Browsing by Author "Shaw, Stanley"

Now showing items 1-13 of 13

    • Aging Syndrome Genes and Premature Coronary Artery Disease 

      Low, Adrian F; O'Donnell, Christopher Joseph; Kathiresan, Sekar; Everett, Brendan Murphy; Chae, Claudia Un-Yong; Shaw, Stanley Yang; Ellinor, Patrick Thomas; MacRae, Calum A (BioMed Central, 2005)
      Background: Vascular disease is a feature of aging, and coronary vascular events are a major source of morbidity and mortality in rare premature aging syndromes. One such syndrome is caused by mutations in the lamin A/C ...

    • Development of phenotype algorithms using electronic medical records and incorporating natural language processing 

      Liao, Katherine P; Cai, Tianxi; Savova, Guergana K; Murphy, Shawn N; Karlson, Elizabeth W; Ananthakrishnan, Ashwin N; Gainer, Vivian S; Shaw, Stanley Y; Xia, Zongqi; Szolovits, Peter; Churchill, Susanne; Kohane, Isaac (BMJ Publishing Group Ltd., 2015)
      Electronic medical records are emerging as a major source of data for clinical and translational research studies, although phenotypes of interest need to be accurately defined first. This article provides an overview of ...

    • Disease Allele-Dependent Small-Molecule Sensitivities in Blood Cells from Monogenic Diabetes 

      Shaw, Stanley Yang; Blodgett, David M.; Ma, Maggie S.; Westly, Elizabeth C.; Clemons, Paul A.; Subramanian, Aravind; Schreiber, Stuart L. (Proceedings of the National Academy of Sciences, 2010)
      Even as genetic studies identify alleles that influence human disease susceptibility, it remains challenging to understand their functional significance and how they contribute to disease phenotypes. Here, we describe an ...

    • Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines 

      Yelensky, Roman; Bonakdar, Sasha; Wolfish, Cara S.; Cotsapas, Chris; Rivas, Manuel; Dermitzakis, Emmanouil T.; Choy, Edwin; Plenge, Robert M.; Saxena, Richa; De Jager, Philip Lawrence; Shaw, Stanley Yang; Slavik, Jacqueline Marie; Cahir-McFarland, Ellen D.; Kieff, Elliott D.; Hafler, David A.; Daly, Mark Joseph; Altshuler, David Matthew (Public Library of Science, 2008)
      Lymphoblastoid cell lines (LCLs), originally collected as renewable sources of DNA, are now being used as a model system to study genotype–phenotype relationships in human cells, including searches for QTLs influencing ...

    • High-Throughput Phenotyping With Electronic Medical Record Data Using a Common Semi-Supervised Approach (PheCAP) 

      Zhang, Yichi; Cai, Tianrun; Yu, Sheng; Cho, Kelly; Hong, Chuan; Sun, Jiehuan; Huang, Jie; Xia, Zongqi; Castro, Victor; Gagnon, David; Savova, Guergana; Churchill, Susanne; Gaziano, John; Kohane, Isaac; Cai, Tianxi; Ho, Yuk-Lam; Ananthakrishnan, Ashwin; Shaw, Stanley; Gainer, Vivian; Link, Nicholas; Honerlaw, Jacqueline; Huong, Sicong; Karlson, Elizabeth; Plenge, Robert; Szolovits, Peter; O'Donnell, Christopher; Murphy, Shawn; Liao, Katherine (Springer Science and Business Media LLC, 2019-11-20)
      Phenotypes are the foundation for clinical and genetic studies of disease risk and outcomes. The growth of biobanks linked to electronic medical record (EMR) data has both facilitated and increased the demand for efficient, ...

    • Improving Case Definition of Crohnʼs Disease and Ulcerative Colitis in Electronic Medical Records Using Natural Language Processing 

      Ananthakrishnan, Ashwin; Cai, Tianxi; Savova, Guergana; Cheng, Su-Chun; Chen, Pei; Guzman, Raul; Gainer, Vivian S.; Murphy, Shawn; Szolovits, Peter; Xia, Zongqi; Shaw, Stanley; Churchill, Susanne; Karlson, Elizabeth; Kohane, Isaac; Plenge, Robert M.; Liao, Katherine (Oxford University Press (OUP), 2013-06)
      Introduction Prior studies identifying patients with inflammatory bowel disease (IBD) utilizing administrative codes have yielded inconsistent results. Our objective was to develop a robust electronic medical record (EMR) ...

    • The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells 

      Khor, Bernard; Gagnon, John D; Goel, Gautam; Roche, Marly I; Conway, Kara L; Tran, Khoa; Aldrich, Leslie N; Sundberg, Thomas B; Paterson, Alison M; Mordecai, Scott; Dombkowski, David; Schirmer, Melanie; Tan, Pauline H; Bhan, Atul K; Roychoudhuri, Rahul; Restifo, Nicholas P; O'Shea, John J; Medoff, Benjamin D; Shamji, Alykhan F; Schreiber, Stuart L; Sharpe, Arlene H; Shaw, Stanley Y; Xavier, Ramnik J (eLife Sciences Publications, Ltd, 2015)
      The balance between Th17 and T regulatory (Treg) cells critically modulates immune homeostasis, with an inadequate Treg response contributing to inflammatory disease. Using an unbiased chemical biology approach, we identified ...

    • Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts 

      Liao, Katherine P.; Ananthakrishnan, Ashwin N.; Kumar, Vishesh; Xia, Zongqi; Cagan, Andrew; Gainer, Vivian S.; Goryachev, Sergey; Chen, Pei; Savova, Guergana K.; Agniel, Denis; Churchill, Susanne; Lee, Jaeyoung; Murphy, Shawn N.; Plenge, Robert M.; Szolovits, Peter; Kohane, Isaac; Shaw, Stanley Y.; Karlson, Elizabeth W.; Cai, Tianxi (Public Library of Science, 2015)
      Background: Typically, algorithms to classify phenotypes using electronic medical record (EMR) data were developed to perform well in a specific patient population. There is increasing interest in analyses which can allow ...

    • Modeling Disease Severity in Multiple Sclerosis Using Electronic Health Records 

      Xia, Zongqi; Secor, Elizabeth; Chibnik, Lori B.; Bove, Riley M.; Cheng, Suchun; Chitnis, Tanuja; Cagan, Andrew; Gainer, Vivian S.; Chen, Pei J.; Liao, Katherine P.; Shaw, Stanley Y.; Ananthakrishnan, Ashwin N.; Szolovits, Peter; Weiner, Howard L.; Karlson, Elizabeth W.; Murphy, Shawn N.; Savova, Guergana K.; Cai, Tianxi; Churchill, Susanne E.; Plenge, Robert M.; Kohane, Isaac S.; De Jager, Philip L. (Public Library of Science, 2013)
      Objective: To optimally leverage the scalability and unique features of the electronic health records (EHR) for research that would ultimately improve patient care, we need to accurately identify patients and extract ...

    • Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors 

      Vafai, Scott B.; Mevers, Emily; Higgins, Kathleen W.; Fomina, Yevgenia; Zhang, Jianming; Mandinova, Anna; Newman, David; Shaw, Stanley Y.; Clardy, Jon; Mootha, Vamsi K. (Public Library of Science, 2016)
      Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS). Idebenone and menadione ...

    • Normalization of Plasma 25-Hydroxy Vitamin D Is Associated with Reduced Risk of Surgery in Crohn’s Disease 

      Ananthakrishnan, Ashwin; Cagan, Andrew; Gainer, Vivian S.; Cai, Tianxi; Cheng, Su-Chun; Savova, Guergana; Chen, Pei; Szolovits, Peter; Xia, Zongqi; De Jager, Philip; Shaw, Stanley; Churchill, Susanne; Karlson, Elizabeth; Kohane, Isaac; Plenge, Robert; Murphy, Shawn; Liao, Katherine (Oxford University Press (OUP), 2013-08-01)
      Introduction Vitamin D may have an immunological role in Crohn’s disease (CD) and ulcerative colitis (UC). Retrospective studies suggested a weak association between vitamin D status and disease activity but have significant ...

    • STARS Is Essential to Maintain Cardiac Development and Function In Vivo via a SRF Pathway 

      Chong, Nelson W.; Koekemoer, Andrea L.; Ounzain, Samir; Samani, Nilesh J.; Shin, Jordan T.; Shaw, Stanley Yang (Public Library of Science, 2012)
      Background: STARS (STriated muscle Activator of Rho Signaling) is a sarcomeric protein expressed early in cardiac development that acts as an acute stress sensor for pathological remodeling. However the role of STARS in ...

    • Use of Chronic Oral Anticoagulation and Associated Outcomes Among Patients Undergoing Percutaneous Coronary Intervention 

      Secemsky, Eric A.; Butala, Neel M.; Kartoun, Uri; Mahmood, Sadiqa; Wasfy, Jason H.; Kennedy, Kevin F.; Shaw, Stanley Y.; Yeh, Robert W. (John Wiley and Sons Inc., 2016)
      Background: Contemporary rates of oral anticoagulant (OAC) therapy and associated outcomes among patients undergoing percutaneous coronary intervention (PCI) have been poorly described. Methods and Results: Using data from ...