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Browsing CAS: Computer Science: Scholarly Papers by Title

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Browsing CAS: Computer Science: Scholarly Papers by Title

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  • Andken, Benjamin B; Lim, In; Benson, Gary; Vincent, John J; Ferenc, Matthew T; Heinrich, Bianca; Jarzylo, Larissa A; Man, Heng-Ye; Deshler, James O (BioMed Central, 2007-7-30)
    BACKGROUND. Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a ...
  • Rachlin, John; Cohen, Dikla Dotan; Cantor, Charles; Kasif, Simon (2006-11-28)
    Network models are a fundamental tool for the visualization and analysis of molecular interactions occurring in biological systems. While broadly illuminating the molecular machinery of the cell, graphical representations ...
  • Giordano, Joti; Ge, Yongchao; Gelfand, Yevgeniy; Abrusán, György; Benson, Gary; Warburton, Peter E (Public Library of Science, 2007-7-13)
    The constant bombardment of mammalian genomes by transposable elements (TEs) has resulted in TEs comprising at least 45% of the human genome. Because of their great age and abundance, TEs are important in comparative ...
  • Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-9-18)
    BACKGROUND. Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is ...
  • Hennessey, Jason; Hill, Chris; Denhardt, Ian; Viggnesh, Venugopal; Silvis, George; Krieger, Orran; Desnoyers, Peter (2014 IEEE High Performance Extreme Computing Conference (HPEC ‘14), 2014-09)
    We describe a “Hardware as a Service (HaaS)” tool for isolating pools of compute, storage and networking resources. The goal of HaaS is to enable dynamic and flexible, user-level provisioning of pools of ...
  • Theriault, Diane H.; Fuller, Nathan W.; Jackson, Brandon E.; Bluhm, Evan; Evangelista, Dennis; Wu, Zheng; Betke, Margrit; Hedrick, Tyson L. (The Company of Biologists, Ltd., 2014-02-27)
    Stereo videography is a powerful technique for quantifying the kinematics and behavior of animals, but it can be challenging to use in an outdoor field setting. We here present a workflow and associated software for ...
  • Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-11-29)
    BACKGROUND. Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network ...
  • Gelfand, Yevgeniy; Rodriguez, Alfredo; Benson, Gary (Oxford University Press, 2006-12-14)
    Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory ...
  • Desnoyers, Peter; Hennessey, Jason; Holden, Brent; Krieger, Orran; Rudolph, Larry; Young, Adam (2015-03)
    We are developing a new public cloud, the Mas- sachusetts Open Cloud (MOC) based on the model of an Open Cloud eXchange (OCX). We discuss in this paper the vision of an OCX and how we ...

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