Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. - Cui Tao; Harold R. Solbrig; Deepak K. Sharma; Wei-Qi Wei; Guergana K. Savova; Christopher G. Chute (ISWC (2), 2010)

Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR. - Lisa Bastarache; Wei-Qi Wei; Joshua C. Denny (AMIA, 2012)

Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes. - Wei-Qi Wei; Lisa Bastarache; Joshua C. Denny (AMIA, 2012)

Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study. - 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; et al. (J. Am. Medical Informatics Assoc., 2012)

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. - 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 (J. Am. Medical Informatics Assoc., 2012)

Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems. - Lisa Bastarache; Wei-Qi Wei; Joshua C. Denny (AMIA, 2013)

Using PheWAS and Natural Language Processing to Discover Clinical Associations for Congenital Chest Deformities. - Christine M. McEvoy; Robert J. Carroll; Lisa Bastarache; Wei-Qi Wei; Joshua C. Denny (AMIA, 2013)

Validation and Enhancement of a Computable Medication Indication Resource (MEDI) Using a Large Practice-based Dataset. - Wei-Qi Wei; Jonathan D. Mosley; Lisa Bastarache; Joshua C. Denny (AMIA, 2013)

Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages. - Yonghui Wu; Jianbo Lei; Wei-Qi Wei; Buzhou Tang; Joshua C. Denny; S. Trent Rosenbloom; Randolph A. Miller; Dario A. Giuse; Kai Zheng 002; Hua Xu 001 (MedInfo, 2013)

The absence of longitudinal data limits the accuracy of high-throughput clinical phenotyping for identifying type 2 diabetes mellitus subjects. - Wei-Qi Wei; Cynthia L. Leibson; Jeanine E. Ransom; Abel N. Kho; Christopher G. Chute (Int. J. Medical Informatics, 2013)

Development and evaluation of an ensemble resource linking medications to their indications. - Wei-Qi Wei; Robert M. Cronin; Hua Xu 001; Thomas A. Lasko; Lisa Bastarache; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2013)

Terminology representation guidelines for biomedical ontologies in the semantic web notations. - Cui Tao; Jyotishman Pathak; Harold R. Solbrig; Wei-Qi Wei; Christopher G. Chute (J. Biomed. Informatics, 2013)

Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype. - Wei-Qi Wei; Pedro L. Teixeira; Huan Mo; Robert M. Cronin; Jeremy L. Warner; Joshua C. Denny (AMIA, 2014)

Quantifying Tobacco Exposure Using Clinical Notes and Natural Language Processing to Enable Lung Cancer Screening. - Travis Osterman; Wei-Qi Wei; Joshua C. Denny (AMIA, 2015)

PheWAS Network Analysis and Visualization. - 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 (AMIA, 2015)

Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. - Cosmin Adrian Bejan; Wei-Qi Wei; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2015)

Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. - Wei-Qi Wei; Pedro L. Teixeira; Huan Mo; Robert M. Cronin; Jeremy L. Warner; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2016)

Association of BMI and Obesity Genetic Risk Score with Surgical Procedures Through a Procedure-wide Association Study. - Jamie R. Robinson; Zongyang Mou; Lisa Bastarache; Wei-Qi Wei; Robert J. Carroll; Joshua C. Denny (AMIA, 2017)

A Phenome-Wide Association Study (PheWAS) of Iron Deficiency in a Large Electronic Health Record Database. - Patrick Wu; Joshua C. Denny; Wei-Qi Wei (AMIA, 2017)

Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. - 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; et al. (J. Am. Medical Informatics Assoc., 2017)

Using Topic Modeling to Identify Relationship between LPA Variant and Disease Phenotypes. - Juan Zhao 003; QiPing Feng; Patrick Wu; Joshua C. Denny; Wei-Qi Wei (AMIA, 2018)

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. - 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; et al. (BIBM, 2018)

Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs. - Patrick Wu; QiPing Feng; Joshua C. Denny; Wei-Qi Wei (AMIA, 2019)

Deep Learning Using Electronic Health Records and Genetic Data to Predict Cardiovascular Diseases. - Juan Zhao 003; QiPing Feng; Patrick Wu; Joshua C. Denny; Wei-Qi Wei (AMIA, 2019)

Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE network. - Xinyuan Zhang 003; 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; et al. (PSB, 2019)

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. - Ning Shang; Cong Liu 020; 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 001; et al. (J. Biomed. Informatics, 2019)

Detecting time-evolving phenotypic topics via tensor factorization on electronic health records: Cardiovascular disease case study. - Juan Zhao 003; Yun Zhang; David J. Schlueter; Patrick Wu; Vern Eric Kerchberger; S. Trent Rosenbloom; Quinn Stanton Wells; QiPing Feng; Joshua C. Denny; Wei-Qi Wei (J. Biomed. Informatics, 2019)

The All of Us Research Program Researcher Workbench Phenotype Library: Five Disease Implementations. - 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; et al. (AMIA, 2020)

Detecting National Institutes of Health's funding interests and trends using Machine Learning. - Juan Zhao 003; Yu Wang; QiPing Feng; Wei-Qi Wei (AMIA, 2020)

PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. - Neil S. Zheng; QiPing Feng; Vern Eric Kerchberger; Juan Zhao 003; Todd L. Edwards; Nancy J. Cox; C. Michael Stein; Dan M. Roden; Joshua C. Denny; Wei-Qi Wei (J. Am. Medical Informatics Assoc., 2020)

Early Detect COVID-19 Presenting Symptoms and Characteristics Using Natural Language Processing on Electronic Health Records. - Juan Zhao 003; Monika E. Grabowska; Wei-Qi Wei (AMIA, 2021)

Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation. - 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 (AMIA, 2021)

Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. - 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 020; Todd Lingren; et al. (AMIA, 2021)

Natural language processing to identify lupus nephritis phenotype in electronic health records. - Yu Deng; Jennifer A. Pacheco; Anh H. Chung; Chengsheng Mao; Joshua C. Smith; Juan Zhao 003; Wei-Qi Wei; April Barnado; Chunhua Weng; Cong Liu 020; Adam Cordon; Jingzhi Yu; et al. (CoRR, 2021)

DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions. - Patrick Wu; Scott D. Nelson; Juan Zhao 003; Cosby A. Stone Jr.; QiPing Feng; Qingxia Chen; Eric A. Larson; Bingshan Li; Nancy J. Cox; C. Michael Stein; Elizabeth Phillips; Dan M. Roden; et al. (J. Am. Medical Informatics Assoc., 2021)

Phenotyping coronavirus disease 2019 during a global health pandemic: Lessons learned from the characterization of an early cohort. - 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; et al. (J. Biomed. Informatics, 2021)

Genomic considerations for FHIR®; eMERGE implementation lessons. - 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; et al. (J. Biomed. Informatics, 2021)

ConceptWAS: A high-throughput method for early identification of COVID-19 presenting symptoms and characteristics from clinical notes. - Juan Zhao 003; 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 (J. Biomed. Informatics, 2021)

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. - 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; et al. (J. Biomed. Informatics, 2021)

Quantitative disease risk scores from EHR with applications to clinical risk stratification and genetic studies. - Danqing Xu; Chen Wang 146; Atlas Khan; Ning Shang; Zihuai He; Adam S. Gordon; Iftikhar J. Kullo; Shawn N. Murphy; Yizhao Ni; Wei-Qi Wei; Ali Gharavi; Krzysztof Kiryluk; et al. (npj Digit. Medicine, 2021)

Developing and Mapping Pediatric Phecodes (Phecode-Peds). - Monika E. Grabowska; Sara L. Van Driest; Patrick Wu; Wei-Qi Wei (AMIA, 2022)

Evaluating Phenotype Classification Using Synthesized Online Content. - Yanwei Li; Wei-Qi Wei; Juan Zhao 003; Chao Yan; Henry H. Ong (AMIA, 2022)

Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. - Jingzhi Yu; Jennifer A. Pacheco; Anika S. Ghosh; Yuan Luo 001; Chunhua Weng; Ning Shang; Barbara Benoit; David S. Carrell; Robert J. Carroll; Ozan Dikilitas; Robert R. Freimuth; Vivian S. Gainer; et al. (BMC Medical Informatics Decis. Mak., 2022)

Natural language processing to identify lupus nephritis phenotype in electronic health records. - Yu Deng; Jennifer A. Pacheco; Anika S. Ghosh; Anh H. Chung; Chengsheng Mao; Joshua C. Smith; Juan Zhao 003; Wei-Qi Wei; April Barnado; Chad Dorn; Chunhua Weng; Cong Liu 020; et al. (BMC Medical Informatics Decis. Mak., 2022)

Scanning the medical phenome to identify new diagnoses after recovery from COVID-19 in a US cohort. - Vern Eric Kerchberger; Josh F. Peterson; Wei-Qi Wei (J. Am. Medical Informatics Assoc., 2023)

Characterizing variability of electronic health record-driven phenotype definitions. - Pascal S. Brandt; Abel N. Kho; Yuan Luo 001; Jennifer A. Pacheco; Theresa L. Walunas; Hakon Hakonarson; George Hripcsak; Cong Liu 020; Ning Shang; Chunhua Weng; Nephi Walton; David S. Carrell; et al. (J. Am. Medical Informatics Assoc., 2023)

Evaluating resources composing the PheMAP knowledge base to enhance high-throughput phenotyping. - Nicholas C. Wan; Ali A Yaqoob; Henry H. Ong; Juan Zhao 003; Wei-Qi Wei (J. Am. Medical Informatics Assoc., 2023)

Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction. - Fuchen Li; Patrick Wu; Henry H. Ong; Josh F. Peterson; Wei-Qi Wei; Juan Zhao 003 (J. Biomed. Informatics, 2023)

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. - 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; et al. (J. Am. Medical Informatics Assoc., 2023)

Representing and utilizing clinical textual data for real world studies: An OHDSI approach. - Vipina Kuttichi Keloth; Juan M. Banda; Michael J. Gurley; Paul M. Heider; Georgina Kennedy; Hongfang Liu; Feifan Liu; Timothy Miller 002; Karthik Natarajan; Olga V. Patterson; Yifan Peng 002; Kalpana Raja; et al. (J. Biomed. Informatics, 2023)

Improving reporting standards for phenotyping algorithm in biomedical research: 5 fundamental dimensions. - Wei-Qi Wei; Robb Rowley; Angela M. Wood; Jacqueline Macarthur; Peter J. Embí; Spiros C. Denaxas (J. Am. Medical Informatics Assoc., 2024)

Large language models facilitate the generation of electronic health record phenotyping algorithms. - Chao Yan 004; 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; et al. (J. Am. Medical Informatics Assoc., 2024)

Leveraging generative AI to prioritize drug repurposing candidates for Alzheimer's disease with real-world clinical validation. - Chao Yan 004; 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 (npj Digit. Medicine, 2024)

Developing and evaluating pediatric phecodes (Peds-Phecodes) for high-throughput phenotyping using electronic health records. - 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 (J. Am. Medical Informatics Assoc., 2024)

Beyond Phecodes: leveraging PheMAP to identify patients lacking diagnosis codes in electronic health records. - Chao Yan 004; Monika E. Grabowska; Rut Thakkar; Alyson L. Dickson; Peter J. Embí; QiPing Feng; Joshua C. Denny; Vern Eric Kerchberger; Bradley A. Malin; Wei-Qi Wei (J. Am. Medical Informatics Assoc., 2025)