Volume 15 Supplement 5

Selected articles from the Third IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2013): Genomics

Research

Edited by Vladmir Filkov, Ananth Kalyanaraman, Yury Khudyakov, Ion Mandoiu, Sanguthevar Rajeskaran, Knut Reinert and Alex 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 peer review process was overseen by the Supplement Editors in accordance with BioMed Central's peer review guidelines for supplements. The Supplement Editors declare that they have no competing interests.

Third IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2013). Go to conference site.

New Orleans, LA, USA12-14 June 2013

Related articles have been published in a supplement to BMC Bioinformatics.

Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure

Drug resistance has become a severe challenge for treatment of HIV infections. Mutations accumulate in the HIV genome and make certain drugs ineffective. Prediction of resistance from genotype data is a valuab...

Authors: Xiaxia Yu, Irene T Weber and Robert W Harrison

Citation: BMC Genomics 2014 15(Suppl 5):S1

Content type: Research Published on: 14 July 2014
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RandAL: a randomized approach to aligning DNA sequences to reference genomes

The alignment of short reads generated by next-generation sequencers to genomes is an important problem in many biomedical and bioinformatics applications. Although many proposed methods work very well on narr...

Authors: Nam S Vo, Quang Tran, Nobal Niraula and Vinhthuy Phan

Citation: BMC Genomics 2014 15(Suppl 5):S2

Content type: Research Published on: 14 July 2014
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Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees

One of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply ad...

Authors: Lijun Liu, Victor Missirian, Matthew Zinkgraf, Andrew Groover and Vladimir Filkov

Citation: BMC Genomics 2014 15(Suppl 5):S3

Content type: Research Published on: 14 July 2014
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Next-generation sequencing reveals large connected networks of intra-host HCV variants

Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV)...

Authors: David S Campo, Zoya Dimitrova, Lilian Yamasaki, Pavel Skums, Daryl TY Lau, Gilberto Vaughan, Joseph C Forbi, Chong-Gee Teo and Yury Khudyakov

Citation: BMC Genomics 2014 15(Suppl 5):S4

Content type: Research Published on: 14 July 2014
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Efficient and scalable scaffolding using optical restriction maps

In the next generation sequencing techniques millions of short reads are produced from a genomic sequence at a single run. The chances of low read coverage to some regions of the sequence are very high. The re...

Authors: Subrata Saha and Sanguthevar Rajasekaran

Citation: BMC Genomics 2014 15(Suppl 5):S5

Content type: Research Published on: 14 July 2014
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A memory-efficient algorithm to obtain splicing graphs and de novoexpression estimates from de Bruijn graphs of RNA-Seq data

The recent advance of high-throughput sequencing makes it feasible to study entire transcriptomes through the application of de novo sequence assembly algorithms. While a popular strategy is to first construct an...

Authors: Sing-Hoi Sze and Aaron M Tarone

Citation: BMC Genomics 2014 15(Suppl 5):S6

Content type: Research Published on: 14 July 2014
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Transcriptome assembly and quantification from Ion Torrent RNA-Seq data

High throughput RNA sequencing (RNA-Seq) can generate whole transcriptome information at the single transcript level providing a powerful tool with multiple interrelated applications including transcriptome re...

Authors: Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Ion Mӑndoiu and Alex Zelikovsky

Citation: BMC Genomics 2014 15(Suppl 5):S7

Content type: Research Published on: 14 July 2014
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Selected articles from the Third IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2013): Genomics

Research

Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure

RandAL: a randomized approach to aligning DNA sequences to reference genomes

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees

Next-generation sequencing reveals large connected networks of intra-host HCV variants

Efficient and scalable scaffolding using optical restriction maps

A memory-efficient algorithm to obtain splicing graphs and de novoexpression estimates from de Bruijn graphs of RNA-Seq data

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data

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