IEEE Transactions on NanoBioscience

Issue 3 • Sept. 2004

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  • Table of contents

    Publication Year: 2004, Page(s): c1
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  • IEEE Transactions on NanoBioscience publication information

    Publication Year: 2004, Page(s): c2
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  • Guest Editorial Special Section on Molecular and Cellular Systems Biology

    Publication Year: 2004, Page(s):141 - 143
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  • Computational approach to systems biology: from fraction to integration and beyond

    Publication Year: 2004, Page(s):144 - 152
    Cited by:  Papers (14)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (526 KB) | HTML iconHTML

    Systems biology is an approach to understanding the workings of whole biological systems. The various methods used for systems analyses range from experimental to computational. In this paper, we describe basic concepts of systems biology, modeling challenges that arise from the massively parallel interaction among components in biological systems, and what lies beyond integration of modular knowl... View full abstract»

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  • Agent-based computational modeling of wounded epithelial cell monolayers

    Publication Year: 2004, Page(s):153 - 163
    Cited by:  Papers (70)  |  Patents (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1317 KB) | HTML iconHTML

    Computational modeling of biological systems, or in silico biology, is an emerging tool for understanding structure and order in biological tissues. Computational models of the behavior of epithelial cells in monolayer cell culture have been developed and used to predict the healing characteristics of scratch wounds made to urothelial cell cultures maintained in low- and physiological [Ca2+ View full abstract»

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  • Towards cooperative frameworks for modeling and integrating biological processes knowledge

    Publication Year: 2004, Page(s):164 - 171
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (173 KB) | HTML iconHTML

    Data organization has become a strategic target for biologists due to the increasing volume of genomic data available for them. For this purpose, we need a complete knowledge model for representing biological system. In this paper, we deal with both processes for the creation and integration of shareable, reusable domain models within biology, which is a critical issue. In particular, this work in... View full abstract»

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  • Mathematical modeling of complex regulatory networks

    Publication Year: 2004, Page(s):172 - 179
    Cited by:  Papers (12)  |  Patents (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (289 KB) | HTML iconHTML

    Cellular regulation comprises overwhelmingly complex interactions between genes and proteins that ultimately will only be rendered understandable by employing formal approaches. Developing large-scale mathematical models of such systems in an efficient and reliable way, however, requires careful evaluation of structuring principles for the models, of the description of the system dynamics, and of ... View full abstract»

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  • Hunting drug targets by systems-level modeling of gene expression profiles

    Publication Year: 2004, Page(s):180 - 191
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2152 KB) | HTML iconHTML

    Structural learning of Bayesian networks applied to sets of genome-wide expression patterns has been recently discovered as a potentially useful tool for the systems-level statistical description of gene interactions. We train and analyze Bayesian networks with the goal of inferring biological aspects of gene function. Our two-component approach focuses on supporting the drug discovery process by ... View full abstract»

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  • Web-based information retrieval system for the prediction of metabolic pathways

    Publication Year: 2004, Page(s):192 - 199
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (448 KB) | HTML iconHTML

    Analysis of metabolic pathways is a central topic in understanding the relationship between genotype and phenotype. The rapid accumulation of biological data provides the possibility of studying metabolic pathways both at the genomic and metabolic levels. Our motivation is to develop a conceptual framework and computational system that will allow retrieval of metabolic information and prediction o... View full abstract»

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  • Modeling and simulation of intracellular dynamics: choosing an appropriate framework

    Publication Year: 2004, Page(s):200 - 207
    Cited by:  Papers (63)  |  Patents (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (236 KB) | HTML iconHTML

    Systems biology is a reemerging paradigm which, among other things, focuses on mathematical modeling and simulation of biochemical reaction networks in intracellular processes. For most simulation tools and publications, they are usually characterized by either preferring stochastic simulation or rate equation models. The use of stochastic simulation is occasionally accompanied with arguments agai... View full abstract»

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  • Evolvable social agents for bacterial systems modeling

    Publication Year: 2004, Page(s):208 - 216
    Cited by:  Papers (13)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1088 KB) | HTML iconHTML

    We present two approaches to the individual-based modeling (IbM) of bacterial ecologies and evolution using computational tools. The IbM approach is introduced, and its important complementary role to biosystems modeling is discussed. A fine-grained model of bacterial evolution is then presented that is based on networks of interactivity between computational objects representing genes and protein... View full abstract»

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  • Dynamic ion channel activation scheduling in patch clamp on a chip

    Publication Year: 2004, Page(s):217 - 224
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (270 KB) | HTML iconHTML

    In 2002, Fertig et al. made a remarkable invention: the first successful demonstration of a patch clamp on a chip-a planar quartz-based biological chip that contains up to several hundred ion channels. This patch-clamp chip can be used in massively parallel screens for ion channel activity, thereby providing a high-throughput screening tool for drug discovery efforts. In this paper, we propose com... View full abstract»

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  • Electric fields within cells as a function of membrane resistivity-a model study

    Publication Year: 2004, Page(s):225 - 231
    Cited by:  Papers (9)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (477 KB) | HTML iconHTML

    Externally applied electric fields play an important role in many therapeutic modalities, but the fields they produce inside cells remain largely unknown. This study makes use of a three-dimensional model to determine the electric field that exists in the intracellular domain of a 10-μm spherical cell exposed to an applied field of 100 V/cm. The transmembrane potential resulting from the applie... View full abstract»

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  • Special issue on ion channels–bio-nanotubes

    Publication Year: 2004, Page(s): 232
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  • Special issue on biophotonics

    Publication Year: 2004, Page(s): 233
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  • The 2nd International Neural Conference on Engineering

    Publication Year: 2004, Page(s): 234
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  • IEEE-EMBS Special Topic Conference on Microtechnologies in Medicine and Biology

    Publication Year: 2004, Page(s): 235
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  • 27th Annual International Conference of the IEEE Engineering in Medicine and Biology Society

    Publication Year: 2004, Page(s): 236
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  • IEEE Transactions on NanoBioscience Information for authors

    Publication Year: 2004, Page(s): c3
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  • Blank page [back cover]

    Publication Year: 2004, Page(s): c4
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Aims & Scope

The IEEE Transactions on NanoBioscience publishes basic and applied papers dealing both with engineering, physics, chemistry, modeling and computer science and with biology and medicine with respect to molecules, cells, tissues. The content of acceptable papers ranges from practical/clinical/environmental applications to formalized mathematical theory.

Full Aims & Scope

Meet Our Editors

Editor-in-Chief
Henry Hess
Department of Biomedical Engineering
Columbia University