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Volume 14 Supplement 2

Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics


Edited by Cenk Sahinalp and Steven Jones

Publication of this supplement was funded by the authors.

The Eleventh Asia Pacific Bioinformatics Conference (APBC 2013). Go to conference site.

Vancouver, Canada21-24 January 2013

  1. One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequenicng (WES) is a popular alternative to whole genome sequencing (WGS) to study disease specific genomic v...

    Authors: Kaushalya C Amarasinghe, Jason Li and Saman K Halgamuge
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S2

    The Erratum to this article has been published in BMC Bioinformatics 2013 14:S26

  2. MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved mi...

    Authors: Joseph W Carl Jr, Joanne Trgovcich and Sridhar Hannenhalli
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S3
  3. Functional RNA molecules participate in numerous biological processes, ranging from gene regulation to protein synthesis. Analysis of functional RNA motifs and elements in RNA sequences can obtain useful infor...

    Authors: Tzu-Hao Chang, Hsi-Yuan Huang, Justin Bo-Kai Hsu, Shun-Long Weng, Jorng-Tzong Horng and Hsien-Da Huang
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S4
  4. Even a single amino acid substitution in a protein sequence may result in significant changes in protein stability, structure, and therefore in protein function as well. In the post-genomic era, computational ...

    Authors: Lukas Folkman, Bela Stantic and Abdul Sattar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S6
  5. Gene expression profiles can show significant changes when genetically diseased cells are compared with non-diseased cells. Biological networks are often used to identify active subnetworks (ASNs) of the diseases...

    Authors: Raj K Gaire, Lorey Smith, Patrick Humbert, James Bailey, Peter J Stuckey and Izhak Haviv
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S7
  6. Markov state models have been widely used to study conformational changes of biological macromolecules. These models are built from short timescale simulations and then propagated to extract long timescale dyn...

    Authors: Chen Gu, Huang-Wei Chang, Lutz Maibaum, Vijay S Pande, Gunnar E Carlsson and Leonidas J Guibas
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S8
  7. Polyadenylation is present in all three domains of life, making it the most conserved post-transcriptional process compared with splicing and 5'-capping. Even though most mammalian poly(A) sites contain a high...

    Authors: Eric S Ho, Samuel I Gunderson and Siobain Duffy
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S9
  8. The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions....

    Authors: Chun-Yu Lin, Yung-Chiang Chen, Yu-Shu Lo and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S11
  9. In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classificatio...

    Authors: Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger and Chung-Shou Liao
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S12
  10. The over consumption of fossil fuels has led to growing concerns over climate change and global warming. Increasing research activities have been carried out towards alternative viable biofuel sources. Of seve...

    Authors: Nguyen Xuan Vinh, Madhu Chetty, Ross Coppel, Sandeep Gaudana and Pramod P Wangikar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S14
  11. Gene Ontology (GO) has been widely used in biological databases, annotation projects, and computational analyses. Although the three GO categories are structured as independent ontologies, the biological relat...

    Authors: Jiajie Peng, Jin Chen and Yadong Wang
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S15
  12. Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein stru...

    Authors: Mahmood A Rashid, MA Hakim Newton, Md Tamjidul Hoque, Swakkhar Shatabda, Duc Nghia Pham and Abdul Sattar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S16
  13. Optimization procedures to identify gene knockouts for targeted biochemical overproduction have been widely in use in modern metabolic engineering. Flux balance analysis (FBA) framework has provided conceptual...

    Authors: Shaogang Ren, Bo Zeng and Xiaoning Qian
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S17
  14. The triplet distance is a distance measure that compares two rooted trees on the same set of leaves by enumerating all sub-sets of three leaves and counting how often the induced topologies of the tree are equ...

    Authors: Andreas Sand, Gerth Stølting Brodal, Rolf Fagerberg, Christian NS Pedersen and Thomas Mailund
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S18
  15. Given a protein's amino acid sequence, the protein structure prediction problem is to find a three dimensional structure that has the native energy level. For many decades, it has been one of the most challeng...

    Authors: Swakkhar Shatabda, MA Hakim Newton, Mahmood A Rashid, Duc Nghia Pham and Abdul Sattar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S19
  16. Disulfide bonds constitute one of the most important cross-linkages in proteins and significantly influence protein structure and function. At the state-of-the-art, various methodological frameworks have been ...

    Authors: Rahul Singh and William Murad
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S20
  17. The pandemic 2009-H1N1 influenza virus circulated in the human population and caused thousands deaths worldwide. Studies on pandemic influenza vaccines have shown that T cell recognition to conserved epitopes ...

    Authors: Chinh TT Su, Christian Schönbach and Chee-Keong Kwoh
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S21
  18. Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free gra...

    Authors: Zsuzsanna Sükösd, Bjarne Knudsen, James WJ Anderson, Ádám Novák, Jørgen Kjems and Christian NS Pedersen
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S22
  19. Searching for members of characterized ncRNA families containing pseudoknots is an important component of genome-scale ncRNA annotation. However, the state-of-the-art known ncRNA search is based on context-fre...

    Authors: Cheng Yuan and Yanni Sun
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S25

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

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