Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. - Joshua C. Denny; Josh F. Peterson; Neesha N. Choma; Hua Xu 001; Randolph A. Miller; Lisa Bastarache; Neeraja B. Peterson (AMIA, 2009)

Tracking medical students' clinical experiences using natural language processing. - Joshua C. Denny; Lisa Bastarache; Elizabeth Ann Sastre; Anderson Spickard III (J. Biomed. Informatics, 2009)

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. - 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 (Bioinform., 2010)

Extracting timing and status descriptors for colonoscopy testing from electronic medical records. - Joshua C. Denny; Josh F. Peterson; Neesha N. Choma; Hua Xu 001; Randolph A. Miller; Lisa Bastarache; Neeraja B. Peterson (J. Am. Medical Informatics Assoc., 2010)

Integrating existing natural language processing tools for medication extraction from discharge summaries. - Son Doan; Lisa Bastarache; Sergio Klimkowski; Joshua C. Denny; Hua Xu 001 (J. Am. Medical Informatics Assoc., 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)

Using PheWAS to Assess Pleiotropy of Genetic Risk Scores for Rheumatoid Arthritis and Coronary Artery Disease in the eMERGE Network. - Robert J. Carroll; Katherine P. Liao; Anne E. Eyler; Lisa Bastarache; Dana C. Crawford; Peggy L. Peissig; Jyotishman Pathak; David Carrell; Abel N. Kho; Rongling Li; Daniel R. Masys; Gail P. Jarvik; et al. (AMIA, 2012)

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

A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing. - Eugenia R. McPeek Hinz; Lisa Bastarache; Joshua C. Denny (HISB, 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)

Open Source R Implementation of the PheWAS Methodology. - Robert J. Carroll; Lisa Bastarache; Joshua C. Denny (AMIA, 2013)

A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype. - Eugenia R. McPeek Hinz; Joshua C. Denny; Lisa Bastarache (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)

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)

Phenome-Wide Association Studies Using NLP-Derived Concepts. - Pedro L. Teixeira; Robert J. Carroll; Lisa Bastarache; Peter Speltz; Joshua C. Smith; Joshua C. Denny (AMIA, 2014)

R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. - Robert J. Carroll; Lisa Bastarache; Joshua C. Denny (Bioinform., 2014)

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)

Sub-Phenotyping of Crohn's Disease Using a Large Electronic Record Cohort. - Jamie R. Robinson; Lisa Bastarache; Robert J. Carroll; Elizabeth A. Scoville; David A. Schwartz; Joshua C. Denny (AMIA, 2017)

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)

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)

Computable Longitudinal Patient Trajectories. - Jeremy L. Warner; Guergana Savova; Noemie Elhadad; Lisa Bastarache; David Gotz (AMIA, 2018)

Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease. - 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 (J. Am. Medical Informatics Assoc., 2019)

Developing a Phenotype Risk Score for Opioid Adverse Events. - Leigh Anne Tang; Sarah DeLozier; Lisa Bastarache; Colin Walsh; Joshua C. Denny (AMIA, 2020)

Using Genomic Association Replication Rates as an EHR Quality Measure via the Phenotype-Genotype Reference Map (PGRM). - Sarah DeLozier; Josh F. Peterson; Joshua C. Denny; Lisa Bastarache (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)

Systematic replication of smoking disease associations in the All of Us Research Program. - 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 (AMIA, 2021)

Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers. - Subha Madhavan; Lisa Bastarache; Jeffrey S. Brown; Atul J. Butte; David A. Dorr; Peter J. Embí; Charles P. Friedman; Kevin B. Johnson; Jason H. Moore; Isaac S. Kohane; Philip R. O. Payne; Jessica D. Tenenbaum; 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)

The PheRS R package: Phenotype risk score generation and analysis tool using electronic health record data. - Layla Aref; Lisa Bastarache; Jake Hughey (AMIA, 2022)

Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS. - Rebecca Irlmeier; Jacob J. Hughey; Lisa Bastarache; Joshua C. Denny; Qingxia Chen (Bioinform., 2022)

A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. - Ken Wiley; Laura Findley; Madison Goldrich; Tejinder K. Rakhra-Burris; Ana Stevens; Pamela Williams; Carol J. Bult; Rex L. Chisholm; Patricia Deverka; Geoffrey S. Ginsburg; Eric D. Green; Gail P. Jarvik; et al. (J. Am. Medical Informatics Assoc., 2022)

The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants. - Layla Aref; Lisa Bastarache; Jacob J. Hughey (Bioinform., 2022)

Knowledgebase strategies to aid interpretation of clinical correlation research. - William W. Stead; Adam Lewis; Nunzia B. Giuse; Taneya Y. Koonce; Lisa Bastarache (J. Am. Medical Informatics Assoc., 2023)

Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics. - Megan M. Shuey; William W. Stead; Ida Aka; April L. Barnado; Lisa Bastarache; Elly Brokamp; Meredith Campbell; Robert J. Carroll; Jeffrey A. Goldstein; Adam Lewis; Beth A. Malow; Jonathan D. Mosley; et al. (Bioinform., 2023)

Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research Program. - 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; et al. (J. Am. Medical Informatics Assoc., 2023)

Comparison of phenomic profiles in the All of Us Research Program against the US general population and the UK Biobank. - Chenjie Zeng; David J. Schlueter; Tam C. Tran; Anav Babbar; Thomas Cassini; Lisa Bastarache; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2024)

Disentangling the phenotypic patterns of hypertension and chronic hypotension. - William W. Stead; Adam Lewis; Nunzia B. Giuse; Annette M. Williams; Italo Biaggioni; Lisa Bastarache (J. Biomed. Informatics, 2024)

Identifying and Extracting Rare Diseases and Their Phenotypes with Large Language Models. - Cathy Shyr; Yan Hu; Lisa Bastarache; Alex Cheng; Rizwan Hamid; Paul A. Harris; Hua Xu 001 (J. Heal. Informatics Res., 2024)

Unmet social needs and diverticulitis: a phenotyping algorithm and cross-sectional analysis. - Thomas E. Ueland; Samuel A Younan; Parker T. Evans; Jessica Sims; Megan M. Shroder; Alexander T. Hawkins; Richard Peek; Xinnan Niu; Lisa Bastarache; Jamie R. Robinson (J. Am. Medical Informatics Assoc., 2025)