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InCoB2012 Conference: from biological data to knowledge to technological breakthroughs.

ABSTRACT: Ten years ago when Asia-Pacific Bioinformatics Network held the first International Conference on Bioinformatics (InCoB) in Bangkok its theme was North-South Networking. At that time InCoB aimed to provide biologists and bioinformatics researchers in the Asia-Pacific region a forum to meet, interact with, and disseminate knowledge about the burgeoning field of bioinformatics. Meanwhile InCoB has evolved into a major regional bioinformatics conference that attracts not only talented and established scientists from the region but increasingly also from East Asia, North America and Europe. Since 2006 InCoB yielded 114 articles in BMC Bioinformatics supplement issues that have been cited nearly 1,000 times to date. In part, these developments reflect the success of bioinformatics education and continuous efforts to integrate and utilize bioinformatics in biotechnology and biosciences in the Asia-Pacific region. A cross-section of research leading from biological data to knowledge and to technological applications, the InCoB2012 theme, is introduced in this editorial. Other highlights included sessions organized by the Pan-Asian Pacific Genome Initiative and a Machine Learning in Immunology competition. InCoB2013 is scheduled for September 18-21, 2013 at Suzhou, China.

SUBMITTER: Schonbach C

PROVIDER: S-EPMC3521245 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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InCoB2012 Conference: from biological data to knowledge to technological breakthroughs.

Schönbach Christian C Tongsima Sissades S Chan Jonathan J Brusic Vladimir V Tan Tin Wee TW Ranganathan Shoba S

BMC bioinformatics 20121213

Ten years ago when Asia-Pacific Bioinformatics Network held the first International Conference on Bioinformatics (InCoB) in Bangkok its theme was North-South Networking. At that time InCoB aimed to provide biologists and bioinformatics researchers in the Asia-Pacific region a forum to meet, interact with, and disseminate knowledge about the burgeoning field of bioinformatics. Meanwhile InCoB has evolved into a major regional bioinformatics conference that attracts not only talented and establish ...[more]

PMID: 23281929

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Project description:Background: Many tools used to analyze microarrays in different conditions have been described. However, the integration of the deregulated genes within coherent metabolic pathways is lacking. Currently no objective selection criterion, based on biological functions exists, to determine a threshold demonstrating that a gene is indeed differentially expressed. Methodology/Principal Findings: To improve transcriptomic analysis of microarrays, we propose a new statistical approach, which takes into account biological parameters. We present an iterative method to optimise the selection of differentially expressed gene in two experimental conditions. The stringency level of gene selection was associated simultaneously with the p-value of expression variation and the occurrence rate parameter, which is associated with the percentage of donors whose transcriptomic profile is similar. Our method intertwines stringency level settings, biological data and a knowledge database to highlight molecular interactions using networks and pathways. Analysis performed during iterations helped us select the optimal threshold required for the most pertinent selection of differently expressed genes. Conclusions/significance: We have applied this approach to the well documented mechanism of human macrophage response to lipopolysaccharide stimulation. For example, we thus verified that our method was able to determine with the highest degree of accuracy the best threshold for selecting genes, which are truly differentially expressed. Macrophages isolated from six heathy donnor was/or not stimulated. Paired data, i.e. LPS stimulated macrophages versus unstimulated macrophages from the same donor have been compared (eg, Donor1_LPS vs Donor1_NT; see processed data file linked below). The six comparaisons have been globaly analyse using two parameters, i.e. threshod and occurency, associated with a request of a database knowledge. Both parameters has been tune to define the best setting allowing to optimize the selection of differentially expressed genes

Dataset Information

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs.

Publications

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs.

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