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Volume 7 Supplement 5

APBioNet - Fifth International Conference on Bioinformatics (InCoB2006)

Proceedings

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

International Conference in Bioinformatics - InCoB2006.

New Delhi, India18-20 December 2006

  1. 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...

    Authors: Shoba Ranganathan, Martti Tammi, Michael Gribskov and Tin Wee Tan
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S1
  2. Automatic annotation of sequenced eukaryotic genomes integrates a combination of methodologies such as ab-initio methods and alignment of homologous genes and/or proteins. For example, annotation of the zebrafish...

    Authors: Alan Christoffels, Richard Bartfai, Hamsa Srinivasan, Hans Komen and Laszlo Orban
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S2
  3. 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...

    Authors: Asif M Khan, AT Heiny, Kenneth X Lee, KN Srinivasan, Tin Wee Tan, J Thomas August and Vladimir Brusic
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S4
  4. 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...

    Authors: Sourangshu Bhattacharya, Chiranjib Bhattacharyya and Nagasuma R Chandra
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S5
  5. Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence inf...

    Authors: Abdur R Sikder and Albert Y Zomaya
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S6
  6. 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...

    Authors: Joo Chuan Tong, Tin Wee Tan, Animesh A Sinha and Shoba Ranganathan
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S7
  7. 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...

    Authors: 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
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S8
  8. A key post genomics challenge is to identify how genes in an organism come together and perform physiological functions. An important first step in this direction is to identify transcriptional units, operons ...

    Authors: Sarita Ranjan, Ranjit Kumar Gundu and Akash Ranjan
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S9
  9. 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...

    Authors: Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S11
  10. 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...

    Authors: Urmila Kulkarni-Kale, Shriram G Bhosle, G Sunitha Manjari, Manali Joshi, Sandeep Bansode and Ashok S Kolaskar
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S12
  11. 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...

    Authors: HH Lin, LY Han, HL Zhang, CJ Zheng, B Xie, ZW Cao and YZ Chen
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S13
  12. 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...

    Authors: Lawrence JK Wee, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S14
  13. 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...

    Authors: AKMA Baten, BCH Chang, SK Halgamuge and Jason Li
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S15

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

  14. 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 ...

    Authors: Xiaomei Wu, Lei Zhu, Jie Guo, Cong Fu, Hongjun Zhou, Dong Dong, Zhenbo Li, Da-Yong Zhang and Kui Lin
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S16
  15. 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...

    Authors: Anita Suresh and Chandra Verma
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S17
  16. 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...

    Authors: 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
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S18
  17. 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...

    Authors: Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, YL Ramachandra and Akhilesh Pandey
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S19
  18. 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...

    Authors: Rahul Thadani and Martti T Tammi
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S20
  19. The number of k-words shared between two sequences is a simple and effcient alignment-free sequence comparison method. This statistic, D2, has been used for the clustering of EST sequences. Sequence comparison ba...

    Authors: Sylvain Forêt, Miriam R Kantorovitz and Conrad J Burden
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S21
  20. Although short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells, its gene silencing efficacy varies markedly and there are only a few consistencies among the recently...

    Authors: Shigeru Takasaki, Yoshihiro Kawamura and Akihiko Konagaya
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S22

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