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

LATTE: Label-efficient Incident Phenotyping from Longitudinal Electronic Health Records. - Wen, Jun; Hou, Jue; Bonzel, Clara-Lea; Zhao, Yihan; Castro, Victor M.; Gainer, Vivian S.; Weisenfeld, Dana; Cai, Tianrun; Ho, Yuk-Lam; Panickan, Vidul Ayakulangara; Costa, Lauren; Hong, Chuan; et al. (CoRR, 2023)

The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics. - Castro, Victor M.; Gainer, Vivian S.; Wattanasin, Nich; Benoit, Barbara; Cagan, Andrew; Ghosh, Bhaswati; Goryachev, Sergey; Metta, Reeta; Park, Heekyong; Wang, Taowei David; Mendis, Michael; Rees, Martin; et al. (J. Am. Medical Informatics Assoc., 2022)

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

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

Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. - Pacheco, Jennifer A.; Rasmussen, Luke V.; Wiley, Ken; Person, Thomas N.; Cronkite, David J.; Sohn, Sunghwan; Murphy, Shawn N.; Gundelach, Justin H.; Gainer, Vivian S.; Castro, Victor M.; Liu, Cong; Lingren, Todd; et al. (2021)

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

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

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

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

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

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

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

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

Enabling phenotypic big data with PheNorm. - Yu, Sheng; Ma, Yumeng; Gronsbell, Jessica L.; Cai, Tianrun A.; Ananthakrishnan, Ashwin N.; Gainer, Vivian S.; Churchill, Susanne E.; Szolovits, Peter; Murphy, Shawn N.; Kohane, Isaac S.; Liao, Katherine P.; Cai, Tianxi (J. Am. Medical Informatics Assoc., 2018)

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

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

Surrogate-assisted feature extraction for high-throughput phenotyping. - Yu, Sheng; Chakrabortty, Abhishek; Liao, Katherine P.; Cai, Tianrun A.; Ananthakrishnan, Ashwin N.; Gainer, Vivian S.; Churchill, Susanne E.; Szolovits, Peter; Murphy, Shawn N.; Kohane, Isaac S.; Cai, Tianxi (J. Am. Medical Informatics Assoc., 2017)

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

High-throughput Phenotyping via Denoised Normal Mixture Transformation. - Yu, Sheng; Ma, Yumeng; Gronsbell, Jessica L.; Liao, Katherine P.; Cai, Tianrun A.; Ananthakrishnan, Ashwin N.; Gainer, Vivian S.; Churchill, Susanne E.; Szolovits, Peter; Murphy, Shawn N.; Kohane, Isaac S.; Cai, Tianxi (2017)

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

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

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

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

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

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

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

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

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

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

Portability of an algorithm to identify rheumatoid arthritis in electronic health records. - Carroll, Robert J.; Thompson, William K.; Eyler, Anne E.; Mandelin, Arthur M.; Cai, Tianxi; Zink, Raquel M.; Pacheco, Jennifer A.; Boomershine, Chad S.; Lasko, Thomas A.; Xu, Hua; Karlson, Elizabeth W.; Pérez, Raúl G.; et al. (J. Am. Medical Informatics Assoc., 2012)

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

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

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

Architecture of the Open-source Clinical Research Chart from Informatics for Integrating Biology and the Bedside. - Murphy, Shawn N.; Mendis, Michael; Hackett, Kristel; Kuttan, Rajesh; Pan, Wensong; Phillips, Lori C.; Gainer, Vivian S.; Berkowicz, David; Glaser, John P.; Kohane, Isaac S.; Chueh, Henry C. (2007)

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