A Visual Interface Designed for Novice Users to find Research Patient Cohorts in a Large Biomedical Database. - Shawn N. Murphy; Vivian S. Gainer; Henry C. Chueh (AMIA, 2003)

Architecture of the Open-source Clinical Research Chart from Informatics for Integrating Biology and the Bedside. - 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 (AMIA, 2007)

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). - Shawn N. Murphy; Griffin M. Weber; Michael Mendis; Vivian S. Gainer; Henry C. Chueh; Susanne E. Churchill; Isaac S. Kohane (J. Am. Medical Informatics Assoc., 2010)

Strategies for maintaining patient privacy in i2b2. - Shawn N. Murphy; Vivian S. Gainer; Michael Mendis; Susanne E. Churchill; Isaac S. Kohane (J. Am. Medical Informatics Assoc., 2011)

Implementing a pharmacovigilance framework using data from electronic medical records. - Victor M. Castro; Vivian S. Gainer; Christopher Herrick; Shawn N. Murphy; Wannapa Kay Mahamaneerat (AMIA, 2012)

Portability of an algorithm to identify rheumatoid arthritis in electronic health records. - 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 001; Elizabeth W. Karlson; Raúl G. Pérez; et al. (J. Am. Medical Informatics Assoc., 2012)

Integrating Information from Unstructured Text with Structured Clinical Data from an Electronic Medical Record to Improve Patient Cohort Identification. - Victor M. Castro; Sergey Goryachev; Christopher Herrick; Vivian S. Gainer; Martin Rees; Shawn N. Murphy (AMIA, 2014)

Informatics for Integrating Biology and the Bedside (I2b2) Clinical Trials (CT) Patient Ascertainment Suite. - Shawn N. Murphy; Nich Wattanasin; Susanne E. Churchill; Isaac S. Kohane; Vivian S. Gainer (AMIA, 2014)

Evaluation of matched control algorithms in EHR-based phenotyping studies: A case study of inflammatory bowel disease comorbidities. - Victor M. Castro; W. Kay Apperson; Vivian S. Gainer; Ashwin N. Ananthakrishnan; Alyssa P. Goodson; Taowei David Wang; Christopher D. Herrick; Shawn N. Murphy (J. Biomed. Informatics, 2014)

Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records. - Uri Kartoun; Vishesh Kumar; Su-Chun Cheng; Sheng Yu 002; Katherine P. Liao; Elizabeth W. Karlson; Ashwin N. Ananthakrishnan; Zongqi Xia; Vivian S. Gainer; Andrew Cagan; Guergana Savova; Pei J. Chen; et al. (AMIA, 2015)

Computable Phenotypes enabled by the i2b2 Validation Platform. - Shawn N. Murphy; Vivian S. Gainer; Victor M. Castro; Alyssa P. Goodson; Lori C. Phillips; Sheng Yu 002; Tianxi Cai (AMIA, 2015)

Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. - Chen Lin 002; Elizabeth W. Karlson; Dmitriy Dligach; Monica P. Ramirez; Timothy A. Miller; Huan Mo; Natalie S. Braggs; Andrew Cagan; Vivian S. Gainer; Joshua C. Denny; Guergana K. Savova (J. Am. Medical Informatics Assoc., 2015)

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. - Sheng Yu 002; Katherine P. Liao; Stanley Y. Shaw; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Tianxi Cai (J. Am. Medical Informatics Assoc., 2015)

Export data from i2b2 using the new download data web client plugin. - Nich Wattanasin; Taowei David Wang; Bhaswati Ghosh; Reeta Metta; Vivian S. Gainer; Shawn N. Murphy (AMIA, 2016)

Defining a Statistically Valid Type 2 Diabetes Cohort in the Partners HealthCare EMR. - Alyssa P. Goodson; Andrew Cagan; Vivian S. Gainer; Christopher D. Herrick; Kelly Bell; Tianxi Cai; Shawn N. Murphy (CRI, 2016)

Building Better Timeline Interactions for Patient Chart Reviews. - Heekyong Park; Taowei David Wang; Vivian S. Gainer; Victor M. Castro; Shawn N. Murphy (AMIA, 2017)

High-throughput Phenotyping via Denoised Normal Mixture Transformation. - Sheng Yu 002; 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 (AMIA, 2017)

Applying Computed Phenotypes Derived from Electronic Health Records in the Partners HealthCare Biobank Using i2b2. - Victor M. Castro; Nich Wattanasin; Vivian S. Gainer; Bhaswati Ghosh; Shawn N. Murphy (CRI, 2017)

Surrogate-assisted feature extraction for high-throughput phenotyping. - Sheng Yu 002; 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 (J. Am. Medical Informatics Assoc., 2017)

High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS. - Katherine P. Liao; Jiehuan Sun; Tianrun A. Cai; Nicholas B. Link; Chuan Hong; Jie Huang 030; Jennifer E. Huffman; Jessica L. Gronsbell; Lauren Costa; Victor M. Castro; Vivian S. Gainer; Shawn N. Murphy; et al. (AMIA, 2018)

A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. - Jennifer A. Pacheco; Luke V. Rasmussen; Richard C. Kiefer; Thomas R. Campion Jr.; Peter Speltz; Robert J. Carroll; Sarah C. Stallings; Huan Mo; Monika Ahuja; Guoqian Jiang; Eric R. LaRose; Peggy L. Peissig; et al. (J. Am. Medical Informatics Assoc., 2018)

Enabling phenotypic big data with PheNorm. - Sheng Yu 002; 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 (J. Am. Medical Informatics Assoc., 2018)

sureLDA: A Novel Multi-Disease Automated Phenotyping Method for the Electronic Health Record. - Yuri Ahuja; Doudou Zhou; Zeling He; Jiehuan Sun; Victor M. Castro; Vivian S. Gainer; Shawn N. Murphy; Chuan Hong; Tianxi Cai (AMIA, 2019)

Scalable Process to Generate Aggregated Patient Data for Analysis. - Nich Wattanasin; Taowei David Wang; Vivian S. Gainer; Shawn N. Murphy (AMIA, 2019)

High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. - Katherine P. Liao; Jiehuan Sun; Tianrun A. Cai; Nicholas B. Link; Chuan Hong; Jie Huang 030; Jennifer E. Huffman; Jessica L. Gronsbell; Yichi Zhang; Yuk-Lam Ho; Victor M. Castro; Vivian S. Gainer; et al. (J. Am. Medical Informatics Assoc., 2019)

Facilitating phenotype transfer using a common data model. - George Hripcsak; Ning Shang; Peggy L. Peissig; Luke V. Rasmussen; Cong Liu 020; Barbara Benoit; Robert J. Carroll; David S. Carrell; Joshua C. Denny; Ozan Dikilitas; Vivian S. Gainer; Kayla Marie Howell; et al. (J. Biomed. Informatics, 2019)

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. - Ning Shang; Cong Liu 020; Luke V. Rasmussen; Casey N. Ta; Robert J. Carroll; Barbara Benoit; Todd Lingren; Ozan Dikilitas; Frank D. Mentch; David S. Carrell; Wei-Qi Wei; Yuan Luo 001; et al. (J. Biomed. Informatics, 2019)

HistoriView: An Interactive and Scalable Visual Exploratory Plugin for Longitudinal Patient Data Review. - Heekyong Park; Taowei David Wang; Vivian S. Gainer; Victor M. Castro; Nich Wattanasin; Shawn N. Murphy (AMIA, 2020)

sureLDA: A multidisease automated phenotyping method for the electronic health record. - Yuri Ahuja; Doudou Zhou; Zeling He; Jiehuan Sun; Victor M. Castro; Vivian S. Gainer; Shawn N. Murphy; Chuan Hong; Tianxi Cai (J. Am. Medical Informatics Assoc., 2020)

Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. - 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 020; Todd Lingren; et al. (AMIA, 2021)

A Novel Data Portal to Enable COVID-19 Data Integration and Analysis. - Nich Wattanasin; Victor M. Castro; Vivian S. Gainer; Barbara Benoit; Andrew Cagan; Reeta Metta; Shawn N. Murphy (AMIA, 2021)

Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. - Ning Shang; Atlas Khan; Fernanda Polubriaginof; Francesca Zanoni; Karla Mehl; David Fasel; Paul E. Drawz; Robert J. Carroll; Joshua C. Denny; Matthew A. Hathcock; Adelaide M. Arruda-Olson; Peggy L. Peissig; et al. (npj Digit. Medicine, 2021)

The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics. - 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; et al. (J. Am. Medical Informatics Assoc., 2022)

Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. - Jingzhi Yu; Jennifer A. Pacheco; Anika S. Ghosh; Yuan Luo 001; Chunhua Weng; Ning Shang; Barbara Benoit; David S. Carrell; Robert J. Carroll; Ozan Dikilitas; Robert R. Freimuth; Vivian S. Gainer; et al. (BMC Medical Informatics Decis. Mak., 2022)

LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. - Jun Wen; Jue Hou; Clara-Lea Bonzel; Yihan Zhao; Victor M. Castro; Vivian S. Gainer; Dana Weisenfeld; Tianrun Cai; Yuk-Lam Ho; Vidul Ayakulangara Panickan; Lauren Costa; Chuan Hong; et al. (Patterns, 2024)