Emerging strengths in Asia Pacific bioinformatics

  • Shoba Ranganathan1, 2Email author,

    Affiliated with

    • Wen-Lian Hsu3, 4,

      Affiliated with

      • Ueng-Cheng Yang5 and

        Affiliated with

        • Tin Wee Tan2

          Affiliated with

          BMC Bioinformatics20089(Suppl 12):S1

          DOI: 10.1186/1471-2105-9-S12-S1

          Published: 12 December 2008

          Abstract

          The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20–23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

          Review policy

          Papers submitted to these proceedings were peer-reviewed by at least two reviewers, from the APBioNet/InCoB program committee members and external experts as required (listed in Additional File 1). InCoB2008 also provided multi-track submissions, with the inclusion of new sessions to present research highlights from recent publications and for showcasing technology developments. With tutorials aimed at introducing new concepts and advancing current practices, and a specialist workshop on bioinformatics education, InCoB2008 has achieved the status of a comprehensive international bioinformatics meeting in the Asia Pacific.

          The aim of the editors was to select only the best papers from more than a dozen Asia Pacific countries. From the 47 full paper submissions, 33 were short listed for oral presentation. This supplement features 24 papers, reflecting an overall acceptance rate of 51%, with seven more appearing in the online journal, Bioinformation [15]. The impressive extent of collaboration in bioinformatics research in the region is demonstrated by the permutations of co-authorship, variously involving papers from Australia, China, Hong Kong, India, Japan, Korea, Singapore, Taiwan, Thailand, UK and USA. A brief review of the various themes follows.

          MicroRNAs

          The discovery in 2004 of very short regulatory RNA segments, termed micro RNAs (miRNAs), has provoked intense research. Chang et al. [16] propose a novel relaxed variable kernel density estimator for predicting species-specific miRNA precursors, particularly suited to taxa distant from humans. The identification of false positives from such predictions is provided by Leung et al. [17], using a clustering approach. The biomolecules that these miRNAs bind to are predicted accurately by the support vector machine classification method of Yang et al. [18] while Tran et al. [19] explore the regulatory networks controlled by miRNAs.

          Transcriptome analysis

          The regulatory role of RNAs is dependent on their binding to specific proteins. Cheng et al. [20] present a novel position-specific scoring matrix method, of high sensitivity, for predicting the RNA-binding sites on proteins. Transcription regulation depends on the binding of several factors based on the presence of distinct signal regions. Lu et al. [21] propose a new algorithm to extract these transcription factor binding sites from a set of unaligned gene sequences. Eukaryotic genes are assembled from a set of exons, from which the intervening intronic elements have been spliced out. A new feature-based splice site detection method has been developed by Baten et al. [22] to accurately delineate the architecture of a multi-exonic gene.

          SNPs

          Single nucleotide polymorphisms (SNPs) are key elements in genomics research, importantly for correlating genetic variations with disease outcomes. VarDetect (Ngamphiw et al. [23]) is a new generation tool for the accurate detection of SNPs, while the functional implications of these variations can be assessed using FANS (Liu et al. [24]).

          Protein analysis

          Understanding protein interactions and networks can provide a deep insight into the functions of biological molecules generally. Lee et al. [25] have extended our knowledge of protein interactions to 18 species, using orthologous interacting pairs. Interactions between proteins are characterized by the surface features of their three dimensional structures. Chang et al. [26] propose a new approach to compute protein solvent accessibility, which will facilitate protein tertiary structure prediction from sequence. The conservation of functional residues in a protein or a domain is critical to maintaining biological function. The evolutionary forces acting on mutation sites can be appraised with WPSMaker (Lee et al. [27]). The functional significance of active site residues in an enzyme has been explored by in silico ligand docking by Gowthaman et al. [28], in the interests of developing anti-HIV drugs.

          Protein trafficking

          Proteins are functional only if they are transported to specific cellular compartments. Choo and Ranganathan [29] report the involvement of flanking residues from the mature protein moiety in a large-scale analysis of experimentally validation secretory signal peptides, while Mizuno et al. [30] have experimentally evaluated predicted peroxisomal targeting signals.

          Systems biology

          Temporal changes in the interactions and concentrations of biological molecules are critical to systems biology. Using model systems, Wu et al. [31] present a new approach to dynamic sensitivity analysis.

          Immunoinformatics

          As part of our quest to efficiently address healthcare issues, delving through the ever-increasing biomedical literature presents an immense challenge. Tsai et al [32] propose a new system to convert their machine-learning based text analysis output into standardized biomedical annotations. Yang et al. [33] have compiled a database linking genetic variations to disease, while Wang et al. [34] address the issue of immunoglobulin heavy chain diversity to allow understanding antibody maturation and antibody-based therapy design. Lim et al. [35] propose a new method for predicting the allergenicity of a protein from its sequence information while Lin et al. [36] have evaluated the efficacy of available major histocompatibility complex Class II peptide binding prediction servers for effective vaccine design. Hsu et al. [37] have combined candidate disease gene information for genetic studies with protein interaction networks to propose a pathogenetic disease model for schizophrenia.

          Biodiversity informatics

          The application of bioinformatics approaches to data from several other areas such as biodiversity and ecology is only logical [9]. In this area, Lim et al. [38] have developed an integrated Korean biodiversity and genetic information retrieval system to link species information with molecular data. Gaikwad et al. [39] have created a customary medicinal plant knowledge base, impressively integrating taxonomy, phytochemistry, biogeography and the biological activities of customary medicinal plant species with chemoinformatics, to facilitate the discovery of novel bioactive compounds.

          Conclusion

          Considering the scope and depth of topics covered in this issue, Asia Pacific bioinformatics research has maintained its level of research achievement, previously set with high standards in 2006. This area is now acknowledged to be a core research discipline in our educational and research institutions. The efforts expended into setting up the bioinformatics resource infrastructure have started to yield dividends, with a number of papers bearing the names of graduate research students as first authors.

          Further, bioinformatics is now considered essential to provide substantial support to genomics and health research, as reported by workers from Thailand [40]. Regional meetings such as the recent Second ASEAN-China International Bioinformatics Workshop and the Third East Asia Bioinformation Network meeting [41], held in Singapore in 2008, focus on specific applications of local relevance and cooperation, such as bioinformatics in traditional medicines and in emerging infectious diseases. Such endeavours are essential in addressing issues on human resource development in bioinformatics and in combating global health threats. After 10 years, APBioNet is well positioned "to foster the growth of Bioinformatics and its allied disciplines in the Asia Pacific" [2], and to sustain a new generation of researchers in the 'post-omic' era.

          Declarations

          Acknowledgements

          We are grateful for the local organizers of the InCoB2008 conference, especially Ms Serena Lee, National Yang-Ming University, Taipei, Taiwan. We thank the referees for their dedication and effort in reviewing the manuscripts and Dr John Candlish for his editorial assistance. We also thank BMC Bioinformatics for their support and encouragement.

          This article has been published as part of BMC Bioinformatics Volume 9 Supplement 12, 2008: Asia Pacific Bioinformatics Network (APBioNet) Seventh International Conference on Bioinformatics (InCoB2008). The full contents of the supplement are available online at http://​www.​biomedcentral.​com/​1471-2105/​9?​issue=​S12.

          Authors’ Affiliations

          (1)
          Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University
          (2)
          Department of Biochemistry, Yong Loo Lin School of Medicine, National, University of Singapore
          (3)
          Institute of Information Science, Academia Sinica, Nankang
          (4)
          Department of Computer Science, National Tsing-Hua University
          (5)
          Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University

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          Copyright

          © Ranganathan et al. 2008

          This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.