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2020 – today
- 2023
[j56]Liqin Wang, Heekyong Park
, Sachin Vallamkonda, Diane L. Seger, Suzanne V. Blackley, Pamela M. Garabedian, Foster R. Goss, Kimberly G. Blumenthal, David W. Bates, Shawn N. Murphy, Li Zhou:
Dynamic reaction picklist for improving allergy reaction documentation: A usability study. Int. J. Medical Informatics 170: 104939 (2023)- [j55]Amelia L. M. Tan, Emily J. Getzen, Meghan R. Hutch, Zachary H. Strasser, Alba Gutiérrez-Sacristán, Trang T. Le, Arianna Dagliati, Michele Morris, David A. Hanauer, Bertrand Moal, Clara-Lea Bonzel, William Yuan, Lorenzo Chiudinelli, Priam Das, Harrison G. Zhang, Bruce J. Aronow, Paul Avillach, Gabriel A. Brat, Tianxi Cai, Chuan Hong, William G. La Cava, He Hooi Will Loh, Yuan Luo, Shawn N. Murphy, Kee Yuan Hgiam, Gilbert S. Omenn, Lav P. Patel, Malarkodi J. Samayamuthu, Emily R. Shriver, Zahra Shakeri Hossein Abad, Byorn W. L. Tan, Shyam Visweswaran, Xuan Wang, Griffin M. Weber, Zongqi Xia, Bertrand Verdy, Qi Long, Danielle L. Mowery, John H. Holmes:
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record? J. Biomed. Informatics 139: 104306 (2023) - 2022
- [j54]Kavishwar B. Wagholikar, Layne Ainsworth, David Zelle, Kira Chaney, Michael Mendis, Jeffery G. Klann, Alexander J. Blood, Angela Miller, Rupendra Chulyadyo, Michael Oates, William J. Gordon, Samuel J. Aronson, Benjamin M. Scirica, Shawn N. Murphy:
I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform. Bioinform. 38(20): 4833-4836 (2022) - [j53]Shawn N. Murphy, Shyam Visweswaran, Michael J. Becich, Thomas R. Campion Jr., Boyd M. Knosp, Genevieve Melton-Meaux, Leslie A. Lenert:
Research data warehouse best practices: catalyzing national data sharing through informatics innovation. J. Am. Medical Informatics Assoc. 29(4): 581-584 (2022) - [j52]Victor M. Castro, Vivian S. Gainer, Nich Wattanasin, Barbara Benoit, Andrew Cagan, Bhaswati Ghosh, Sergey Goryachev, Reeta Metta, Heekyong Park, Taowei David Wang, Michael Mendis, Martin Rees, Christopher Herrick, Shawn N. Murphy:
The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics. J. Am. Medical Informatics Assoc. 29(4): 643-651 (2022) - [j51]Marc P. Maurits, Ilya Korsunsky, Soumya Raychaudhuri, Shawn N. Murphy, Jordan W. Smoller, Scott T. Weiss, Thomas W. J. Huizinga, Marcel J. T. Reinders, Elizabeth W. Karlson, Erik van den Akker, Rachel Knevel:
A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history. J. Am. Medical Informatics Assoc. 29(5): 761-769 (2022) - [j50]Hossein Estiri, Zachary H. Strasser, Sina Rashidian, Jeffrey G. Klann, Kavishwar B. Wagholikar, Thomas H. McCoy Jr., Shawn N. Murphy:
An objective framework for evaluating unrecognized bias in medical AI models predicting COVID-19 outcomes. J. Am. Medical Informatics Assoc. 29(8): 1334-1341 (2022) - [j49]Vladimir I. Valtchinov, Shawn N. Murphy, Ronilda Lacson, Nikolay Ikonomov, Bingxue K. Zhai, Katherine P. Andriole, Justin F. Rousseau, Dick Hanson, Isaac S. Kohane, Ramin Khorasani:
Analytics to monitor local impact of the Protecting Access to Medicare Act's imaging clinical decision support requirements. J. Am. Medical Informatics Assoc. 29(11): 1870-1878 (2022) - [j48]Doudou Zhou, Ziming Gan, Xu Shi, Alina Patwari, Everett Neil Rush, Clara-Lea Bonzel, Vidul Ayakulangara Panickan, Chuan Hong, Yuk-Lam Ho, Tianrun Cai, Lauren Costa, Xiaoou Li, Victor M. Castro, Shawn N. Murphy, Gabriel A. Brat, Griffin M. Weber, Paul Avillach, J. Michael Gaziano, Kelly Cho, Katherine P. Liao, Junwei Lu, Tianxi Cai:
Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization. J. Biomed. Informatics 133: 104147 (2022) - [j47]Xuan Wang, Harrison G. Zhang, Xin Xiong, Chuan Hong, Griffin M. Weber, Gabriel A. Brat, Clara-Lea Bonzel, Yuan Luo, Rui Duan, Nathan P. Palmer, Meghan R. Hutch, Alba Gutiérrez-Sacristán, Riccardo Bellazzi, Luca Chiovato, Kelly Cho, Arianna Dagliati, Hossein Estiri, Noelia García-Barrio, Romain Griffier, David A. Hanauer, Yuk-Lam Ho, John H. Holmes, Mark S. Keller, Jeffrey G. Klann, Sehi L'Yi, Sara Lozano-Zahonero, Sarah Maidlow, Adeline Makoudjou, Alberto Malovini, Bertrand Moal, Jason H. Moore, Michele Morris, Danielle L. Mowery, Shawn N. Murphy, Antoine Neuraz, Kee Yuan Ngiam, Gilbert S. Omenn, Lav P. Patel, Miguel Pedrera-Jiménez, Andrea Prunotto, Malarkodi J. Samayamuthu, Fernando J. Sanz Vidorreta, Emily Schriver, Petra Schubert, Pablo Serrano-Balazote, Andrew M. South, Amelia L. M. Tan, Byorn W. L. Tan, Valentina Tibollo, Patric Tippmann, Shyam Visweswaran, Zongqi Xia, William Yuan, Daniela Zöller, Isaac S. Kohane, Paul Avillach, Zijian Guo, Tianxi Cai:
SurvMaximin: Robust federated approach to transporting survival risk prediction models. J. Biomed. Informatics 134: 104176 (2022) - [j46]Jingzhi Yu, Jennifer A. Pacheco, Anika S. Ghosh, Yuan Luo, Chunhua Weng, Ning Shang, Barbara Benoit, David S. Carrell, Robert J. Carroll, Ozan Dikilitas, Robert R. Freimuth, Vivian S. Gainer, Hakon Hakonarson, George Hripcsak, Iftikhar J. Kullo, Frank D. Mentch, Shawn N. Murphy, Peggy L. Peissig, Andrea H. Ramirez, Nephi Walton, Wei-Qi Wei, Luke V. Rasmussen:
Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Medical Informatics Decis. Mak. 22(1): 23 (2022) - [c102]Arianna Dagliati, Zachary H. Strasser, Rebecca Mesa, Zahra Shakeri, Alaleh Azhir, Riccardo Bellazzi, Shawn N. Murphy, Hossein Estiri:
A Deductive Data-Driven Pipeline Powered by MLHO for Post-Acute Sequelae of COVID-19 (PASC) Phenotyping. AMIA 2022 - [c101]Jeffrey G. Klann, Michael Mendis, Kevin Bui, Griffin M. Weber, Diane Keogh, Shawn N. Murphy:
Informatics for Integrating Biology and the Bedside (i2b2) in 2022: Single Sign On and Synthetic Data. AMIA 2022 - [c100]Jeffrey G. Klann, Zachary H. Strasser, Chris J. Kennedy, Meghan Hutch, John H. Holmes, Gabriel A. Brat, Shawn N. Murphy:
Distinguishing Admissions Specifically for COVID-19 from Incidental SARS-CoV-2 Admissions. AMIA 2022 - [c99]Genevieve Melton-Meaux, Leslie Lenert, Michael J. Becich, Shawn N. Murphy, Thomas R. Campion Jr.:
Research Patient Data Repositories: Perspectives from JAMIA Special Issue Editors on the Next Generation of Multi-Institutional Data Sharing. AMIA 2022 - [c98]Liqin Wang, Heekyong Park, Sachin Vallamkonda, Diane L. Seger, Suzanne V. Blackley, Pamela M. Garabedian, Foster R. Goss, Kimberly G. Blumenthal, David W. Bates, Shawn N. Murphy, Li Zhou:
Dynamic Reaction Picklist for Improving Allergy Reaction Documentation: A Usability Study. AMIA 2022 - [c97]Mark G. Weiner, Charles Bailey, Richard R. Moffitt, Shawn N. Murphy:
The Informatics of RECOVER: Understanding the Post Acute Sequelae of SARS-CoV-2 Infection. AMIA 2022 - 2021
- [j45]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) - [j44]Hossein Estiri, Sebastien Vasey, Shawn N. Murphy:
Generative transfer learning for measuring plausibility of EHR diagnosis records. J. Am. Medical Informatics Assoc. 28(3): 559-568 (2021) - [j43]Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy:
High-throughput phenotyping with temporal sequences. J. Am. Medical Informatics Assoc. 28(4): 772-781 (2021) - [j42]Jeffrey G. Klann, Hossein Estiri, Griffin M. Weber, Bertrand Moal, Paul Avillach, Chuan Hong, Amelia L. M. Tan, Brett K. Beaulieu-Jones, Victor M. Castro, Thomas Maulhardt, Alon Geva, Alberto Malovini, Andrew M. South, Shyam Visweswaran, Michele Morris, Malarkodi J. Samayamuthu, Gilbert S. Omenn, Kee Yuan Ngiam, Kenneth D. Mandl, Martin Boeker, Karen L. Olson, Danielle L. Mowery, Robert W. Follett, David A. Hanauer, Riccardo Bellazzi, Jason H. Moore, Ne-Hooi Will Loh, Douglas S. Bell, Kavishwar B. Wagholikar, Luca Chiovato, Valentina Tibollo, Siegbert Rieg, Anthony L. L. J. Li, Vianney Jouhet, Emily Schriver, Zongqi Xia, Meghan Hutch, Yuan Luo, Isaac S. Kohane, Gabriel A. Brat, Shawn N. Murphy:
Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data. J. Am. Medical Informatics Assoc. 28(7): 1411-1420 (2021) - [j41]Harrison G. Zhang, Boris P. Hejblum, Griffin M. Weber, Nathan P. Palmer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Katherine P. Liao, Isaac S. Kohane, Tianxi Cai:
ATLAS: an automated association test using probabilistically linked health records with application to genetic studies. J. Am. Medical Informatics Assoc. 28(12): 2582-2592 (2021) - [j40]Sheng He, Diana Pereira, Juan David Perez, Randy L. Gollub, Shawn N. Murphy, Sanjay Prabhu, Rudolph Pienaar, Richard L. Robertson, Patricia Ellen Grant, Yangming Ou:
Multi-channel attention-fusion neural network for brain age estimation: Accuracy, generality, and interpretation with 16, 705 healthy MRIs across lifespan. Medical Image Anal. 72: 102091 (2021) - [c96]Jeffrey G. Klann, Michael Mendis, Peter Rice, Rudy Potenzone, Louisa May Klann, Griffin M. Weber, Diane Keogh, Shawn N. Murphy:
Integrating Informatics for Integrating Biology and the Bedside with tranSMART: Flexible Data Warehousing with Complex Analytics. AMIA 2021 - [c95]Jeffrey G. Klann, Griffin M. Weber, Emma Perez, William Yuan, Gabriel A. Brat, Shawn N. Murphy:
Combining Chart Review and Hospital System Dynamics for Electronic Health Record Phenotyping in an International COVID-19 Research Network. AMIA 2021 - [c94]Shawn N. Murphy, Hossein Estiri, Arianna Dagliati, Riccardo Bellazzi, John H. Holmes:
Temporal Phenotypic Pathways of Post-Acute Sequelae of SARS-CoV-2 by an International Consortium for Clinical Characterization of COVID-19 (4CE). AMIA 2021 - [c93]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, Todd Lingren, Frank D. Mentch, Agnes S. Sundaresan, Garrett Eickelberg, Valerie Willis, Al'ona Furmanchuk, Roshan Patel, David S. Carrell, Marc S. Williams, Elizabeth W. Karlson, Jodell E. Linder, Yuan Luo, Chunhua Weng, Wei-Qi Wei:
Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. AMIA 2021 - [c92]Zachary H. Strasser, Hossein Estiri, Shawn N. Murphy:
A Machine Learning Approach for Identifying Emergent Phenotypes Associated with a Previous COVID Infection. AMIA 2021 - [c91]Nich Wattanasin, Victor M. Castro, Vivian S. Gainer, Barbara Benoit, Andrew Cagan, Reeta Metta, Shawn N. Murphy:
A Novel Data Portal to Enable COVID-19 Data Integration and Analysis. AMIA 2021 - 2020
- [j39]Kavishwar B. Wagholikar, Hossein Estiri, Marykate Murphy, Shawn N. Murphy:
Polar labeling: silver standard algorithm for training disease classifiers. Bioinform. 36(10): 3200-3206 (2020) - [j38]Yuri Ahuja, Doudou Zhou, Zeling He, Jiehuan Sun, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, Chuan Hong, Tianxi Cai:
sureLDA: A multidisease automated phenotyping method for the electronic health record. J. Am. Medical Informatics Assoc. 27(8): 1235-1243 (2020) - [j37]Hossein Estiri, Zachary H. Strasser, Jeffery G. Klann, Thomas H. McCoy Jr., Kavishwar B. Wagholikar, Sebastien Vasey, Victor M. Castro, Marykate Murphy, Shawn N. Murphy:
Transitive Sequencing Medical Records for Mining Predictive and Interpretable Temporal Representations. Patterns 1(4): 100051 (2020) - [c90]Hossein Estiri, Sebastien Vasey, Shawn N. Murphy:
Transitive Sequential Pattern Mining for Discrete Clinical Data. AIME 2020: 414-424 - [c89]Hossein Estiri, Sebastien Vasey, Jeffrey G. Klann, Victor M. Castro, Shawn N. Murphy:
Generative Transfer Learning for Measuring Plausibility of EHR Diagnosis Records Over Time. AMIA 2020 - [c88]Jeffrey G. Klann, Michael Mendis, Diane Keogh, Shawn N. Murphy:
Informatics for Integrating Biology and the Bedside (i2b2) in 2020: Supporting Large Ontologies and REDcap Surveys. AMIA 2020 - [c87]Douglas MacFadden, Shawn N. Murphy, Griffin M. Weber, Anupama Maram:
National Informatics Infrastructure Responding to the COVID-19 Pandemic. AMIA 2020 - [c86]Shawn N. Murphy, Hossein Estiri, Zachary H. Strasser, Kavishwar B. Wagholikar, Victor M. Castro:
High-throughput Phenotyping with EHR Sequences. AMIA 2020 - [c85]Heekyong Park, Taowei David Wang, Vivian S. Gainer, Victor M. Castro, Nich Wattanasin, Shawn N. Murphy:
HistoriView: An Interactive and Scalable Visual Exploratory Plugin for Longitudinal Patient Data Review. AMIA 2020 - [c84]Sheng He, Randy L. Gollub, Shawn N. Murphy, Juan David Perez, Sanjay Prabhu, Rudolph Pienaar, Richard L. Robertson, Patricia Ellen Grant, Yangming Ou:
Brain Age Estimation Using LSTM on Children's Brain MRI. ISBI 2020: 1-4 - [i2]Sheng He, Randy L. Gollub, Shawn N. Murphy, Juan David Perez, Sanjay Prabhu, Rudolph Pienaar, Richard L. Robertson, Patricia Ellen Grant, Yangming Ou:
Brain Age Estimation Using LSTM on Children's Brain MRI. CoRR abs/2002.09045 (2020) - [i1]Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy:
Individualized Prediction of COVID-19 Adverse outcomes with MLHO. CoRR abs/2008.03869 (2020)
2010 – 2019
- 2019
- [j36]Hossein Estiri, Shawn N. Murphy:
Semi-supervised encoding for outlier detection in clinical observation data. Comput. Methods Programs Biomed. 181 (2019) - [j35]Hossein Estiri, Jeffrey G. Klann, Sarah R. Weiler, Ernest Alema-Mensah, R. Joseph Applegate, Galina Lozinski, Nandan Patibandla, Kun Wei, William G. Adams, Marc D. Natter, Elizabeth O. Ofili, Brian Ostasiewski, Alexander Quarshie, Gary E. Rosenthal, Elmer V. Bernstam, Kenneth D. Mandl, Shawn N. Murphy:
A federated EHR network data completeness tracking system. J. Am. Medical Informatics Assoc. 26(7): 637-645 (2019) - [j34]Katherine P. Liao, Jiehuan Sun, Tianrun A. Cai, Nicholas B. Link, Chuan Hong, Jie Huang, Jennifer E. Huffman, Jessica L. Gronsbell, Yichi Zhang, Yuk-Lam Ho, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, Christopher J. O'Donnell, J. Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu:
High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. J. Am. Medical Informatics Assoc. 26(11): 1255-1262 (2019) - [j33]George Hripcsak, Ning Shang, Peggy L. Peissig, Luke V. Rasmussen, Cong Liu, Barbara Benoit, Robert J. Carroll, David S. Carrell, Joshua C. Denny, Ozan Dikilitas, Vivian S. Gainer, Kayla Marie Howell, Jeffrey G. Klann, Iftikhar J. Kullo, Todd Lingren, Frank D. Mentch, Shawn N. Murphy, Karthik Natarajan, Chunhua Weng:
Facilitating phenotype transfer using a common data model. J. Biomed. Informatics 96 (2019) - [j32]Hossein Estiri, Jeffrey G. Klann, Shawn N. Murphy:
A clustering approach for detecting implausible observation values in electronic health records data. BMC Medical Informatics Decis. Mak. 19(1): 142:1-142:16 (2019) - [c83]Yuri Ahuja, Doudou Zhou, Zeling He, Jiehuan Sun, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, Chuan Hong, Tianxi Cai:
sureLDA: A Novel Multi-Disease Automated Phenotyping Method for the Electronic Health Record. AMIA 2019 - [c82]Hossein Estiri, Thomas H. McCoy, Shawn N. Murphy:
EHR Sequencing: A Novel Approach for Constructing Predictive and Interpretable Data Representations from EHR Data. AMIA 2019 - [c81]Jeffrey G. Klann, Nich Wattanasin, Michael Mendis, Matthew A. Joss, Hossein Estiri, Kavishwar B. Wagholikar, Shawn N. Murphy:
Ontologies Enabling Computable Tables. AMIA 2019 - [c80]Kavishwar B. Wagholikar, Samuel J. Aronson, Benjamin Morgan Scirica, Akshay S. Desai, Shawn N. Murphy:
Patient Stratification Process for enabling Clinical Interventions. AMIA 2019 - [c79]Kavishwar B. Wagholikar, Christina M. Fischer, Alyssa P. Goodson, Christopher Herrick, Taylor Maclean, Katelyn Smith, Liliana Fera, Thomas Gaziano, Jacqueline Dunning, Joshua Bosque-Hamilton, Lina Matta, Eloy Toscano, Brent Richter, Layne Ainsworth, Michael Oates, Samuel J. Aronson, Calum A. MacRae, Benjamin Morgan Scirica, Akshay S. Desai, Shawn N. Murphy:
Dynamic Phenotyping to facilitate Accrual for Prospective Clinical studies: A Case Study in Heart Failure. AMIA 2019 - [c78]Kavishwar B. Wagholikar, Vishal Vernekar, Akshay Zagade, Yuri Ostrovsky, Shek-Wayne Chan, Alyssa P. Goodson, Ameet Pathak, Corey Glynn, Christopher Herrick, Shawn N. Murphy:
Stratification of Patient Population for enabling data-driven Clinical Interventions using I2b2. AMIA 2019 - [c77]Nich Wattanasin, Taowei David Wang, Vivian S. Gainer, Shawn N. Murphy:
Scalable Process to Generate Aggregated Patient Data for Analysis. AMIA 2019 - [c76]Akshay Zagade, Vishal Vernekar, Shek-Wayne Chan, Kavishwar B. Wagholikar, Rupendra Chulyadyo, Yuri Ostrovsky, Alyssa P. Goodson, Ameet Pathak, Christopher Herrick, Shawn N. Murphy:
Plugin for importing spreadsheets into Informatics for Integrating Biology and the Bedside platform. AMIA 2019 - 2018
- [j31]Hossein Estiri, Behzad Abounia Omran, Shawn N. Murphy:
kluster: An Efficient Scalable Procedure for Approximating the Number of Clusters in Unsupervised Learning. Big Data Res. 13: 38-51 (2018) - [j30]Hossein Estiri, Kari A. Stephens, Jeffrey G. Klann, Shawn N. Murphy:
Exploring completeness in clinical data research networks with DQe-c. J. Am. Medical Informatics Assoc. 25(1): 17-24 (2018) - [j29]Sheng Yu, Yumeng Ma, Jessica L. Gronsbell, Tianrun A. Cai, Ashwin N. Ananthakrishnan, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Katherine P. Liao, Tianxi Cai:
Enabling phenotypic big data with PheNorm. J. Am. Medical Informatics Assoc. 25(1): 54-60 (2018) - [j28]Jeffrey G. Klann, Lori C. Phillips, Christopher Herrick, Matthew A. Joss, Kavishwar B. Wagholikar, Shawn N. Murphy:
Web services for data warehouses: OMOP and PCORnet on i2b2. J. Am. Medical Informatics Assoc. 25(10): 1331-1338 (2018) - [j27]Samuel J. Aronson, Lawrence J. Babb, Darren C. Ames, Richard A. Gibbs, Eric Venner, John J. Connelly, Keith Marsolo, Chunhua Weng, Marc S. Williams, Andrea L. Hartzler, Wayne H. Liang, James D. Ralston, Emily Beth Devine, Shawn N. Murphy, Christopher G. Chute, Pedro J. Caraballo, Iftikhar J. Kullo, Robert R. Freimuth, Luke V. Rasmussen, Firas H. Wehbe, Josh F. Peterson, Jamie R. Robinson, Ken Wiley, Casey Overby Taylor, eMERGE Network EHRI Working Group:
Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example. J. Am. Medical Informatics Assoc. 25(10): 1375-1381 (2018) - [j26]Kavishwar B. Wagholikar, Christina M. Fischer, Alyssa P. Goodson, Christopher D. Herrick, Martin Rees, Eloy Toscano, Calum A. MacRae, Benjamin M. Scirica, Akshay S. Desai, Shawn N. Murphy:
Extraction of Ejection Fraction from Echocardiography Notes for Constructing a Cohort of Patients having Heart Failure with reduced Ejection Fraction (HFrEF). J. Medical Syst. 42(11): 209:1-209:12 (2018) - [j25]Kavishwar B. Wagholikar, Pralav P. Dessai, Javier Sanz, Michael Mendis, Douglas S. Bell, Shawn N. Murphy:
Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers. BMC Medical Informatics Decis. Mak. 18(1): 66:1-66:6 (2018) - [j24]Yangming Ou, Lilla Zöllei, Xiao Da, Kallirroi Retzepi, Shawn N. Murphy, Elizabeth R. Gerstner, Bruce R. Rosen, Patricia Ellen Grant, Jayashree Kalpathy-Cramer, Randy L. Gollub:
Field of View Normalization in Multi-Site Brain MRI. Neuroinformatics 16(3-4): 431-444 (2018) - [c75]Guoqian Jiang, Jon D. Duke, Daniella Meeker, Mitra Rocca, Harold R. Solbrig, Shawn N. Murphy:
Using HL7 FHIR to Improve Standardization and Interoperability of Common Data Models for Clinical and Translational Research. AMIA 2018 - [c74]Jeffrey G. Klann, Stanley Boykin, Marc D. Natter, Margaret Vella, Douglas MacFadden, Sarah R. Weiler, Sebastian Schneeweiss, Kenneth D. Mandl, Shawn N. Murphy:
Accessible Research Commons for Health: Four Years Into the PCORnet Journey. AMIA 2018 - [c73]Katherine P. Liao, Jiehuan Sun, Tianrun A. Cai, Nicholas B. Link, Chuan Hong, Jie Huang, Jennifer E. Huffman, Jessica L. Gronsbell, Lauren Costa, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, J. Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu, Tianxi Cai:
High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS. AMIA 2018 - [c72]Harold R. Solbrig, Na Hong, Shawn N. Murphy, Guoqian Jiang:
Automated Population of an i2b2 Clinical Data Warehouse using FHIR. AMIA 2018 - [r2]Shawn N. Murphy:
Data Warehousing for Clinical Research. Encyclopedia of Database Systems (2nd ed.) 2018 - 2017
- [j23]Jorge L. Bernal-Rusiel, Nicolas Rannou, Randy L. Gollub, Steve Pieper, Shawn N. Murphy, Richard Robertson, Patricia E. Grant, Rudolph Pienaar:
Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization. Frontiers Neuroinformatics 11: 32 (2017) - [j22]Kavishwar B. Wagholikar, Joshua C. Mandel, Jeffrey G. Klann, Nich Wattanasin, Michael Mendis, Christopher G. Chute, Kenneth D. Mandl, Shawn N. Murphy:
SMART-on-FHIR implemented over i2b2. J. Am. Medical Informatics Assoc. 24(2): 398-402 (2017) - [j21]Griffin M. Weber, William G. Adams, Elmer V. Bernstam, Jonathan P. Bickel, Kathe P. Fox, Keith Marsolo, Vijay A. Raghavan, Alexander Turchin, Xiaobo Zhou, Shawn N. Murphy, Kenneth D. Mandl:
Biases introduced by filtering electronic health records for patients with "complete data". J. Am. Medical Informatics Assoc. 24(6): 1134-1141 (2017) - [j20]Sheng Yu, Abhishek Chakrabortty, Katherine P. Liao, Tianrun A. Cai, Ashwin N. Ananthakrishnan, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Tianxi Cai:
Surrogate-assisted feature extraction for high-throughput phenotyping. J. Am. Medical Informatics Assoc. 24(e1): e143-e149 (2017) - [c71]Hossein Estiri, Jeffrey G. Klann, Kavishwar B. Wagholikar, Shawn N. Murphy:
Applying unsupervised learning to characterize rare observations in clinical data: the DQe-p tool. AMIA 2017 - [c70]Christopher Herrick, Alyssa P. Goodson, Wayne Chan, Lori C. Phillips, Michael Mendis, Shawn N. Murphy:
Integrating Patient Registries into Enterprise wide Patient-Discovery Strategies. AMIA 2017 - [c69]Jeffrey G. Klann, Matthew A. Joss, Kevin Embree, Shawn N. Murphy:
Reuse of PCORnet Data to Support the Precision Medicine Initiative: Data Model Harmonization. AMIA 2017 - [c68]Jeffrey G. Klann, Kavishwar B. Wagholikar, Lori C. Phillips, Matthew A. Joss, Shawn N. Murphy:
Web-Service-Enabled Apps for Research: SMART-on-FHIR for OMOP and PCORNet. AMIA 2017 - [c67]Heekyong Park, Taowei David Wang, Vivian S. Gainer, Victor M. Castro, Shawn N. Murphy:
Building Better Timeline Interactions for Patient Chart Reviews. AMIA 2017 - [c66]Sheng Yu, Yumeng Ma, Jessica L. Gronsbell, Katherine P. Liao, Tianrun A. Cai, Ashwin N. Ananthakrishnan, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Tianxi Cai:
High-throughput Phenotyping via Denoised Normal Mixture Transformation. AMIA 2017 - [c65]Shawn N. Murphy:
Instrumenting the Health Care Enterprise for Discovery in the Course of Clinical Care. BCB 2017: 632 - [c64]Ania Berchuck, Michael G. Kahn, Shelley A. Rusincovitch, Daniella Meeker, Shawn N. Murphy, Ravi Bhosale, Keith Marsolo, Michael E. Matheny, L. Russell Waitman, Rachel Hess:
Strategic Assessment and Planning for the PCORnet Common Data Model. CRI 2017 - [c63]Victor M. Castro, Nich Wattanasin, Vivian S. Gainer, Bhaswati Ghosh, Shawn N. Murphy:
Applying Computed Phenotypes Derived from Electronic Health Records in the Partners HealthCare Biobank Using i2b2. CRI 2017 - [c62]Hossein Estiri, Kari A. Stephens, Jeffrey G. Klann, Shawn N. Murphy:
Exploring Completeness in Clinical Data Research Networks with DQe-c. CRI 2017 - [c61]Jeffrey G. Klann, Daniella Meeker, Marc B. Rosenman, Shawn N. Murphy:
Data Fitness-for-Use: A Method to Maximize Utility of Poor-Quality Data? CRI 2017 - [c60]Jeffrey G. Klann, Vijay A. Raghavan, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy:
Needs-Driven Data Completeness Dashboard in a Multi-Site Research Network. CRI 2017 - [c59]Jeffrey G. Klann, Vijay A. Raghavan, Chunhua Weng, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy:
Needs-Driven Data Completeness Assessment for Clinical Research. CRI 2017 - [c58]Shawn N. Murphy, Christopher D. Herrick, Michael Mendis, Lori C. Phillips, Wayne Chan, Alyssa J. Porter, Griffin M. Weber, Susanne E. Churchill, Isaac S. Kohane:
Creating a Patient Information Commons from Multiple Research Informatics Platforms. CRI 2017 - [c57]Lori C. Phillips, Christopher D. Herrick, Shawn N. Murphy:
i2b2 on OMOP CDM. CRI 2017 - [c56]Kavishwar B. Wagholikar, Rahul Jain, Eliel Oliveira, Joshua C. Mandel, Jeffrey G. Klann, Ricardo Colas, Prasad Patil, Kuladip Yadav, Kenneth D. Mandl, Shawn N. Murphy:
Evolving Research Data Sharing Networks to Clinical App Sharing Networks. CRI 2017 - 2016
- [j19]Jeffrey G. Klann, Aaron Abend, Vijay A. Raghavan, Kenneth D. Mandl, Shawn N. Murphy:
Data interchange using i2b2. J. Am. Medical Informatics Assoc. 23(5): 909-915 (2016) - [c55]Jeffrey G. Klann, Vijay A. Raghavan, Michael Mendis, Douglas MacFadden, Sarah R. Weiler, Kenneth D. Mandl, Shawn N. Murphy:
Comparison of Data Models used in Research Data Repositories for Electronic Phenotyping. AMIA 2016 - [c54]Jeffrey G. Klann, Vijay A. Raghavan, Douglas MacFadden, Sarah R. Weiler, Kenneth D. Mandl, Shawn N. Murphy:
Data Topography of a Large Multi-Site Research Network. AMIA 2016 - [c53]Kavishwar B. Wagholikar, Rahul Jain, Eliel Oliveira, Henry Chu, Harshal Shah, Joshua C. Mandel, Jeffrey G. Klann, Sohail Rao, Kenneth D. Mandl, Shawn N. Murphy, Thomas Carton:
Cajun Codefest 4.0 on SMART-on-FHIR apps for Diabetes. AMIA 2016 - [c52]Kavishwar B. Wagholikar, Rahul Jain, Eliel Oliveira, Joshua C. Mandel, Jeffrey G. Klann, Prasad Patil, Kenneth D. Mandl, Shawn N. Murphy, Thomas Carton:
Evaluation of SMART-on-FHIR I2b2 cell using PCORNET data model. AMIA 2016 - [c51]Nich Wattanasin, Taowei David Wang, Bhaswati Ghosh, Reeta Metta, Vivian S. Gainer, Shawn N. Murphy:
Export data from i2b2 using the new download data web client plugin. AMIA 2016 - [c50]Alyssa P. Goodson, Andrew Cagan, Vivian S. Gainer, Christopher D. Herrick, Kelly Bell, Tianxi Cai, Shawn N. Murphy:
Defining a Statistically Valid Type 2 Diabetes Cohort in the Partners HealthCare EMR. CRI 2016 - [c49]Jeffrey G. Klann, Vijay A. Raghavan, Douglas MacFadden, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy:
Comparison of Two Distributed Data Network Approaches: Democratic and Self-Governed vs. Centrally Managed. CRI 2016 - [c48]Jeffrey G. Klann, Vijay A. Raghavan, Douglas MacFadden, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy:
Multi-site Data Completeness Analysis: Application to Laboratory Results in a Large Distributed Research Network. CRI 2016 - [c47]Lori C. Phillips, Shawn N. Murphy:
Improving i2b2 Ontology Medications Mappings with RxMix. CRI 2016 - [c46]Philip Trevvett, Shawn N. Murphy, Lori C. Phillips, Bhanu Bahl:
Using Medication Terminologies NDF-RT and RxNorm for Implementing a Medications Ingredient Hierarchy in a SHRINE/i2b2 use case. CRI 2016 - [c45]