Volume 10 Supplement 3

Eighth International Conference on Bioinformatics (InCoB2009):Computational Biology


Edited by Shoba Ranganathan, Frank Eisenhaber, Joo Chuan Tong and Tin Wee Tan

Asia Pacific Bioinformatics Network (APBioNet) Eighth International Conference on Bioinformatics (InCoB2009). Go to conference site.


7-11 September 2009

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  1. Introduction

    Extending Asia Pacific bioinformatics into new realms in the "-omics" era

    The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics...

    Shoba Ranganathan, Frank Eisenhaber, Joo Chuan Tong and Tin Wee Tan

    BMC Genomics 2009 10(Suppl 3):S1

    Published on: 3 December 2009

  2. Proceedings

    BOAT: Basic Oligonucleotide Alignment Tool

    Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymor...

    Shu-Qi Zhao, Jun Wang, Li Zhang, Jiong-Tang Li, Xiaocheng Gu, Ge Gao and Liping Wei

    BMC Genomics 2009 10(Suppl 3):S2

    Published on: 3 December 2009

  3. Proceedings

    RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation

    Polymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools...

    Jittima Piriyapongsa, Chumpol Ngamphiw, Anunchai Assawamakin, Pongsakorn Wangkumhang, Payiarat Suwannasri, Uttapong Ruangrit, Gallissara Agavatpanitch and Sissades Tongsima

    BMC Genomics 2009 10(Suppl 3):S4

    Published on: 3 December 2009

  4. Proceedings

    Computational identification and experimental validation of PPRE motifs in NHE1 and MnSOD genes of Human

    Activation of PPARs has been reported to inhibit the proliferation of malignant cells from different lineages. They are involved in transcription regulation of genes upon activation by a ligand. The binding of...

    Gireedhar Venkatachalam, Alan Prem Kumar, Loo Ser Yue, Shazib Pervaiz, Marie Veronique Clement and Meena Kishore Sakharkar

    BMC Genomics 2009 10(Suppl 3):S5

    Published on: 3 December 2009

  5. Proceedings

    A multi-factor model for caspase degradome prediction

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

    Lawrence JK Wee, Joo Chuan Tong, Tin Wee Tan and Shoba Ranganathan

    BMC Genomics 2009 10(Suppl 3):S6

    Published on: 3 December 2009

  6. Proceedings

    Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

    Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB)...

    Wenwei Yang, Ke Jin, Xing Xie, Dongsheng Li, Jigang Yang, Li Wang, Ning Gu, Yang Zhong and Ling V Sun

    BMC Genomics 2009 10(Suppl 3):S7

    Published on: 3 December 2009

  7. Proceedings

    BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources

    DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on ...

    Jeongheui Lim, Sang-Yoon Kim, Sungmin Kim, Hae-Seok Eo, Chang-Bae Kim, Woon Kee Paek, Won Kim and Jong Bhak

    BMC Genomics 2009 10(Suppl 3):S8

    Published on: 3 December 2009

  8. Proceedings

    TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome

    DNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and mi...

    Piroon Jenjaroenpun and Vladimir A Kuznetsov

    BMC Genomics 2009 10(Suppl 3):S9

    Published on: 3 December 2009

  9. Proceedings

    MitoVariome: a variome database of human mitochondrial DNA

    Mitochondrial sequence variation provides critical information for studying human evolution and variation. Mitochondrial DNA provides information on the origin of humans, and plays a substantial role in forens...

    Yong Seok Lee, Woo-Yeon Kim, Mihyun Ji, Ji Han Kim and Jong Bhak

    BMC Genomics 2009 10(Suppl 3):S12

    Published on: 3 December 2009

  10. Proceedings

    MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads

    Next-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcr...

    Hua Bao, Yuanyan Xiong, Hui Guo, Renchao Zhou, Xuemei Lu, Zhen Yang, Yang Zhong and Suhua Shi

    BMC Genomics 2009 10(Suppl 3):S13

    Published on: 3 December 2009

  11. Proceedings

    MINER: exploratory analysis of gene interaction networks by machine learning from expression data

    The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "...

    Sidath Randeni Kadupitige, Kin Chun Leung, Julia Sellmeier, Jane Sivieng, Daniel R Catchpoole, Michael E Bain and Bruno A Gaëta

    BMC Genomics 2009 10(Suppl 3):S17

    Published on: 3 December 2009

  12. Proceedings

    PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

    Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organis...

    Seong-Jin Park, Jong-Soon Choi, Byoung-Chul Kim, Seong-Woong Jho, Jea-Woon Ryu, Daeui Park, Kyung-A Lee, Jong Bhak and Seung Il Kim

    BMC Genomics 2009 10(Suppl 3):S18

    Published on: 3 December 2009

  13. Proceedings

    Comparative study of protein-protein interaction observed in PolyGalacturonase-Inhibiting Proteins from Phaseolus vulgaris and Glycine max and PolyGalacturonase from Fusarium moniliforme

    The PolyGalacturonase-Inhibiting Proteins (PGIP) of plant cell wall limit the invasion of phytopathogenic organisms by interacting with the enzyme PolyGalacturonase (PG) they secrete to degrade pectin present ...

    Aditi Maulik, Hiren Ghosh and Soumalee Basu

    BMC Genomics 2009 10(Suppl 3):S19

    Published on: 3 December 2009

  14. Proceedings

    MitoInteractome: Mitochondrial protein interactome database, and its application in 'aging network' analysis

    Mitochondria play a vital role in the energy production and apoptotic process of eukaryotic cells. Proteins in the mitochondria are encoded by nuclear and mitochondrial genes. Owing to a large increase in the ...

    Rohit Reja, AJ Venkatakrishnan, Jungwoo Lee, Byoung-Chul Kim, Jea-Woon Ryu, Sungsam Gong, Jong Bhak and Daeui Park

    BMC Genomics 2009 10(Suppl 3):S20

    Published on: 3 December 2009

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