Volume 7 Supplement 2

Third Annual MCBIOS Conference. Bioinformatics: A Calculated Discovery


Edited by Jonathan D Wren (Senior Editor), Stephen Winters-Hilt, Yuriy Gusev, Andrey Ptitsyn

Third Annual MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. Bioinformatics: A Calculated Discovery.

Baton Rouge, LA, USA

2-4 March, 2006

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  1. Proceedings

    A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity

    Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is p...

    Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O Elasri and Youping Deng

    BMC Bioinformatics 2006 7(Suppl 2):S2

    Published on: 26 September 2006

  2. Proceedings

    Support Vector Machine Implementations for Classification & Clustering

    We describe Support Vector Machine (SVM) applications to classification and clustering of channel current data. SVMs are variational-calculus based methods that are constrained to have structural risk minimiza...

    Stephen Winters-Hilt, Anil Yelundur, Charlie McChesney and Matthew Landry

    BMC Bioinformatics 2006 7(Suppl 2):S4

    Published on: 26 September 2006

  3. Proceedings

    RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers

    Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selec...

    Venkata Thodima, Mehdi Pirooznia and Youping Deng

    BMC Bioinformatics 2006 7(Suppl 2):S6

    Published on: 26 September 2006

  4. Proceedings

    EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

    Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed E

    Laila A Nahum, Matthew T Reynolds, Zhengyuan O Wang, Jeremiah J Faith, Rahul Jonna, Zhi J Jiang, Thomas J Meyer and David D Pollock

    BMC Bioinformatics 2006 7(Suppl 2):S7

    Published on: 26 September 2006

  5. Proceedings

    Independent Component Analysis-motivated Approach to Classificatory Decomposition of Cortical Evoked Potentials

    Independent Component Analysis (ICA) proves to be useful in the analysis of neural activity, as it allows for identification of distinct sources of activity. Applied to measurements registered in a controlled ...

    Tomasz G Smolinski, Roger Buchanan, Grzegorz M Boratyn, Mariofanna Milanova and Astrid A Prinz

    BMC Bioinformatics 2006 7(Suppl 2):S8

    Published on: 26 September 2006

  6. Proceedings

    Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells

    The Thymidine kinase (Tk) mutants generated from the widely used L5178Y mouse lymphoma assay fall into two categories, small colony and large colony. Cells from the large colonies grow at a normal rate while cell...

    Tao Han, Jianyong Wang, Weida Tong, Martha M Moore, James C Fuscoe and Tao Chen

    BMC Bioinformatics 2006 7(Suppl 2):S9

    Published on: 26 September 2006

  7. Proceedings

    Permutation test for periodicity in short time series data

    Periodic processes, such as the circadian rhythm, are important factors modulating and coordinating transcription of genes governing key metabolic pathways. Theoretically, even small fluctuations in the orches...

    Andrey A Ptitsyn, Sanjin Zvonic and Jeffrey M Gimble

    BMC Bioinformatics 2006 7(Suppl 2):S10

    Published on: 26 September 2006

  8. Proceedings

    Hidden Markov Model Variants and their Application

    Markov statistical methods may make it possible to develop an unsupervised learning process that can automatically identify genomic structure in prokaryotes in a comprehensive way. This approach is based on mu...

    Stephen Winters-Hilt

    BMC Bioinformatics 2006 7(Suppl 2):S14

    Published on: 26 September 2006

  9. Proceedings

    DNA Molecule Classification Using Feature Primitives

    We present a novel strategy for classification of DNA molecules using measurements from an alpha-Hemolysin channel detector. The proposed approach provides excellent classification performance for five differe...

    Raja Tanveer Iqbal, Matthew Landry and Stephen Winters-Hilt

    BMC Bioinformatics 2006 7(Suppl 2):S15

    Published on: 26 September 2006

  10. Proceedings

    Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale)

    Comfrey is consumed by humans as a vegetable and a tea, and has been used as an herbal medicine for more than 2000 years. Comfrey, however, is hepatotoxic in livestock and humans and carcinogenic in experiment...

    Nan Mei, Lei Guo, Lu Zhang, Leming Shi, Yongming Andrew Sun, Chris Fung, Carrie L Moland, Stacey L Dial, James C Fuscoe and Tao Chen

    BMC Bioinformatics 2006 7(Suppl 2):S16

    Published on: 26 September 2006

  11. Proceedings

    Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions

    DNA microarrays, which have been increasingly used to monitor mRNA transcripts at a global level, can provide detailed insight into cellular processes involved in response to drugs and toxins. This is leading ...

    Tao Han, Cathy D Melvin, Leming Shi, William S Branham, Carrie L Moland, P Scott Pine, Karol L Thompson and James C Fuscoe

    BMC Bioinformatics 2006 7(Suppl 2):S17

    Published on: 26 September 2006

  12. Proceedings

    Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor α agonists

    Fibrates are a unique hypolipidemic drugs that lower plasma triglyceride and cholesterol levels through their action as peroxisome proliferator-activated receptor alpha (PPARα) agonists. The activation of PPAR...

    Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey Dial, Alex Wong, Kshama Mehta, Ernice Blann, Leming Shi, Weida Tong and Yvonne P Dragan

    BMC Bioinformatics 2006 7(Suppl 2):S18

    Published on: 26 September 2006

  13. Proceedings

    Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats

    Aristolochic acid (AA) is the active component of herbal drugs derived from Aristolochia species that have been used for medicinal purposes since antiquity. AA, however, induced nephropathy and urothelial cancer ...

    Tao Chen, Lei Guo, Lu Zhang, Leming Shi, Hong Fang, Yongming Sun, James C Fuscoe and Nan Mei

    BMC Bioinformatics 2006 7(Suppl 2):S20

    Published on: 26 September 2006

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