Volume 10 Supplement 11

Proceedings of the Sixth Annual MCBIOS Conference. Transformational Bioinformatics: Delivering Value from Genomes


Edited by Jonathan D Wren (Senior Editor), Yuriy Gusev, Raphael D Isokpehi, Dan Berleant, Ulisses Braga-Neto, Dawn Wilkins and Susan Bridges

Sixth Annual MCBIOS Conference. Transformational Bioinformatics: Delivering Value from Genomes. Go to conference site.

Starkville, MS, USA

20-21 February 2009

  1. Proceedings

    Facilitating functional annotation of chicken microarray data

    Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest...

    Teresia J Buza, Ranjit Kumar, Cathy R Gresham, Shane C Burgess and Fiona M McCarthy

    BMC Bioinformatics 2009 10(Suppl 11):S2

    Published on: 8 October 2009

  2. Proceedings

    Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

    As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modificati...

    Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen L Reichel, Nathan R Stewart, Ryan D Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Robert W Sykes, Jason N Burris, Joseph J Bozell, Max Zong-Ming Cheng…

    BMC Bioinformatics 2009 10(Suppl 11):S3

    Published on: 8 October 2009

  3. Proceedings

    HPD: an online integrated human pathway database enabling systems biology studies

    Pathway-oriented experimental and computational studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gen...

    Sudhir R Chowbina, Xiaogang Wu, Fan Zhang, Peter M Li, Ragini Pandey, Harini N Kasamsetty and Jake Y Chen

    BMC Bioinformatics 2009 10(Suppl 11):S5

    Published on: 8 October 2009

  4. Proceedings

    Structural and functional-annotation of an equine whole genome oligoarray

    The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for ...

    Lauren A Bright, Shane C Burgess, Bhanu Chowdhary, Cyprianna E Swiderski and Fiona M McCarthy

    BMC Bioinformatics 2009 10(Suppl 11):S8

    Published on: 8 October 2009

  5. Proceedings

    Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes

    Nanomaterials are being manufactured on a commercial scale for use in medical, diagnostic, energy, component and communications industries. However, concerns over the safety of engineered nanomaterials have su...

    Amin Zollanvari, Mary Jane Cunningham, Ulisses Braga-Neto and Edward R Dougherty

    BMC Bioinformatics 2009 10(Suppl 11):S10

    Published on: 8 October 2009

  6. Proceedings

    Site-specific impacts on gene expression and behavior in fathead minnows (Pimephales promelas) exposed in situ to streams adjacent to sewage treatment plants

    Environmental monitoring for pharmaceuticals and endocrine disruptors in the aquatic environment traditionally employs a variety of methods including analytical chemistry, as well as a variety of histological ...

    Natàlia Garcia-Reyero, Ira R Adelman, Dalma Martinović, Li Liu and Nancy D Denslow

    BMC Bioinformatics 2009 10(Suppl 11):S11

    Published on: 8 October 2009

  7. Proceedings

    NATbox: a network analysis toolbox in R

    There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as ...

    Shweta S Chavan, Michael A Bauer, Marco Scutari and Radhakrishnan Nagarajan

    BMC Bioinformatics 2009 10(Suppl 11):S14

    Published on: 8 October 2009

  8. Proceedings

    Novel software package for cross-platform transcriptome analysis (CPTRA)

    Next-generation sequencing techniques enable several novel transcriptome profiling approaches. Recent studies indicated that digital gene expression profiling based on short sequence tags has superior performa...

    Xin Zhou, Zhen Su, R Douglas Sammons, Yanhui Peng, Patrick J Tranel, C Neal Stewart and Joshua S Yuan

    BMC Bioinformatics 2009 10(Suppl 11):S16

    Published on: 8 October 2009

  9. Proceedings

    An automated proteomic data analysis workflow for mass spectrometry

    Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be i...

    Ken Pendarvis, Ranjit Kumar, Shane C Burgess and Bindu Nanduri

    BMC Bioinformatics 2009 10(Suppl 11):S17

    Published on: 8 October 2009

  10. Proceedings

    Graph ranking for exploratory gene data analysis

    Microarray technology has made it possible to simultaneously monitor the expression levels of thousands of genes in a single experiment. However, the large number of genes greatly increases the challenges of a...

    Cuilan Gao, Xin Dang, Yixin Chen and Dawn Wilkins

    BMC Bioinformatics 2009 10(Suppl 11):S19

    Published on: 8 October 2009

  11. Proceedings

    Integrating phenotype and gene expression data for predicting gene function

    This paper presents a framework for integrating disparate data sets to predict gene function. The algorithm constructs a graph, called an integrated similarity graph, by computing similarities based upon both ...

    Brandon M Malone, Andy D Perkins and Susan M Bridges

    BMC Bioinformatics 2009 10(Suppl 11):S20

    Published on: 8 October 2009