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Proceedings of the IEEE

Issue 8 • Date Aug. 2008

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Displaying Results 1 - 21 of 21
  • [Front cover]

    Publication Year: 2008, Page(s): C1
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  • Proceedings of the IEEE publication information

    Publication Year: 2008, Page(s): C2
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  • Table of contents

    Publication Year: 2008, Page(s):1245 - 1246
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  • The Quantum Limit to Moore's Law

    Publication Year: 2008, Page(s):1247 - 1248
    Cited by:  Papers (5)
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    Freely Available from IEEE
  • Editorial to the Special Issue on Computational Systems Biology

    Publication Year: 2008, Page(s):1249 - 1253
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  • CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

    Publication Year: 2008, Page(s):1254 - 1265
    Cited by:  Papers (54)  |  Patents (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1379 KB) | HTML iconHTML

    Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed a modeling/simulating tool called CellDesigner. CellDesigner primarily has capabilities to visualize, model, and simulate gene-regulatory and biochemical networks. Two major characteristics embedded in CellDesigner boost i... View full abstract»

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  • The Simbios National Center: Systems Biology in Motion

    Publication Year: 2008, Page(s):1266 - 1280
    Cited by:  Papers (20)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1566 KB) | HTML iconHTML

    Physics-based simulation is needed to understand the function of biological structures and can be applied across a wide range of scales, from molecules to organisms. Simbios (the national center for physics-based simulation of biological structures, http://www.simbios.stanford.edu/</weblink>) is one of seven NIH-supported national centers for biomedical computation. This article provides an ... View full abstract»

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  • Multigraph Conditions for Multistability, Oscillations and Pattern Formation in Biochemical Reaction Networks

    Publication Year: 2008, Page(s):1281 - 1291
    Cited by:  Papers (7)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (476 KB) | HTML iconHTML

    We represent interactions among biochemical species using a directed multigraph, which is a generalization of a more commonly used digraph. We show that network properties that are known to lead to multistability or oscillations, such as the existence of a positive feedback cycle, can be generalized to ldquocritical subnetworksrdquo that can contain several cycles. We also derive corresponding gra... View full abstract»

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  • The Future of Large-Scale Collaborative Proteomics

    Publication Year: 2008, Page(s):1292 - 1309
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1107 KB) | HTML iconHTML

    The postgenomics era has witnessed a rapid change in biological methods for knowledge elucidation and pharmacological approaches to biomarker discovery. Differential expression of proteins in health and disease holds the key to early diagnosis and accelerated drug discovery. This approach, however, has also brought an explosion of data complexity not mirrored by existing progress in proteome infor... View full abstract»

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  • Computational Systems Bioinformatics and Bioimaging for Pathway Analysis and Drug Screening

    Publication Year: 2008, Page(s):1310 - 1331
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2590 KB) | HTML iconHTML

    The premise of today's drug development is that the mechanism of a disease is highly dependent upon underlying signaling and cellular pathways. Such pathways are often composed of complexes of physically interacting genes, proteins, or biochemical activities coordinated by metabolic intermediates, ions, and other small solutes and are investigated with molecular biology approaches in genomics, pro... View full abstract»

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  • Fuzzy Fractal Analysis of Molecular Imaging Data

    Publication Year: 2008, Page(s):1332 - 1347
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1714 KB) | HTML iconHTML

    Recent advances in biomedicine, pharmacology, and biotechnology open doors to the understanding how diseases are developed at the molecular and physiological level. This gain of understanding tremendously helps facilitate the design and discovery of drugs for therapeutic treatment. Despite the advances in the technology and new knowledge in systems biology, drug discovery is still a low process wi... View full abstract»

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  • Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods

    Publication Year: 2008, Page(s):1348 - 1360
    Cited by:  Papers (6)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (936 KB) | HTML iconHTML

    Automated image analysis provides a powerful tool when quantifying various characteristics of cell populations. Previously, the validation of image analysis results has been a task of expert biologist, who has manually analyzed the images and provided the ground truth to which the proposed analysis results have been compared. The traditional validation approach, prone to errors and variation, is u... View full abstract»

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  • Modeling and Analyzing Biological Oscillations in Molecular Networks

    Publication Year: 2008, Page(s):1361 - 1385
    Cited by:  Papers (16)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (747 KB) | HTML iconHTML

    One of the major challenges for postgenomic biology is to understand how genes, proteins, and small molecules dynamically interact to form molecular networks which facilitate sophisticated biological functions. In this paper, we present a survey on recent developments on modelling molecular networks and analyzing synchronization of bio-oscillators in multicellular systems from the viewpoint of sys... View full abstract»

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  • Signals and Systems: Towards a Systems Biology of Signal Transduction

    Publication Year: 2008, Page(s):1386 - 1397
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (531 KB) | HTML iconHTML

    Systems biology seeks to understand how the behavior of cells and organisms arises from the collective interactions of their component molecules. I will discuss how signal transduction- the process by which cells sense and respond to external signals - is being reconsidered from a systems perspective. This relies on ideas and concepts from the physical sciences coupled to new experimental strategi... View full abstract»

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  • Stability and Time-Delay Modeling of Negative Feedback Loops

    Publication Year: 2008, Page(s):1398 - 1410
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (613 KB) | HTML iconHTML

    Negative feedback loops are a common cellular motif underlying many important gene regulation pathways, and therefore a clear understanding of their dynamics is important for the study of gene regulation. Here we analyze the linear stability of negative feedback loops with and without explicit time delays. When the degradation rates of each loop component are identical, we derive the analytical so... View full abstract»

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  • Centrality, Network Capacity, and Modularity as Parameters to Analyze the Core-Periphery Structure in Metabolic Networks

    Publication Year: 2008, Page(s):1411 - 1420
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1696 KB) | HTML iconHTML

    Genome-scale metabolic networks of organisms are normally very large and complex. Previous studies have shown that they are organized in a hierarchical and modular manner. In particular, a core-periphery modular organization structure has been proposed for metabolic networks. However, no methods or parameters are available in the literature to quantitatively evaluate or find the hierarchical and m... View full abstract»

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  • The Lymph Node B Cell Immune Response: Dynamic Analysis In-Silico

    Publication Year: 2008, Page(s):1421 - 1443
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (3610 KB) | HTML iconHTML Multimedia Media

    Lymph nodes are organs in which lymphocytes respond to antigens to generate, among other cell types, plasma cells that secrete specific antibodies and memory lymphocytes for enhanced future responses to the antigen. To achieve these ends, the lymph node (LN) has to orchestrate the meeting and interactions between the antigen and various cell types including the rare clones of B cells and T cells b... View full abstract»

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  • Electrical Engineering Hall of Fame: Dugald C. Jackson

    Publication Year: 2008, Page(s):1444 - 1446
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    Freely Available from IEEE
  • Future Special Issues/Special Sections of the Proceedings

    Publication Year: 2008, Page(s):1447 - 1448
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    Freely Available from IEEE
  • IEEE Potentials is looking for article submissions

    Publication Year: 2008, Page(s): C3
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  • [Back cover]

    Publication Year: 2008, Page(s): C4
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Aims & Scope

The most highly-cited general interest journal in electrical engineering and computer science, the Proceedings is the best way to stay informed on an exemplary range of topics.

Full Aims & Scope

Meet Our Editors

Editor-in-Chief
H. Joel Trussell
North Carolina State University