Vivian S. Gainer

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 27

Top Topics

Rheumatoid Arthritis

Electronic Medical Record

Natural Language Processing

Top Venues

J. Am. Medical Informatics Assoc.

J. Biomed. Informatics

Publications

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, J. Michael Gaziano, Katherine P. Liao, Junwei Lu, Kelly Cho, Tianxi Cai
LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. Patterns 5 (1) (2024)
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, J. Michael Gaziano, Katherine P. Liao, Junwei Lu, Kelly Cho, Tianxi Cai
LATTE: Label-efficient Incident Phenotyping from Longitudinal Electronic Health Records. CoRR (2023)
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) (2022)
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) (2022)
Ning Shang, Atlas Khan, Fernanda Polubriaginof, Francesca Zanoni, Karla Mehl, David Fasel, Paul E. Drawz, Robert J. Carrol, Joshua C. Denny, Matthew A. Hathcock, Adelaide M. Arruda-Olson, Peggy L. Peissig, Richard A. Dart, Murray H. Brilliant, Eric B. Larson, David S. Carrell, Sarah A. Pendergrass, Shefali Setia Verma, Marylyn D. Ritchie, Barbara Benoit, Vivian S. Gainer, Elizabeth W. Karlson, Adam S. Gordon, Gail P. Jarvik, Ian B. Stanaway, David R. Crosslin, Sumit Mohan, Iuliana Ionita-Laza, Nicholas P. Tatonetti, Ali G. Gharavi, George Hripcsak, Chunhua Weng, Krzysztof Kiryluk
Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. npj Digit. Medicine 4 (2021)
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)
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)
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)
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) (2020)
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)
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)
Nich Wattanasin, Taowei David Wang, Vivian S. Gainer, Shawn N. Murphy
Scalable Process to Generate Aggregated Patient Data for Analysis. AMIA (2019)
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) (2019)
Ning Shang, Cong Liu, 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, Vivian S. Gainer, Iftikhar J. Kullo, Jennifer A. Pacheco, Hakon Hakonarson, Theresa L. Walunas, Joshua C. Denny, Chunhua Weng
Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. J. Biomed. Informatics 99 (2019)
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)
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, Ning Shang, Barbara Benoit, Vivian S. Gainer, Kenneth Borthwick, Kathryn L. Jackson, Ambrish Sharma, Andy Yizhou Wu, Abel N. Kho, Dan M. Roden, Jyotishman Pathak, Joshua C. Denny, William K. Thompson
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. J. Am. Medical Informatics Assoc. 25 (11) (2018)
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) (2018)
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) (2017)
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)
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)
Heekyong Park, Taowei David Wang, Vivian S. Gainer, Victor M. Castro, Shawn N. Murphy
Building Better Timeline Interactions for Patient Chart Reviews. AMIA (2017)
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)
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)
Shawn N. Murphy, Vivian S. Gainer, Victor M. Castro, Alyssa P. Goodson, Lori C. Phillips, Sheng Yu, Tianxi Cai
Computable Phenotypes enabled by the i2b2 Validation Platform. AMIA (2015)
Chen Lin, 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
Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. J. Am. Medical Informatics Assoc. 22 (e1) (2015)
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
Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records. AMIA (2015)
Sheng Yu, Katherine P. Liao, Stanley Y. Shaw, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Tianxi Cai
Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. J. Am. Medical Informatics Assoc. 22 (5) (2015)
Victor M. Castro, W. Kay Apperson, Vivian S. Gainer, Ashwin N. Ananthakrishnan, Alyssa P. Goodson, Taowei David Wang, Christopher D. Herrick, Shawn N. Murphy
Evaluation of matched control algorithms in EHR-based phenotyping studies: A case study of inflammatory bowel disease comorbidities. J. Biomed. Informatics 52 (2014)
Victor M. Castro, Sergey Goryachev, Christopher Herrick, Vivian S. Gainer, Martin Rees, Shawn N. Murphy
Integrating Information from Unstructured Text with Structured Clinical Data from an Electronic Medical Record to Improve Patient Cohort Identification. AMIA (2014)
Shawn N. Murphy, Nich Wattanasin, Susanne E. Churchill, Isaac S. Kohane, Vivian S. Gainer
Informatics for Integrating Biology and the Bedside (I2b2) Clinical Trials (CT) Patient Ascertainment Suite. AMIA (2014)
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
Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J. Am. Medical Informatics Assoc. 19 (e1) (2012)
Victor M. Castro, Vivian S. Gainer, Christopher Herrick, Shawn N. Murphy, Wannapa Kay Mahamaneerat
Implementing a pharmacovigilance framework using data from electronic medical records. AMIA (2012)
Shawn N. Murphy, Vivian S. Gainer, Michael Mendis, Susanne E. Churchill, Isaac S. Kohane
Strategies for maintaining patient privacy in i2b2. J. Am. Medical Informatics Assoc. 18 (Supplement) (2011)
Shawn N. Murphy, Griffin M. Weber, Michael Mendis, Vivian S. Gainer, Henry C. Chueh, Susanne E. Churchill, Isaac S. Kohane
Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J. Am. Medical Informatics Assoc. 17 (2) (2010)
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
Architecture of the Open-source Clinical Research Chart from Informatics for Integrating Biology and the Bedside. AMIA (2007)
Shawn N. Murphy, Vivian S. Gainer, Henry C. Chueh
A Visual Interface Designed for Novice Users to find Research Patient Cohorts in a Large Biomedical Database. AMIA (2003)