Now showing items 1-20 of 62

    • Absolute Enrichment: Gene Set Enrichment Analysis for Homeostatic Systems 

      Saxena, Vishal; Orgill, Dennis Paul; Kohane, Isaac Samuel (Oxford University Press, 2006)
      The Gene Set Enrichment Analysis (GSEA) identifies sets of genes that are differentially regulated in one direction. Many homeostatic systems will include one limb that is upregulated in response to a downregulation of ...
    • Analysis of Gene Expression in a Developmental Context Emphasizes Distinct Biological Leitmotifs in Human Cancers 

      Naxerova, Kamila; Bult, Carol J; Peaston, Anne; Fancher, Karen; Knowles, Barbara B; Kasif, Simon; Kohane, Isaac Samuel (BioMed Central, 2008)
      A systematic analysis of the relationship between the neoplastic and developmental transcriptome provides an outline of global trends in cancer gene expression.
    • Are Meaningful Use Stage 2 certified EHRs ready for interoperability? Findings from the SMART C-CDA Collaborative 

      D'Amore, John D; Mandel, Joshua C; Kreda, David A; Swain, Ashley; Koromia, George A; Sundareswaran, Sumesh; Alschuler, Liora; Dolin, Robert H; Mandl, Kenneth D; Kohane, Isaac S; Ramoni, Rachel B (BMJ Publishing Group, 2014)
      Background and objective Upgrades to electronic health record (EHR) systems scheduled to be introduced in the USA in 2014 will advance document interoperability between care providers. Specifically, the second stage of the ...
    • Automated Validation Of Genetic Variants From Large Databases: Ensuring That Variant References Refer To The Same Genomic Locations 

      Tong, Mark Y.; Cassa, Christopher Anthony; Kohane, Isaac Samuel (Oxford University Press, 2011)
      Accurate annotations of genomic variants are necessary to achieve full-genome clinical interpretations that are scientifically sound and medically relevant. Many disease associations, especially those reported before the ...
    • Availability and Quality of Paraffin Blocks Identified in Pathology Archives: A Multi-Institutional Study by the Shared Pathology Informatics Network (SPIN) 

      Patel, Ashokkumar A; Gupta, Dilipkumar; Seligson, David; Hattab, Eyas M; Balis, Ulysses J; Ulbright, Thomas M; Berman, Jules J; Dry, Sarah; Schirripa, Osvaldo; Becich, Michael J; Parwani, Anil V; Kohane, Isaac Samuel; Gilbertson, John R; Yu, Hong (BioMed Central, 2007)
      Background: Shared Pathology Informatics Network (SPIN) is a tissue resource initiative that utilizes clinical reports of the vast amount of paraffin-embedded tissues routinely stored by medical centers. SPIN has an ...
    • Calculating the Return on Investment of Mobile Healthcare 

      Oriol, Nancy Elizabeth; Cote, Paul J; Vavasis, Anthony P; Bennet, Jennifer; DeLorenzo, Darien; Blanc, Philip; Kohane, Isaac Samuel (BioMed Central, 2009)
      Background: Mobile health clinics provide an alternative portal into the healthcare system for the medically disenfranchised, that is, people who are underinsured, uninsured or who are otherwise outside of mainstream ...
    • Cambogin is Preferentially Cytotoxic to Cells Expressing PDGFR 

      Tian, Ze; Shen, Jie; Wang, Fengfei; Xiao, Peigen; Yang, Junshan; Lei, Hetian; Kazlauskas, Andrius; Kohane, Isaac Samuel; Wu, Erxi (Public Library of Science, 2011)
      Platelet-derived growth factor receptors (PDGFRs) have been implicated in a wide array of human malignancies, including medulloblastoma (MB), the most common brain tumor of childhood. Although significant progress in MB ...
    • Characteristics and Predictive Value of Blood Transcriptome Signature in Males with Autism Spectrum Disorders 

      Kong, Sek Won; Collins, Christin D.; Shimizu-Motohashi, Yuko; Holm, Ingrid A.; Campbell, Malcolm G.; Lee, In-Hee; Brewster, Stephanie J.; Hanson, Ellen M.; Harris, Heather; Lowe, Kathryn R.; Saada, Adrianna; Mora, Andrea; Madison, Kimberly; Hundley, Rachel; Egan, Jessica; McCarthy, Jillian; Eran, Ally; Galdzicki, Michal; Rappaport, Leonard; Kunkel, Louis M.; Kohane, Isaac S. (Public Library of Science, 2012)
      Autism Spectrum Disorders (ASD) is a spectrum of highly heritable neurodevelopmental disorders in which known mutations contribute to disease risk in 20% of cases. Here, we report the results of the largest blood transcriptome ...
    • The Co-Morbidity Burden of Children and Young Adults with Autism Spectrum Disorders 

      Wattanasin, Nich; Churchill, Susanne; Kohane, Isaac Samuel; McMurry, Andrew; MacFadden, Douglas; Rappaport, Leonard Allan; Kunkel, Louis Martens; Bickel, Jonathan; Spence, Sarah J.; Murphy, Shawn Norman; Weber, Griffin M. (Public Library of Science, 2012)
      Objectives: Use electronic health records Autism Spectrum Disorder (ASD) to assess the comorbidity burden of ASD in children and young adults. Study Design: A retrospective prevalence study was performed using a distributed ...
    • Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells 

      Wu, Erxi; Palmer, Nathan; Tian, Ze; Moseman, Annie P.; Galdzicki, Michal; Wang, Xuetao; Berger, Bonnie; Zhang, Hongbing; Kohane, Isaac Samuel (Public Library of Science, 2008)
      Despite the growing understanding of PDGF signaling, studies of PDGF function have encountered two major obstacles: the functional redundancy of PDGFRα and PDGFRβ in vitro and their distinct roles in vivo. Here we used ...
    • A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey 

      Patel, Chirag J.; Pho, Nam; McDuffie, Michael; Easton-Marks, Jeremy; Kothari, Cartik; Kohane, Isaac S.; Avillach, Paul (Nature Publishing Group, 2016)
      The National Health and Nutrition Examination Survey (NHANES) is a population survey implemented by the Centers for Disease Control and Prevention (CDC) to monitor the health of the United States whose data is publicly ...
    • 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 ...
    • Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis 

      Kong, Sek Won; Sahin, Mustafa; Collins, Christin D; Wertz, Mary H; Campbell, Malcolm G; Leech, Jarrett D; Krueger, Dilja; Bear, Mark F; Kunkel, Louis M; Kohane, Isaac S (BioMed Central, 2014)
      Background: Fragile X syndrome and tuberous sclerosis are genetic syndromes that both have a high rate of comorbidity with autism spectrum disorder (ASD). Several lines of evidence suggest that these two monogenic disorders ...
    • Early Detection of Poor Adherers to Statins: Applying Individualized Surveillance to Pay for Performance 

      Zimolzak, Andrew J.; Spettell, Claire M.; Fernandes, Joaquim; Fusaro, Vincent A.; Palmer, Nathan P.; Saria, Suchi; Kohane, Isaac S.; Jonikas, Magdalena A.; Mandl, Kenneth D. (Public Library of Science, 2013)
      Background: Medication nonadherence costs $300 billion annually in the US. Medicare Advantage plans have a financial incentive to increase medication adherence among members because the Centers for Medicare and Medicaid ...
    • Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder 

      Lingren, Todd; Chen, Pei; Bochenek, Joseph; Doshi-Velez, Finale; Manning-Courtney, Patty; Bickel, Julie; Wildenger Welchons, Leah; Reinhold, Judy; Bing, Nicole; Ni, Yizhao; Barbaresi, William; Mentch, Frank; Basford, Melissa; Denny, Joshua; Vazquez, Lyam; Perry, Cassandra; Namjou, Bahram; Qiu, Haijun; Connolly, John; Abrams, Debra; Holm, Ingrid A.; Cobb, Beth A.; Lingren, Nataline; Solti, Imre; Hakonarson, Hakon; Kohane, Isaac S.; Harley, John; Savova, Guergana (Public Library of Science, 2016)
      Objective: Cohort selection is challenging for large-scale electronic health record (EHR) analyses, as International Classification of Diseases 9th edition (ICD-9) diagnostic codes are notoriously unreliable disease ...
    • Electronic Patient-Physician Communication: Problems and Promise 

      Mandl, Kenneth David; Kohane, Isaac Samuel; Brandt, Allan M. (American College of Physicians, 1998)
      A critical mass of Internet users will soon enable wide diffusion of electronic communication within medical practice. E-mail between physicians and patients offers important opportunities for better communication. Linking ...
    • EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children 

      Namjou, Bahram; Keddache, Mehdi; Marsolo, Keith; Wagner, Michael; Lingren, Todd; Cobb, Beth; Perry, Cassandra; Kennebeck, Stephanie; Holm, Ingrid A.; Li, Rongling; Crimmins, Nancy A.; Martin, Lisa; Solti, Imre; Kohane, Isaac S.; Harley, John B. (Frontiers Media S.A., 2013)
      Common variations at the loci harboring the fat mass and obesity gene (FTO), MC4R, and TMEM18 are consistently reported as being associated with obesity and body mass index (BMI) especially in adult population. In order ...
    • Expression differences by continent of origin point to the immortalization process 

      Davis, Adam Robert; Kohane, Isaac Samuel (Oxford University Press, 2009)
      Analysis of recently available microarray expression data sets obtained from immortalized cell lines of the individuals represented in the HapMap project have led to inconclusive comparisons across cohorts with different ...
    • Extracting Physician Group Intelligence from Electronic Health Records to Support Evidence Based Medicine 

      Weber, Griffin M.; Kohane, Isaac S. (Public Library of Science, 2013)
      Evidence-based medicine employs expert opinion and clinical data to inform clinical decision making. The objective of this study is to determine whether it is possible to complement these sources of evidence with information ...
    • Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: A pilot study 

      Hoogenboom, Wouter S.; Perlis, Roy; Smoller, Jordan W; Zeng-Treitler, Qing; Gainer, Vivian S.; Murphy, Shawn Norman; Churchill, Susanne E.; Kohane, Isaac Samuel; Shenton, Martha Elizabeth; Iosifescu, Dan (Elsevier BV, 2013)
      For certain research questions related to long-term outcomes or to rare disorders, designing prospective studies is impractical or prohibitively expensive. Such studies could instead utilize clinical and magnetic resonance ...