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2020 – today
- 2024
[j29]Monika E. Grabowska
, Sara L. Van Driest, Jamie R. Robinson, Anna E. Patrick, Chris Guardo, Srushti Gangireddy, Henry H. Ong, QiPing Feng, Robert J. Carroll, Prince J. Kannankeril, Wei-Qi Wei:
Developing and evaluating pediatric phecodes (Peds-Phecodes) for high-throughput phenotyping using electronic health records. J. Am. Medical Informatics Assoc. 31(2): 386-395 (2024)- [j28]Wei-Qi Wei, Robb Rowley, Angela M. Wood, Jacqueline Macarthur, Peter J. Embí, Spiros C. Denaxas:
Improving reporting standards for phenotyping algorithm in biomedical research: 5 fundamental dimensions. J. Am. Medical Informatics Assoc. 31(4): 1036-1041 (2024) - [j27]Chao Yan, Henry H. Ong, Monika E. Grabowska, Matthew S. Krantz, Wu-Chen Su, Alyson L. Dickson, Josh F. Peterson, QiPing Feng, Dan M. Roden, C. Michael Stein, Vern Eric Kerchberger, Bradley A. Malin, Wei-Qi Wei:
Large language models facilitate the generation of electronic health record phenotyping algorithms. J. Am. Medical Informatics Assoc. 31(9): 1994-2001 (2024) - [j26]Chao Yan, Monika E. Grabowska, Alyson L. Dickson, Bingshan Li, Zhexing Wen, Dan M. Roden, C. Michael Stein, Peter J. Embí, Josh F. Peterson, QiPing Feng, Bradley A. Malin, Wei-Qi Wei:
Leveraging generative AI to prioritize drug repurposing candidates for Alzheimer's disease with real-world clinical validation. npj Digit. Medicine 7(1) (2024) - 2023
- [j25]Vern Eric Kerchberger, Josh F. Peterson, Wei-Qi Wei:
Scanning the medical phenome to identify new diagnoses after recovery from COVID-19 in a US cohort. J. Am. Medical Informatics Assoc. 30(2): 233-244 (2023) - [j24]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) - [j23]Nicholas C. Wan, Ali A Yaqoob, Henry H. Ong, Juan Zhao, Wei-Qi Wei:
Evaluating resources composing the PheMAP knowledge base to enhance high-throughput phenotyping. J. Am. Medical Informatics Assoc. 30(3): 456-465 (2023) - [j22]Emily R. Pfaff, Andrew T. Girvin, Miles Crosskey, Srushti Gangireddy, Hiral Master, Wei-Qi Wei, Vern Eric Kerchberger, Mark G. Weiner, Paul A. Harris, Melissa A. Basford, Christopher Lunt, Christopher G. Chute, Richard A. Moffitt, Melissa A. Haendel:
De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the All of Us data repository. J. Am. Medical Informatics Assoc. 30(7): 1305-1312 (2023) - [j21]Fuchen Li, Patrick Wu, Henry H. Ong, Josh F. Peterson, Wei-Qi Wei, Juan Zhao:
Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction. J. Biomed. Informatics 138: 104294 (2023) - [j20]Vipina Kuttichi Keloth, Juan M. Banda, Michael J. Gurley, Paul M. Heider, Georgina Kennedy, Hongfang Liu, Feifan Liu, Timothy A. Miller, Karthik Natarajan, Olga V. Patterson, Yifan Peng, Kalpana Raja, Ruth M. Reeves, Masoud Rouhizadeh, Jianlin Shi, Xiaoyan Wang, Yanshan Wang, Wei-Qi Wei, Andrew E. Williams, Rui Zhang, Rimma Belenkaya, Christian G. Reich, Clair Blacketer, Patrick B. Ryan, George Hripcsak, Noémie Elhadad, Hua Xu:
Representing and utilizing clinical textual data for real world studies: An OHDSI approach. J. Biomed. Informatics 142: 104343 (2023) - 2022
- [j19]Jingzhi Yu, Jennifer A. Pacheco, Anika S. Ghosh, Yuan Luo, Chunhua Weng, Ning Shang, Barbara Benoit, David S. Carrell, Robert J. Carroll, Ozan Dikilitas, Robert R. Freimuth, Vivian S. Gainer, Hakon Hakonarson, George Hripcsak, Iftikhar J. Kullo, Frank D. Mentch, Shawn N. Murphy, Peggy L. Peissig, Andrea H. Ramirez, Nephi Walton, Wei-Qi Wei, Luke V. Rasmussen:
Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Medical Informatics Decis. Mak. 22(1): 23 (2022) - [j18]Yu Deng, Jennifer A. Pacheco, Anika S. Ghosh, Anh H. Chung, Chengsheng Mao, Joshua C. Smith, Juan Zhao, Wei-Qi Wei, April Barnado, Chad Dorn, Chunhua Weng, Cong Liu, Adam Cordon, Jingzhi Yu, Yacob Tedla, Abel Kho, Rosalind Ramsey-Goldman, Theresa Walunas, Yuan Luo:
Natural language processing to identify lupus nephritis phenotype in electronic health records. BMC Medical Informatics Decis. Mak. 22-S(2): 348 (2022) - [c24]Monika E. Grabowska, Sara L. Van Driest, Patrick Wu, Wei-Qi Wei:
Developing and Mapping Pediatric Phecodes (Phecode-Peds). AMIA 2022 - [c23]Yanwei Li, Wei-Qi Wei, Juan Zhao, Chao Yan, Henry H. Ong:
Evaluating Phenotype Classification Using Synthesized Online Content. AMIA 2022 - 2021
- [j17]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) - [j16]Neil S. Zheng, Jeremy L. Warner, Travis J. Osterman, Quinn Stanton Wells, Xiao-Ou Shu, Stephen A. Deppen, Seth J. Karp, Shon Dwyer, QiPing Feng, Nancy J. Cox, Josh F. Peterson, C. Michael Stein, Dan M. Roden, Kevin B. Johnson, Wei-Qi Wei:
A retrospective approach to evaluating potential adverse outcomes associated with delay of procedures for cardiovascular and cancer-related diagnoses in the context of COVID-19. J. Biomed. Informatics 113: 103657 (2021) - [j15]Juan Zhao, Monika E. Grabowska, Vern Eric Kerchberger, Joshua C. Smith, H. Nur Eken, QiPing Feng, Josh F. Peterson, S. Trent Rosenbloom, Kevin B. Johnson, Wei-Qi Wei:
ConceptWAS: A high-throughput method for early identification of COVID-19 presenting symptoms and characteristics from clinical notes. J. Biomed. Informatics 117: 103748 (2021) - [j14]Sarah DeLozier, Sarah Bland, Melissa McPheeters, Quinn Stanton Wells, Eric Farber-Eger, Cosmin Adrian Bejan, Daniel Fabbri, S. Trent Rosenbloom, Dan M. Roden, Kevin B. Johnson, Wei-Qi Wei, Josh F. Peterson, Lisa Bastarache:
Phenotyping coronavirus disease 2019 during a global health pandemic: Lessons learned from the characterization of an early cohort. J. Biomed. Informatics 117: 103777 (2021) - [j13]Mullai Murugan, Lawrence J. Babb, Casey Overby Taylor, Luke V. Rasmussen, Robert R. Freimuth, Eric Venner, Fei Yan, Victoria Yi, Stephen J. Granite, Hana Zouk, Samuel J. Aronson, Kevin Power, Alexander Fedotov, David R. Crosslin, David Fasel, Gail P. Jarvik, Hakon Hakonarson, Hana Bangash, Iftikhar J. Kullo, John J. Connolly, Jordan G. Nestor, Pedro J. Caraballo, Wei-Qi Wei, Ken Wiley, Heidi L. Rehm, Richard A. Gibbs:
Genomic considerations for FHIR®; eMERGE implementation lessons. J. Biomed. Informatics 118: 103795 (2021) - [j12]Danqing Xu, Chen Wang, Atlas Khan, Ning Shang, Zihuai He, Adam S. Gordon, Iftikhar J. Kullo, Shawn N. Murphy, Yizhao Ni, Wei-Qi Wei, Ali Gharavi, Krzysztof Kiryluk, Chunhua Weng, Iuliana Ionita-Laza:
Quantitative disease risk scores from EHR with applications to clinical risk stratification and genetic studies. npj Digit. Medicine 4 (2021) - [c22]Juan Zhao, Monika E. Grabowska, Wei-Qi Wei:
Early Detect COVID-19 Presenting Symptoms and Characteristics Using Natural Language Processing on Electronic Health Records. AMIA 2021 - [c21]Spiros C. Denaxas, Ge Liu, QiPing Feng, Ghazaleh Fatemifar, Lisa Bastarache, Vern Eric Kerchberger, Aroon D. Hingorani, R. Tom Lumbers, Josh F. Peterson, Wei-Qi Wei, Harry Hemingway:
Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation. AMIA 2021 - [c20]Jennifer A. Pacheco, Luke V. Rasmussen, Ken Wiley, Thomas N. Person, David J. Cronkite, Sunghwan Sohn, Shawn N. Murphy, Justin H. Gundelach, Vivian S. Gainer, Victor M. Castro, Cong Liu, Todd Lingren, Frank D. Mentch, Agnes S. Sundaresan, Garrett Eickelberg, Valerie Willis, Al'ona Furmanchuk, Roshan Patel, David S. Carrell, Marc S. Williams, Elizabeth W. Karlson, Jodell E. Linder, Yuan Luo, Chunhua Weng, Wei-Qi Wei:
Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. AMIA 2021 - [i2]Yu Deng, Jennifer A. Pacheco, Anh H. Chung, Chengsheng Mao, Joshua C. Smith, Juan Zhao, Wei-Qi Wei, April Barnado, Chunhua Weng, Cong Liu, Adam Cordon, Jingzhi Yu, Yacob Tedla, Abel N. Kho, Rosalind Ramsey-Goldman, Theresa Walunas, Yuan Luo:
Natural language processing to identify lupus nephritis phenotype in electronic health records. CoRR abs/2112.10821 (2021) - 2020
- [j11]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) - [c19]Izabelle P. Humes, Roxana Loperena-Cortes, Melissa A. Basford, Kelsey R. Mayo, Joseph DiPaolo, David J. Schlueter, Jun Qian, Wei-Qi Wei, Robert J. Carroll, David Glazer, Paul A. Harris, Anthony A. Philippakis, Dan M. Roden, Andrea H. Ramirez:
The All of Us Research Program Researcher Workbench Phenotype Library: Five Disease Implementations. AMIA 2020 - [c18]Juan Zhao, Yu Wang, QiPing Feng, Wei-Qi Wei:
Detecting National Institutes of Health's funding interests and trends using Machine Learning. AMIA 2020
2010 – 2019
- 2019
- [j10]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) - [j9]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) - [c17]Patrick Wu, QiPing Feng, Joshua C. Denny, Wei-Qi Wei:
Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs. AMIA 2019 - [c16]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 - [c15]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 - 2018
- [c14]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 - [c13]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 - [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
- [j8]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) - [c12]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 - [c11]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 - 2016
- [j7]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) - 2015
- [j6]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) - [c10]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 - [c9]Yaomin Xu, Todd L. Edwards, Lisa Bastarache, Rebecca N. Jerome, Shilin Zho, Eric Torstenson, Wei-Qi Wei, Jana Shirey-Rice, Erica A. Bowton, Yu Shyr, Jill M. Pulley, Joshua C. Denny:
PheWAS Network Analysis and Visualization. AMIA 2015 - 2014
- [c8]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 - 2013
- [j5]Wei-Qi Wei, Cynthia L. Leibson, Jeanine E. Ransom, Abel N. Kho, Christopher G. Chute:
The absence of longitudinal data limits the accuracy of high-throughput clinical phenotyping for identifying type 2 diabetes mellitus subjects. Int. J. Medical Informatics 82(4): 239-247 (2013) - [j4]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) - [j3]Cui Tao, Jyotishman Pathak, Harold R. Solbrig, Wei-Qi Wei, Christopher G. Chute:
Terminology representation guidelines for biomedical ontologies in the semantic web notations. J. Biomed. Informatics 46(1): 128-138 (2013) - [c7]Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny:
Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems. AMIA 2013 - [c6]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 - [c5]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 - [c4]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 - 2012
- [j2]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) - [j1]Wei-Qi Wei, Cynthia L. Leibson, Jeanine E. Ransom, Abel N. Kho, Pedro J. Caraballo, High Seng Chai, Barbara P. Yawn, Jennifer A. Pacheco, Christopher G. Chute:
Impact of data fragmentation across healthcare centers on the accuracy of a high-throughput clinical phenotyping algorithm for specifying subjects with type 2 diabetes mellitus. J. Am. Medical Informatics Assoc. 19(2): 219-224 (2012) - [c3]Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny:
Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR. AMIA 2012 - [c2]Wei-Qi Wei, Lisa Bastarache, Joshua C. Denny:
Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes. AMIA 2012 - 2010
- [c1]Cui Tao, Harold R. Solbrig, Deepak K. Sharma, Wei-Qi Wei, Guergana K. Savova, Christopher G. Chute:
Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. ISWC (2) 2010: 241-256
Coauthor Index
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