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Joshua Charles Denny

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2024
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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
[j82]
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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): 427-437 (2023)
[j81]
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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)
[j80]
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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)
2022
[j79]
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  - journals/bioinformatics/IrlmeierHBDC22
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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)
[j78]
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Huan Mo, Joshua C. Denny:
The U.S. National Library of Medicine's impact on precision and genomic medicine. Inf. Serv. Use 42(1): 71-80 (2022)
[j77]
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  - journals/patterns/RamirezSSHQRLMB22
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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:
The All of Us Research Program: Data quality, utility, and diversity. Patterns 3(8): 100570 (2022)
2021
[j76]
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  - journals/bioinformatics/StrayerSSDPX21
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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): 1778-1780 (2021)
[j75]
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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): 126-131 (2021)
[j74]
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  - journals/jamia/Zayas-CabanCRDW21
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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): 1345-1352 (2021)
[j73]
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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): 1421-1430 (2021)
[j72]
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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:
Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. npj Digit. Medicine 4 (2021)
2020
[j71]
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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): 407-418 (2020)
[j70]
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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): 1675-1687 (2020)
2019
[j69]
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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): 1314-1322 (2019)
[j68]
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  - journals/jamia/BastaracheHGBDZ19
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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)
[j67]
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  - journals/jbi/HripcsakSPRLBCC19
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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)
[j66]
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  - journals/jbi/ZhaoZSWKRWFDW19
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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:
Detecting time-evolving phenotypic topics via tensor factorization on electronic health records: Cardiovascular disease case study. J. Biomed. Informatics 98 (2019)
[j65]
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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)
[j64]
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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:
Automated grouping of medical codes via multiview banded spectral clustering. J. Biomed. Informatics 100 (2019)
2018
[j63]
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  - journals/aci/SmithCDRJM18
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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. 09(02): 313-325 (2018)
[j62]
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  - journals/bioinformatics/ChoiCBMRDD18
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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): 2988-2996 (2018)
[j61]
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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): 61-71 (2018)
[j60]
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  - journals/jamia/BolandPLMCINSYS18
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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:
Uncovering exposures responsible for birth season - disease effects: a global study. J. Am. Medical Informatics Assoc. 25(3): 275-288 (2018)
[j59]
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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): 1540-1546 (2018)
2017
[j58]
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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: 110-120 (2017)
[j57]
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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)
[j56]
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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): e79-e86 (2017)
[j55]
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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): 35-44 (2017)
2016
[j54]
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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:
Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. Appl. Clin. Inform. 07(03): 693-706 (2016)
[j53]
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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. 07(03): 870-882 (2016)
[j52]
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  - journals/artmed/RichessonSPKD16
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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: 57-61 (2016)
[j51]
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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): 413-419 (2016)
[j50]
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Lewis J. Frey, Elmer V. Bernstam, Joshua C. Denny:
Precision medicine informatics. J. Am. Medical Informatics Assoc. 23(4): 668-670 (2016)
[j49]
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  - journals/jamia/KirbySRBGPPTPCE16
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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): 1046-1052 (2016)
[j48]
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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): e131-e137 (2016)
[j47]
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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): e20-e27 (2016)
[j46]
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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: 232-242 (2016)
2015
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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:
Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J. Am. Medical Informatics Assoc. 22(1): 179-191 (2015)
[j44]
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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): 324-329 (2015)
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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): 1220-1230 (2015)
[j42]
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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): 1251-1260 (2015)
[j41]
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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:
Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. J. Am. Medical Informatics Assoc. 22(e1): e151-e161 (2015)
[j40]
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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): e162-e176 (2015)
[j39]
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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: 82-93 (2015)
[j38]
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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: 292-299 (2015)
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Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu:
A study of active learning methods for named entity recognition in clinical text. J. Biomed. Informatics 58: 11-18 (2015)
[j36]
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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(S-1): S2 (2015)
[j35]
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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)
2014
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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)
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Wei Xie, Murat Kantarcioglu, William S. Bush, Dana C. Crawford, Joshua C. Denny, Raymond Heatherly, Bradley A. Malin:
SecureMA: protecting participant privacy in genetic association meta-analysis. Bioinform. 30(23): 3334-3341 (2014)
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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:
Predicting changes in hypertension control using electronic health records from a chronic disease management program. J. Am. Medical Informatics Assoc. 21(2): 337-344 (2014)
[j31]
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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:
Design patterns for the development of electronic health record-driven phenotype extraction algorithms. J. Biomed. Informatics 51: 280-286 (2014)
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Joyce C. Ho, Joydeep Ghosh, Steven R. Steinhubl, Walter F. Stewart, Joshua C. Denny, Bradley A. Malin, Jimeng Sun:
Limestone: High-throughput candidate phenotype generation via tensor factorization. J. Biomed. Informatics 52: 199-211 (2014)
[j29]
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Raymond Heatherly, Joshua C. Denny, Jonathan L. Haines, Dan M. Roden, Bradley A. Malin:
Size matters: How population size influences genotype-phenotype association studies in anonymized data. J. Biomed. Informatics 52: 243-250 (2014)
2013
[j28]
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Ruth M. Reeves, Ferdo R. Ong, Michael E. Matheny, Joshua C. Denny, Dominik Aronsky, Glenn T. Gobbel, Diane Montella, Theodore Speroff, Steven H. Brown:
Detecting temporal expressions in medical narratives. Int. J. Medical Informatics 82(2): 118-127 (2013)
[j27]
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Mei Liu, Eugenia Renne McPeek Hinz, Michael Edwin Matheny, Joshua C. Denny, Jonathan Scott Schildcrout, Randolph A. Miller, Hua Xu:
Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records. J. Am. Medical Informatics Assoc. 20(3): 420-426 (2013)
[j26]
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Nicholas P. Tatonetti, Joshua C. Denny, Russ B. Altman:
Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al. J. Am. Medical Informatics Assoc. 20(3): 591 (2013)
[j25]
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Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Joshua C. Denny, Hua Xu:
A hybrid system for temporal information extraction from clinical text. J. Am. Medical Informatics Assoc. 20(5): 828-835 (2013)
[j24]
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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)
[j23]
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Richard H. Epstein, Paul St. Jacques, Michael Stockin, Brian Rothman, Jesse M. Ehrenfeld, Joshua C. Denny:
Automated identification of drug and food allergies entered using non-standard terminology. J. Am. Medical Informatics Assoc. 20(5): 962-968 (2013)
[j22]
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Jung-Wei Fan, Elly W. Yang, Min Jiang, Rashmi Prasad, Richard M. Loomis, Daniel Zisook, Joshua C. Denny, Hua Xu, Yang Huang:
Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. J. Am. Medical Informatics Assoc. 20(6): 1168-1177 (2013)
2012
[j21]
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Yanxin Lu, Hua Xu, Neeraja B. Peterson, Qi Dai, Min Jiang, Joshua C. Denny, Mei Liu:
Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches. Int. J. Data Min. Bioinform. 6(4): 447-459 (2012)
[j20]
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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:
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. 19(2): 212-218 (2012)
[j19]
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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:
Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. J. Am. Medical Informatics Assoc. 19(2): 225-234 (2012)
[j18]
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Shane P. Stenner, Kevin B. Johnson, Joshua C. Denny:
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. 19(3): 368-374 (2012)
[j17]
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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:
Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J. Am. Medical Informatics Assoc. 19(e1) (2012)
[j16]
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Joshua C. Denny:
Chapter 13: Mining Electronic Health Records in the Genomics Era. PLoS Comput. Biol. 8(12) (2012)
2011
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S. Trent Rosenbloom, Joshua C. Denny, Hua Xu, Nancy M. Lorenzi, William W. Stead, Kevin B. Johnson:
Data from clinical notes: a perspective on the tension between structure and flexible documentation. J. Am. Medical Informatics Assoc. 18(2): 181-186 (2011)
[j14]
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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:
Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. J. Am. Medical Informatics Assoc. 18(4): 387-391 (2011)
[j13]
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Min Jiang, Yukun Chen, Mei Liu, S. Trent Rosenbloom, Subramani Mani, Joshua C. Denny, Hua Xu:
A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J. Am. Medical Informatics Assoc. 18(5): 601-606 (2011)
[j12]
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Hua Xu, Samir AbdelRahman, Yanxin Lu, Joshua C. Denny, Son Doan:
Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences. J. Biomed. Informatics 44(6): 1068-1075 (2011)
2010
[j11]
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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)
[j10]
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Mei Liu, Joshua C. Denny, Subramani Mani, Yukun Chen, Yong Hu, Hua Xu:
Identifying potential drugs that induce QT prolongation using electronic medical records. BMC Bioinform. 11(S-4): P2 (2010)
[j9]
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Hua Xu, Shane P. Stenner, Son Doan, Kevin B. Johnson, Lemuel R. Waitman, Joshua C. Denny:
Application of information technology: MedEx: a medication information extraction system for clinical narratives. J. Am. Medical Informatics Assoc. 17(1): 19-24 (2010)
[j8]
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Grigorios Loukides, Joshua C. Denny, Bradley A. Malin:
The disclosure of diagnosis codes can breach research participants' privacy. J. Am. Medical Informatics Assoc. 17(3): 322-327 (2010)
[j7]
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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]
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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)
[j5]
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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:
An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records. J. Biomed. Informatics 43(6): 914-923 (2010)
2009
[j4]
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Joshua C. Denny, Randolph A. Miller, Lemuel R. Waitman, Mark Arrieta, Josh F. Peterson:
Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor. Int. J. Medical Informatics 78(Supplement-1): S34-S42 (2009)
[j3]
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Joshua C. Denny, Anderson Spickard III, Kevin B. Johnson, Neeraja B. Peterson, Josh F. Peterson, Randolph A. Miller:
Research Paper: Evaluation of a Method to Identify and Categorize Section Headers in Clinical Documents. J. Am. Medical Informatics Assoc. 16(6): 806-815 (2009)
[j2]
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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)
2003
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Joshua C. Denny, Jeffrey D. Smithers, Randolph A. Miller, Anderson Spickard III:
Research Paper: "Understanding" Medical School Curriculum Content Using KnowledgeMap. J. Am. Medical Informatics Assoc. 10(4): 351-362 (2003)

Conference and Workshop Papers

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2021
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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
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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
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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
[c115]
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Leigh Anne Tang, Sarah DeLozier, Lisa Bastarache, Colin Walsh, Joshua C. Denny:
Developing a Phenotype Risk Score for Opioid Adverse Events. AMIA 2020
2019
[c114]
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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
[c113]
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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
[c112]
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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
[c111]
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Patrick Wu, QiPing Feng, Joshua C. Denny, Wei-Qi Wei:
Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs. AMIA 2019
[c110]
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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
[c109]
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Ergin Soysal, Jeremy L. Warner, Jingqi Wang, Min Jiang, Krysten Harvey, Sandeep Kumar Jain, Xiao Dong, Hsing-yi Song, Harish Siddhanamatha, Liwei Wang, Qi Dai, Qingxia Chen, Xianglin Du, Cui Tao, Ping Yang, Joshua Charles Denny, Hongfang Liu, Hua Xu:
Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. MedInfo 2019: 1041-1045
[c108]
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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:
Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE network. PSB 2019: 272-283
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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: 711-719
2018
[c106]
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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
[c105]
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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
[c104]
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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
[c103]
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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
[c102]
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Joshua C. Denny:
Huge Cohorts, Genomics, and Clinical Data to Personalize Medicine. BCB 2018: 562
[c101]
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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: 1143-1146
[c100]
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Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. PSB 2018: 389-399
2017
[c99]
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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
[c98]
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Cosmin Adrian Bejan, Joshua C. Denny:
A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects. AMIA 2017
[c97]
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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
[c96]
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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
[c95]
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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
[c94]
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Andrea H. Ramirez, Anthony A. 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
[c93]
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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]
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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
[c91]
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Peter Speltz, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, William K. Thompson, Guoqian Jiang, Jyotishman Pathak, Joshua C. Denny:
The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs. AMIA 2017
[c90]
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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
[c89]
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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
[c88]
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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
[c87]
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Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu:
Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. CRI 2017
[c86]
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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: 214-223
[c85]
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Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. PSB 2017: 348-355
[c84]
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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: 545-556
2016
[c83]
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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
[c82]
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Yang Huang, Hua Xu, Joshua C. Denny:
Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations. AMIA 2016
[c81]
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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
[c80]
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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
[c79]
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Huan Mo, Guoqian Jiang, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson:
A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. CRI 2016
[c78]
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  - conf/cri/SolomonidesADOT16
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Anthony E. Solomonides, Russ B. Altman, Joshua C. Denny, Larry Ozeran, Jessica D. Tenenbaum:
The Many Meanings of Precision Medicine. CRI 2016
[c77]
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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
[c76]
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Jessica D. Tenenbaum, Subha Madhavan, Robert R. Freimuth, Joshua C. Denny, Lewis J. Frey:
Translational Bioinformatics 101. PSB 2016: 552-556
2015
[c75]
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Yukun Chen, Sungrim Moon, Thomas A. Lasko, Qiaozhu Mei, Jingqi Wang, Trevor Cohen, Qingxia Chen, Joshua C. Denny, Hua Xu:
Real Time Active Learning Study for Clinical Named Entity Recognition. AMIA 2015
[c74]
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Alex C. Cheng, Marc Beller, Joshua C. Denny:
Predicting Clinical Laboratory Turnaround Time. AMIA 2015
[c73]
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Robert M. Cronin, Daniel Fabbri, Joshua C. Denny, Gretchen Purcell Jackson:
Automated Classification of Consumer Health Information Needs in Patient Portal Messages. AMIA 2015
[c72]
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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
[c71]
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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
[c70]
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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
[c69]
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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
[c68]
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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
[c67]
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Jennifer A. Pacheco, Abel N. Kho, Jyotishman Pathak, Joshua C. Denny, Shawn N. Murphy:
(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping. AMIA 2015
[c66]
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Jyotishman Pathak, Joshua C. Denny, William K. Thompson, Luke V. Rasmussen:
PhEMA: Phenotype Modeling, Sharing and Execution Architecture. AMIA 2015
[c65]
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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
[c64]
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Jessica D. Tenenbaum, Joshua C. Denny, David Flannery, Douglas B. Fridsma, Marc S. Williams:
Building the Computational Workforce for Precision Medicine. AMIA 2015
[c63]
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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
[c62]
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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: 1265-1274
[c61]
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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: 1098
2014
[c60]
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Cosmin Adrian Bejan, Joshua C. Denny:
Learning to Identify Treatment Relations in Clinical Text. AMIA 2014
[c59]
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Robert J. Carroll, Jeremy L. Warner, Anne E. Eyler, Charles Moore, Jayanth Doss, Katherine P. Liao, Robert M. Plenge, Joshua C. Denny:
PheWAS and Genetics Define Subphenotypes in Drug Response. AMIA 2014
[c58]
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Yukun Chen, Jesse O. Wrenn, Hua Xu, Anderson Spickard III, Ralf Habermann, James S. Powers, Joshua C. Denny:
Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies. AMIA 2014
[c57]
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Yukun Chen, Yaoyun Zhang, Qiaozhu Mei, Dead Account, Joshua C. Denny, Hua Xu:
A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions. AMIA 2014
[c56]
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Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, Hua Xu:
Applying Active Learning to Word Sense Disambiguation in a Real-Time Setting. AMIA 2014
[c55]
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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:
A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project. AMIA 2014
[c54]
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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:
Evaluation of Existing Phenotype Authoring Tools for Clinical Research. AMIA 2014
[c53]
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Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu:
Identifying Metastases from Pathology Reports in Lung Cancer Patients. AMIA 2014
[c52]
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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
[c51]
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Wei-Qi Wei, Pedro L. Teixeira, Huan Mo, Robert M. Cronin, Jeremy L. Warner, Joshua C. Denny:
Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype. AMIA 2014
[c50]
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Hua Xu, Qingxia Chen, Jeremy L. Warner, Han Xue, Min Jiang, Anushi Shah, Melinda Aldrich, Qi Dai, Joshua C. Denny:
Mining electronic health record data to detect drug-repurposing signals for cancers. AMIA 2014
[c49]
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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:
Qualitative evaluation of three phenotype information models to find methotrexate liver injury. AMIA 2014
[c48]
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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? DTMBIO@CIKM 2014: 1
[c47]
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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:
Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies. EvoApplications 2014: 939-951
[c46]
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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:
Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients. Pacific Symposium on Biocomputing 2014: 253-264
2013
[c45]
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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]
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Robert J. Carroll, Lisa Bastarache, Joshua C. Denny:
Open Source R Implementation of the PheWAS Methodology. AMIA 2013
[c43]
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Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu:
A Study of Active Learning Methods for Clinical Entities Recognition. AMIA 2013
[c42]
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Richard H. Epstein, Jesse M. Ehrenfeld, Michael Stockin, Paul St. Jacques, Brian Rothman, Joshua C. Denny:
Automated Identification of Drug and Food Allergies Entered in EHRs Using Non-Standard Terminology. AMIA 2013
[c41]
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Eugenia R. McPeek Hinz, Joshua C. Denny, Lisa Bastarache:
A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype. AMIA 2013
[c40]
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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
[c39]
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Jeremy L. Warner, Gil Alterovitz, Joshua C. Denny, Robert Fassett, Kevin S. Hughes:
Sharing of Genomic Information: Perspectives from Stakeholders. AMIA 2013
[c38]
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Jeremy L. Warner, Quan Ding, David A. Kreda, Zi'ou Zheng, Keshav Gupta, Joshua C. Denny, Gil Alterovitz:
Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information. AMIA 2013
[c37]
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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
[c36]
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Laura K. Wiley, Josh F. Peterson, Joshua C. Denny, William S. Bush:
Establishing the Need for Personalized Medicine: Simvastatin Exposure Among a SLCO1B1 Variant Population. AMIA 2013
[c35]
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Yonghui Wu, S. Trent Rosenbloom, Joshua C. Denny, Randolph A. Miller, Dario A. Giuse, Hua Xu:
Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries. AMIA 2013
[c34]
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Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu:
Messaging to your doctors: understanding patient-provider communications via a portal system. CHI 2013: 1739-1748
[c33]
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Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Min Song, Hua Xu:
A prototype application for real-time recognition and disambiguation of clinical abbreviations. DTMBIO 2013: 7-8
[c32]
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Buzhou Tang, Yonghui Wu, Min Jiang, Joshua C. Denny, Hua Xu:
Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model. CLEF (Working Notes) 2013
[c31]
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Yonghui Wu, Buzhou Tang, Min Jiang, Sungrim Moon, Joshua C. Denny, Hua Xu:
Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. CLEF (Working Notes) 2013
[c30]
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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:
Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages. MedInfo 2013: 662-666
[c29]
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Jeremy L. Warner, Joshua C. Denny, David A. Kreda, Gil Alterovitz:
Analytic Approaches to Phenotypic Complexity. MedInfo 2013: 1267
2012
[c28]
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Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny:
Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR. AMIA 2012
[c27]
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Haresh Bhatia, Eugenia R. McPeek Hinz, Joshua C. Denny:
Establishing Drug Treatment discovery rate of MedEx. AMIA 2012
[c26]
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Min Jiang, Joshua C. Denny, Buzhou Tang, Hongxin Cao, Hua Xu:
Extracting Semantic Lexicons from Discharge Summaries using Machine Learning and the C-Value Method. AMIA 2012
[c25]
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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:
A Study of Transportability of an Existing Smoking Status Detection Module across Institutions. AMIA 2012
[c24]
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  - conf/amia/ManiCECD12
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Subramani Mani, Yukun Chen, Tom Elasy, Warren Clayton, Joshua C. Denny:
Type 2 Diabetes Risk Forecasting from EMR Data using Machine Learning. AMIA 2012
[c23]
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Jyotishman Pathak, Aref Al-Kali, Jayant Talwalkar, Abel N. Kho, Joshua C. Denny, Sean P. Murphy, Kevin Bruce, Matthew J. Durski, Christopher G. Chute:
Using Electronic Health Records to Identify Patient Cohorts for Drug-Induced Thrombocytopenia, Neutropenia and Liver Injury. AMIA 2012
[c22]
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Joshua Pruitt, Peter Speltz, Jacqueline Kirby, Melissa A. Basford, Jonathan L. Haines, Joshua C. Denny:
PheKB.org: An Online Collaboration Tool for Phenotype Algorithm Research. AMIA 2012
[c21]
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Anushi Shah, Min Jiang, Yonghui Wu, Joshua C. Denny, Hua Xu:
MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text. AMIA 2012
[c20]
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  - conf/amia/SunZXD12
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  - https://dblp.org/rec/conf/amia/SunZXD12
Si Sun, Xiaomu Zhou, Hua Xu, Joshua C. Denny:
Understanding Patient-Provider Communication via a Patient Portal. AMIA 2012
[c19]
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  - conf/amia/ThompsonRPPDKMP12
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William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Peggy L. Peissig, Joshua C. Denny, Abel N. Kho, Aaron W. Miller, Jyotishman Pathak:
An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms. AMIA 2012
[c18]
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  - conf/amia/WeiBD12
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Wei-Qi Wei, Lisa Bastarache, Joshua C. Denny:
Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes. AMIA 2012
[c17]
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Yonghui Wu, Joshua C. Denny, Samuel Rosenbloom, Randolph A. Miller, Dario A. Giuse, Hua Xu:
A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. AMIA 2012
[c16]
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  dblp key:
  - conf/amia/XuACPDLSXLFLD12
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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:
Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies. AMIA 2012
[c15]
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  - conf/asist/SunZDR012
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Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu:
Understanding patient-provider communication entered via a patient portal system. ASIST 2012: 1-4
[c14]
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  - conf/asist/SunZDR012a
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Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu:
Understanding patient-provider communication entered via a patient portal system. ASIST 2012: 1-4
[c13]
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  - conf/hisb/LiuMWHDSMX12
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Mei Liu, Michael E. Matheny, Yonghui Wu, Eugenia R. McPeek Hinz, Joshua C. Denny, Jonathan S. Schildcrout, Randolph A. Miller, Hua Xu:
Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data. HISB 2012: 131
[c12]
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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
2009
[c11]
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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
2008
[c10]
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Joshua C. Denny, Randolph A. Miller, Kevin B. Johnson, Anderson Spickard III:
Development and Evaluation of a Clinical Note Section Header Terminology. AMIA 2008
2007
[c9]
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  - conf/amia/CampionDWLW07
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Thomas R. Campion Jr., Joshua C. Denny, Stuart T. Weinberg, Nancy M. Lorenzi, L. Russell Waitman:
Analysis of a Computerized Sign-out Tool: Identification of Unanticipated Uses and Contradictory Content. AMIA 2007
[c8]
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Joshua C. Denny, Josh F. Peterson:
Identifying QT prolongation from ECG impressions using Natural Language Processing and Negation Detection. MedInfo 2007: 1283-1288
2006
[c7]
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Benjamin P. Rosenbaum, Joshua C. Denny, Anderson Spickard III:
Analysis of Medical Student Content Searches that Resulted in Unidentified UMLS Concepts. AMIA 2006
2005
[c6]
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Joshua C. Denny, Anderson Spickard III, Randolph A. Miller, Jonathan S. Schildcrout, Dawood Darbar, S. Trent Rosenbloom, Josh F. Peterson:
Identifying UMLS concepts from ECG Impressions using Knowledge Map. AMIA 2005
[c5]
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Firas H. Wehbe, Joshua C. Denny, Anderson Spickard III:
Can Users Estimate Their Usage of a Web-Based Application? Validating a Self-Report Usage Questionnaire. AMIA 2005
2003
[c4]
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Joshua C. Denny, Plomarz R. Irani, Firas H. Wehbe, Jeffrey D. Smithers, Anderson Spickard III:
The KnowledgeMap Project: Development of a Concept-Based Medical School Curriculum Database. AMIA 2003
[c3]
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  - conf/amia/WehbeAPDS03
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Firas H. Wehbe, Brian Armstrong, Matthew R. Peachey, Joshua C. Denny, Anderson Spickard III:
Formative Evaluation to Guide Early Deployment of an Online Content Management Tool for Medical Curriculum. AMIA 2003
2002
[c2]
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Joshua C. Denny, Jeffrey D. Smithers, Anderson Spickard III, Randolph A. Miller:
A New Tool to Identify Key Biomedical Concepts in Text Documents, with Special Application to Curriculum Content. AMIA 2002
[c1]
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  - conf/amia/SmithersDSM02
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Jeffrey D. Smithers, Joshua C. Denny, Anderson Spickard III, Randolph A. Miller:
Using Concept Markers to Find Genetics Content in a Medical School Curriculum. AMIA 2002

Informal and Other Publications

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What is the meaning of the colors in the publication lists?

2018
[i1]
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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 abs/1811.06183 (2018)

Coauthor Index

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