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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, USA23-24 February 2008

  1. Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genomic variation and can cause phenotypic differences between individuals, including diseases. Bases are subject to various levels of selec...

    Authors: Vinayak Kulkarni, Mounir Errami, Robert Barber and Harold R Garner
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S3
  2. 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 ...

    Authors: 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
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S4
  3. New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many soft...

    Authors: Tianxiao Huan, Andrey Y Sivachenko, Scott H Harrison and Jake Y Chen
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S5
  4. 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....

    Authors: Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola and Hesham Ali
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S6
  5. Most existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (sim...

    Authors: Arun Rawat, Georg J Seifert and Youping Deng
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S7
  6. Advances in DNA microarray technology portend that molecular signatures from which microarray will eventually be used in clinical environments and personalized medicine. Derivation of biomarkers is a large ste...

    Authors: Zhenqiang Su, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins and Weida Tong
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S9
  7. 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...

    Authors: 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…
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S10
  8. 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 ...

    Authors: Cory B Giles and Jonathan D Wren
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S11
  9. 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...

    Authors: Brian Roux and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S12
  10. 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...

    Authors: Alexander Churbanov and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S13
  11. 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...

    Authors: Jerzy S Zielinski, Nidhal Bouaynaya, Dan Schonfeld and William O'Neill
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S14
  12. 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 ...

    Authors: Minho Chae, Robert J Shmookler Reis and John J Thaden
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S15
  13. Biological chemistry is very stereospecific. Nonetheless, the diastereotopic oxygen atoms of diphosphate-containing molecules in the Protein Data Bank (PDB) are often given names that do not uniquely distingui...

    Authors: Christopher A Bottoms and Dong Xu
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S16
  14. 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...

    Authors: 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
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S17
  15. 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...

    Authors: Taewon Lee, Varsha G Desai, Cruz Velasco, Robert J S Reis and Robert R Delongchamp
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S20

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