Shawn N. Murphy

175 papers A* 1B 1Misc 82Journal 71Unranked 18

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	An autonomous agentic workflow for clinical detection of cognitive concerns using large language models. npj Digit. Medicine Jiazi Tian, Pedram J. Fard, Cameron Cagan, Neguine Rezaii, Rebeka Bustamante Rocha, Liqin Wang, Valdery Moura Junior, Deborah Blacker, Jennifer S. Haas, Chirag J. Patel, Shawn N. Murphy, Lidia M. V. R. Moura, Hossein Estiri
2026	J	`jnl`	Optimization Instability in Autonomous Agentic Workflows for Clinical Symptom Detection. CoRR Cameron Cagan, Pedram J. Fard, Jiazi Tian, Jingya Cheng, Shawn N. Murphy, Hossein Estiri
2025	J	`jnl`	An Agentic AI Workflow for Detecting Cognitive Concerns in Real-world Data. CoRR Jiazi Tian, Liqin Wang, Pedram J. Fard, Valdery Moura Junior, Deborah Blacker, Jennifer S. Haas, Chirag J. Patel, Shawn N. Murphy, Lidia M. V. R. Moura, Hossein Estiri
2025	J	`jnl`	Comparing patient-reported symptoms and structured clinician documentation in electronic health records. J. Am. Medical Informatics Assoc. Victor M. Castro, Vivian S. Gainer, Danielle M. Crookes, Shawn N. Murphy, Justin Manjourides
2025	J	`jnl`	The Average Patient Fallacy. CoRR Alaleh Azhir, Shawn N. Murphy, Hossein Estiri
2024	J	`jnl`	Environment Scan of Generative AI Infrastructure for Clinical and Translational Science. CoRR Betina Idnay, Zihan Xu, William G. Adams, Mohammad Adibuzzaman, Nicholas R. Anderson, Neil Bahroos, Douglas S. Bell, Cody Bumgardner, Thomas R. Campion Jr., Victor M. Castro, James J. Cimino, I. Glenn Cohen, David A. Dorr, Peter L. Elkin, Jungwei W. Fan, Todd Ferris, David J. Foran, David A. Hanauer, Mike Hogarth, Kun Huang, Jayashree Kalpathy-Cramer, Manoj Kandpal, Niranjan S. Karnik, Avnish Katoch, Albert M. Lai, Christophe G. Lambert, Lang Li, Christopher J. Lindsell, Jinze Liu, Zhiyong Lu, Yuan Luo, Peter McGarvey, Eneida A. Mendonça, Parsa Mirhaji, Shawn N. Murphy, John D. Osborne, Ioannis Ch. Paschalidis, Paul A. Harris, Fred W. Prior, Nicholas J. Shaheen, Nawar Shara, Ida Sim, Umberto Tachinardi, Lemuel R. Waitman, Rosalind J. Wright, Adrian H. Zai, Kai Zheng, Sandra Soo-Jin Lee, Bradley A. Malin, Karthik Natarajan, W. Nicholson Price, Rui Zhang, Yiye Zhang, Hua Xu, Jiang Bian, Chunhua Weng, Yifan Peng
2024	J	`jnl`	Towards cross-application model-agnostic federated cohort discovery. J. Am. Medical Informatics Assoc. Nicholas J. Dobbins, Michele Morris, Eugene Sadhu, Douglas MacFadden, Marc-Danie Nazaire, William Simons, Griffin M. Weber, Shawn N. Murphy, Shyam Visweswaran
2023	J	`jnl`	A broadly applicable approach to enrich electronic-health-record cohorts by identifying patients with complete data: a multisite evaluation. J. Am. Medical Informatics Assoc. Jeffrey G. Klann, Darren W. Henderson, Michele Morris, Hossein Estiri, Griffin M. Weber, Shyam Visweswaran, Shawn N. Murphy
2023	J	`jnl`	Dynamic reaction picklist for improving allergy reaction documentation: A usability study. Int. J. Medical Informatics 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
2023	J	`jnl`	Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record? J. Biomed. Informatics 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, Priyam 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
2023	J	`jnl`	tSPM+; a high-performance algorithm for mining transitive sequential patterns from clinical data. CoRR Jonas Hügel, Ulrich Sax, Shawn N. Murphy, Hossein Estiri
2022	Misc	`conf`	A Deductive Data-Driven Pipeline Powered by MLHO for Post-Acute Sequelae of COVID-19 (PASC) Phenotyping. AMIA Arianna Dagliati, Zachary H. Strasser, Rebecca Mesa, Zahra Shakeri, Alaleh Azhir, Riccardo Bellazzi, Shawn N. Murphy, Hossein Estiri
2022	J	`jnl`	A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history. J. Am. Medical Informatics Assoc. 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
2022	J	`jnl`	An objective framework for evaluating unrecognized bias in medical AI models predicting COVID-19 outcomes. J. Am. Medical Informatics Assoc. Hossein Estiri, Zachary H. Strasser, Sina Rashidian, Jeffrey G. Klann, Kavishwar B. Wagholikar, Thomas H. McCoy Jr., Shawn N. Murphy
2022	J	`jnl`	Analytics to monitor local impact of the Protecting Access to Medicare Act's imaging clinical decision support requirements. J. Am. Medical Informatics Assoc. 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
2022	Misc	`conf`	Distinguishing Admissions Specifically for COVID-19 from Incidental SARS-CoV-2 Admissions. AMIA Jeffrey G. Klann, Zachary H. Strasser, Chris J. Kennedy, Meghan Hutch, John H. Holmes, Gabriel A. Brat, Shawn N. Murphy
2022	Misc	`conf`	Dynamic Reaction Picklist for Improving Allergy Reaction Documentation: A Usability Study. AMIA 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
2022	J	`jnl`	I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform. Bioinform. Kavishwar B. Wagholikar, Layne Ainsworth, David Zelle, Kira Chaney, Michael Mendis, Jeffrey G. Klann, Alexander J. Blood, Angela Miller, Rupendra Chulyadyo, Michael Oates, William J. Gordon, Samuel J. Aronson, Benjamin M. Scirica, Shawn N. Murphy
2022	Misc	`conf`	Informatics for Integrating Biology and the Bedside (i2b2) in 2022: Single Sign On and Synthetic Data. AMIA Jeffrey G. Klann, Michael Mendis, Kevin Bui, Griffin M. Weber, Diane Keogh, Shawn N. Murphy
2022	J	`jnl`	International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. npj Digit. Medicine Harrison G. Zhang, Arianna Dagliati, Zahra Shakeri Hossein Abad, Xin Xiong, Clara-Lea Bonzel, Zongqi Xia, Bryce W. Q. Tan, Paul Avillach, Gabriel A. Brat, Chuan Hong, Michele Morris, Shyam Visweswaran, Lav P. Patel, Alba Gutiérrez-Sacristán, David A. Hanauer, John H. Holmes, Malarkodi Jebathilagam Samayamuthu, Florence T. Bourgeois, Sehi L'Yi, Sarah E. Maidlow, Bertrand Moal, Shawn N. Murphy, Zachary H. Strasser, Antoine Neuraz, Kee Yuan Ngiam, Ne-Hooi Will Loh, Gilbert S. Omenn, Andrea Prunotto, Lauren A. Dalvin, Jeffrey G. Klann, Petra Schubert, Fernando J. Sanz Vidorreta, Vincent Benoit, Guillaume Verdy, Ramakanth Kavuluru, Hossein Estiri, Yuan Luo, Alberto Malovini, Valentina Tibollo, Riccardo Bellazzi, Kelly Cho, Yuk-Lam Ho, Amelia L. M. Tan, Byorn W. L. Tan, Nils Gehlenborg, Sara Lozano-Zahonero, Vianney Jouhet, Luca Chiovato, Bruce J. Aronow, Emma M. S. Toh, Wei Gen Scott Wong, Sara Pizzimenti, Kavishwar B. Wagholikar, Mauro Bucalo, Tianxi Cai, Andrew M. South, Isaac S. Kohane, Griffin M. Weber
2022	J	`jnl`	Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization. J. Biomed. Informatics 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, John Michael Gaziano, Kelly Cho, Katherine P. Liao, Junwei Lu, Tianxi Cai
2022	Misc	`conf`	Research Patient Data Repositories: Perspectives from JAMIA Special Issue Editors on the Next Generation of Multi-Institutional Data Sharing. AMIA Genevieve Melton-Meaux, Leslie Lenert, Michael J. Becich, Shawn N. Murphy, Thomas R. Campion Jr.
2022	J	`jnl`	Research data warehouse best practices: catalyzing national data sharing through informatics innovation. J. Am. Medical Informatics Assoc. Shawn N. Murphy, Shyam Visweswaran, Michael J. Becich, Thomas R. Campion Jr., Boyd M. Knosp, Genevieve Melton-Meaux, Leslie A. Lenert
2022	J	`jnl`	SurvMaximin: Robust federated approach to transporting survival risk prediction models. J. Biomed. Informatics 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 E. 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
2022	Misc	`conf`	The Informatics of RECOVER: Understanding the Post Acute Sequelae of SARS-CoV-2 Infection. AMIA Mark G. Weiner, Charles Bailey, Richard R. Moffitt, Shawn N. Murphy
2022	J	`jnl`	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. 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
2022	J	`jnl`	Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Medical Informatics Decis. Mak. 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
2021	Misc	`conf`	A Machine Learning Approach for Identifying Emergent Phenotypes Associated with a Previous COVID Infection. AMIA Zachary H. Strasser, Hossein Estiri, Shawn N. Murphy
2021	Misc	`conf`	A Novel Data Portal to Enable COVID-19 Data Integration and Analysis. AMIA Nich Wattanasin, Victor M. Castro, Vivian S. Gainer, Barbara Benoit, Andrew Cagan, Reeta Metta, Shawn N. Murphy
2021	J	`jnl`	ATLAS: an automated association test using probabilistically linked health records with application to genetic studies. J. Am. Medical Informatics Assoc. 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
2021	J	`jnl`	Clinical knowledge extraction via sparse embedding regression (KESER) with multi-center large scale electronic health record data. npj Digit. Medicine Chuan Hong, Everett Neil Rush, Molei Liu, Doudou Zhou, Jiehuan Sun, Aaron Sonabend W., Victor M. Castro, Petra Schubert, Vidul Ayakulangara Panickan, Tianrun Cai, Lauren Costa, Zeling He, Nicholas B. Link, Ronald G. Hauser, John Michael Gaziano, Shawn N. Murphy, George Ostrouchov, Yuk-Lam Ho, Edmon Begoli, Junwei Lu, Kelly Cho, Katherine P. Liao, Tianxi Cai
2021	Misc	`conf`	Combining Chart Review and Hospital System Dynamics for Electronic Health Record Phenotyping in an International COVID-19 Research Network. AMIA Jeffrey G. Klann, Griffin M. Weber, Emma Perez, William Yuan, Gabriel A. Brat, Shawn N. Murphy
2021	Misc	`conf`	Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. AMIA 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
2021	J	`jnl`	Generative transfer learning for measuring plausibility of EHR diagnosis records. J. Am. Medical Informatics Assoc. Hossein Estiri, Sebastien Vasey, Shawn N. Murphy
2021	J	`jnl`	High-throughput phenotyping with temporal sequences. J. Am. Medical Informatics Assoc. Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy
2021	Misc	`conf`	Integrating Informatics for Integrating Biology and the Bedside with tranSMART: Flexible Data Warehousing with Complex Analytics. AMIA Jeffrey G. Klann, Michael Mendis, Peter Rice, Rudy Potenzone, Louisa May Klann, Griffin M. Weber, Diane Keogh, Shawn N. Murphy
2021	J	`jnl`	Multi-channel attention-fusion neural network for brain age estimation: Accuracy, generality, and interpretation with 16, 705 healthy MRIs across lifespan. Medical Image Anal. 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
2021	J	`jnl`	Predicting COVID-19 mortality with electronic medical records. npj Digit. Medicine Hossein Estiri, Zachary H. Strasser, Jeffrey G. Klann, Pourandokht Naseri, Kavishwar B. Wagholikar, Shawn N. Murphy
2021	J	`jnl`	Quantitative disease risk scores from EHR with applications to clinical risk stratification and genetic studies. npj Digit. Medicine Danqing Xu, Chen Wang, Atlas Khan, Ning Shang, Zihuai He, Adam S. Gordon, Iftikhar J. Kullo, Shawn N. Murphy, Yizhao Ni, Wei-Qi Wei, Ali Gharavi, Krzysztof Kiryluk, Chunhua Weng, Iuliana Ionita-Laza
2021	Misc	`conf`	Temporal Phenotypic Pathways of Post-Acute Sequelae of SARS-CoV-2 by an International Consortium for Clinical Characterization of COVID-19 (4CE). AMIA Shawn N. Murphy, Hossein Estiri, Arianna Dagliati, Riccardo Bellazzi, John H. Holmes
2021	J	`jnl`	The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J. Am. Medical Informatics Assoc. 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
2021	J	`jnl`	Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data. J. Am. Medical Informatics Assoc. 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
2020	—	`conf`	Brain Age Estimation Using LSTM on Children's Brain MRI. ISBI Sheng He, Randy L. Gollub, Shawn N. Murphy, Juan David Perez, Sanjay Prabhu, Rudolph Pienaar, Richard L. Robertson, Patricia Ellen Grant, Yangming Ou
2020	J	`jnl`	Brain Age Estimation Using LSTM on Children's Brain MRI. CoRR Sheng He, Randy L. Gollub, Shawn N. Murphy, Juan David Perez, Sanjay Prabhu, Rudolph Pienaar, Richard L. Robertson, Patricia Ellen Grant, Yangming Ou
2020	Misc	`conf`	Generative Transfer Learning for Measuring Plausibility of EHR Diagnosis Records Over Time. AMIA Hossein Estiri, Sebastien Vasey, Jeffrey G. Klann, Victor M. Castro, Shawn N. Murphy
2020	Misc	`conf`	High-throughput Phenotyping with EHR Sequences. AMIA Shawn N. Murphy, Hossein Estiri, Zachary H. Strasser, Kavishwar B. Wagholikar, Victor M. Castro
2020	Misc	`conf`	HistoriView: An Interactive and Scalable Visual Exploratory Plugin for Longitudinal Patient Data Review. AMIA Heekyong Park, Taowei David Wang, Vivian S. Gainer, Victor M. Castro, Nich Wattanasin, Shawn N. Murphy
2020	J	`jnl`	Individualized Prediction of COVID-19 Adverse outcomes with MLHO. CoRR Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy
2020	Misc	`conf`	Informatics for Integrating Biology and the Bedside (i2b2) in 2020: Supporting Large Ontologies and REDcap Surveys. AMIA Jeffrey G. Klann, Michael Mendis, Diane Keogh, Shawn N. Murphy
2020	J	`jnl`	International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. npj Digit. Medicine Gabriel A. Brat, Griffin M. Weber, Nils Gehlenborg, Paul Avillach, Nathan P. Palmer, Luca Chiovato, James J. Cimino, Lemuel R. Waitman, Gilbert S. Omenn, Alberto Malovini, Jason H. Moore, Brett K. Beaulieu-Jones, Valentina Tibollo, Shawn N. Murphy, Sehi L'Yi, Mark S. Keller, Riccardo Bellazzi, David A. Hanauer, Arnaud Serret-Larmande, Alba Gutiérrez-Sacristán, John J. Holmes, Douglas S. Bell, Kenneth D. Mandl, Robert W. Follett, Jeffrey G. Klann, Douglas A. Murad, Luigia Scudeller, Mauro Bucalo, Katie G. Kirchoff, Jean B. Craig, Jihad S. Obeid, Vianney Jouhet, Romain Griffier, Sébastien Cossin, Bertrand Moal, Lav P. Patel, Antonio Bellasi, Hans-Ulrich Prokosch, Detlef Kraska, Piotr Sliz, Amelia L. M. Tan, Kee Yuan Ngiam, Alberto Zambelli, Danielle L. Mowery, Emily Schriver, Batsal Devkota, Robert L. Bradford, Mohamad Daniar, Christel Daniel, Vincent Benoit, Romain Bey, Nicolas Paris, Patricia Serre, Nina Orlova, Julien Dubiel, Martin Hilka, Anne-Sophie Jannot, Stéphane Bréant, Judith Leblanc, Nicolas Griffon, Anita Burgun, Mélodie Bernaux, Arnaud Sandrin, Elisa Salamanca, Sylvie Cormont, Thomas Ganslandt, Tobias Gradinger, Julien Champ, Martin Boeker, Patricia Martel, Loic Estève, Alexandre Gramfort, Olivier Grisel, Damien Leprovost, Thomas Moreau, Gaël Varoquaux, Jill-Jênn Vie, Demian Wassermann, Arthur Mensch, Charlotte Caucheteux, Christian Haverkamp, Guillaume Lemaitre, Silvano Bosari, Ian D. Krantz, Andrew M. South, Tianxi Cai, Isaac S. Kohane
2020	Misc	`conf`	National Informatics Infrastructure Responding to the COVID-19 Pandemic. AMIA Douglas MacFadden, Shawn N. Murphy, Griffin M. Weber, Anupama Maram
2020	J	`jnl`	Polar labeling: silver standard algorithm for training disease classifiers. Bioinform. Kavishwar B. Wagholikar, Hossein Estiri, Marykate Murphy, Shawn N. Murphy
2020	J	`jnl`	Transitive Sequencing Medical Records for Mining Predictive and Interpretable Temporal Representations. Patterns Hossein Estiri, Zachary H. Strasser, Jeffrey G. Klann, Thomas H. McCoy Jr., Kavishwar B. Wagholikar, Sebastien Vasey, Victor M. Castro, Marykate Murphy, Shawn N. Murphy
2020	B	`conf`	Transitive Sequential Pattern Mining for Discrete Clinical Data. AIME Hossein Estiri, Sebastien Vasey, Shawn N. Murphy
2020	J	`jnl`	sureLDA: A multidisease automated phenotyping method for the electronic health record. J. Am. Medical Informatics Assoc. Yuri Ahuja, Doudou Zhou, Zeling He, Jiehuan Sun, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, Chuan Hong, Tianxi Cai
2019	J	`jnl`	A clustering approach for detecting implausible observation values in electronic health records data. BMC Medical Informatics Decis. Mak. Hossein Estiri, Jeffrey G. Klann, Shawn N. Murphy
2019	J	`jnl`	A federated EHR network data completeness tracking system. J. Am. Medical Informatics Assoc. 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
2019	Misc	`conf`	Dynamic Phenotyping to facilitate Accrual for Prospective Clinical studies: A Case Study in Heart Failure. AMIA 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
2019	Misc	`conf`	EHR Sequencing: A Novel Approach for Constructing Predictive and Interpretable Data Representations from EHR Data. AMIA Hossein Estiri, Thomas H. McCoy, Shawn N. Murphy
2019	J	`jnl`	Facilitating phenotype transfer using a common data model. J. Biomed. Informatics 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
2019	J	`jnl`	High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. J. Am. Medical Informatics Assoc. 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, John Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu
2019	Misc	`conf`	Ontologies Enabling Computable Tables. AMIA Jeffrey G. Klann, Nich Wattanasin, Michael Mendis, Matthew A. Joss, Hossein Estiri, Kavishwar B. Wagholikar, Shawn N. Murphy
2019	Misc	`conf`	Patient Stratification Process for enabling Clinical Interventions. AMIA Kavishwar B. Wagholikar, Samuel J. Aronson, Benjamin Morgan Scirica, Akshay S. Desai, Shawn N. Murphy
2019	Misc	`conf`	Plugin for importing spreadsheets into Informatics for Integrating Biology and the Bedside platform. AMIA Akshay Zagade, Vishal Vernekar, Shek-Wayne Chan, Kavishwar B. Wagholikar, Rupendra Chulyadyo, Yuri Ostrovsky, Alyssa P. Goodson, Ameet Pathak, Christopher Herrick, Shawn N. Murphy
2019	Misc	`conf`	Scalable Process to Generate Aggregated Patient Data for Analysis. AMIA Nich Wattanasin, Taowei David Wang, Vivian S. Gainer, Shawn N. Murphy
2019	J	`jnl`	Semi-supervised encoding for outlier detection in clinical observation data. Comput. Methods Programs Biomed. Hossein Estiri, Shawn N. Murphy
2019	Misc	`conf`	Stratification of Patient Population for enabling data-driven Clinical Interventions using I2b2. AMIA Kavishwar B. Wagholikar, Vishal Vernekar, Akshay Zagade, Yuri Ostrovsky, Shek-Wayne Chan, Alyssa P. Goodson, Ameet Pathak, Corey Glynn, Christopher Herrick, Shawn N. Murphy
2019	Misc	`conf`	sureLDA: A Novel Multi-Disease Automated Phenotyping Method for the Electronic Health Record. AMIA Yuri Ahuja, Doudou Zhou, Zeling He, Jiehuan Sun, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, Chuan Hong, Tianxi Cai
2018	Misc	`conf`	Accessible Research Commons for Health: Four Years Into the PCORnet Journey. AMIA Jeffrey G. Klann, Stanley Boykin, Marc D. Natter, Margaret Vella, Douglas MacFadden, Sarah R. Weiler, Sebastian Schneeweiss, Kenneth D. Mandl, Shawn N. Murphy
2018	Misc	`conf`	Automated Population of an i2b2 Clinical Data Warehouse using FHIR. AMIA Harold R. Solbrig, Na Hong, Shawn N. Murphy, Guoqian Jiang
2018	—	`ch.`	Data Warehousing for Clinical Research. Encyclopedia of Database Systems (2nd ed.) Shawn N. Murphy
2018	J	`jnl`	Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example. J. Am. Medical Informatics Assoc. 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
2018	J	`jnl`	Enabling phenotypic big data with PheNorm. J. Am. Medical Informatics Assoc. 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
2018	J	`jnl`	Exploring completeness in clinical data research networks with DQe-c. J. Am. Medical Informatics Assoc. Hossein Estiri, Kari A. Stephens, Jeffrey G. Klann, Shawn N. Murphy
2018	J	`jnl`	Extraction of Ejection Fraction from Echocardiography Notes for Constructing a Cohort of Patients having Heart Failure with reduced Ejection Fraction (HFrEF). J. Medical Syst. 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
2018	J	`jnl`	Field of View Normalization in Multi-Site Brain MRI. Neuroinformatics 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
2018	Misc	`conf`	High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS. AMIA 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, John Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu, Tianxi Cai
2018	J	`jnl`	Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers. BMC Medical Informatics Decis. Mak. Kavishwar B. Wagholikar, Pralav P. Dessai, Javier Sanz, Michael Mendis, Douglas S. Bell, Shawn N. Murphy
2018	Misc	`conf`	Using HL7 FHIR to Improve Standardization and Interoperability of Common Data Models for Clinical and Translational Research. AMIA Guoqian Jiang, Jon D. Duke, Daniella Meeker, Mitra Rocca, Harold R. Solbrig, Shawn N. Murphy
2018	J	`jnl`	Web services for data warehouses: OMOP and PCORnet on i2b2. J. Am. Medical Informatics Assoc. Jeffrey G. Klann, Lori C. Phillips, Christopher Herrick, Matthew A. Joss, Kavishwar B. Wagholikar, Shawn N. Murphy
2017	—	`conf`	Applying Computed Phenotypes Derived from Electronic Health Records in the Partners HealthCare Biobank Using i2b2. CRI Victor M. Castro, Nich Wattanasin, Vivian S. Gainer, Bhaswati Ghosh, Shawn N. Murphy
2017	Misc	`conf`	Applying unsupervised learning to characterize rare observations in clinical data: the DQe-p tool. AMIA Hossein Estiri, Jeffrey G. Klann, Kavishwar B. Wagholikar, Shawn N. Murphy
2017	J	`jnl`	Biases introduced by filtering electronic health records for patients with "complete data". J. Am. Medical Informatics Assoc. 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
2017	Misc	`conf`	Building Better Timeline Interactions for Patient Chart Reviews. AMIA Heekyong Park, Taowei David Wang, Vivian S. Gainer, Victor M. Castro, Shawn N. Murphy
2017	—	`conf`	Creating a Patient Information Commons from Multiple Research Informatics Platforms. CRI 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
2017	—	`conf`	Data Fitness-for-Use: A Method to Maximize Utility of Poor-Quality Data? CRI Jeffrey G. Klann, Daniella Meeker, Marc B. Rosenman, Shawn N. Murphy
2017	—	`conf`	Evolving Research Data Sharing Networks to Clinical App Sharing Networks. CRI 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
2017	—	`conf`	Exploring Completeness in Clinical Data Research Networks with DQe-c. CRI Hossein Estiri, Kari A. Stephens, Jeffrey G. Klann, Shawn N. Murphy
2017	Misc	`conf`	High-throughput Phenotyping via Denoised Normal Mixture Transformation. AMIA 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
2017	—	`conf`	Instrumenting the Health Care Enterprise for Discovery in the Course of Clinical Care. BCB Shawn N. Murphy
2017	Misc	`conf`	Integrating Patient Registries into Enterprise wide Patient-Discovery Strategies. AMIA Christopher Herrick, Alyssa P. Goodson, Wayne Chan, Lori C. Phillips, Michael Mendis, Shawn N. Murphy
2017	—	`conf`	Needs-Driven Data Completeness Assessment for Clinical Research. CRI Jeffrey G. Klann, Vijay A. Raghavan, Chunhua Weng, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy
2017	—	`conf`	Needs-Driven Data Completeness Dashboard in a Multi-Site Research Network. CRI Jeffrey G. Klann, Vijay A. Raghavan, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy
2017	J	`jnl`	Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization. Frontiers Neuroinformatics Jorge L. Bernal-Rusiel, Nicolas Rannou, Randy L. Gollub, Steve Pieper, Shawn N. Murphy, Richard Robertson, Patricia Ellen Grant, Rudolph Pienaar
2017	Misc	`conf`	Reuse of PCORnet Data to Support the Precision Medicine Initiative: Data Model Harmonization. AMIA Jeffrey G. Klann, Matthew A. Joss, Kevin Embree, Shawn N. Murphy
2017	J	`jnl`	SMART-on-FHIR implemented over i2b2. J. Am. Medical Informatics Assoc. Kavishwar B. Wagholikar, Joshua C. Mandel, Jeffrey G. Klann, Nich Wattanasin, Michael Mendis, Christopher G. Chute, Kenneth D. Mandl, Shawn N. Murphy
2017	—	`conf`	Strategic Assessment and Planning for the PCORnet Common Data Model. CRI 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
2017	J	`jnl`	Surrogate-assisted feature extraction for high-throughput phenotyping. J. Am. Medical Informatics Assoc. 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
2017	Misc	`conf`	Web-Service-Enabled Apps for Research: SMART-on-FHIR for OMOP and PCORNet. AMIA Jeffrey G. Klann, Kavishwar B. Wagholikar, Lori C. Phillips, Matthew A. Joss, Shawn N. Murphy
2017	—	`conf`	i2b2 on OMOP CDM. CRI Lori C. Phillips, Christopher D. Herrick, Shawn N. Murphy
2016	Misc	`conf`	Cajun Codefest 4.0 on SMART-on-FHIR apps for Diabetes. AMIA 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
2016	Misc	`conf`	Comparison of Data Models used in Research Data Repositories for Electronic Phenotyping. AMIA Jeffrey G. Klann, Vijay A. Raghavan, Michael Mendis, Douglas MacFadden, Sarah R. Weiler, Kenneth D. Mandl, Shawn N. Murphy
2016	—	`conf`	Comparison of Two Distributed Data Network Approaches: Democratic and Self-Governed vs. Centrally Managed. CRI Jeffrey G. Klann, Vijay A. Raghavan, Douglas MacFadden, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy
2016	Misc	`conf`	Data Topography of a Large Multi-Site Research Network. AMIA Jeffrey G. Klann, Vijay A. Raghavan, Douglas MacFadden, Sarah R. Weiler, Kenneth D. Mandl, Shawn N. Murphy
2016	J	`jnl`	Data interchange using i2b2. J. Am. Medical Informatics Assoc. Jeffrey G. Klann, Aaron Abend, Vijay A. Raghavan, Kenneth D. Mandl, Shawn N. Murphy
2016	—	`conf`	Defining a Statistically Valid Type 2 Diabetes Cohort in the Partners HealthCare EMR. CRI Alyssa P. Goodson, Andrew Cagan, Vivian S. Gainer, Christopher D. Herrick, Kelly Bell, Tianxi Cai, Shawn N. Murphy
2016	Misc	`conf`	Evaluation of SMART-on-FHIR I2b2 cell using PCORNET data model. AMIA Kavishwar B. Wagholikar, Rahul Jain, Eliel Oliveira, Joshua C. Mandel, Jeffrey G. Klann, Prasad Patil, Kenneth D. Mandl, Shawn N. Murphy, Thomas Carton
2016	Misc	`conf`	Export data from i2b2 using the new download data web client plugin. AMIA Nich Wattanasin, Taowei David Wang, Bhaswati Ghosh, Reeta Metta, Vivian S. Gainer, Shawn N. Murphy
2016	—	`conf`	Improving i2b2 Ontology Medications Mappings with RxMix. CRI Lori C. Phillips, Shawn N. Murphy
2016	—	`conf`	Multi-site Data Completeness Analysis: Application to Laboratory Results in a Large Distributed Research Network. CRI Jeffrey G. Klann, Vijay A. Raghavan, Douglas MacFadden, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy
2016	—	`conf`	Read only SMART on FHIR Façade for I2b2. CRI Kavishwar B. Wagholikar, Joshua C. Mandel, Jeffrey G. Klann, Nich Wattanasin, Michael Mendis, Christopher G. Chute, Kenneth D. Mandl, Shawn N. Murphy
2016	—	`conf`	Using Medication Terminologies NDF-RT and RxNorm for Implementing a Medications Ingredient Hierarchy in a SHRINE/i2b2 use case. CRI Philip Trevvett, Shawn N. Murphy, Lori C. Phillips, Bhanu Bahl
2015	Misc	`conf`	(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping. AMIA Jennifer A. Pacheco, Abel N. Kho, Jyotishman Pathak, Joshua C. Denny, Shawn N. Murphy
2015	J	`jnl`	A numerical similarity approach for using retired Current Procedural Terminology (CPT) codes for electronic phenotyping in the Scalable Collaborative Infrastructure for a Learning Health System (SCILHS). BMC Medical Informatics Decis. Mak. Jeffrey G. Klann, Lori C. Phillips, Alexander Turchin, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy
2015	J	`jnl`	Brain extraction in pediatric ADC maps, toward characterizing neuro-development in multi-platform and multi-institution clinical images. NeuroImage Yangming Ou, Randy L. Gollub, Kallirroi Retzepi, Nathaniel Reynolds, Rudolph Pienaar, Steve Pieper, Shawn N. Murphy, Patricia Ellen Grant, Lilla Zöllei
2015	Misc	`conf`	Computable Phenotypes enabled by the i2b2 Validation Platform. AMIA Shawn N. Murphy, Vivian S. Gainer, Victor M. Castro, Alyssa P. Goodson, Lori C. Phillips, Sheng Yu, Tianxi Cai
2015	Misc	`conf`	Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records. AMIA Uri Kartoun, Vishesh Kumar, Su-Chun Cheng, Sheng Yu, Katherine P. Liao, Elizabeth W. Karlson, Ashwin N. Ananthakrishnan, Zongqi Xia, Vivian S. Gainer, Andrew Cagan, Guergana Savova, Pei J. Chen, Shawn N. Murphy, Susanne E. Churchill, Isaac S. Kohane, Peter Szolovits, Tianxi Cai, Stanley Y. Shaw
2015	J	`jnl`	High Throughput Tools to Access Images from Clinical Archives for Research. J. Digit. Imaging Shawn N. Murphy, Christopher Herrick, Yanbing Wang, Taowei David Wang, Darren Sack, Katherine P. Andriole, Jesse Wei, Nathaniel Reynolds, Wendy Plesniak, Bruce R. Rosen, Steven D. Pieper, Randy L. Gollub
2015	Misc	`conf`	SCILHS Data Mart Creation Plugin. AMIA Michael Mendis, Janice Donahoe, Jeffrey G. Klann, Vijay A. Raghavan, Lori C. Phillips, Alexander Turchin, Shawn N. Murphy
2015	Misc	`conf`	Supporting Multi-sourced Medication Information in i2b2. AMIA Jeffrey G. Klann, Pascal B. Pfiffner, Marc D. Natter, Emily Conner, Paul Blazejewski, Shawn N. Murphy, Kenneth D. Mandl
2015	J	`jnl`	Taking advantage of continuity of care documents to populate a research repository. J. Am. Medical Informatics Assoc. Jeffrey G. Klann, Michael Mendis, Lori C. Phillips, Alyssa P. Goodson, Beatriz H. Rocha, Howard S. Goldberg, Nich Wattanasin, Shawn N. Murphy
2015	Misc	`conf`	The Scalable Collaborative Infrastructure for a Learning Health System. AMIA Jeffrey G. Klann, Marc D. Natter, Douglas MacFadden, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy
2015	Misc	`conf`	The Scalable Collaborative Infrastructure for a Learning Health System: Facilitating Agile Comparative Effectiveness Research. AMIA Jeffrey G. Klann, Marc D. Natter, Douglas MacFadden, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy
2015	J	`jnl`	Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. J. Am. Medical Informatics Assoc. Sheng Yu, Katherine P. Liao, Stanley Y. Shaw, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Tianxi Cai
2014	J	`jnl`	Brief communication: Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture. J. Am. Medical Informatics Assoc. Kenneth D. Mandl, Isaac S. Kohane, Douglas McFadden, Griffin M. Weber, Marc D. Natter, Joshua C. Mandel, Sebastian Schneeweiss, Sarah Weiler, Jeffrey G. Klann, Jonathan P. Bickel, William G. Adams, Yaorong Ge, Xiaobo Zhou, James Perkins, Keith Marsolo, Elmer V. Bernstam, John Showalter, Alexander Quarshie, Elizabeth O. Ofili, George Hripcsak, Shawn N. Murphy
2014	Misc	`conf`	Enabling Patient-Centric Comparative Effectiveness Research in i2b2. AMIA Jeffrey G. Klann, Lori C. Phillips, Kenneth D. Mandl, Shawn N. Murphy
2014	J	`jnl`	Evaluation of matched control algorithms in EHR-based phenotyping studies: A case study of inflammatory bowel disease comorbidities. J. Biomed. Informatics Victor M. Castro, W. Kay Apperson, Vivian S. Gainer, Ashwin N. Ananthakrishnan, Alyssa P. Goodson, Taowei David Wang, Christopher D. Herrick, Shawn N. Murphy
2014	Misc	`conf`	Handling Clinical and Next Generation Sequencing data: new strategies in i2b2 and tranSMART. AMIA Shawn N. Murphy, Riccardo Bellazzi, Matteo Gabetta, Paul Avillach, Lori C. Phillips
2014	Misc	`conf`	Improving the Review of Individual Patients in a Clinical Data Repository. AMIA Nich Wattanasin, Michael Mendis, Kenneth D. Mandl, Isaac S. Kohane, Shawn N. Murphy
2014	Misc	`conf`	Informatics for Integrating Biology and the Bedside (I2b2) Clinical Trials (CT) Patient Ascertainment Suite. AMIA Shawn N. Murphy, Nich Wattanasin, Susanne E. Churchill, Isaac S. Kohane, Vivian S. Gainer
2014	Misc	`conf`	Integrating Information from Unstructured Text with Structured Clinical Data from an Electronic Medical Record to Improve Patient Cohort Identification. AMIA Victor M. Castro, Sergey Goryachev, Christopher Herrick, Vivian S. Gainer, Martin Rees, Shawn N. Murphy
2014	J	`jnl`	Query Health: standards-based, cross-platform population health surveillance. J. Am. Medical Informatics Assoc. Jeffrey G. Klann, Michael D. Buck, Jeffrey S. Brown, Marc Hadley, Richard Elmore, Griffin M. Weber, Shawn N. Murphy
2013	Misc	`conf`	Amassing Pediatric Brain MRI's to Understand "Normal" using Mi2b2. AMIA Shawn N. Murphy, Christopher Herrick, Victor M. Castro, Randy L. Gollub, Nathaniel Reynolds, Patricia Ellen Grant
2013	Misc	`conf`	Integrating the CCDA for Real-Time Patient Data in the i2b2 Platform. AMIA Nich Wattanasin, Michael Mendis, Joshua C. Mandel, Rachel B. Ramoni, Kenneth D. Mandl, Isaac S. Kohane, Shawn N. Murphy
2013	Misc	`conf`	Organization and Transformation of Next-Generation Sequencing Data for Use within i2b2. AMIA Lori C. Phillips, Shawn N. Murphy, Isaac S. Kohane
2013	Misc	`conf`	Query Health: One Step Toward a Learning Health System. AMIA Jeffrey G. Klann, Michael D. Buck, Jeffrey S. Brown, Shawn N. Murphy, Douglas B. Fridsma
2013	Misc	`conf`	Research Informatics : Re-engineering the Research Enterprise. AMIA Mark G. Weiner, Philip R. O. Payne, Peter J. Embí, Shawn N. Murphy
2013	Misc	`conf`	Using SMART and i2b2 to Efficiently Identify Adverse Events. AMIA Jeffrey G. Klann, Rachel L. Ramoni, Shawn N. Murphy
2012	J	`jnl`	A translational engine at the national scale: informatics for integrating biology and the bedside. J. Am. Medical Informatics Assoc. Isaac S. Kohane, Susanne E. Churchill, Shawn N. Murphy
2012	Misc	`conf`	Apps to display patient data, making SMART available in the i2b2 platform. AMIA Nich Wattanasin, Alyssa Porter, Stella Ubaha, Michael Mendis, Lori C. Phillips, Joshua C. Mandel, Rachel L. Ramoni, Kenneth D. Mandl, Isaac S. Kohane, Shawn N. Murphy
2012	Misc	`conf`	Building the SMART Platforms Ecosystem: Toward an Apps-Based Health Information Economy. AMIA Kenneth D. Mandl, Brian D. Athey, Daniel S. Fritsch, Shawn N. Murphy, Will Ross
2012	J	`jnl`	Clinical Bioinformatics: challenges and opportunities. BMC Bioinform. Riccardo Bellazzi, Marco Masseroli, Shawn N. Murphy, Amnon Shabo, Paolo Romano
2012	Misc	`conf`	Data Sharing: Incentives and Governance Issues in Industry and Academia. AMIA Suzanne Bakken, Michael N. Cantor, Shawn N. Murphy, Lisa M. Schilling
2012	Misc	`conf`	Implementing a pharmacovigilance framework using data from electronic medical records. AMIA Victor M. Castro, Vivian S. Gainer, Christopher Herrick, Shawn N. Murphy, Wannapa Kay Mahamaneerat
2012	Misc	`conf`	Integrating Substitutable Medical Apps, Reusable Technologies (SMART) in the i2b2 Platform. AMIA Nich Wattanasin, Alyssa Porter, Stella Ubaha, Michael Mendis, Lori C. Phillips, Joshua C. Mandel, Rachel L. Ramoni, Kenneth D. Mandl, Isaac S. Kohane, Shawn N. Murphy
2012	J	`jnl`	Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J. Am. Medical Informatics Assoc. 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, Elizabeth W. Karlson, Raúl G. Pérez, Vivian S. Gainer, Shawn N. Murphy, Eric M. Ruderman, Richard M. Pope, Robert M. Plenge, Abel N. Kho, Katherine P. Liao, Joshua C. Denny
2012	Misc	`conf`	Query Health and i2b2: Enabling Standards-based, Multiplatform Population Health Queries. AMIA Jeffrey G. Klann, Shawn N. Murphy
2012	Misc	`conf`	Rethinking the "Honest Broker" in the Changing Face of Security and Privacy. AMIA Luke V. Rasmussen, Brian D. Athey, Andrew D. Boyd, Bradley A. Malin, Shawn N. Murphy
2012	Misc	`conf`	Supporting Population Queries and Clinical Trials in i2b2 with SMART. AMIA Shawn N. Murphy, Michael Mendis, Nich Wattanasin, Alyssa Porter, Stella Ubaha, Lori C. Phillips, Joshua C. Mandel, Rachel L. Ramoni, Kenneth D. Mandl, Isaac S. Kohane
2012	Misc	`conf`	The Medical App Store, Research Data Repositories, and Physician Cognitive Overload: Uniting Three Large, Multisite Grants for Health Care Transformation. AMIA Jeffrey G. Klann, Adam Wright, Allison B. McCoy, Shawn N. Murphy
2012	J	`jnl`	The SMART Platform: early experience enabling substitutable applications for electronic health records. J. Am. Medical Informatics Assoc. Kenneth D. Mandl, Joshua C. Mandel, Shawn N. Murphy, Elmer V. Bernstam, Rachel L. Ramoni, David A. Kreda, J. Michael McCoy, Ben Adida, Isaac S. Kohane
2011	J	`jnl`	Strategies for maintaining patient privacy in i2b2. J. Am. Medical Informatics Assoc. Shawn N. Murphy, Vivian S. Gainer, Michael Mendis, Susanne E. Churchill, Isaac S. Kohane
2010	J	`jnl`	Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J. Am. Medical Informatics Assoc. Shawn N. Murphy, Griffin M. Weber, Michael Mendis, Vivian S. Gainer, Henry C. Chueh, Susanne E. Churchill, Isaac S. Kohane
2009	—	`conf`	A PSO/ACO approach to knowledge discovery in a pharmacovigilance context. GECCO (Companion) Margarita Sordo, Gabriela Ochoa, Shawn N. Murphy
2009	J	`jnl`	Application of Information Technology: The Shared Health Research Information Network (SHRINE): A Prototype Federated Query Tool for Clinical Data Repositories. J. Am. Medical Informatics Assoc. Griffin M. Weber, Shawn N. Murphy, Andrew J. McMurry, Douglas MacFadden, Daniel J. Nigrin, Susanne E. Churchill, Isaac S. Kohane
2009	—	`ch.`	Data Warehousing for Clinical Research. Encyclopedia of Database Systems Shawn N. Murphy
2008	J	`jnl`	A National Human Neuroimaging Collaboratory Enabled by the Biomedical Informatics Research Network (BIRN). IEEE Trans. Inf. Technol. Biomed. David B. Keator, Jeffrey S. Grethe, Daniel S. Marcus, I. Burak Özyurt, Syam Gadde, Shawn N. Murphy, Steve Pieper, Douglas N. Greve, R. Notestine, Henry Jeremy Bockholt, Philip M. Papadopoulos
2008	A*	`conf`	Aligning temporal data by sentinel events: discovering patterns in electronic health records. CHI Taowei David Wang, Catherine Plaisant, Alexander J. Quinn, Roman Stanchak, Shawn N. Murphy, Ben Shneiderman
2007	Misc	`conf`	Architecture of the Open-source Clinical Research Chart from Informatics for Integrating Biology and the Bedside. AMIA Shawn N. Murphy, Michael Mendis, Kristel Hackett, Rajesh Kuttan, Wensong Pan, Lori C. Phillips, Vivian S. Gainer, David Berkowicz, John P. Glaser, Isaac S. Kohane, Henry C. Chueh
2006	Misc	`conf`	A Web Portal that Enables Collaborative Use of Advanced Medical Image Processing and Informatics Tools through the Biomedical Informatics Research Network (BIRN). AMIA Shawn N. Murphy, Michael Mendis, Jeffrey S. Grethe, Randy L. Gollub, David N. Kennedy, Bruce R. Rosen
2006	Misc	`conf`	Calculating the Benefits of a Research Patient Data Repository. AMIA Ruth Nalichowski, Diane Keogh, Henry C. Chueh, Shawn N. Murphy
2006	J	`jnl`	Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system. BMC Medical Informatics Decis. Mak. Qing T. Zeng, Sergey Goryachev, Scott T. Weiss, Margarita Sordo, Shawn N. Murphy, Ross Lazarus
2006	Misc	`conf`	Integration of Clinical and Genetic Data in the i2b2 Architecture. AMIA Shawn N. Murphy, Michael Mendis, David A. Berkowitz, Isaac S. Kohane, Henry C. Chueh
2006	Misc	`conf`	Mapping Tool for Maintaining Vocabulary Relationships. AMIA Kristel Hackett, Isaac S. Kohane, Henry C. Chueh, Shawn N. Murphy
2005	Misc	`conf`	Concept-Value Pair Extraction from Semi-Structured Clinical Narrative: A Case Study Using Echocardiogram Reports. AMIA Jeanhee Chung, Shawn N. Murphy
2003	Misc	`conf`	A Visual Interface Designed for Novice Users to find Research Patient Cohorts in a Large Biomedical Database. AMIA Shawn N. Murphy, Vivian S. Gainer, Henry C. Chueh
2002	Misc	`conf`	A security architecture for query tools used to access large biomedical databases. AMIA Shawn N. Murphy, Henry C. Chueh
2001	Misc	`conf`	Visual Query Tool for Integrating Clinical and Genetic Data in the Partners Healthcare System. AMIA Shawn N. Murphy, Henry C. Chueh
2000	Misc	`conf`	Visual query tool for finding patient cohorts from a clinical data warehouse of the partners HealthCare system. AMIA Shawn N. Murphy, G. Octo Barnett, Henry C. Chueh
1999	Misc	`conf`	Deriving Patient Profiles from Clinical Repositories. AMIA Rajneesh Behal, Shawn N. Murphy, G. Octo Barnett, Henry C. Chueh
1999	Misc	`conf`	Optimizing healthcare research data warehouse design through past COSTAR query analysis. AMIA Shawn N. Murphy, Mary Morgan, G. Octo Barnett, Henry C. Chueh
1998	J	`jnl`	Research Paper: The GuideLine Interchange Format: A Model for Representing Guidelines. J. Am. Medical Informatics Assoc. Lucila Ohno-Machado, John H. Gennari, Shawn N. Murphy, Nilesh L. Jain, Samson W. Tu, Diane E. Oliver, Edward Pattison-Gordon, Robert A. Greenes, Edward H. Shortliffe, G. Octo Barnett
1998	Misc	`conf`	Using web technology and Java mobile software agents to manage outside referrals. AMIA Shawn N. Murphy, T. Ng, Dean F. Sittig, G. Octo Barnett
1997	Misc	`conf`	Puya: a method of attracting attention to relevant physical findings. AMIA W. D. de Estrada, Shawn N. Murphy, G. Octo Barnett
1997	Misc	`conf`	Using software agents to maintain autonomous patient registries for clinical research. AMIA Shawn N. Murphy, Usman Rabbani, G. Octo Barnett