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  • 2017
    • Best Practices for HPC Center
      Worldwide Best Practices in Partnerships between HPC Centers and Industrial Users Sponsored by: The National Center for Supercomputing Applications (NCSA) ...
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    • Perspectives on Research in Artificial Intelligence and Artificial General Intelligence Relevant to DoD
      JASON report of January 2017...
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    • Joint Agency Assessment of the Responses to the Request for Information (RFI) on “Science Drivers Requiring Capable Exascale High Performance Computing”
      PLEASE CLICK ON THE PDF FILE ON THE FRONT PAGE This report provides a joint assessment by the National Institutes of Health (NIH), Department of Energy (DOE) and National Science Foundation (NSF) of the scientific and engineering research community's science drivers requiring capable exascale ...
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    • Antigenic Determinants of Der p 1: Specificity and Cross-Reactivity Associated with IgE Antibody Recognition
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    • Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode
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  • 2016
    • BioNetGen 2.2: advances in rule-based modeling.
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    • Sharing brain mapping statistical results with the neuroimaging data model.
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    • Optimization and Control of Agent-Based Models in Biology: A Perspective
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    • Quantitative human cell encyclopedia
      Scientists gathered to discuss the necessity, feasibility, and challenges of generating a quantitative catalog of the components in human cells that is essential for our understanding of human physiology in health and disease and to support future breakthroughs in treating diseases. This report sum...
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    • Council on Library and Information Resources Report Examines Federal Public Access Plans and Their Implications for the Cultural Heritage Community
      New U.S. government requirements for exposing and managing federally funded research data add urgency to the call for curating data that can be used, reused, and exploited by future generations, according to a new report ...
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    • Staying Alive: Measuring Intact Viable Microbes with Electrospray Ionization Mass Spectrometry.
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    • Metabolomics: beyond biomarkers and towards mechanisms
      Metabolomics, which is the profiling of metabolites in biofluids, cells and tissues, is routinely applied as a tool for biomarker discovery. Owing to innovative developments in informatics and analytical technologies, and the integration of orthogonal biological approaches, it is now possible to ex...
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    • Endothelial to mesenchymal transition is common in atherosclerotic lesions and is associated with plaque instability
      Endothelial to mesenchymal transition (EndMT) plays a major role during development, and also contributes to several adult cardiovascular diseases. Importantly, mesenchymal cells including fibroblasts are prominent in atherosclerosis, with key functions including regulation of: inflammation, matrix...
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    • Proteome-wide covalent ligand discovery in native biological systems.
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    • Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials.
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    • An R Package for Finlay-Wilkinson Regression that Incorporates Genomic/Pedigree Information and Covariance Structures Between Environments
      The Finlay-Wilkinson regression (FW) is a popular method among plant breeders to describe genotype by environment interaction. The standard implementation is a two-step procedure that uses environment (sample) means as covariates in a within-line ordinary least squares (OLS)regression. This procedu...
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    • Breast Imaging in the Era of Big Data: Structured Reporting and Data Mining
      OBJECTIVE. The purpose of this article is to describe structured reporting and the development of large databases for use in data mining in breast imaging. CONCLUSION. The results of millions of breast imaging examinations are reported with structured tools based on the BI-RADS lexicon. Much of ...
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    • Predicting protein function and other biomedical characteristics with heterogeneous ensembles
      Prediction problems in biomedical sciences, including protein function prediction (PFP), are generally quite difficult. This is due in part to incomplete knowledge of the cellular phenomenon of interest, the appropriateness and data quality of the variables and measurements used for prediction, as ...
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    • The Quantitative-MFG Test: A Linear Mixed Effect Model to Detect Maternal-Offspring Gene Interactions
      Maternal-offspring gene interactions, aka maternal-fetal genotype (MFG) incompatibilities, are neglected in complex diseases and quantitative trait studies. They are implicated in birth to adult onset diseases but there are limited ways to investigate their influence on quantitative traits. We pres...
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  • 2015
    • Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits
      Traditional coarse-graining based on a reduced number of interaction sites often entails a significant sacrifice of chemical accuracy. As analternative, we present a method for simulating large systems composed of interacting macromolecules using an energy tabulation strategy previously devised for...
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    • Charting a Path to Success in Virtual Screening.
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    • Computational challenges of structure-based approaches applied to HIV.
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    • A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA.
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