Volume 14 Supplement 9

Selected articles from the 8th International Symposium on Bioinformatics Research and Applications (ISBRA'12)

Methodology Articles

Edited by Russell Schwartz, Rajshekhar Sunderraman, Jianxin Wang and Alexander Zelikovsky

Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The content of the supplement is based on presentations made at ISBRA 2012, the conference was partially supported by U.S. NSF award IIS-1237310. Articles have undergone the journal’s standard peer-review process for supplements. The Supplement Editors declare that they have no competing interests.

8th International Symposium on Bioinformatics Research and Applications (ISBRA'12). Go to conference site.

Dallas, TX, USA

21-23 May 2012

  1. Methodology Article

    Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

    High throughput parallel sequencing, RNA-Seq, has recently emerged as an appealing alternative to microarray in identifying differentially expressed genes (DEG) between biological groups. However, there still ...

    Xiao Xu, Yuanhao Zhang, Jennie Williams, Eric Antoniou, W Richard McCombie, Song Wu, Wei Zhu, Nicholas O Davidson, Paula Denoya and Ellen Li

    BMC Bioinformatics 2013 14(Suppl 9):S1

    Published on: 28 June 2013

  2. Methodology Article

    Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows

    Highly mutable RNA viruses exist in infected hosts as heterogeneous populations of genetically close variants known as quasispecies. Next-generation sequencing (NGS) allows for analysing a large number of vira...

    Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion Mandoiu, Yury Khudyakov and Alex Zelikovsky

    BMC Bioinformatics 2013 14(Suppl 9):S2

    Published on: 28 June 2013

  3. Methodology Article

    PoPLAR: Portal for Petascale Lifescience Applications and Research

    We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in...

    Bhanu Rekapalli, Paul Giblock and Christopher Reardon

    BMC Bioinformatics 2013 14(Suppl 9):S3

    Published on: 28 June 2013

  4. Methodology Article

    MGC: a metagenomic gene caller

    Computational gene finding algorithms have proven their robustness in identifying genes in complete genomes. However, metagenomic sequencing has presented new challenges due to the incomplete and fragmented na...

    Achraf El Allali and John R Rose

    BMC Bioinformatics 2013 14(Suppl 9):S6

    Published on: 28 June 2013

  5. Methodology Article

    Solving the molecular distance geometry problem with inaccurate distance data

    We present a new iterative algorithm for the molecular distance geometry problem with inaccurate and sparse data, which is based on the solution of linear systems, maximum cliques, and a minimization of nonlin...

    Michael Souza, Carlile Lavor, Albert Muritiba and Nelson Maculan

    BMC Bioinformatics 2013 14(Suppl 9):S7

    Published on: 28 June 2013