Volume 9 Supplement 9

Proceedings of the Fifth Annual MCBIOS Conference. Systems Biology: Bridging the Omics

Proceedings

Edited by Jonathan D Wren (Senior Editor), Yuriy Gusev, Dawn Wilkins, Susan Bridges, Stephen Winters-Hilt and James Fuscoe

Fifth Annual MCBIOS Conference. Systems Biology: Bridging the Omics. Go to conference site.

Oklahoma City, OK, USA

23-24 February 2008

  1. Proceedings

    From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells

    A statistically robust and biologically-based approach for analysis of microarray data is described that integrates independent biological knowledge and data with a global F-test for finding genes of interest ...

    Mikhail G Dozmorov, Kimberly D Kyker, Paul J Hauser, Ricardo Saban, David D Buethe, Igor Dozmorov, Michael B Centola, Daniel J Culkin and Robert E Hurst

    BMC Bioinformatics 2008 9(Suppl 9):S4

    Published on: 12 August 2008

  2. Proceedings

    MTAP: The Motif Tool Assessment Platform

    In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences....

    Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola and Hesham Ali

    BMC Bioinformatics 2008 9(Suppl 9):S6

    Published on: 12 August 2008

  3. Proceedings

    The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

    Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not repr...

    Leming Shi, Wendell D Jones, Roderick V Jensen, Stephen C Harris, Roger G Perkins, Federico M Goodsaid, Lei Guo, Lisa J Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur, Wenjun Bao, Catalin C Barbacioru, Vincent Bertholet, Xiaoxi Megan Cao…

    BMC Bioinformatics 2008 9(Suppl 9):S10

    Published on: 12 August 2008

  4. Proceedings

    Large-scale directional relationship extraction and resolution

    Relationships between entities such as genes, chemicals, metabolites, phenotypes and diseases in MEDLINE are often directional. That is, one may affect the other in a positive or negative manner. Detection of ...

    Cory B Giles and Jonathan D Wren

    BMC Bioinformatics 2008 9(Suppl 9):S11

    Published on: 12 August 2008

  5. Proceedings

    Hybrid MM/SVM structural sensors for stochastic sequential data

    In this paper we present preliminary results stemming from a novel application of Markov Models and Support Vector Machines to splice site classification of Intron-Exon and Exon-Intron (5' and 3') splice sites...

    Brian Roux and Stephen Winters-Hilt

    BMC Bioinformatics 2008 9(Suppl 9):S12

    Published on: 12 August 2008

  6. Proceedings

    Clustering ionic flow blockade toggles with a Mixture of HMMs

    Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties with potential implications for DNA sequencing. The α-Hemolysin transmembr...

    Alexander Churbanov and Stephen Winters-Hilt

    BMC Bioinformatics 2008 9(Suppl 9):S13

    Published on: 12 August 2008

  7. Proceedings

    Time-dependent ARMA modeling of genomic sequences

    Over the past decade, many investigators have used sophisticated time series tools for the analysis of genomic sequences. Specifically, the correlation of the nucleotide chain has been studied by examining the...

    Jerzy S Zielinski, Nidhal Bouaynaya, Dan Schonfeld and William O'Neill

    BMC Bioinformatics 2008 9(Suppl 9):S14

    Published on: 12 August 2008

  8. Proceedings

    An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks

    Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector ...

    Minho Chae, Robert J Shmookler Reis and John J Thaden

    BMC Bioinformatics 2008 9(Suppl 9):S15

    Published on: 12 August 2008

  9. Proceedings

    Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

    Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associated with phenotypic traits such as diseas...

    Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming Shi, Roger Perkins, Hong Fang, Joshua Xu, James J Chen, Tao Han, Jim Kaput, James C Fuscoe and Weida Tong

    BMC Bioinformatics 2008 9(Suppl 9):S17

    Published on: 12 August 2008

  10. Proceedings

    Testing for treatment effects on gene ontology

    In studies that use DNA arrays to assess changes in gene expression, it is preferable to measure the significance of treatment effects on a group of genes from a pathway or functional category such as gene ont...

    Taewon Lee, Varsha G Desai, Cruz Velasco, Robert J S Reis and Robert R Delongchamp

    BMC Bioinformatics 2008 9(Suppl 9):S20

    Published on: 12 August 2008