Volume 14 Supplement 2

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

Proceedings

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, Canada

21-24 January 2013

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  1. Proceedings

    CoNVEX: copy number variation estimation in exome sequencing data using HMM

    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...

    Kaushalya C Amarasinghe, Jason Li and Saman K Halgamuge

    BMC Bioinformatics 2013 14(Suppl 2):S2

    Published on: 21 January 2013

  2. Proceedings

    Widespread evidence of viral miRNAs targeting host pathways

    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...

    Joseph W Carl, Joanne Trgovcich and Sridhar Hannenhalli

    BMC Bioinformatics 2013 14(Suppl 2):S3

    Published on: 21 January 2013

  3. Proceedings

    An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs

    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...

    Tzu-Hao Chang, Hsi-Yuan Huang, Justin Bo-Kai Hsu, Shun-Long Weng, Jorng-Tzong Horng and Hsien-Da Huang

    BMC Bioinformatics 2013 14(Suppl 2):S4

    Published on: 21 January 2013

  4. Proceedings

    Discovery and analysis of consistent active sub-networks in cancers

    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...

    Raj K Gaire, Lorey Smith, Patrick Humbert, James Bailey, Peter J Stuckey and Izhak Haviv

    BMC Bioinformatics 2013 14(Suppl 2):S7

    Published on: 21 January 2013

  5. Proceedings

    Building Markov state models with solvent dynamics

    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...

    Chen Gu, Huang-Wei Chang, Lutz Maibaum, Vijay S Pande, Gunnar E Carlsson and Leonidas J Guibas

    BMC Bioinformatics 2013 14(Suppl 2):S8

    Published on: 21 January 2013

  6. Proceedings

    A multispecies polyadenylation site model

    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...

    Eric S Ho, Samuel I Gunderson and Siobain Duffy

    BMC Bioinformatics 2013 14(Suppl 2):S9

    Published on: 21 January 2013

  7. Proceedings

    Reconstruction of phyletic trees by global alignment of multiple metabolic networks

    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...

    Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger and Chung-Shou Liao

    BMC Bioinformatics 2013 14(Suppl 2):S12

    Published on: 21 January 2013

  8. Proceedings

    A model of the circadian clock in the cyanobacterium Cyanothece sp. ATCC 51142

    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...

    Nguyen Xuan Vinh, Madhu Chetty, Ross Coppel, Sandeep Gaudana and Pramod P Wangikar

    BMC Bioinformatics 2013 14(Suppl 2):S14

    Published on: 21 January 2013

  9. Proceedings

    Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice

    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...

    Mahmood A Rashid, MA Hakim Newton, Md Tamjidul Hoque, Swakkhar Shatabda, Duc Nghia Pham and Abdul Sattar

    BMC Bioinformatics 2013 14(Suppl 2):S16

    Published on: 21 January 2013

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