An efficient approach for surveillance of childhood diabetes by type derived from electronic health record data: the SEARCH for Diabetes in Youth Study. - Victor W. Zhong; Jihad S. Obeid; Jean B. Craig; Emily R. Pfaff; Joan Thomas; Lindsay M. Jaacks; Daniel P. Beavers; Timothy S. Carey; Jean M. Lawrence; Dana Dabelea; Richard F. Hamman; Deborah A. Bowlby; et al. (J. Am. Medical Informatics Assoc., 2016)

FDTool: a Python application to mine for functional dependencies and candidate keys in tabular data. - Matt Buranosky; Elmar Stellnberger; Emily R. Pfaff; David Díaz-Gutiérrez; Cavin Ward-Caviness (F1000Research, 2018)

SMOREs : Synergistic Medication Organizer for RxNorm and Expansions, a Tool For Improving Semantic Relationships of Institutional Medications to Standardized Ontologies. - Robert L. Bradford; Marshall Clark; Emily R. Pfaff (AMIA, 2019)

A novel approach for exposing and sharing clinical data: the Translator Integrated Clinical and Environmental Exposures Service. - Karamarie Fecho; Emily R. Pfaff; Hao Xu 006; James Champion; Steve Cox 001; Lisa Stillwell; David B. Peden; Chris Bizon; Ashok Kumar Krishnamurthy 001; Alexander Tropsha; Stanley C. Ahalt (J. Am. Medical Informatics Assoc., 2019)

Recruiting for a pragmatic trial using the electronic health record and patient portal: successes and lessons learned. - Emily R. Pfaff; Adam Lee; Robert L. Bradford; Jinhee Pae; Clarence Potter; Paul Blue; Patricia Knoepp; Kristie Thompson; Christianne L. Roumie; David Crenshaw; Remy Servis; Darren A. DeWalt (J. Am. Medical Informatics Assoc., 2019)

Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon. - Karamarie Fecho; Stanley C. Ahalt; Saravanan Arunachalam; James Champion; Christopher G. Chute; Sarah Davis; Kenneth Gersing; Gustavo Glusman; Jennifer Hadlock; Jewel Lee; Emily R. Pfaff; Max Robinson; et al. (J. Biomed. Informatics, 2019)

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. - Xingmin Aaron Zhang; Amy Yates; Nicole A. Vasilevsky; Jean-Philippe F. Gourdine; Tiffany J. Callahan; Leigh C. Carmody; Daniel Danis; Marcin P. Joachimiak; Vida Ravanmehr; Emily R. Pfaff; James Champion; Kimberly Robasky; et al. (npj Digit. Medicine, 2019)

Utilizing Encrypted Hashes to Link Patient Cohorts via Streamlined SAS Programs. - Robert L. Bradford; Sofia Dard; Emily R. Pfaff; Ashok K. Krishnamurthy 001 (AMIA, 2020)

FHIR PIT: an open software application for spatiotemporal integration of clinical data and environmental exposures data. - Hao Xu 006; Steven Cox 001; Lisa Stillwell; Emily R. Pfaff; James Champion; Stanley C. Ahalt; Karamarie Fecho (BMC Medical Informatics Decis. Mak., 2020)

Cohort Identification Using Semantic Web Technologies: Ontologies and Triplestores as Engines for Complex Computable Phenotyping. - Emily R. Pfaff (2020)

National COVID Cohort Collaborative (N3C) Case-control Buddies. - Marshall Clark; Adam M. Lee; Emily R. Pfaff; Kristin Kostka; Matvey B. Palchuk; Lora Lingrey; Michele Morris; Robert T. Miller (AMIA, 2021)

Enabling Longitudinal Exploratory Analysis of Clinical COVID Data. - David Borland; Irena Brain; Karamarie Fecho; Emily R. Pfaff; Hao Xu 006; James Champion; Chris Bizon; David Gotz (VAHC, 2021)

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Rui Zhang 028; et al. (CoRR, 2021)

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. - Melissa A. Haendel; Christopher G. Chute; Tellen D. Bennett; David A. Eichmann; Justin Guinney; Warren A. Kibbe; Philip R. O. Payne; Emily R. Pfaff; Peter N. Robinson; Joel H. Saltz; Heidi Spratt; Christine Suver; et al. (J. Am. Medical Informatics Assoc., 2021)

CAMP FHIR: Clinical Asset Mapping Program for FHIR. - James Champion; Paul Kovach; Asiyah Ahmad; Anna Jojic; Buck Bohac; Adam M. Lee; Patrick Conway; Emily R. Pfaff (AMIA, 2022)

Maximizing Interoperability, Enriching EHR Data: Transforming HL7 FHIR Data to RDF Using the FHIR RDF Playground. - James Champion; Eric Prud'hommeaux; David Booth; Gaurav Vaidya; James P. Balhoff; Deepak K. Sharma; Guoqian Jiang; Emily R. Pfaff (AMIA, 2022)

HIPAA Safe Harbor (HuSH) Common Data Models for Education. - Sofia Z. Dard; James Champion; Robert L. Bradford; Adam M. Lee; Emily R. Pfaff (AMIA, 2022)

Modeling a Cancer Symptom Control Domain Using HL7 FHIR: Applicability of the Minimal Common Oncology Data Elements (mCODE). - Nan Huo; Yue Yu; Nansu Zong; Andrea Cheville; Claude Nanjo; Eric Prud'hommeaux; Deirdre Pachman; Guohui Xiao 001; Emily R. Pfaff; Christopher G. Chute; Guoqian Jiang; Kathryn J. Ruddy (AMIA, 2022)

Relational FHIR: Converting FHIR's Hierarchal Schema. - Adam M. Lee; Paul Kovach; James Champion; Patrick Conway; Emily R. Pfaff (AMIA, 2022)

A Comparative Study on the Capability of Real-World Antineoplastic Drug Data Collection by CanMED, ATC and HemOnc. - Yue Yu; Kathryn J. Ruddy; Nan Huo; Nansu Zong; Deirdre Pachman; Christopher G. Chute; Emily R. Pfaff; Andrea Cheville; Guoqian Jiang (AMIA, 2022)

Implementing a New FHIR RDF Specification for Semantic Clinical Data Using a JSON-LD-based Approach. - Deepak K. Sharma; Eric Prud'hommeaux; David Booth; Kevin J. Peterson; Daniel J. Stone; Harold Solbrig; Guohui Xiao 001; Emily R. Pfaff; Guoqian Jiang (SWAT4HCLS, 2022)

Leveraging Open Electronic Health Record Data and Environmental Exposures Data to Derive Insights Into Rare Pulmonary Disease. - Karamarie Fecho; Stanley C. Ahalt; Michael Knowles; Ashok K. Krishnamurthy 001; Margaret Leigh; Kenneth Morton; Emily R. Pfaff; Max Wang; Hong Yi (Frontiers Artif. Intell., 2022)

Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset. - Katie R. Bradwell; Jacob T. Wooldridge; Benjamin R. C. Amor; Tellen D. Bennett; Adit Anand; Carolyn Bremer; Yun Jae Yoo; Zhenglong Qian; Steven G. Johnson; Emily R. Pfaff; Andrew T. Girvin; Amin Manna; et al. (J. Am. Medical Informatics Assoc., 2022)

Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. - Emily R. Pfaff; Andrew T. Girvin; Davera Gabriel; Kristin Kostka; Michele Morris; Matvey B. Palchuk; Harold P. Lehmann; Benjamin R. C. Amor; Mark Bissell; Katie R. Bradwell; Sigfried Gold; Stephanie S. Hong; et al. (J. Am. Medical Informatics Assoc., 2022)

Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C). - Jason A. Thomas; Randi E. Foraker; Noa Zamstein; Jon D. Morrow; Philip R. O. Payne; Adam B. Wilcox; Melissa A. Haendel; Christopher G. Chute; Kenneth R. Gersing; Anita Walden; Tellen D. Bennett; David A. Eichmann; et al. (J. Am. Medical Informatics Assoc., 2022)

Supporting research, protecting data: one institution's approach to clinical data warehouse governance. - Kellie M. Walters; Anna Jojic; Emily R. Pfaff; Marie Rape; Donald C. Spencer; Nicholas J. Shaheen; Brent Lamm; Timothy S. Carey (J. Am. Medical Informatics Assoc., 2022)

FHIR-Ontop-OMOP: Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model. - Guohui Xiao 001; Emily R. Pfaff; Eric Prud'hommeaux; David Booth; Deepak K. Sharma; Nan Huo; Yue Yu; Nansu Zong; Kathryn J. Ruddy; Christopher G. Chute; Guoqian Jiang (J. Biomed. Informatics, 2022)

Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. - Yue Yu; Nansu Zong; Andrew Wen; Sijia Liu 002; Daniel J. Stone; David Knaack; Alanna M. Chamberlain; Emily R. Pfaff; Davera Gabriel; Christopher G. Chute; Nilay Shah; Guoqian Jiang (J. Biomed. Informatics, 2022)

International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. - Griffin M. Weber; Chuan Hong; Zongqi Xia; Nicolas Paris; Miguel Pedrera-Jiménez; Ashley C. Pfaff; Emily R. Pfaff; Danielle Pillion; Sara Pizzimenti; Hans-Ulrich Prokosch; Robson A. Prudente; Andrea Prunotto; et al. (npj Digit. Medicine, 2022)

FHIR-Ontop-OMOP: Querying OMOP clinical databases as FHIR-compliant Clinical Knowledge Graphs. - Guohui Xiao 001; Emily R. Pfaff; Eric Prud'hommeaux; David Booth; Deepak K. Sharma; Nan Huo; Yue Yu; Nansu Zong; Kathryn J. Ruddy; Christopher G. Chute; Guoqian Jiang (SWAT4HCLS, 2023)

Clinical encounter heterogeneity and methods for resolving in networked EHR data: a study from N3C and RECOVER programs. - Peter Leese; Adit Anand; Andrew T. Girvin; Amin Manna; Saaya Patel; Yun Jae Yoo; Rachel Wong; Melissa A. Haendel; Christopher G. Chute; Tellen D. Bennett; Janos G. Hajagos; Emily R. Pfaff; et al. (J. Am. Medical Informatics Assoc., 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)

An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Dalton Schutte; et al. (J. Am. Medical Informatics Assoc., 2023)

Finding Long-COVID: temporal topic modeling of electronic health records from the N3C and RECOVER programs. - Shawn T. O'Neil; Charisse R. Madlock-Brown; Kenneth Wilkins; Brenda M. McGrath; Hannah E. Davis; Gina S. Assaf; Hannah Wei; Parya Zareie; Evan T. French; Johanna Loomba; Julie A. McMurry; Andrea Zhou; et al. (npj Digit. Medicine, 2024)

Code for Publication: Insights from an N3C RECOVER EHR-based cohort study characterizing SARS-CoV-2 reinfections and Long COVID. - Emily Hadley; Yun Jae Yoo; Saaya Patel; Andrea Zhou; Bryan Laraway; Rachel Wong; Alexander Preiss; Hannah E. Davis; Daniel Brannock; Christopher G. Chute; Emily R. Pfaff; Johanna Loomba; et al. (Zenodo, 2024)

National COVID Cohort Collaborative data enhancements: a path for expanding common data models. - Kellie M. Walters; Marshall Clark; Sofia Dard; Stephanie S. Hong; Elizabeth Kelly; Kristin Kostka; Adam M. Lee; Robert T. Miller; Michele Morris; Matvey B. Palchuk; Emily R. Pfaff; Adam B. Wilcox; et al. (J. Am. Medical Informatics Assoc., 2025)