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检索条件"任意字段=Proceedings of the IEEE Computational Systems Bioinformatics Conference, CSB"

共 409 条记录，以下是81-90 订阅

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A Scalable Architecture for Intrusion-Detection systems Based on a Broadband Network of Embedded Set-Top Boxes

A Scalable Architecture for Intrusion-Detection Systems Base...

引用

54th ieee International Midwest Symposium on Circuits and systems (MWSCAS)

作者： Neill, Richard Carloni, Luca P. Columbia Univ Dept Comp Sci New York NY 10027 USA

ISBN: (纸本)9781612848570

As the processing power of set-top box (STB) devices continnes to grow with each new product generation and multiple service operators directly manage millions of these devices through a dedicated broadband network, we propose to harness this massive aggregate computational power to execute large-scale parallel applications. We present a prototype implementation of a heterogeneous distributed embedded system that combines a complete head-end cable system with a DOCSIS broadband network of STBs and an interoperable embedded implementation of Open MPI running on the STB operating system. We demonstrate the operations and performance of this system by reporting the experimental results that we obtained for the execution of various instances of Multiple Sequence Alignment, a parallel bioinformatics application. Based on these results we propose a new distributed embedded system architecture for highly-scalable intrusion-detection systems.

关键词： Broadband communication DOCSIS broadband network Frequency modulation Linux Radio frequency Servers Transform coding bioinformatics bioinformatics application computer networks dedicated broadband network embedded set-top boxes embedded systems head end cable system heterogeneous distributed embedded system intrusion detection systems large scale parallel applications massive aggregate computational power multiple sequence alignment scalable architecture security of data set-top boxes

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Exploring the use of stem-loop characteristics for pinpointing structural RNA genes

Exploring the use of stem-loop characteristics for pinpointi...

引用

proceedings of the ieee computational systems bioinformatics conference, csb

作者： K. Noel K.C. Wiese School of Interactive Arts and Technology Simon Fraser University Surrey BC Canada

Our goal is to determine whether a stem-loop metric or combination of stem-loop metrics can be used to identify structural RNAs along genomic sequences across the entire GC content spectrum. Herein we describe the first step towards this goal by comparing selected stem-loop metric valuations between structural RNAs and their genomic counterparts.

关键词： RNA bioinformatics Genomics Sequences Art Cities and towns Road transportation Cost accounting Energy measurement Displays

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Mining estrogen microarray data: an approach using contrast data analysis

Mining estrogen microarray data: an approach using contrast ...

引用

proceedings of the ieee computational systems bioinformatics conference, csb

作者： Haili Jiao Peixin Yang Zhengxin Chen Department of Computer Science University of Nebraska Omaha USA Department of OB/GYN University of Nebraska Medical Center USA

Estrogen is a steroid hormone, secreted by ovarian antral follicles, which regulates divergent functions of ovarian granulosa cells ranging from differentiation, apoptosis and proliferation. Cellular signals of estrogen are transduced by its cohort receptors. Estrogen receptors belong to nuclear receptor superfamily and comprise two subtypes, namely, estrogen receptor alpha (ER-a) and estrogen receptor beta (ER-ß).

关键词： Data mining Data analysis Computer science bioinformatics Phased arrays Erbium Biochemistry Breast cancer Prostate cancer RNA

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Using Clouds for Metagenomics: A Case Study

Using Clouds for Metagenomics: A Case Study

引用

ieee International conference on Cluster Computing (Cluster 2009)

作者： Wilkening, Jared Wilke, Andreas Desai, Narayan Meyer, Folker Argonne Natl Lab Div Math & Comp Sci Argonne IL 60439 USA

ISBN: (纸本)9781424450114

Cutting-edge sequencing systems produce data at a prodigious rate;and the analysis of these datasets requires significant computing resources. Cloud computing provides a tantalizing possibility for on-demand access to computing resources. However, many open questions remain. We present here a performance assessment of BLAST on real metagenomics data in a cloud setting, in order to determine the viability of this approach. BLAST is one of the premier applications in bioinformatics and computational biology and is assumed to consume the vast majority of resources in that area.

关键词： bioinformatics

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Inferring genetic networks from microarray data

Inferring genetic networks from microarray data

引用

proceedings of the ieee computational systems bioinformatics conference, csb

作者： S. Martin G. Davidson E. May J.-L. Faulon M. Werner-Washburne Computational Biology Sandia National Laboratories Albuquerque NM USA Department of Biology University of New Mexico Albuquerque NM USA

In theory, it should be possible to infer realistic genetic networks from time series microarray data. In practice, however, network discovery has proved problematic. The three major challenges are 1) inferring the network; 2) estimating the stability of the inferred network; and 3) making the network visually accessible to the user. Here we describe a method, tested on publicly available time series microarray data, which addresses these concerns.

关键词： Genetics Inference algorithms Clustering algorithms Partitioning algorithms Stability bioinformatics Logic Laboratories computational biology Testing

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Gene length and alternative transcription in fruit fly

Gene length and alternative transcription in fruit fly

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： B. Budagyan A. Loraine University of Alabama Birmingham UK

Alternative transcription, in which a single gene may give rise to multiple variant mRNA forms, is widely recognized as an important source of protein diversity in complex, eukaryotic genomes. Here we show that in the Drosophila genome, larger genes with greater numbers of exons tend to be alternatively transcribed to a greater degree than smaller genes with fewer exons. In addition, we show that a log-normal distribution provides a good approximation for gene length distributions in Drosophila and that an exponential function relates the number of variants produced per gene with average exon count.

关键词： bioinformatics Genomics Testing Proteins Statistical distributions Data mining Data processing Computer languages Log-normal distribution Shape

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Multiple RNA structure alignment

Multiple RNA structure alignment

引用

proceedings of the ieee computational systems bioinformatics conference, csb

作者： Zhuozhi Wang Kaizhong Zhang Experimental Therapeutics Research University Heath Network Toronto ONT Canada Department of Computer Science University of Western Ontario London ONT Canada

RNA structures can be viewed as a kind of special strings with some characters bonded with each other. The question of aligning two RNA structures has been studied for a while, and there are several successful algorithms that are based upon different models. In this paper, by adopting the model introduced in a paper by Z. Wang et al. (2001) we propose two algorithms to attack the question of aligning multiple RNA structures. We reduce the multiple RNA structure alignment problem to the problem of aligning two RNA structure alignments.

关键词： RNA Sequences Biological system modeling DNA Proteins bioinformatics Computer science Bonding Councils Displays

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Probabilistic consistency analysis for gene selection

Probabilistic consistency analysis for gene selection

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： S. Mukherjee S.J. Roberts Department of Engineering Science University of Oxford Oxford UK

A great deal of recent research has focused on the problem of selecting differentially expressed genes from microarray data ('gene selection'). Recent theoretical work has shown that the effectiveness of a gene selection algorithm can be captured as a probability called 'selection accuracy'. Unfortunately, in practice, there tends to be relatively little known about the very features upon which selection accuracy depends, making it difficult to choose a suitable method. In this paper we present a 'consistency analysis' which allows the inference of posterior distributions over selection accuracy from data. The utility of our approach lies in the fact that it can be used to assess gene selection algorithms in a practical but principled manner, and thus choose an appropriate method for given experimental data.

关键词： Inference algorithms bioinformatics Biological systems Data engineering Graphical models Statistics

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A rule-based framework for gene regulation pathways discovery

A rule-based framework for gene regulation pathways discover...

引用

ieee conference on bioinformatics

作者： B. Wilczynski T. Hvidsten A. Kryshtafovych L. Stubbs J. Komorowski K. Fidelis University of Warmia and Mazury Warsaw Poland Lawrence Livermore National Laboratories Livermore CA USA Linnaeus Centre for Bioinformatics Uppsala Sweden

We present a novel approach for rule discovery in the area of gene regulation. The method is based on supervised machine learning and is designed to reveal relationships between transcription factors and gene expression. As a representation of the gene regulatory circuit we have chosen a special form of the IF-THEN rules associating predefined features, taken here as a generalized idea of transcription factor binding sites in gene regulatory regions, with the corresponding gene expression profiles.

关键词： bioinformatics

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Eulerian path methods for multiple sequence alignment

Eulerian path methods for multiple sequence alignment

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ieee conference on bioinformatics

作者： M.S. Waterman Y. Zhang Department of Biological Science University of Southern California Los Angeles CA USA Department of Mathematics University of Southern California Los Angeles CA USA

With the rapid increase in the size of genome sequence databases, the multiple sequence alignment problem is increasingly important and often requires the alignment of a large number of sequences. Beginning in 1975, many heuristic algorithms have been created to improve the speed of computation and the quality of alignment. We introduce a novel approach that is fundamentally distinct from all currently available methods. Our motivation comes from the Eulerian method for fragment assembly in DNA sequence determination, that transforms all the DNA sequencing fragments into a de Bruijn graph and then reduces sequence assembly to a Eulerian path problem.

关键词： Sequences DNA bioinformatics Assembly Biology Mathematics Genomics Databases Heuristic algorithms computational modeling

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