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Bioinformatics, Systems Biology and Intelligent Computing, 2009. IJCBS '09. International Joint Conference on

Date 3-5 Aug. 2009

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Displaying Results 1 - 25 of 129
  • [Front cover]

    Publication Year: 2009, Page(s): C1
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  • [Title page i]

    Publication Year: 2009, Page(s): i
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  • [Title page iii]

    Publication Year: 2009, Page(s): iii
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  • [Copyright notice]

    Publication Year: 2009, Page(s): iv
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  • Table of contents

    Publication Year: 2009, Page(s):v - xiv
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  • Message from General Chair

    Publication Year: 2009, Page(s): xv
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  • Message from Program Chairs

    Publication Year: 2009, Page(s): xvi
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  • Organizing Committee

    Publication Year: 2009, Page(s): xvii
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  • Steering Committee

    Publication Year: 2009, Page(s):xviii - xix
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  • Program Committee

    Publication Year: 2009, Page(s):xx - xxii
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  • list-reviewer

    Publication Year: 2009, Page(s):xxiii - xxiv
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  • Planery Keynote Abstracts

    Publication Year: 2009, Page(s):xxv - xxxvii
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (545 KB)

    Provides an abstract for each of the keynote presentations and a brief professional biography of each presenter. The complete presentations were not made available for publication as part of the conference proceedings. View full abstract»

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  • Gene Selection for Microarray Expression Data with Imbalanced Sample Distributions

    Publication Year: 2009, Page(s):3 - 9
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1104 KB) | HTML iconHTML

    Microarray expression data, which contain expression levels of a large number of simultaneously observed genes, have been used in many scientific research and clinical studies. Due to its high dimensionalities, selecting a small number of genes has shown to be beneficial for tasks such as building prediction models for molecular classification of cancers. Traditional gene selection methods, howeve... View full abstract»

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  • Redundant Gene Selection Based on Particle Swarm Optimization

    Publication Year: 2009, Page(s):10 - 16
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (865 KB) | HTML iconHTML

    Redundant gene selection is an important topic in the field of bioinformatics. This paper proposes a novel algorithm on Redundant Gene Selection by Particle Swarm Optimization (RGS-PSO), which tries to find a compact gene subset with great predictive ability. Compared with the previous works, RGS-PSO measures the redundancy of feature set by the maximum feature inter-correlation, which is more rea... View full abstract»

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  • Investigating Gene and MicroRNA Expression in Glioblastoma

    Publication Year: 2009, Page(s):17 - 22
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1655 KB) | HTML iconHTML

    Glioblastoma is the most common primary brain tumor in adults. Here we present an integrated analysis of microRNA expression and gene expression in 237 tumor tissues and 10 normal tissues. We indentified 1,236 genes, and 131 pathways significantly differentially expressed between tumor and normal tissues. We also indentified 98 differentially expressed microRNAs, 22 of which have been reported to ... View full abstract»

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  • Discovery of Biomarker Genes from Earthworm Microarray Data by Discriminant Analysis and Clustering

    Publication Year: 2009, Page(s):23 - 29
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (451 KB) | HTML iconHTML

    Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. A variety of toxicological effects have been associated with explosive compounds 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX). Here we devel... View full abstract»

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  • PBC: A Software Framework Facilitating Pattern-Based Clustering for Microarray Data Analysis

    Publication Year: 2009, Page(s):30 - 36
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1410 KB) | HTML iconHTML

    Microarray data produces expression pattern of thousands of genes at once. Grouping these gene expression patterns to have each group convey some biologically meaningful sight entails use of a clustering method. Two problems exist when attempting to use conventional clustering methods for the microarray data analysis. Presence of outliers skews the mean value computation which, in turn influences ... View full abstract»

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  • Cross-Domain Neurobiology Data Integration and Exploration

    Publication Year: 2009, Page(s):37 - 43
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1003 KB) | HTML iconHTML

    Understanding the biomedical implications of data from high throughput experiments requires solutions for effective cross-scale and cross-domain data exploration. Our work integrates molecular level data with high level biological functions using anatomical structure as a scaffold. The flex-based pubanatomy Web application we developed enables highly interactive visual exploration of literature an... View full abstract»

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  • Study DNA Microarray Gene Expression Data of Alzheimer's Disease by Independent Component Analysis

    Publication Year: 2009, Page(s):44 - 47
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1053 KB) | HTML iconHTML

    Rapid progress in deciphering the biological mechanism of Alzheimer's disease (AD) has arisen from the application of molecular and cell biology to this complex disorder of the limbic and association cortices. The precise diagnosis of AD, however, has little progress and is also a challenging task. In this study, we investigate the DNA gene expression data of AD based on independent component anal... View full abstract»

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  • Probabilistic Model Based Hough Transform for Detection of Co-expression Patterns in Three-Color cDNA Microarray Data

    Publication Year: 2009, Page(s):48 - 51
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (869 KB) | HTML iconHTML

    Three-color cDNA microarrays built on normal-disease-drug samples can be used to assess the effects of a drug on the genomic scale. We have recently shown that the Hough transform (HT) applied to a two-dimensional representation of the three color intensities can be used to detect groups of co-expressed genes. However, the standard HT is not well suited for the purpose because: (1) the essayed gen... View full abstract»

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  • Multiclass Gene Selection on Microarray Data Using l1-norm Least Square Regression

    Publication Year: 2009, Page(s):52 - 55
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (911 KB) | HTML iconHTML

    A new univariate filter method for multiclass gene selection is proposed based on l1-norm least square regression. The numerical experiment shows that the method is, at least, comparable to two popular methods: ANOVA and BSS/WSS. View full abstract»

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  • Framework for Knowledge-Based Integrative Analysis of Microarray Data

    Publication Year: 2009, Page(s):56 - 59
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1019 KB) | HTML iconHTML

    The whole genome DNA microarrays make it possible to monitor the expression of nearly all the genes in an organism and have been widely used in scientific and industrial fields. The challenges no longer lie in obtaining the data, but rather in interpreting the results to reveal the mechanisms of biological significance. A recent established method GSEA assesses whether priori defined gene sets sho... View full abstract»

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  • Genome Evolution in Malaria Parasites: I. Core Genome Components

    Publication Year: 2009, Page(s):63 - 69
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (978 KB) | HTML iconHTML

    Malaria is one of the most common infectious diseases that affect millions of people globally. It is caused by protozoan parasites in the genus Plasmodium. Existing antimalarials have lost efficacy thanks to the emergence of resistant parasite populations and the incidence of the disease is on the rise. It is believed that the completion of the genome sequence of the human malaria parasite Plasmod... View full abstract»

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  • Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units

    Publication Year: 2009, Page(s):70 - 76
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1028 KB) | HTML iconHTML

    Recent advances in highly parallel, multithreaded, manycore Graphics Processing Units (GPUs) have been enabling massive parallel implementations of many applications in bioinformatics. In this paper, we describe a parallel implementation of genome-wide association studies (GWAS) using Compute Unified Device Architecture (CUDA). Using a single NVIDIA GTX 280 graphics card, we achieve speedups of ab... View full abstract»

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  • Genomic Comparison of Bacterial Species Based on Metabolic Characteristics

    Publication Year: 2009, Page(s):77 - 83
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1412 KB) | HTML iconHTML

    In this work, we developed a novel method to generate comparison trees based on characteristics collected from metabolic networks of bacteria. We characterize each bacterial genomepsilas metabolism by the occurrence frequencies of various chemical reactions classified by enzyme commission numbers, and by the correlation of the reaction types for any two consecutive reactions in pathways present in... View full abstract»

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