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2020 – today
- 2023
[j18]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, Richard A. Moffitt:
Clinical encounter heterogeneity and methods for resolving in networked EHR data: a study from N3C and RECOVER programs. J. Am. Medical Informatics Assoc. 30(6): 1125-1136 (2023)- [j17]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) - [j16]Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30(12): 2036-2040 (2023) - [c12]Guohui Xiao, 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:
FHIR-Ontop-OMOP: Querying OMOP clinical databases as FHIR-compliant Clinical Knowledge Graphs. SWAT4HCLS 2023: 165-166 - 2022
- [j15]Karamarie Fecho, Stanley C. Ahalt, Michael Knowles, Ashok K. Krishnamurthy, Margaret Leigh, Kenneth Morton, Emily R. Pfaff, Max Wang, Hong Yi:
Leveraging Open Electronic Health Record Data and Environmental Exposures Data to Derive Insights Into Rare Pulmonary Disease. Frontiers Artif. Intell. 5 (2022) - [j14]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, Johanna Loomba, Amin Manna, Julie A. McMurry, Emily Niehaus, Nabeel Qureshi, Anita Walden, Xiaohan Tanner Zhang, Richard L. Zhu, Richard A. Moffitt, Christopher G. Chute, William G. Adams, Shaymaa Al-Shukri, Alfred Anzalone, Ahmad Baghal, Tellen D. Bennett, Elmer V. Bernstam, Mark M. Bissell, Brian Bush, Thomas R. Campion Jr., Victor Castro, Jack Chang, Deepa D. Chaudhari, Wenjin Chen, San Chu, James J. Cimino, Keith A. Crandall, Mark Crooks, Sara J. Deakyne Davies, John Dipalazzo, David A. Dorr, Dan Eckrich, Sarah E. Eltinge, Daniel G. Fort, George Golovko, Snehil Gupta, Melissa A. Haendel, Janos G. Hajagos, David A. Hanauer, Brett M. Harnett, Ronald Horswell, Nancy Huang, Steven G. Johnson, Michael Kahn, Kamil Khanipov, Curtis Kieler, Katherine Ruiz De Luzuriaga, Sarah E. Maidlow, Ashley Martinez, Jomol Mathew, James C. McClay, Gabriel McMahan, Brian Melancon, Stéphane M. Meystre, Lucio Miele, Hiroki Morizono, Ray Pablo, Lav P. Patel, Jimmy Phuong, Daniel J. Popham, Claudia P. Pulgarin, Carlos Santos, Indra Neil Sarkar, Nancy Sazo, Soko Setoguchi, Selvin Soby, Sirisha Surampalli, Christine Suver, Uma Maheswara Reddy Vangala, Shyam Visweswaran, James von Oehsen, Kellie M. Walters, Laura K. Wiley, David A. Williams, Adrian H. Zai:
Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. J. Am. Medical Informatics Assoc. 29(4): 609-618 (2022) - [j13]Kellie M. Walters, Anna Jojic, Emily R. Pfaff, Marie Rape, Donald C. Spencer, Nicholas J. Shaheen, Brent Lamm, Timothy S. Carey:
Supporting research, protecting data: one institution's approach to clinical data warehouse governance. J. Am. Medical Informatics Assoc. 29(4): 707-712 (2022) - [j12]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, Emily Niehaus, Stephanie S. Hong, Xiaohan Tanner Zhang, Richard L. Zhu, Mark Bissell, Nabeel Qureshi, Joel H. Saltz, Melissa A. Haendel, Christopher G. Chute, Harold P. Lehmann, Richard A. Moffitt:
Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset. J. Am. Medical Informatics Assoc. 29(7): 1172-1182 (2022) - [j11]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, Justin Guinney, Warren A. Kibbe, Hongfang Liu, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Justin Starren, Christine Suver, Chunlei Wu, Davera Gabriel, Stephanie S. Hong, Kristin Kostka, Harold P. Lehmann, Richard A. Moffitt, Michele Morris, Matvey B. Palchuk, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Mark M. Bissell, Marshall Clark, Andrew T. Girvin, Adam M. Lee, Robert T. Miller, Kellie M. Walters, Yooree Chae, Connor Cook, Alexandra Dest, Racquel R. Dietz, Thomas Dillon, Patricia A. Francis, Rafael Fuentes, Alexis Graves, Andrew J. Neumann, Shawn T. O'Neil, Usman Sheikh, Andréa M. Volz, Elizabeth Zampino, Christopher P. Austin, Samuel Bozzette, Mariam Deacy, Nicole Garbarini, Michael G. Kurilla, Sam G. Michael, Joni L. Rutter, Meredith Temple-O'Connor, Katie Rebecca Bradwell, Amin Manna, Nabeel Qureshi, Mary Morrison Saltz, Julie A. McMurry, Carolyn T. Bramante, Jeremy Richard Harper, Wenndy Hernandez, Farrukh M. Koraishy, Federico Mariona, Saidulu Mattapally, Amit Saha, Satyanarayana Vedula, Yujuan Fu, Nisha Mathews, Ofer Mendelevitch:
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). J. Am. Medical Informatics Assoc. 29(8): 1350-1365 (2022) - [j10]Yue Yu, Nansu Zong, Andrew Wen, Sijia Liu, Daniel J. Stone, David Knaack, Alanna M. Chamberlain, Emily R. Pfaff, Davera Gabriel, Christopher G. Chute, Nilay Shah, Guoqian Jiang:
Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. J. Biomed. Informatics 127: 104002 (2022) - [j9]Guohui Xiao, 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:
FHIR-Ontop-OMOP: Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model. J. Biomed. Informatics 134: 104201 (2022) - [j8]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, Víctor Quirós-González, Maryna Raskin, Siegbert Rieg, Gustavo Roig-Domínguez, Pablo Rojo, Paula Rubio-Mayo, Paolo Sacchi, Carlos Sáez, Elisa Salamanca, Malarkodi Jebathilagam Samayamuthu, L. Nelson Sanchez-Pinto, Arnaud Sandrin, Nandhini Santhanam, Janaina C. C. Santos, Fernando J. Sanz Vidorreta, Maria Savino, Jürgen Schüttler, Luigia Scudeller, Neil J. Sebire, Pablo Serrano-Balazote, Patricia Serre, Arnaud Serret-Larmande, Mohsin Shah, Zahra Shakeri Hossein Abad, Domenick Silvio, Piotr Sliz, Jiyeon Son, Charles Sonday, Andrew M. South, Francesca Sperotto, Zachary H. Strasser, Bryce W. Q. Tan, Suzana E. Tanni, Deanne M. Taylor, Ana I. Terriza-Torres, Patric Tippmann, Emma M. S. Toh, Yi-Ju Tseng, Andrew K. Vallejos, Gaël Varoquaux, Margaret E. Vella, Guillaume Verdy, Jill-Jênn Vie, Michele Vitacca, Kavishwar B. Wagholikar, Lemuel R. Waitman, Demian Wassermann, Martin Wolkewitz, Scott Wong, Xin Xiong, Ye Ye, Nadir Yehya, William Yuan, Alberto Zambelli, Harrison G. Zhang, Daniela Zöller, Valentina Zuccaro, Chiara Zucco:
International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. npj Digit. Medicine 5 (2022) - [c11]James Champion, Paul Kovach, Asiyah Ahmad, Anna Jojic, Buck Bohac, Adam M. Lee, Patrick Conway, Emily R. Pfaff:
CAMP FHIR: Clinical Asset Mapping Program for FHIR. AMIA 2022 - [c10]James Champion, Eric Prud'hommeaux, David Booth, Gaurav Vaidya, James P. Balhoff, Deepak K. Sharma, Guoqian Jiang, Emily R. Pfaff:
Maximizing Interoperability, Enriching EHR Data: Transforming HL7 FHIR Data to RDF Using the FHIR RDF Playground. AMIA 2022 - [c9]Sofia Z. Dard, James Champion, Robert L. Bradford, Adam M. Lee, Emily R. Pfaff:
HIPAA Safe Harbor (HuSH) Common Data Models for Education. AMIA 2022 - [c8]Nan Huo, Yue Yu, Nansu Zong, Andrea Cheville, Claude Nanjo, Eric Prud'hommeaux, Deirdre Pachman, Guohui Xiao, Emily R. Pfaff, Christopher G. Chute, Guoqian Jiang, Kathryn J. Ruddy:
Modeling a Cancer Symptom Control Domain Using HL7 FHIR: Applicability of the Minimal Common Oncology Data Elements (mCODE). AMIA 2022 - [c7]Adam M. Lee, Paul Kovach, James Champion, Patrick Conway, Emily R. Pfaff:
Relational FHIR: Converting FHIR's Hierarchal Schema. AMIA 2022 - [c6]Yue Yu, Kathryn J. Ruddy, Nan Huo, Nansu Zong, Deirdre Pachman, Christopher G. Chute, Emily R. Pfaff, Andrea Cheville, Guoqian Jiang:
A Comparative Study on the Capability of Real-World Antineoplastic Drug Data Collection by CanMED, ATC and HemOnc. AMIA 2022 - [c5]Deepak K. Sharma, Eric Prud'hommeaux, David Booth, Kevin J. Peterson, Daniel J. Stone, Harold Solbrig, Guohui Xiao, Emily R. Pfaff, Guoqian Jiang:
Implementing a New FHIR RDF Specification for Semantic Clinical Data Using a JSON-LD-based Approach. SWAT4HCLS 2022: 82-86 - 2021
- [j7]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, John Wilbanks, Adam B. Wilcox, Andrew E. Williams, Chunlei Wu, Clair Blacketer, Robert L. Bradford, James J. Cimino, Marshall Clark, Evan W. Colmenares, Patricia A. Francis, Davera Gabriel, Alexis Graves, Raju Hemadri, Stephanie S. Hong, George Hripcsak, Dazhi Jiao, Jeffrey G. Klann, Kristin Kostka, Adam M. Lee, Harold P. Lehmann, Lora Lingrey, Robert T. Miller, Michele Morris, Shawn N. Murphy, Karthik Natarajan, Matvey B. Palchuk, Usman Sheikh, Harold Solbrig, Shyam Visweswaran, Anita Walden, Kellie M. Walters, Griffin M. Weber, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Andrew T. Girvin, Amin Manna, Nabeel Qureshi, Michael G. Kurilla, Sam G. Michael, Lili M. Portilla, Joni L. Rutter, Christopher P. Austin, Ken R. Gersing:
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J. Am. Medical Informatics Assoc. 28(3): 427-443 (2021) - [c4]Marshall Clark, Adam M. Lee, Emily R. Pfaff, Kristin Kostka, Matvey B. Palchuk, Lora Lingrey, Michele Morris, Robert T. Miller:
National COVID Cohort Collaborative (N3C) Case-control Buddies. AMIA 2021 - [c3]David Borland, Irena Brain, Karamarie Fecho, Emily R. Pfaff, Hao Xu, James Champion, Chris Bizon, David Gotz:
Enabling Longitudinal Exploratory Analysis of Clinical COVID Data. VAHC 2021: 19-24 - [i3]David Borland, Irena Brain, Karamarie Fecho, Emily R. Pfaff, Hao Xu, James Champion, Chris Bizon, David Gotz:
Enabling Longitudinal Exploratory Analysis of Clinical COVID Data. CoRR abs/2108.11476 (2021) - [i2]Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR abs/2110.10780 (2021) - 2020
- [j6]Hao Xu, Steven Cox, Lisa Stillwell, Emily R. Pfaff, James Champion, Stanley C. Ahalt, Karamarie Fecho:
FHIR PIT: an open software application for spatiotemporal integration of clinical data and environmental exposures data. BMC Medical Informatics Decis. Mak. 20(1): 53 (2020) - [c2]Robert L. Bradford, Sofia Dard, Emily R. Pfaff, Ashok K. Krishnamurthy:
Utilizing Encrypted Hashes to Link Patient Cohorts via Streamlined SAS Programs. AMIA 2020
2010 – 2019
- 2019
- [j5]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:
Recruiting for a pragmatic trial using the electronic health record and patient portal: successes and lessons learned. J. Am. Medical Informatics Assoc. 26(1): 44-49 (2019) - [j4]Karamarie Fecho, Emily R. Pfaff, Hao Xu, James Champion, Steve Cox, Lisa Stillwell, David B. Peden, Chris Bizon, Ashok Kumar Krishnamurthy, Alexander Tropsha, Stanley C. Ahalt:
A novel approach for exposing and sharing clinical data: the Translator Integrated Clinical and Environmental Exposures Service. J. Am. Medical Informatics Assoc. 26(10): 1064-1073 (2019) - [j3]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, Eric Sid, Casey N. Ta, Hao Xu, Richard L. Zhu, Qian Zhu, David B. Peden:
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. J. Biomed. Informatics 100 (2019) - [j2]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, Hao Xu, Karamarie Fecho, Nephi A. Walton, Richard L. Zhu, Justin Ramsdill, Christopher J. Mungall, Sebastian Köhler, Melissa A. Haendel, Clement J. McDonald, Daniel J. Vreeman, David B. Peden, Tellen D. Bennett, James A. Feinstein, Blake Martin, Adrianne L. Stefanski, Lawrence E. Hunter, Christopher G. Chute, Peter N. Robinson:
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. npj Digit. Medicine 2 (2019) - [c1]Robert L. Bradford, Marshall Clark, Emily R. Pfaff:
SMOREs : Synergistic Medication Organizer for RxNorm and Expansions, a Tool For Improving Semantic Relationships of Institutional Medications to Standardized Ontologies. AMIA 2019 - 2018
- [i1]Matt Buranosky, Elmar Stellnberger, Emily R. Pfaff, David Díaz-Gutiérrez, Cavin Ward-Caviness:
FDTool: a Python application to mine for functional dependencies and candidate keys in tabular data. F1000Research 7: 1667 (2018) - 2016
- [j1]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, Catherine Pihoker, Sharon H. Saydah, Elizabeth J. Mayer-Davis:
An efficient approach for surveillance of childhood diabetes by type derived from electronic health record data: the SEARCH for Diabetes in Youth Study. J. Am. Medical Informatics Assoc. 23(6): 1060-1067 (2016)
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