A Highly Specific Algorithm for Identifying Asthma Cases and Controls for Genome-Wide Association Studies. - Jennifer A. Pacheco; Pedro C. Avila; Jason A. Thompson; May Law; Jihan A. Quraishi; Alyssa K. Greiman; Eric M. Just; Abel N. Kho (AMIA, 2009)

A Geographic Exploration of Colon Polyps. - Anna Roberts; Arun Muthalagu; Jennifer A. Pacheco; William K. Thompson; Andrew Gawron; Abel N. Kho (AMIA, 2012)

An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms. - William K. Thompson; Luke V. Rasmussen; Jennifer A. Pacheco; Peggy L. Peissig; Joshua C. Denny; Abel N. Kho; Aaron W. Miller; Jyotishman Pathak (AMIA, 2012)

Open Source Workflow Tools for Electronic Health Record Based Phenotyping Algorithms. - William K. Thompson; Luke V. Rasmussen; Jennifer A. Pacheco; Anna Roberts; Arun Muthalagu; Abel N. Kho (AMIA, 2012)

Portability of an algorithm to identify rheumatoid arthritis in electronic health records. - 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 001; Elizabeth W. Karlson; Raúl G. Pérez; et al. (J. Am. Medical Informatics Assoc., 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)

Automating Extraction and Calculation of Daily Dose and Duration for Medications in EHRs. - Jennifer A. Pacheco; William K. Thompson; Kathryn L. Jackson; Abel N. Kho (AMIA, 2014)

Evaluation of Existing Phenotype Authoring Tools for Clinical Research. - Luke V. Rasmussen; Jie Xu 011; Ruijue Liu; Qian Zhu 003; Jennifer A. Pacheco; Jyotishman Pathak; William K. Thompson; Joshua C. Denny; Huan Mo; Richard C. Kiefer; Peter Speltz; Enid N. H. Montague (AMIA, 2014)

Qualitative evaluation of three phenotype information models to find methotrexate liver injury. - Qian Zhu 003; Huan Mo; Luke V. Rasmussen; Andrew R. Post; Jennifer A. Pacheco; Jie Xu 011; Richard C. Kiefer; Peter Speltz; Enid N. H. Montague; William K. Thompson; Joshua C. Denny; Jyotishman Pathak (AMIA, 2014)

Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies. - 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; et al. (EvoApplications, 2014)

Design patterns for the development of electronic health record-driven phenotype extraction algorithms. - 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 (J. Biomed. Informatics, 2014)

Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study. - Guoqian Jiang; Harold R. Solbrig; Richard C. Kiefer; Luke V. Rasmussen; Huan Mo; Jennifer A. Pacheco; Enid N. H. Montague; Jie Xu 011; Peter Speltz; William K. Thompson; Joshua C. Denny; Christopher G. Chute; et al. (AMIA, 2015)

A Genome- and Phenome- Wide Study of Diverticulosis. - 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; et al. (AMIA, 2015)

Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME. - Huan Mo; Jennifer A. Pacheco; Richard C. Kiefer; Luke V. Rasmussen; Jyotishman Pathak; Joshua C. Denny; William K. Thompson (AMIA, 2015)

Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools. - Enid N. H. Montague; Jie Xu 011; Luke V. Rasmussen; Joshua C. Denny; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Peter Speltz; William K. Thompson; Jyotishman Pathak (AMIA, 2015)

(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping. - Jennifer A. Pacheco; Abel N. Kho; Jyotishman Pathak; Joshua C. Denny; Shawn N. Murphy (AMIA, 2015)

Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR). - Rishika De; Shefali S. Verma; Fotios Drenos; Emily Rose Holzinger; Michael Holmes; Molly A. Hall; David R. Crosslin; David Carrell; Hakon Hakonarson; Gail P. Jarvik; Eric B. Larson; Jennifer A. Pacheco; et al. (BioData Min., 2015)

Desiderata for computable representations of electronic health records-driven phenotype algorithms. - Huan Mo; William K. Thompson; Luke V. Rasmussen; Jennifer A. Pacheco; Guoqian Jiang; Richard C. Kiefer; Qian Zhu 003; Jie Xu 011; Enid N. H. Montague; David S. Carrell; Todd Lingren; Frank D. Mentch; et al. (J. Am. Medical Informatics Assoc., 2015)

Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. - Jie Xu 011; Luke V. Rasmussen; Pamela L. Shaw; Guoqian Jiang; Richard C. Kiefer; Huan Mo; Jennifer A. Pacheco; Peter Speltz; Qian Zhu 003; Joshua C. Denny; Jyotishman Pathak; William K. Thompson; et al. (J. Am. Medical Informatics Assoc., 2015)

Personalized Heart Disease Risk Manager: A Tool for Patients and Clinicians to Manage Cardiovascular Risk. - Raja Arul Cholan; Jennifer A. Pacheco; Gene Ren; Laura Hickerson (AMIA, 2016)

An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution. - Guoqian Jiang; William K. Thompson; Luke V. Rasmussen; Richard C. Kiefer; Jennifer A. Pacheco; Huan Mo; Peter Speltz; Joshua C. Denny; Jyotishman Pathak (AMIA, 2016)

Design and Implementation of an Ancillary Genomics System for the Return of Pharmacogenetic Results. - Luke V. Rasmussen; Maureen E. Smith; Federico Almaraz; Stephen D. Persell; Laura Rasmussen-Torvik; Jennifer A. Pacheco; Carl Christensen; Timothy M. Herr; Firas H. Wehbe; Justin Starren (AMIA, 2016)

A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. - Huan Mo; Guoqian Jiang; Jennifer A. Pacheco; Richard C. Kiefer; Luke V. Rasmussen; Jyotishman Pathak; Joshua C. Denny; William K. Thompson (CRI, 2016)

A multi-institution evaluation of clinical profile anonymization. - Raymond Heatherly; Luke V. Rasmussen; Peggy L. Peissig; Jennifer A. Pacheco; Paul A. Harris; Joshua C. Denny; Bradley A. Malin (J. Am. Medical Informatics Assoc., 2016)

PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. - 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; et al. (J. Am. Medical Informatics Assoc., 2016)

Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. - Guoqian Jiang; Richard C. Kiefer; Luke V. Rasmussen; Harold R. Solbrig; Huan Mo; Jennifer A. Pacheco; Jie Xu 011; Enid N. H. Montague; William K. Thompson; Joshua C. Denny; Christopher G. Chute; Jyotishman Pathak (J. Biomed. Informatics, 2016)

A Machine Learning-Based Approach for Identifying Atopic Dermatitis in Adults from Electronic Health Records. - Erin N. Gustafson; Al'ona Furmanchuk; Jennifer A. Pacheco; Firas H. Wehbe; Kathryn L. Jackson; Abel N. Kho; William K. Thompson; Jonathan Silverberg (AMIA, 2017)

Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository. - Richard C. Kiefer; Luke V. Rasmussen; Jennifer A. Pacheco; Peter Speltz; Joshua C. Denny; William K. Thompson; Jyotishman Pathak; Guoqian Jiang (AMIA, 2017)

Portable Precision Phenotype Algorithm for Chronic Rhinosinusitis. - Jennifer A. Pacheco; Agnes S. Sundaresan; Kenneth M. Borthwick; Sergio E. Chiarella; David T. Coleman; Andy Yizhou Wu; Abel N. Kho; M. Geoffrey Hayes; Marc S. Williams (AMIA, 2017)

Sensi-steps: Using Patient-Generated Data to Prevent Post-stroke Falls. - Angela Smith; Ada Ng; Eleanor R. Burgess; Jennifer A. Pacheco; Noah D. Weingarten (AMIA, 2017)

The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs. - Peter Speltz; Luke V. Rasmussen; Richard C. Kiefer; Jennifer A. Pacheco; William K. Thompson; Guoqian Jiang; Jyotishman Pathak; Joshua C. Denny (AMIA, 2017)

A Machine Learning Algorithm for Identifying Atopic Dermatitis in Adults from Electronic Health Records. - Erin N. Gustafson; Jennifer A. Pacheco; Firas H. Wehbe; Jonathan Silverberg; William K. Thompson (ICHI, 2017)

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)

A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. - 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; et al. (J. Am. Medical Informatics Assoc., 2018)

Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. - Prakash Adekkanattu; Guoqian Jiang; Yuan Luo 001; Paul R. Kingsbury; Zhenxing Xu; Luke V. Rasmussen; Jennifer A. Pacheco; Richard C. Kiefer; Daniel J. Stone; Pascal S. Brandt; Liang Yao; Yizhen Zhong; et al. (AMIA, 2019)

Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms. - Luke V. Rasmussen; Pascal S. Brandt; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Prakash Adekkanattu; Jessica S. Ancker; Fei Wang 001; Zhenxing Xu; Jyotishman Pathak; Yuan Luo 001 (AMIA, 2019)

Assessing the Concordance of Clinical Classification Criteria for Lupus Between Electronic Health Records and a Physician Curated Registry. - Theresa L. Walunas; Anika S. Ghosh; Jennifer A. Pacheco; Kathryn L. Jackson; Anh H. Chung; Daniel L. Erickson; Karen Mancera-Cuevas; Rosalind Ramsey-Goldman; Abel N. Kho (MedInfo, 2019)

Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care. - Zhenxing Xu; Yuan Luo 001; Prakash Adekkanattu; Jessica S. Ancker; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Luke V. Rasmussen; Jyotishman Pathak; Fei Wang 001 (MedInfo, 2019)

Identification of Predictive Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks. - Zhenxing Xu; Jingyuan Chou; Xi Sheryl Zhang; Yuan Luo 001; Tamara Isakova; Prakash Adekkanattu; Jessica S. Ancker; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Luke V. Rasmussen; Jyotishman Pathak; et al. (CoRR, 2019)

An ancillary genomics system to support the return of pharmacogenomic results. - Luke V. Rasmussen; Maureen E. Smith; Federico Almaraz; Stephen D. Persell; Laura J. Rasmussen-Torvik; Jennifer A. Pacheco; Rex L. Chisholm; Carl Christensen; Timothy M. Herr; Firas H. Wehbe; Justin B. Starren (J. Am. Medical Informatics Assoc., 2019)

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. - Na Hong; Andrew Wen; Daniel J. Stone; Shintaro Tsuji; Paul R. Kingsbury; Luke V. Rasmussen; Jennifer A. Pacheco; Prakash Adekkanattu; Fei Wang 001; Yuan Luo 001; Jyotishman Pathak; Hongfang Liu; et al. (J. Biomed. Informatics, 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)

Feasibility of Cross-Platform EHR-Driven Phenotyping Using Clinical Quality Language. - Pascal S. Brandt; Richard C. Kiefer; Jennifer A. Pacheco; Prakash Adekkanattu; Evan Sholle; Faraz S. Ahmad; Jie Xu 012; Zhenxing Xu; Jessica S. Ancker; Fei Wang 001; Yuan Luo 001; Guoqian Jiang; et al. (AMIA, 2020)

Identification of Alzheimer's Disease Subtypes from Electronic Health Records Using a Data-Driven Approach. - Jie Xu 012; Fei Wang 001; Zhenxing Xu; Prakash Adekkanattu; Pascal S. Brandt; Guoqian Jiang; Richard C. Kiefer; Yuan Luo 001; Chengsheng Mao; Jennifer A. Pacheco; Luke V. Rasmussen; Yiye Zhang; et al. (AMIA, 2020)

Identifying sub-phenotypes of acute kidney injury using structured and unstructured electronic health record data with memory networks. - Zhenxing Xu; Jingyuan Chou; Xi Sheryl Zhang; Yuan Luo 001; Tamara Isakova; Prakash Adekkanattu; Jessica S. Ancker; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Luke V. Rasmussen; Jyotishman Pathak; et al. (J. Biomed. Informatics, 2020)

Multi-site Evaluation of Longitudinal Changes in Ejection Fraction in Heart Failure Patients Through Data-driven Phenotyping. - Prakash Adekkanattu; Jennifer A. Pacheco; Joseph Kabariti; Daniel J. Stone; Yue Yu; Parag Goyal; Faraz S. Ahmad; Guoqian Jiang; Yuan Luo 001; Luke V. Rasmussen; Pascal S. Brandt; Zhenxing Xu; et al. (AMIA, 2021)

Supporting EHR-based Cohort Discovery Through User-centered Design: Results of an Early Formative Usability Study. - Natalie C. Benda; Pascal S. Brandt; Jessica S. Ancker; Jennifer A. Pacheco; Prakash Adekkanattu; Guoqian Jiang; Jyotishman Pathak; Luke V. Rasmussen (AMIA, 2021)

A Deep Learning Framework Using a Pre-trained BERT Model to Predict the Risk of Progression from Mild Cognitive Impairment to Alzheimer's Disease. - Chengsheng Mao; Jie Xu 012; Luke V. Rasmussen; Jennifer A. Pacheco; Guoqian Jiang; Fei Wang 001; Richard Isaacson; Jyotishman Pathak; Yuan Luo 001 (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)

FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. - Daniel J. Stone; Sijia Liu 002; Yuan Luo 001; Andrew Wen; Nansu Zong; Luke V. Rasmussen; Prakash Adekkanattu; Pascal S. Brandt; Jennifer A. Pacheco; Fei Wang 001; Cui Tao; Jyotishman Pathak; et al. (AMIA, 2021)

On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. - Andrew Wen; Luke V. Rasmussen; Daniel J. Stone; Sijia Liu 002; Prakash Adekkanattu; Pascal S. Brandt; Jennifer A. Pacheco; Yuan Luo 001; Fei Wang 001; Jyotishman Pathak; Hongfang Liu; Guoqian Jiang (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)

AD-BERT: Using Pre-trained contextualized embeddings to Predict the Progression from Mild Cognitive Impairment to Alzheimer's Disease. - Chengsheng Mao; Jie Xu 012; Luke V. Rasmussen; Yikuan Li; Prakash Adekkanattu; Jennifer A. Pacheco; Borna Bonakdarpour; Robert Vassar; Guoqian Jiang; Fei Wang 001; Jyotishman Pathak; Yuan Luo 001 (CoRR, 2022)

Design and validation of a FHIR-based EHR-driven phenotyping toolbox. - Pascal S. Brandt; Jennifer A. Pacheco; Prakash Adekkanattu; Evan Sholle; Sajjad Abedian; Daniel J. Stone; David Knaack; Jie Xu 012; Zhenxing Xu; Yifan Peng 002; Natalie C. Benda; Fei Wang 001; et al. (J. Am. Medical Informatics Assoc., 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)

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)

AD-BERT: Using pre-trained language model to predict the progression from mild cognitive impairment to Alzheimer's disease. - Chengsheng Mao; Jie Xu 012; Luke V. Rasmussen; Yikuan Li; Prakash Adekkanattu; Jennifer A. Pacheco; Borna Bonakdarpour; Robert Vassar; Li Shen; Guoqian Jiang; Fei Wang 001; Jyotishman Pathak; et al. (J. Biomed. Informatics, 2023)