Volume 13 Supplement 15
Ninth Annual MCBIOS Conference. Dealing with the Omics Data Deluge
Proceedings
Edited by Jonathan Wren, Susan Bridges, Doris Kupfer, Dennis Burian, Mikhail Dozmorov and Rakesh Kaundal
Proceedings of the Ninth Annual MCBIOS Conference. Dealing with the Omics Data Deluge. Go to conference site.
Oxford, MS, USA17-18 February 2012
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Citation: BMC Bioinformatics 2012 13(Suppl 15):S1
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PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries
Over the past decade, pathway and gene-set enrichment analysis has evolved into the study of high-throughput functional genomics. Owing to poorly annotated and incomplete pathway data, researchers have begun t...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S2 -
Implementation of multiple-instance learning in drug activity prediction
In the context of drug discovery and development, much effort has been exerted to determine which conformers of a given molecule are responsible for the observed biological activity. In this work we aimed to p...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S3 -
Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
Computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. Identification of transcriptional start sites, demar...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S4 -
Computational workflow for analysis of gain and loss of genes in distantly related genomes
Early evolution of animals led to profound changes in body plan organization, symmetry and the rise of tissue complexity including formation of muscular and nervous systems. This process was associated with ma...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S5 -
Investigating drug repositioning opportunities in FDA drug labels through topic modeling
Drug repositioning offers an opportunity to revitalize the slowing drug discovery pipeline by finding new uses for currently existing drugs. Our hypothesis is that drugs sharing similar side effect profiles ar...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S6 -
IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis
Next-Generation Sequencing (NGS) technologies and Genome-Wide Association Studies (GWAS) generate millions of reads and hundreds of datasets, and there is an urgent need for a better way to accurately interpre...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S7 -
Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses
Multidimensional protein identification technology (MudPIT)-based shot-gun proteomics has been proven to be an effective platform for functional proteomics. In particular, the various sample preparation method...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S8 -
A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins
Members of the phylum Proteobacteria are most prominent among bacteria causing plant diseases that result in a diminution of the quantity and quality of food produced by agriculture. To ameliorate these losses...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S9 -
Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis
NAC domain transcription factors are important transcriptional regulators involved in plant growth, development and stress responses. Recent studies have revealed several classes of NAC transcriptional factors...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S10 -
BirdsEyeView (BEV): graphical overviews of experimental data
Analyzing global experimental data can be tedious and time-consuming. Thus, helping biologists see results as quickly and easily as possible can facilitate biological research, and is the purpose of the softwa...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S11 -
Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization
Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as protei...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S12 -
Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spe...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S13 -
Empirical evaluation of scoring functions for Bayesian network model selection
In this work, we empirically evaluate the capability of various scoring functions of Bayesian networks for recovering true underlying structures. Similar investigations have been carried out before, but they t...
Citation: BMC Bioinformatics 2012 13(Suppl 15):S14
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