Preface
BMC Bioinformatics 2012 13(Suppl 2):I1
Published on: 13 March 2012
Volume 13 Supplement 2
Proceedings from the Great Lakes Bioinformatics Conference 2011
Proceedings
Edited by Robert A Colvin and Jundong Liu
Great Lakes Bioinformatics Conference 2011. Go to conference site.
Athens, OH, USA
2-4 May 2011
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Proceedings
Reordering based integrative expression profiling for microarray classification
Current network-based microarray analysis uses the information of interactions among concerned genes/gene products, but still considers each gene expression individually. We propose an organized knowledge-supe...
BMC Bioinformatics 2012 13(Suppl 2):S1
Published on: 13 March 2012
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Proceedings
A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data
RNA polymerase II (PolII) is essential in gene transcription and ChIP-seq experiments have been used to study PolII binding patterns over the entire genome. However, since PolII enriched regions in the genome ...
BMC Bioinformatics 2012 13(Suppl 2):S2
Published on: 13 March 2012
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Proceedings
Amino acid function and docking site prediction through combining disease variants, structure alignments, sequence alignments, and molecular dynamics: a study of the HMG domain
The DNA binding domain of HMG proteins is known to be important in many diseases, with the Sox sub-family of HMG proteins of particular significance. Numerous natural variants in HMG proteins are associated wi...
BMC Bioinformatics 2012 13(Suppl 2):S3
Published on: 13 March 2012
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Proceedings
THINK Back: KNowledge-based Interpretation of High Throughput data
Results of high throughput experiments can be challenging to interpret. Current approaches have relied on bulk processing the set of expression levels, in conjunction with easily obtained external evidence, su...
BMC Bioinformatics 2012 13(Suppl 2):S4
Published on: 13 March 2012
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Proceedings
Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery
The T box riboswitch controls bacterial transcription by structurally responding to tRNA aminoacylation charging ratios. Knowledge of the thermodynamic stability difference between two competing structural ele...
BMC Bioinformatics 2012 13(Suppl 2):S5
Published on: 13 March 2012
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Proceedings
Evaluation of multiple protein docking structures using correctly predicted pairwise subunits
Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development ...
BMC Bioinformatics 2012 13(Suppl 2):S6
Published on: 13 March 2012
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Proceedings
Constructing patch-based ligand-binding pocket database for predicting function of proteins
Many of solved tertiary structures of unknown functions do not have global sequence and structural similarities to proteins of known function. Often functional clues of unknown proteins can be obtained by pred...
BMC Bioinformatics 2012 13(Suppl 2):S7
Published on: 13 March 2012
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Proceedings
Convergence of genetic influences in comorbidity
Predisposition to complex diseases is explained in part by genetic variation, and complex diseases are frequently comorbid, consistent with pleiotropic genetic variation influencing comorbidity. Genome Wide As...
BMC Bioinformatics 2012 13(Suppl 2):S8
Published on: 13 March 2012
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Proceedings
Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets
Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment ...
BMC Bioinformatics 2012 13(Suppl 2):S9
Published on: 13 March 2012
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Proceedings
Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry
When flow cytometric data on mixtures of cell populations are collected from samples under different experimental conditions, computational methods are needed (a) to classify the samples into similar groups, a...
BMC Bioinformatics 2012 13(Suppl 2):S10
Published on: 13 March 2012
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Proceedings
Fold change and p-value cutoffs significantly alter microarray interpretations
As context is important to gene expression, so is the preprocessing of microarray to transcriptomics. Microarray data suffers from several normalization and significance problems. Arbitrary fold change (FC) cu...
BMC Bioinformatics 2012 13(Suppl 2):S11
Published on: 13 March 2012
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Proceedings
Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data
Using gene co-expression analysis, researchers were able to predict clusters of genes with consistent functions that are relevant to cancer development and prognosis. We applied a weighted gene co-expression n...
BMC Bioinformatics 2012 13(Suppl 2):S12
Published on: 13 March 2012
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Proceedings
Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome
Retrotransposons are mobile DNA elements that spread through genomes via the action of element-encoded reverse transcriptases. They are ubiquitous constituents of most eukaryotic genomes, especially those of h...
BMC Bioinformatics 2012 13(Suppl 2):S13
Published on: 13 March 2012
