Volume 7 Supplement 5

APBioNet - Fifth International Conference on Bioinformatics (InCoB2006)


Edited by Shoba Ranganathan, Martti Tammi, Michael Gribskov, Tin Wee Tan

International Conference in Bioinformatics - InCoB2006.

New Delhi, India

18-20 December 2006

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  1. Introduction

    Establishing bioinformatics research in the Asia Pacific

    In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able t...

    Shoba Ranganathan, Martti Tammi, Michael Gribskov and Tin Wee Tan

    BMC Bioinformatics 2006 7(Suppl 5):S1

    Published on: 18 December 2006

  2. Proceedings

    Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus

    Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antig...

    Asif M Khan, AT Heiny, Kenneth X Lee, KN Srinivasan, Tin Wee Tan, J Thomas August and Vladimir Brusic

    BMC Bioinformatics 2006 7(Suppl 5):S4

    Published on: 18 December 2006

  3. Proceedings

    Projections for fast protein structure retrieval

    In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly impor...

    Sourangshu Bhattacharya, Chiranjib Bhattacharyya and Nagasuma R Chandra

    BMC Bioinformatics 2006 7(Suppl 5):S5

    Published on: 18 December 2006

  4. Proceedings

    Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris

    Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503. The target antigen of PV, des...

    Joo Chuan Tong, Tin Wee Tan, Animesh A Sinha and Shoba Ranganathan

    BMC Bioinformatics 2006 7(Suppl 5):S7

    Published on: 18 December 2006

  5. Proceedings

    Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes

    Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect th...

    Manisha Brahmachary, Christian Schönbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, SPT Krishnan, Chin-Yo Lin, David A Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki and Vladimir B Bajic

    BMC Bioinformatics 2006 7(Suppl 5):S8

    Published on: 18 December 2006

  6. Proceedings

    NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition

    Biomedical named entity recognition (Bio-NER) is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes) do not follow one standard nomenclature. Th...

    Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung and Wen-Lian Hsu

    BMC Bioinformatics 2006 7(Suppl 5):S11

    Published on: 18 December 2006

  7. Proceedings

    Curation of viral genomes: challenges, applications and the way forward

    Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targete...

    Urmila Kulkarni-Kale, Shriram G Bhosle, G Sunitha Manjari, Manali Joshi, Sandeep Bansode and Ashok S Kolaskar

    BMC Bioinformatics 2006 7(Suppl 5):S12

    Published on: 18 December 2006

  8. Proceedings

    Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

    Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diver...

    HH Lin, LY Han, HL Zhang, CJ Zheng, B Xie, ZW Cao and YZ Chen

    BMC Bioinformatics 2006 7(Suppl 5):S13

    Published on: 18 December 2006

  9. Proceedings

    SVM-based prediction of caspase substrate cleavage sites

    Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of such cleavage sites will...

    Lawrence JK Wee, Tin Wee Tan and Shoba Ranganathan

    BMC Bioinformatics 2006 7(Suppl 5):S14

    Published on: 18 December 2006

  10. Proceedings

    Splice site identification using probabilistic parameters and SVM classification

    Recent advances and automation in DNA sequencing technology has created a vast amount of DNA sequence data. This increasing growth of sequence data demands better and efficient analysis methods. Identifying ge...

    AKMA Baten, BCH Chang, SK Halgamuge and Jason Li

    BMC Bioinformatics 2006 7(Suppl 5):S15

    Published on: 18 December 2006

    The Erratum to this article has been published in BMC Bioinformatics 2007 8:241

  11. Proceedings

    SPIDer: Saccharomyces protein-protein interaction database

    Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an ...

    Xiaomei Wu, Lei Zhu, Jie Guo, Cong Fu, Hongjun Zhou, Dong Dong, Zhenbo Li, Da-Yong Zhang and Kui Lin

    BMC Bioinformatics 2006 7(Suppl 5):S16

    Published on: 18 December 2006

  12. Proceedings

    Modelling study of dimerization in mammalian defensins

    Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are con...

    Anita Suresh and Chandra Verma

    BMC Bioinformatics 2006 7(Suppl 5):S17

    Published on: 18 December 2006

  13. Proceedings

    Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology

    Proteins control and mediate many biological activities of cells by interacting with other protein partners. This work presents a statistical model to predict protein interaction networks of Drosophila melanogast...

    Chung-Yen Lin, Shu-Hwa Chen, Chi-Shiang Cho, Chia-Ling Chen, Fan-Kai Lin, Chieh-Hua Lin, Pao-Yang Chen, Chen-Zen Lo and Chao A Hsiung

    BMC Bioinformatics 2006 7(Suppl 5):S18

    Published on: 18 December 2006

  14. Proceedings

    An evaluation of human protein-protein interaction data in the public domain

    Protein-protein interaction (PPI) databases have become a major resource for investigating biological networks and pathways in cells. A number of publicly available repositories for human PPIs are currently av...

    Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, YL Ramachandra and Akhilesh Pandey

    BMC Bioinformatics 2006 7(Suppl 5):S19

    Published on: 18 December 2006

  15. Proceedings

    MicroTar: predicting microRNA targets from RNA duplexes

    The accurate prediction of a comprehensive set of messenger RNAs (targets) regulated by animal microRNAs (miRNAs) remains an open problem. In particular, the prediction of targets that do not possess evolution...

    Rahul Thadani and Martti T Tammi

    BMC Bioinformatics 2006 7(Suppl 5):S20

    Published on: 18 December 2006

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