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IBM Journal of Research and Development

Issue 6 • Nov. 2006

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Displaying Results 1 - 14 of 14
  • Message

    Publication Year: 2006, Page(s):526 - 527
    IEEE is not the copyright holder of this material | PDF file iconPDF (65 KB)
    Freely Available from IEEE
  • Preface

    Publication Year: 2006, Page(s):527 - 528
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (41 KB)

    This issue of the IBM Journal of Research and Development focuses on the growing field of systems biology. While the precise definition of the term “systems biology” is continually undergoing refinement and is open for discussion, researchers agree that the vast quantities of data generated by high-throughput biology, and related techniques used to study living systems, ensure that c... View full abstract»

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  • An assessment of the role of computing in systems biology

    Publication Year: 2006, Page(s):529 - 543
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (205 KB)

    Systems biology is a burgeoning field in which researchers are investigating a flood of new data that is gathered in high-throughput genomics, proteomics, and related analyses. Systems biologists focus on what this data reveals about the functioning of living systems. The large volume of data, and the complexity of living systems, ensures that computing plays a central role in analyzing, modeling,... View full abstract»

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  • Graph data management for molecular and cell biology

    Publication Year: 2006, Page(s):545 - 560
    Cited by:  Papers (2)  |  Patents (2)
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (358 KB)

    As high-throughput biology begins to generate large volumes of systems biology data, the need grows for robust, efficient database systems to support investigations of metabolic and signaling pathways, chemical reaction networks, gene regulatory networks, and protein interaction networks. Network data is frequently represented as graphs, and researchers need to navigate, query and manipulate this ... View full abstract»

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  • The Pathway Editor: A tool for managing complex biological networks

    Publication Year: 2006, Page(s):561 - 573
    Cited by:  Papers (1)
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (369 KB)

    Biological networks are systems of biochemical processes inside a cell that involve cellular constituents such as DNA, RNA, proteins, and various small molecules. Pathway maps are often used to represent the structure of such networks with associated biological information. Several pathway editors exist, and they vary according to specific domains of knowledge. This paper presents a review of exis... View full abstract»

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  • Visualization of complementary systems biology data with parallel heatmaps

    Publication Year: 2006, Page(s):575 - 581
    Cited by:  Papers (1)
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (554 KB)

    The interpretation of large-scale biological data can be aided by the use of appropriate visualization tools. Heatmaps—pattern-revealing aggregate views of data—have emerged as a preferred technique for the display of genomics data, since they provide an extra dimension of information in a two-dimensional display. However, an increasing focus on the integration of data from multiple ... View full abstract»

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  • A spatially detailed myofilament model as a basis for large-scale biological simulations

    Publication Year: 2006, Page(s):583 - 600
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (880 KB)

    The availability of increased computing power will make possible new classes of biological models that include detailed representations of proteins and protein complexes with spatial interactions. We develop such a model of the interaction of actin and myosin within one pair of thick and thin filaments in the cardiac sarcomere. The model includes explicit representations of actin, myosin, and regu... View full abstract»

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  • Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations

    Publication Year: 2006, Page(s):601 - 615
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (309 KB)

    In order to achieve a comprehensive understanding of complex biological systems, researchers must develop new techniques that incorporate key features of the system across all relevant spatial and temporal scales. Recent advances in molecular biology and genetics have generated a wealth of experimental data that provides details with respect to gene-expression patterns and individual gene and prot... View full abstract»

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  • Computational multiscale modeling in the IUPS Physiome Project: Modeling cardiac electromechanics

    Publication Year: 2006, Page(s):617 - 630
    Cited by:  Papers (1)
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (772 KB)

    We present a computational modeling and numerical simulation framework that enables the integration of multiple physics and spatiotemporal scales in models of physiological systems. This framework is the foundation of the IUPS (International Union of Physiological Sciences) Physiome Project. One novel aspect is the use of CellML, an annotated mathematical representation language, to specify model-... View full abstract»

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  • Machine learning methods for transcription data integration

    Publication Year: 2006, Page(s):631 - 643
    Cited by:  Papers (1)
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (257 KB)

    Gene expression is modulated by transcription factors (TFs), which are proteins that generally bind to DNA adjacent to coding regions and initiate transcription. Each target gene can be regulated by more than one TF, and each TF can regulate many targets. For a complete molecular understanding of transcriptional regulation, researchers must first associate each TF with the set of genes that it reg... View full abstract»

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  • Model-based design approaches in drug discovery: A parallel to traditional engineering approaches

    Publication Year: 2006, Page(s):645 - 651
    IEEE is not the copyright holder of this material | Click to expandAbstract | PDF file iconPDF (201 KB)

    Model-based design (MBD) has been successfully applied in the automotive, chemical, and aerospace industries. Here we discuss the possible application of engineering-based MBD approaches to drug discovery. One of the biggest challenges in drug discovery is the high attrition rate of new drugs in development: Many promising candidates prove ineffective or toxic in animal or human testing. More ofte... View full abstract»

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  • Author index for papers in Volume 50

    Publication Year: 2006, Page(s):653 - 657
    IEEE is not the copyright holder of this material | PDF file iconPDF (76 KB)
    Freely Available from IEEE
  • Errata

    Publication Year: 2006, Page(s): 665
    IEEE is not the copyright holder of this material | PDF file iconPDF (82 KB)
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  • Subject index for papers in Volume 50

    Publication Year: 2006, Page(s):659 - 663
    IEEE is not the copyright holder of this material | PDF file iconPDF (67 KB)
    Freely Available from IEEE

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Meet Our Editors

Editor-in-Chief
Clifford A. Pickover
IBM T. J. Watson Research Center