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Joshua Charles Denny
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2020 – today
- 2024
[j83]Chenjie Zeng
, David J. Schlueter, Tam C. Tran, Anav Babbar, Thomas Cassini, Lisa Bastarache, Joshua C. Denny:
Comparison of phenomic profiles in the All of Us Research Program against the US general population and the UK Biobank. J. Am. Medical Informatics Assoc. 31(4): 846-854 (2024)- 2023
- [j82]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]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]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]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]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]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]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]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]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]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]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) - [c118]Sarah DeLozier, Josh F. Peterson, Joshua C. Denny, Lisa Bastarache:
Using Genomic Association Replication Rates as an EHR Quality Measure via the Phenotype-Genotype Reference Map (PGRM). AMIA 2021 - [c117]David J. Schlueter, Lina M. Sulieman, Jacob M. Keaton, Tracey Ferrara, Kyle Webb, Ariel Williams, Francis Ratsimbazafy, Jun Qian, Lisa Bastarache, Andrea H. Ramirez, Joshua C. Denny:
Systematic replication of smoking disease associations in the All of Us Research Program. AMIA 2021 - 2020
- [j71]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]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) - [c116]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]Leigh Anne Tang, Sarah DeLozier, Lisa Bastarache, Colin Walsh, Joshua C. Denny:
Developing a Phenotype Risk Score for Opioid Adverse Events. AMIA 2020
2010 – 2019
- 2019
- [j69]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]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]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]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]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]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) - [c114]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]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]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]Patrick Wu, QiPing Feng, Joshua C. Denny, Wei-Qi Wei:
Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs. AMIA 2019 - [c110]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]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]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 - [c107]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
- [j63]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]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]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]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]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) - [c106]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]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]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]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]Joshua C. Denny:
Huge Cohorts, Genomics, and Clinical Data to Personalize Medicine. BCB 2018: 562 - [c101]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]Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. PSB 2018: 389-399 - [i1]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) - 2017
- [j58]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]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]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]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) - [c99]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]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]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]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]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]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]Jamie R. Robinson, Lisa Bastarache, Robert J. Carroll, Elizabeth A. Scoville, David A. Schwartz, Joshua C. Denny:
Sub-Phenotyping of Crohn's Disease Using a Large Electronic Record Cohort. AMIA 2017 - [c92]Jamie R. Robinson, Zongyang Mou, Lisa Bastarache, Wei-Qi Wei, Robert J. Carroll, Joshua C. Denny:
Association of BMI and Obesity Genetic Risk Score with Surgical Procedures Through a Procedure-wide Association Study. AMIA 2017 - [c91]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]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]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]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]Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu:
Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. CRI 2017 - [c86]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]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]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
- [j54]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]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]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]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]Lewis J. Frey, Elmer V. Bernstam, Joshua C. Denny:
Precision medicine informatics. J. Am. Medical Informatics Assoc. 23(4): 668-670 (2016) - [j49]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]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]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]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) - [c83]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]Yang Huang, Hua Xu, Joshua C. Denny:
Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations. AMIA 2016 - [c81]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]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]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]Anthony E. Solomonides, Russ B. Altman, Joshua C. Denny, Larry Ozeran, Jessica D. Tenenbaum:
The Many Meanings of Precision Medicine. CRI 2016 - [c77]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]Jessica D. Tenenbaum, Subha Madhavan, Robert R. Freimuth, Joshua C. Denny, Lewis J. Frey:
Translational Bioinformatics 101. PSB 2016: 552-556 - 2015
- [j45]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]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) - [j43]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]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]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]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]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]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) - [j37]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]