 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
2019	J	`jnl`	Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease. J. Am. Medical Informatics Assoc. 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
2019	J	`jnl`	Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. J. Biomed. Informatics 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
2019	Misc	`conf`	Quality Analysis of the All of Us Research Program Health Surveys. AMIA 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
2019	Misc	`conf`	medExtractR: A medication extraction algorithm for electronic health records using the R programming language. AMIA Hannah L. Weeks, Cole Beck, Elizabeth McNeer, Cosmin Adrian Bejan, Joshua C. Denny, Leena Choi
2018	J	`jnl`	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. 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
2018	—	`conf`	Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. BIBM 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
2018	J	`jnl`	Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. CoRR 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
2018	Misc	`conf`	Crowdsourcing Clinical Chart Reviews. AMIA Joseph R. Coco, Cheng Ye, Chen Hajaj, Yevgeniy Vorobeychik, Joshua C. Denny, Laurie L. Novak, Bradley A. Malin, Thomas A. Lasko, Daniel Fabbri
2018	Misc	`conf`	EHR Extraction of Longitudinal Exposure to Proton Pump Inhibitors. AMIA Andrea H. Ramirez, Elliot M. Fielstein, QiPing Feng, Henry H. Ong, Jonathan S. Schildcrout, Yaping Shi, Joshua C. Denny, Josh F. Peterson
2018	J	`jnl`	Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects. Bioinform. Leena Choi, Robert J. Carroll, Cole Beck, Jonathan D. Mosley, Dan M. Roden, Joshua C. Denny, Sara L. Van Driest
2018	J	`jnl`	Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions. Appl. Clin. Inform. Joshua C. Smith, Qingxia Chen, Joshua C. Denny, Dan M. Roden, Kevin B. Johnson, Randolph A. Miller
2018	—	`conf`	Huge Cohorts, Genomics, and Clinical Data to Personalize Medicine. BCB Joshua C. Denny
2018	J	`jnl`	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. 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
2018	Misc	`conf`	Phenotyping through Semi-Supervised Tensor Factorization (PSST). AMIA Jette Henderson, Huan He, Bradley A. Malin, Joshua C. Denny, Abel N. Kho, Joydeep Ghosh, Joyce C. Ho
2018	Misc	`conf`	Session Introduction. PSB Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner
2018	J	`jnl`	Uncovering exposures responsible for birth season - disease effects: a global study. J. Am. Medical Informatics Assoc. 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 D. Mooney, Patrick B. Ryan, Yu-Chuan (Jack) Li, Rae Woong Park, Joshua C. Denny, Joel T. Dudley, George Hripcsak, Pierre Gentine, Nicholas P. Tatonetti
2018	Misc	`conf`	Using Topic Modeling to Identify Relationship between LPA Variant and Disease Phenotypes. AMIA Juan Zhao, QiPing Feng, Patrick Wu, Joshua C. Denny, Wei-Qi Wei
2017	Misc	`conf`	A Phenome-Wide Association Study (PheWAS) of Iron Deficiency in a Large Electronic Health Record Database. AMIA Patrick Wu, Joshua C. Denny, Wei-Qi Wei
2017	Misc	`conf`	A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects. AMIA Cosmin Adrian Bejan, Joshua C. Denny
2017	—	`conf`	A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. CRI 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
2017	J	`jnl`	A comparison of rule-based and machine learning approaches for classifying patient portal messages. Int. J. Medical Informatics Robert M. Cronin, Daniel Fabbri, Joshua C. Denny, S. Trent Rosenbloom, Gretchen Purcell Jackson
2017	J	`jnl`	A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). J. Am. Medical Informatics Assoc. Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Lulu Wang, Carmelo Blanquicett, Ergin Soysal, Jun Xu, Hua Xu
2017	J	`jnl`	An active learning-enabled annotation system for clinical named entity recognition. BMC Medical Informatics Decis. Mak. Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Qingxia Chen, Sungrim Moon, Jingqi Wang, Ky Nguyen, Tolulola Dawodu, Trevor Cohen, Joshua C. Denny, Hua Xu
2017	Misc	`conf`	Association of BMI and Obesity Genetic Risk Score with Surgical Procedures Through a Procedure-wide Association Study. AMIA Jamie R. Robinson, Zongyang Mou, Lisa Bastarache, Wei-Qi Wei, Robert J. Carroll, Joshua C. Denny
2017	—	`conf`	Development and Testing of Participant Provided Information Modules for the Precision Medicine Initiative. CRI 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
2017	J	`jnl`	Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. J. Am. Medical Informatics Assoc. 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
2017	—	`conf`	Granite: Diversified, Sparse Tensor Factorization for Electronic Health Record-Based Phenotyping. ICHI Jette Henderson, Joyce C. Ho, Abel N. Kho, Joshua C. Denny, Bradley A. Malin, Jimeng Sun, Joydeep Ghosh
2017	Misc	`conf`	HealthPro: An integrated web application for essential health data and biological specimen collection in the Precision Medicine Initiative. AMIA Kelsey R. Mayo, Robert J. Carroll, Jason Tan, Rebecca Johnston, Celecia M. Scott, Joshua C. Denny, Paul A. Harris
2017	—	`conf`	Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. CRI Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu
2017	Misc	`conf`	Large-Scale Text Mining of Social Determinants from Electronic Health Records: Case Studies of Homelessness and Adverse Childhood Experiences. AMIA 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
2017	Misc	`conf`	Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository. AMIA Richard C. Kiefer, Luke V. Rasmussen, Jennifer A. Pacheco, Peter Speltz, Joshua C. Denny, William K. Thompson, Jyotishman Pathak, Guoqian Jiang
2017	Misc	`conf`	Session Introduction. PSB Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
2017	Misc	`conf`	Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population. PSB Laura K. Wiley, Jacob P. VanHouten, David Samuels, Melinda Aldrich, Dan M. Roden, Josh F. Peterson, Joshua C. Denny
2017	Misc	`conf`	Sub-Phenotyping of Crohn's Disease Using a Large Electronic Record Cohort. AMIA Jamie R. Robinson, Lisa Bastarache, Robert J. Carroll, Elizabeth A. Scoville, David A. Schwartz, Joshua C. Denny
2017	Misc	`conf`	The All of Us Research Program Researcher Portal: Innovative access to Unprecendented Data. AMIA Andrea H. Ramirez, Anthony A. Philippakis, Gonçalo R. Abecasis, Paul A. Harris, Joshua C. Denny
2017	Misc	`conf`	The Data and Research Center of the All of Us Research Program: Framework for a National Cohort Program and Research Opportunities. AMIA Robert J. Carroll, Joshua C. Mandel, Karthik Natarajan, Scott Sutherland, Joshua C. Denny
2017	Misc	`conf`	The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs. AMIA Peter Speltz, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, William K. Thompson, Guoqian Jiang, Jyotishman Pathak, Joshua C. Denny
2016	—	`conf`	A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. CRI Huan Mo, Guoqian Jiang, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson
2016	J	`jnl`	A multi-institution evaluation of clinical profile anonymization. J. Am. Medical Informatics Assoc. Raymond Heatherly, Luke V. Rasmussen, Peggy L. Peissig, Jennifer A. Pacheco, Paul A. Harris, Joshua C. Denny, Bradley A. Malin
2016	Misc	`conf`	An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. AMIA Rui Duan, Ming Cao, Yonghui Wu, Jing Huang, Joshua C. Denny, Hua Xu, Yong Chen
2016	Misc	`conf`	An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution. AMIA Guoqian Jiang, William K. Thompson, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, Huan Mo, Peter Speltz, Joshua C. Denny, Jyotishman Pathak
2016	Misc	`conf`	Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time. AMIA Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, S. Trent Rosenbloom, Ky Nguyen, Tolulola Dawodu, Hua Xu
2016	Misc	`conf`	Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations. AMIA Yang Huang, Hua Xu, Joshua C. Denny
2016	J	`jnl`	Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods. Artif. Intell. Medicine Rachel L. Richesson, Jimeng Sun, Jyotishman Pathak, Abel N. Kho, Joshua C. Denny
2016	J	`jnl`	Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. J. Am. Medical Informatics Assoc. Wei-Qi Wei, Pedro L. Teixeira, Huan Mo, Robert M. Cronin, Jeremy L. Warner, Joshua C. Denny
2016	J	`jnl`	Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. J. Biomed. Informatics 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
2016	J	`jnl`	Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. Appl. Clin. Inform. 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 A. Holm, John Harley, Isaac S. Kohane, Guergana Savova, Nancy Crimmins, Todd Lingren, Vidhu Thaker
2016	—	`conf`	Evaluating Physician Response to Pharmacogenomic-Guided Warfarin Dosing in an Hospitalized Population. CRI Laura K. Wiley, Marc Beller, Julie Field, Josh F. Peterson, Joshua C. Denny
2016	J	`jnl`	Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. J. Am. Medical Informatics Assoc. Laura K. Wiley, Peter Tarczy-Hornoch, Joshua C. Denny, Robert R. Freimuth, Casey L. Overby, Nigam Shah, Ross D. Martin, Indra Neil Sarkar
2016	J	`jnl`	PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J. Am. Medical Informatics Assoc. 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
2016	J	`jnl`	Practical considerations for implementing genomic information resources. Appl. Clin. Inform. 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
2016	J	`jnl`	Precision medicine informatics. J. Am. Medical Informatics Assoc. Lewis J. Frey, Elmer V. Bernstam, Joshua C. Denny
2016	—	`conf`	The Many Meanings of Precision Medicine. CRI Anthony E. Solomonides, Russ B. Altman, Joshua C. Denny, Larry Ozeran, Jessica D. Tenenbaum
2016	Misc	`conf`	Translational Bioinformatics 101. PSB Jessica D. Tenenbaum, Subha Madhavan, Robert R. Freimuth, Joshua C. Denny, Lewis J. Frey
2015	Misc	`conf`	(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping. AMIA Jennifer A. Pacheco, Abel N. Kho, Jyotishman Pathak, Joshua C. Denny, Shawn N. Murphy
2015	Misc	`conf`	A Genome- and Phenome- Wide Study of Diverticulosis. AMIA 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
2015	—	`conf`	A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution. MedInfo 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
2015	J	`jnl`	A study of active learning methods for named entity recognition in clinical text. J. Biomed. Informatics Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu
2015	J	`jnl`	Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. J. Am. Medical Informatics Assoc. Cosmin Adrian Bejan, Wei-Qi Wei, Joshua C. Denny
2015	Misc	`conf`	Automated Classification of Consumer Health Information Needs in Patient Portal Messages. AMIA Robert M. Cronin, Daniel Fabbri, Joshua C. Denny, Gretchen Purcell Jackson
2015	J	`jnl`	Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. J. Am. Medical Informatics Assoc. Chen Lin, 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
2015	J	`jnl`	Building bridges across electronic health record systems through inferred phenotypic topics. J. Biomed. Informatics 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
2015	Misc	`conf`	Building the Computational Workforce for Precision Medicine. AMIA Jessica D. Tenenbaum, Joshua C. Denny, David Flannery, Douglas B. Fridsma, Marc S. Williams
2015	J	`jnl`	Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput. Biol. 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
2015	J	`jnl`	Desiderata for computable representations of electronic health records-driven phenotype algorithms. J. Am. Medical Informatics Assoc. 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
2015	Misc	`conf`	Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study. AMIA 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
2015	Misc	`conf`	Natural Language Processing for Phenotype Extraction: Challenges in Extraction and Representation. AMIA Guergana Savova, Rebecca S. Jacobson, Joshua C. Denny, Nicole L. Washington, Harry Hochheiser
2015	J	`jnl`	Parsing clinical text: how good are the state-of-the-art parsers? BMC Medical Informatics Decis. Mak. Min Jiang, Yang Huang, Jungwei Fan, Buzhou Tang, Joshua C. Denny, Hua Xu
2015	Misc	`conf`	PhEMA: Phenotype Modeling, Sharing and Execution Architecture. AMIA Jyotishman Pathak, Joshua C. Denny, William K. Thompson, Luke V. Rasmussen
2015	Misc	`conf`	PheWAS Network Analysis and Visualization. AMIA 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
2015	Misc	`conf`	Predicting Clinical Laboratory Turnaround Time. AMIA Alex C. Cheng, Marc Beller, Joshua C. Denny
2015	Misc	`conf`	Quantifying Tobacco Exposure Using Clinical Notes and Natural Language Processing to Enable Lung Cancer Screening. AMIA Travis Osterman, Wei-Qi Wei, Joshua C. Denny
2015	Misc	`conf`	Real Time Active Learning Study for Clinical Named Entity Recognition. AMIA Yukun Chen, Sungrim Moon, Thomas A. Lasko, Qiaozhu Mei, Jingqi Wang, Trevor Cohen, Qingxia Chen, Joshua C. Denny, Hua Xu
2015	J	`jnl`	Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. J. Am. Medical Informatics Assoc. 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
2015	A*	`conf`	Rubik: Knowledge Guided Tensor Factorization and Completion for Health Data Analytics. KDD Yichen Wang, Robert Chen, Joydeep Ghosh, Joshua C. Denny, Abel N. Kho, You Chen, Bradley A. Malin, Jimeng Sun
2015	J	`jnl`	Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization. J. Am. Medical Informatics Assoc. Jeremy L. Warner, Joshua C. Denny, David A. Kreda, Gil Alterovitz
2015	Misc	`conf`	Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME. AMIA Huan Mo, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson
2015	Misc	`conf`	Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools. AMIA 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
2015	J	`jnl`	Using natural language processing to provide personalized learning opportunities from trainee clinical notes. J. Biomed. Informatics Joshua C. Denny, Anderson Spickard III, Peter Speltz, Renee Porier, Donna E. Rosenstiel, James S. Powers
2015	J	`jnl`	Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J. Am. Medical Informatics Assoc. Hua Xu, Melinda C. Aldrich, Qingxia Chen, Hongfang Liu, Neeraja B. Peterson, Qi Dai, Mia A. Levy, Anushi Shah, Han Xue, Xiaoyang Ruan, Min Jiang, Ying Li, Jamii St Julien, Jeremy L. Warner, Carol Friedman, Dan M. Roden, Joshua C. Denny
2014	Misc	`conf`	A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions. AMIA Yukun Chen, Yaoyun Zhang, Qiaozhu Mei, Dead Account, Joshua C. Denny, Hua Xu
2014	Misc	`conf`	A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project. AMIA 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, James D. Ralston, Alan R. Shuldiner, Iftikhar J. Kullo, Peter Tarczy-Hornoch, Marc S. Williams
2014	Misc	`conf`	Applying Active Learning to Word Sense Disambiguation in a Real-Time Setting. AMIA Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, Hua Xu
2014	Misc	`conf`	Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies. AMIA Yukun Chen, Jesse O. Wrenn, Hua Xu, Anderson Spickard III, Ralf Habermann, James S. Powers, Joshua C. Denny
2014	J	`jnl`	Design patterns for the development of electronic health record-driven phenotype extraction algorithms. J. Biomed. Informatics 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
2014	Misc	`conf`	Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype. AMIA Wei-Qi Wei, Pedro L. Teixeira, Huan Mo, Robert M. Cronin, Jeremy L. Warner, Joshua C. Denny
2014	Misc	`conf`	Evaluation of Existing Phenotype Authoring Tools for Clinical Research. AMIA Luke V. Rasmussen, Jie Xu, Ruijue Liu, Qian Zhu, Jennifer A. Pacheco, Jyotishman Pathak, William K. Thompson, Joshua C. Denny, Huan Mo, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague
2014	Misc	`conf`	Identifying Metastases from Pathology Reports in Lung Cancer Patients. AMIA Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu
2014	Misc	`conf`	Learning to Identify Treatment Relations in Clinical Text. AMIA Cosmin Adrian Bejan, Joshua C. Denny
2014	J	`jnl`	Limestone: High-throughput candidate phenotype generation via tensor factorization. J. Biomed. Informatics Joyce C. Ho, Joydeep Ghosh, Steven R. Steinhubl, Walter F. Stewart, Joshua C. Denny, Bradley A. Malin, Jimeng Sun
2014	Misc	`conf`	Mining electronic health record data to detect drug-repurposing signals for cancers. AMIA Hua Xu, Qingxia Chen, Jeremy L. Warner, Han Xue, Min Jiang, Anushi Shah, Melinda Aldrich, Qi Dai, Joshua C. Denny
2014	—	`conf`	Parsing Clinical Text: How Good are the State-of-the-Art Parsers? DTMBIO@CIKM Min Jiang, Yang Huang, Jungwei Fan, Buzhou Tang, Joshua C. Denny, Hua Xu
2014	Misc	`conf`	PheWAS and Genetics Define Subphenotypes in Drug Response. AMIA Robert J. Carroll, Jeremy L. Warner, Anne E. Eyler, Charles Moore, Jayanth Doss, Katherine P. Liao, Robert M. Plenge, Joshua C. Denny
2014	Misc	`conf`	Phenome-Wide Association Studies Using NLP-Derived Concepts. AMIA Pedro L. Teixeira, Robert J. Carroll, Lisa Bastarache, Peter Speltz, Joshua C. Smith, Joshua C. Denny
2014	J	`jnl`	Predicting changes in hypertension control using electronic health records from a chronic disease management program. J. Am. Medical Informatics Assoc. Jimeng Sun, Candace D. McNaughton, Ping Zhang, Adam Perer, Aris Gkoulalas-Divanis, Joshua C. Denny, Jacqueline Kirby, Thomas A. Lasko, Alexander Saip, Bradley A. Malin
2014	Misc	`conf`	Qualitative evaluation of three phenotype information models to find methotrexate liver injury. AMIA Qian Zhu, Huan Mo, Luke V. Rasmussen, Andrew R. Post, Jennifer A. Pacheco, Jie Xu, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague, William K. Thompson, Joshua C. Denny, Jyotishman Pathak
2014	J	`jnl`	R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. Bioinform. Robert J. Carroll, Lisa Bastarache, Joshua C. Denny
2014	B	`conf`	Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies. EvoApplications 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, Nathalie Schnetz-Boutaud, Holli H. Dilks, Melissa A. Basford, Jennifer A. Pacheco, Gail P. Jarvik, Rex L. Chisholm, Dan M. Roden, M. Geoffrey Hayes, Dana C. Crawford
2014	J	`jnl`	SecureMA: protecting participant privacy in genetic association meta-analysis. Bioinform. Wei Xie, Murat Kantarcioglu, William S. Bush, Dana C. Crawford, Joshua C. Denny, Raymond Heatherly, Bradley A. Malin
2014	J	`jnl`	Size matters: How population size influences genotype-phenotype association studies in anonymized data. J. Biomed. Informatics Raymond Heatherly, Joshua C. Denny, Jonathan L. Haines, Dan M. Roden, Bradley A. Malin
2014	Misc	`conf`	Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients. Pacific Symposium on Biocomputing 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
2013	Misc	`conf`	A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype. AMIA Eugenia R. McPeek Hinz, Joshua C. Denny, Lisa Bastarache
2013	Misc	`conf`	A Study of Active Learning Methods for Clinical Entities Recognition. AMIA Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu
2013	J	`jnl`	A hybrid system for temporal information extraction from clinical text. J. Am. Medical Informatics Assoc. Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Joshua C. Denny, Hua Xu
2013	—	`conf`	A prototype application for real-time recognition and disambiguation of clinical abbreviations. DTMBIO Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Min Song, Hua Xu
2013	—	`conf`	Analytic Approaches to Phenotypic Complexity. MedInfo Jeremy L. Warner, Joshua C. Denny, David A. Kreda, Gil Alterovitz
2013	—	`conf`	Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages. MedInfo Yonghui Wu, Jianbo Lei, Wei-Qi Wei, Buzhou Tang, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Kai Zheng, Hua Xu
2013	Misc	`conf`	Automated Identification of Drug and Food Allergies Entered in EHRs Using Non-Standard Terminology. AMIA Richard H. Epstein, Jesse M. Ehrenfeld, Michael Stockin, Paul St. Jacques, Brian Rothman, Joshua C. Denny
2013	J	`jnl`	Automated identification of drug and food allergies entered using non-standard terminology. J. Am. Medical Informatics Assoc. Richard H. Epstein, Paul St. Jacques, Michael Stockin, Brian Rothman, Jesse M. Ehrenfeld, Joshua C. Denny
2013	Misc	`conf`	Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries. AMIA Yonghui Wu, S. Trent Rosenbloom, Joshua C. Denny, Randolph A. Miller, Dario A. Giuse, Hua Xu
2013	Misc	`conf`	Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems. AMIA Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny
2013	—	`conf`	Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. CLEF (Working Notes) Yonghui Wu, Buzhou Tang, Min Jiang, Sungrim Moon, Joshua C. Denny, Hua Xu
2013	J	`jnl`	Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records. J. Am. Medical Informatics Assoc. Mei Liu, Eugenia Renne McPeek Hinz, Michael Edwin Matheny, Joshua C. Denny, Jonathan Scott Schildcrout, Randolph A. Miller, Hua Xu
2013	J	`jnl`	Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden J. Am. Medical Informatics Assoc. Nicholas P. Tatonetti, Joshua C. Denny, Russ B. Altman
2013	J	`jnl`	Detecting temporal expressions in medical narratives. Int. J. Medical Informatics Ruth M. Reeves, Ferdo R. Ong, Michael E. Matheny, Joshua C. Denny, Dominik Aronsky, Glenn T. Gobbel, Diane Montella, Theodore Speroff, Steven H. Brown
2013	J	`jnl`	Development and evaluation of an ensemble resource linking medications to their indications. J. Am. Medical Informatics Assoc. Wei-Qi Wei, Robert M. Cronin, Hua Xu, Thomas A. Lasko, Lisa Bastarache, Joshua C. Denny
2013	Misc	`conf`	Establishing the Need for Personalized Medicine: Simvastatin Exposure Among a SLCO1B1 Variant Population. AMIA Laura K. Wiley, Josh F. Peterson, Joshua C. Denny, William S. Bush
2013	A*	`conf`	Messaging to your doctors: understanding patient-provider communications via a portal system. CHI Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu
2013	Misc	`conf`	Open Source R Implementation of the PheWAS Methodology. AMIA Robert J. Carroll, Lisa Bastarache, Joshua C. Denny
2013	Misc	`conf`	Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information. AMIA Jeremy L. Warner, Quan Ding, David A. Kreda, Zi'ou Zheng, Keshav Gupta, Joshua C. Denny, Gil Alterovitz
2013	—	`conf`	Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model. CLEF (Working Notes) Buzhou Tang, Yonghui Wu, Min Jiang, Joshua C. Denny, Hua Xu
2013	J	`jnl`	Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. J. Am. Medical Informatics Assoc. Jungwei Fan, Elly W. Yang, Min Jiang, Rashmi Prasad, Richard M. Loomis, Daniel Zisook, Joshua C. Denny, Hua Xu, Yang Huang
2013	Misc	`conf`	Sharing of Genomic Information: Perspectives from Stakeholders. AMIA Jeremy L. Warner, Gil Alterovitz, Joshua C. Denny, Robert Fassett, Kevin S. Hughes
2013	Misc	`conf`	Using PheWAS and Natural Language Processing to Discover Clinical Associations for Congenital Chest Deformities. AMIA Christine M. McEvoy, Robert J. Carroll, Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny
2013	Misc	`conf`	Validation and Enhancement of a Computable Medication Indication Resource (MEDI) Using a Large Practice-based Dataset. AMIA Wei-Qi Wei, Jonathan D. Mosley, Lisa Bastarache, Joshua C. Denny
2012	—	`conf`	A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing. HISB Eugenia R. McPeek Hinz, Lisa Bastarache, Joshua C. Denny
2012	Misc	`conf`	A Study of Transportability of an Existing Smoking Status Detection Module across Institutions. AMIA Mei Liu, Anushi Shah, Min Jiang, Neeraja B. Peterson, Qi Dai, Melinda Aldrich, Qingxia Chen, Erica A. Bowton, Hongfang Liu, Joshua C. Denny, Hua Xu
2012	Misc	`conf`	A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. AMIA Yonghui Wu, Joshua C. Denny, Samuel Rosenbloom, Randolph A. Miller, Dario A. Giuse, Hua Xu
2012	Misc	`conf`	An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms. AMIA William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Peggy L. Peissig, Joshua C. Denny, Abel N. Kho, Aaron W. Miller, Jyotishman Pathak
2012	J	`jnl`	Chapter 13: Mining Electronic Health Records in the Genomics Era. PLoS Comput. Biol. Joshua C. Denny
2012	Misc	`conf`	Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes. AMIA Wei-Qi Wei, Lisa Bastarache, Joshua C. Denny
2012	—	`conf`	Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data. HISB Mei Liu, Michael E. Matheny, Yonghui Wu, Eugenia R. McPeek Hinz, Joshua C. Denny, Jonathan S. Schildcrout, Randolph A. Miller, Hua Xu
2012	Misc	`conf`	Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR. AMIA Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny
2012	Misc	`conf`	Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies. AMIA Hua Xu, 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
2012	Misc	`conf`	Establishing Drug Treatment discovery rate of MedEx. AMIA Haresh Bhatia, Eugenia R. McPeek Hinz, Joshua C. Denny
2012	Misc	`conf`	Extracting Semantic Lexicons from Discharge Summaries using Machine Learning and the C-Value Method. AMIA Min Jiang, Joshua C. Denny, Buzhou Tang, Hongxin Cao, Hua Xu
2012	J	`jnl`	Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches. Int. J. Data Min. Bioinform. Yanxin Lu, Hua Xu, Neeraja B. Peterson, Qi Dai, Min Jiang, Joshua C. Denny, Mei Liu
2012	J	`jnl`	Focus on health information technology, electronic health records and their financial impact: PASTE: patient-centered SMS text tagging in a medication management system. J. Am. Medical Informatics Assoc. Shane P. Stenner, Kevin B. Johnson, Joshua C. Denny
2012	J	`jnl`	Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. J. Am. Medical Informatics Assoc. 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, Justin B. Starren
2012	Misc	`conf`	MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text. AMIA Anushi Shah, Min Jiang, Yonghui Wu, Joshua C. Denny, Hua Xu
2012	Misc	`conf`	PheKB.org: An Online Collaboration Tool for Phenotype Algorithm Research. AMIA Joshua Pruitt, Peter Speltz, Jacqueline Kirby, Melissa A. Basford, Jonathan L. Haines, Joshua C. Denny
2012	J	`jnl`	Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J. Am. Medical Informatics Assoc. 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, Elizabeth W. Karlson, Raúl G. Pérez, Vivian S. Gainer, Shawn N. Murphy, Eric M. Ruderman, Richard M. Pope, Robert M. Plenge, Abel N. Kho, Katherine P. Liao, Joshua C. Denny
2012	Misc	`conf`	Type 2 Diabetes Risk Forecasting from EMR Data using Machine Learning. AMIA Subramani Mani, Yukun Chen, Tom Elasy, Warren Clayton, Joshua C. Denny
2012	Misc	`conf`	Understanding Patient-Provider Communication via a Patient Portal. AMIA Si Sun, Xiaomu Zhou, Hua Xu, Joshua C. Denny
2012	—	`conf`	Understanding patient-provider communication entered via a patient portal system. ASIST Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu
2012	—	`conf`	Understanding patient-provider communication entered via a patient portal system. ASIST Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu
2012	J	`jnl`	Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study. J. Am. Medical Informatics Assoc. 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, Cynthia L. Leibson, Gail P. Jarvik, David R. Crosslin, Christopher S. Carlson, Katherine M. Newton, Wendy A. Wolf, Rex L. Chisholm, William L. Lowe
2012	Misc	`conf`	Using Electronic Health Records to Identify Patient Cohorts for Drug-Induced Thrombocytopenia, Neutropenia and Liver Injury. AMIA Jyotishman Pathak, Aref Al-Kali, Jayant Talwalkar, Abel N. Kho, Joshua C. Denny, Sean P. Murphy, Kevin Bruce, Matthew J. Durski, Christopher G. Chute
2011	J	`jnl`	A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J. Am. Medical Informatics Assoc. Min Jiang, Yukun Chen, Mei Liu, S. Trent Rosenbloom, Subramani Mani, Joshua C. Denny, Hua Xu
2011	J	`jnl`	Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences. J. Biomed. Informatics Hua Xu, Samir AbdelRahman, Yanxin Lu, Joshua C. Denny, Son Doan
2011	J	`jnl`	Data from clinical notes: a perspective on the tension between structure and flexible documentation. J. Am. Medical Informatics Assoc. S. Trent Rosenbloom, Joshua C. Denny, Hua Xu, Nancy M. Lorenzi, William W. Stead, Kevin B. Johnson
2011	J	`jnl`	Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. J. Am. Medical Informatics Assoc. Hua Xu, Min Jiang, 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, Dan M. Roden, Dana C. Crawford, Joshua C. Denny
2010	J	`jnl`	An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records. J. Biomed. Informatics 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
2010	J	`jnl`	Application of information technology: MedEx: a medication information extraction system for clinical narratives. J. Am. Medical Informatics Assoc. Hua Xu, Shane P. Stenner, Son Doan, Kevin B. Johnson, Lemuel R. Waitman, Joshua C. Denny
2010	J	`jnl`	Extracting timing and status descriptors for colonoscopy testing from electronic medical records. J. Am. Medical Informatics Assoc. Joshua C. Denny, Josh F. Peterson, Neesha N. Choma, Hua Xu, Randolph A. Miller, Lisa Bastarache, Neeraja B. Peterson
2010	J	`jnl`	Identifying potential drugs that induce QT prolongation using electronic medical records. BMC Bioinform. Mei Liu, Joshua C. Denny, Subramani Mani, Yukun Chen, Yong Hu, Hua Xu
2010	J	`jnl`	Integrating existing natural language processing tools for medication extraction from discharge summaries. J. Am. Medical Informatics Assoc. Son Doan, Lisa Bastarache, Sergio Klimkowski, Joshua C. Denny, Hua Xu
2010	J	`jnl`	PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinform. 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
2010	J	`jnl`	The disclosure of diagnosis codes can breach research participants' privacy. J. Am. Medical Informatics Assoc. Grigorios Loukides, Joshua C. Denny, Bradley A. Malin
2009	Misc	`conf`	Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. AMIA Joshua C. Denny, Josh F. Peterson, Neesha N. Choma, Hua Xu, Randolph A. Miller, Lisa Bastarache, Neeraja B. Peterson
2009	J	`jnl`	Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor. Int. J. Medical Informatics Joshua C. Denny, Randolph A. Miller, Lemuel R. Waitman, Mark Arrieta, Josh F. Peterson
2009	J	`jnl`	Research Paper: Evaluation of a Method to Identify and Categorize Section Headers in Clinical Documents. J. Am. Medical Informatics Assoc. Joshua C. Denny, Anderson Spickard III, Kevin B. Johnson, Neeraja B. Peterson, Josh F. Peterson, Randolph A. Miller
2009	J	`jnl`	Tracking medical students' clinical experiences using natural language processing. J. Biomed. Informatics Joshua C. Denny, Lisa Bastarache, Elizabeth Ann Sastre, Anderson Spickard III
2008	Misc	`conf`	Development and Evaluation of a Clinical Note Section Header Terminology. AMIA Joshua C. Denny, Randolph A. Miller, Kevin B. Johnson, Anderson Spickard III
2007	Misc	`conf`	Analysis of a Computerized Sign-out Tool: Identification of Unanticipated Uses and Contradictory Content. AMIA Thomas R. Campion Jr., Joshua C. Denny, Stuart T. Weinberg, Nancy M. Lorenzi, L. Russell Waitman
2007	—	`conf`	Identifying QT prolongation from ECG impressions using Natural Language Processing and Negation Detection. MedInfo Joshua C. Denny, Josh F. Peterson
2006	Misc	`conf`	Analysis of Medical Student Content Searches that Resulted in Unidentified UMLS Concepts. AMIA Benjamin P. Rosenbaum, Joshua C. Denny, Anderson Spickard III
2005	Misc	`conf`	Can Users Estimate Their Usage of a Web-Based Application? Validating a Self-Report Usage Questionnaire. AMIA Firas H. Wehbe, Joshua C. Denny, Anderson Spickard III
2005	Misc	`conf`	Identifying UMLS concepts from ECG Impressions using Knowledge Map. AMIA Joshua C. Denny, Anderson Spickard III, Randolph A. Miller, Jonathan S. Schildcrout, Dawood Darbar, S. Trent Rosenbloom, Josh F. Peterson
2003	Misc	`conf`	Formative Evaluation to Guide Early Deployment of an Online Content Management Tool for Medical Curriculum. AMIA Firas H. Wehbe, Brian Armstrong, Matthew R. Peachey, Joshua C. Denny, Anderson Spickard III
2003	J	`jnl`	Research Paper: "Understanding" Medical School Curriculum Content Using KnowledgeMap. J. Am. Medical Informatics Assoc. Joshua C. Denny, Jeffrey D. Smithers, Randolph A. Miller, Anderson Spickard III
2003	Misc	`conf`	The KnowledgeMap Project: Development of a Concept-Based Medical School Curriculum Database. AMIA Joshua C. Denny, Plomarz R. Irani, Firas H. Wehbe, Jeffrey D. Smithers, Anderson Spickard III
2002	Misc	`conf`	A New Tool to Identify Key Biomedical Concepts in Text Documents, with Special Application to Curriculum Content. AMIA Joshua C. Denny, Jeffrey D. Smithers, Anderson Spickard III, Randolph A. Miller
2002	Misc	`conf`	Using Concept Markers to Find Genetics Content in a Medical School Curriculum. AMIA Jeffrey D. Smithers, Joshua C. Denny, Anderson Spickard III, Randolph A. Miller