Volume 12 Supplement 2

Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2010

Proceedings

Edited by Xiaohua Tony Hu and Taesung Park

IEEE International Conference on Bioinformatics and Biomedicine 2010. Go to conference site.

Hong Kong, P. R. China18-21 December 2010

Sublineage structure analysis of Mycobacterium tuberculosis complex strains using multiple-biomarker tensors

Strains of Mycobacterium tuberculosis complex (MTBC) can be classified into major lineages based on their genotype. Further subdivision of major lineages into sublineages requires multiple biomarkers along with m...

Authors: Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bülent Yener and Kristin P Bennett

Citation: BMC Genomics 2011 12(Suppl 2):S1

Content type: Proceedings

Published on: 27 July 2011
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Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters

Proximity-based methods and co-evolution-based phylogenetic profiles methods have been successfully used for the identification of functionally related genes. Proximity-based methods are effective for physical...

Authors: Vikas Rao Pejaver and Sun Kim

Citation: BMC Genomics 2011 12(Suppl 2):S2

Content type: Proceedings

Published on: 27 July 2011
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FluReF, an automated flu virus reassortment finder based on phylogenetic trees

Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemic...

Authors: Alisa Yurovsky and Bernard M E Moret

Citation: BMC Genomics 2011 12(Suppl 2):S3

Content type: Proceedings

Published on: 27 July 2011
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Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to ...

Authors: Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen and Mihai Pop

Citation: BMC Genomics 2011 12(Suppl 2):S4

Content type: Proceedings

Published on: 27 July 2011
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Building interpretable fuzzy models for high dimensional data analysis in cancer diagnosis

Analysing gene expression data from microarray technologies is a very important task in biology and medicine, and particularly in cancer diagnosis. Different from most other popular methods in high dimensional...

Authors: Zhenyu Wang and Vasile Palade

Citation: BMC Genomics 2011 12(Suppl 2):S5

Content type: Proceedings

Published on: 27 July 2011
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CAMBer: an approach to support comparative analysis of multiple bacterial strains

There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in prom...

Authors: Michal Wozniak, Limsoon Wong and Jerzy Tiuryn

Citation: BMC Genomics 2011 12(Suppl 2):S6

Content type: Proceedings

Published on: 27 July 2011
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Ψ-RA: a parallel sparse index for genomic read alignment

Genomic read alignment involves mapping (exactly or approximately) short reads from a particular individual onto a pre-sequenced reference genome of the same species. Because all individuals of the same specie...

Authors: M Oğuzhan Külekci, Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter and Bojian Xu

Citation: BMC Genomics 2011 12(Suppl 2):S7

Content type: Proceedings

Published on: 27 July 2011
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Evaluation of short read metagenomic assembly

Metagenomic assembly is a challenging problem due to the presence of genetic material from multiple organisms. The problem becomes even more difficult when short reads produced by next generation sequencing te...

Authors: Anveshi Charuvaka and Huzefa Rangwala

Citation: BMC Genomics 2011 12(Suppl 2):S8

Content type: Proceedings

Published on: 27 July 2011
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bNEAT: a Bayesian network method for detecting epistatic interactions in genome-wide association studies

Detecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis and treatment of complex human diseases. A recent study in automatic detection of epistatic interactio...

Authors: Bing Han and Xue-wen Chen

Citation: BMC Genomics 2011 12(Suppl 2):S9

Content type: Proceedings

Published on: 27 July 2011
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Correlating CpG islands, motifs, and sequence variants in human chromosome 21

CpG islands are important regions in DNA. They usually appear at the 5’ end of genes containing GC-rich dinucleotides. When DNA methylation occurs, gene regulation is affected and it sometimes leads to carcino...

Authors: Leah Spontaneo and Nick Cercone

Citation: BMC Genomics 2011 12(Suppl 2):S10

Content type: Proceedings

Published on: 27 July 2011
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Dynamic biclustering of microarray data by multi-objective immune optimization

Newly microarray technologies yield large-scale datasets. The microarray datasets are usually presented in 2D matrices, where rows represent genes and columns represent experimental conditions. Systematic anal...

Authors: Junwan Liu, Zhoujun Li, Xiaohua Hu, Yiming Chen and EK Park

Citation: BMC Genomics 2011 12(Suppl 2):S11

Content type: Proceedings

Published on: 27 July 2011
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Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2010

Proceedings

Sublineage structure analysis of Mycobacterium tuberculosis complex strains using multiple-biomarker tensors

Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters

FluReF, an automated flu virus reassortment finder based on phylogenetic trees

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Building interpretable fuzzy models for high dimensional data analysis in cancer diagnosis

CAMBer: an approach to support comparative analysis of multiple bacterial strains

Ψ-RA: a parallel sparse index for genomic read alignment

Evaluation of short read metagenomic assembly

bNEAT: a Bayesian network method for detecting epistatic interactions in genome-wide association studies

Correlating CpG islands, motifs, and sequence variants in human chromosome 21

Dynamic biclustering of microarray data by multi-objective immune optimization

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