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Volume 8 Supplement 7

Proceedings of the Fourth Annual MCBIOS Conference. Computational Frontiers in Biomedicine

Proceedings

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

Fourth Annual MCBIOS Conference. Computational Frontiers in Biomedicine. Go to conference site.

New Orleans, LA, USA1-3 February 2007

  2. To better understand the response of urinary epithelial (urothelial) cells to Enterococcus faecalis, a uropathogen that exhibits resistance to multiple antibiotics, a genome-wide scan of gene expression was obtai...

    Authors: Mikhail G Dozmorov, Kimberly D Kyker, Ricardo Saban, Nathan Shankar, Arto S Baghdayan, Michael B Centola and Robert E Hurst
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S2
    Content type: Proceedings Published on:

  3. Urine from male Sprague-Dawley rats 25, 40, and 80 days old was analyzed by NMR and UPLC/MS. The effects of data normalization procedures on principal component analysis (PCA) and quantitative analysis of NMR-...

    Authors: Laura K Schnackenberg, Jinchun Sun, Parvaneh Espandiari, Ricky D Holland, Joseph Hanig and Richard D Beger
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S3
    Content type: Proceedings Published on:

  4. Pyrrolizidine alkaloids (PAs) are probably the most common plant constituents that poison livestock, wildlife, and humans worldwide. Riddelliine is isolated from plants grown in the western United States and i...

    Authors: Nan Mei, Lei Guo, Ruqing Liu, James C Fuscoe and Tao Chen
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S4
    Content type: Proceedings Published on:

  6. As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR ...

    Authors: Joshua S Yuan, Jason Burris, Nathan R Stewart, Ayalew Mentewab and C Neal Stewart Jr
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S6
    Content type: Proceedings Published on:

  7. Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test o...

    Authors: Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S Inouye, Kuan Yang, Edward J Perkins and Youping Deng
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S7
    Content type: Proceedings Published on:

  8. Mean-based clustering algorithms such as bisecting k-means generally lack robustness. Although componentwise median is a more robust alternative, it can be a poor center representative for high dimensional data. ...

    Authors: Yuanyuan Ding, Xin Dang, Hanxiang Peng and Dawn Wilkins
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S8
    Content type: Proceedings Published on:

  9. Nanopore detection is based on observations of the ionic current threading a single, highly stable, nanometer-scale channel. The dimensions are such that small biomolecules and biopolymers (like DNA and peptid...

    Authors: Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S9
    Content type: Proceedings Published on:

  10. Synthetic transcription factors (STFs) promise to offer a powerful new therapeutic against Cancer, AIDS, and genetic disease. Currently, 10% of drugs are of this type, including salicylate and tamoxifen. STFs ...

    Authors: Stephen Winters-Hilt, Amanda Davis, Iftekhar Amin and Eric Morales
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S10
    Content type: Proceedings Published on:

  11. Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overh...

    Authors: Karen Thomson, Iftekhar Amin, Eric Morales and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S11
    Content type: Proceedings Published on:

  12. A nanopore detector has a nanometer-scale trans-membrane channel across which a potential difference is established, resulting in an ionic current through the channel in the pA-nA range. A distinctive channel ...

    Authors: Matthew Landry and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S12
    Content type: Proceedings Published on:

  13. The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In order to understand the underlyi...

    Authors: Peng Li, Chaoyang Zhang, Edward J Perkins, Ping Gong and Youping Deng
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S13
    Content type: Proceedings Published on:

  14. 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 alpha-Hemolysin tr...

    Authors: Alexander Churbanov, Carl Baribault and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S14
    Content type: Proceedings Published on:

  16. Multiple recent studies have found aberrant expression profiles of microRNAome in human cancers. While several target genes have been experimentally identified for some microRNAs in various tumors, the global ...

    Authors: Yuriy Gusev, Thomas D Schmittgen, Megan Lerner, Russell Postier and Daniel Brackett
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S16
    Content type: Proceedings Published on:

  18. Support Vector Machines (SVMs) provide a powerful method for classification (supervised learning). Use of SVMs for clustering (unsupervised learning) is now being considered in a number of different ways.

    Authors: Stephen Winters-Hilt and Sam Merat
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S18
    Content type: Proceedings Published on:

  19. Hidden Markov Models (HMMs) provide an excellent means for structure identification and feature extraction on stochastic sequential data. An HMM-with-Duration (HMMwD) is an HMM that can also exactly model the ...

    Authors: Stephen Winters-Hilt and Carl Baribault
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S19
    Content type: Proceedings Published on:

  20. The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions th...

    Authors: Stephen Winters-Hilt, Eric Morales, Iftekhar Amin and Alexander Stoyanov
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S20
    Content type: Proceedings Published on:

  21. Unraveling the mechanisms that regulate gene expression is a major challenge in biology. An important task in this challenge is to identify regulatory elements, especially the binding sites in deoxyribonucleic...

    Authors: Modan K Das and Ho-Kwok Dai
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S21
    Content type: Proceedings Published on:

  23. When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only a portion of the proteotypic peptides associated with each protein will be observ...

    Authors: William S Sanders, Susan M Bridges, Fiona M McCarthy, Bindu Nanduri and Shane C Burgess
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S23
    Content type: Proceedings Published on:

  24. Effective and economical methods for quantitative analysis of high throughput mass spectrometry data are essential to meet the goals of directly identifying, characterizing, and quantifying proteins from a par...

    Authors: Susan M Bridges, G Bryce Magee, Nan Wang, W Paul Williams, Shane C Burgess and Bindu Nanduri
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S24
    Content type: Proceedings Published on:

  25. As the number of fully sequenced genome increases, the need is greater for bioinformatics to predict or annotate genes of a newly sequenced genome. Ever since Eisenberg and his colleagues introduced phylogenet...

    Authors: Raja Loganantharaj and Mazen Atwi
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S25
    Content type: Proceedings Published on:
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