Genome Informatics Vol.23 (2009)

Presented at the The 20th International Conference on Genome Informatics
December 14 - 16, 2009, PACIFICO YOKOHAMA, Japan

Published as: Shinichi Morishita, Sang Yup Lee and Yasubumi Sakakibara
"Genome Informatics Vol.23 (2009)"
Imperial College Press, London

Preface by Shinichi Morishita, Sang Yup Lee and Yasubumi Sakakibara

Acknowlegments

Program Committee

  • Full Talk Papers
  • Keynote Address

    • Papers

    Predicting Protein-Protein Relationships from Literature Using Latent Topics
    Tatsuya Aso, Koji Eguchi
    Genome Informatics Vol.23 (2009): 3-12
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Evaluation of DNA Intramolecular Interactions for Nucleosome Positioning in Yeast
    Michael Fernandez, Satoshi Fujii, Hidetoshi Kono, Akinori Sarai
    Genome Informatics Vol.23 (2009): 13-20
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Quality Control and Reproducibility in DNA Microarray Experiments
    André Fujita, João Sato, Fernando H.L daSilva, Maria C. Galvaõo, Mari C.Sogayar, Satoru Miyano
    Genome Informatics Vol.23 (2009): 21-31
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Comparative Analysis of Topological Patterns in Different Mammalian Networks
    Bjoern Goemann, AnatolijP. Potapov, Michael Ante, Edgar Wingender
    Genome Informatics Vol.23 (2009): 32-45
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Tools for Investigating Mechanisms of Antigenic Variation: New Extensions to varDB
    C.Nelson Hayes, Diego Diez, Nicolas Joannin, Minoru Kanehisa, Mats Wahlgren, Craig E. Wheelock, Susumu Goto
    Genome Informatics Vol.23 (2009): 46-59
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Localized Suffix Array and Its Application to Genome Mapping Problems for Paired-End Short Reads
    Kouichi Kimura, Asako Koike
    Genome Informatics Vol.23 (2009): 60-71
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Comparative Analysis of Aerobic and Anaerobic Prokaryotes to Identify Correlation between Oxygen Requirement and Gene-Gene Functional Association Patterns
    Yaming Lin, Hongwei Wu
    Genome Informatics Vol.23 (2009): 72-84
    [Abstract]   [Full-text HTML]   [Full-text PDF] [Supplementary Data]

    Calculation of Protein-Ligand Binding Free Energy Using Smooth Reaction Path Generation (SRPG) Method; a Comparison of the Explicit Water Model, GB/SA Model and Docking Score Function
    Daisuke Mitomo, Yoshifumi Fukunishi, Junichi Higo, Haruki Nakamura
    Genome Informatics Vol.23 (2009): 85-97
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Structural Insights into the Enzyme Mechanism of a New Family of D-2-Hydroxyacid Dehydrogenases, a Close Homolog of 2-Ketopantoate Reductase
    Sukanta Mondal, Kenji Mizuguchi
    Genome Informatics Vol.23 (2009): 98-105
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Comprehensive Analysis of Sequence-Structure Relationships in the Loop Regions of Proteins
    Shugo Nakamura, Kentaro Shimizu
    Genome Informatics Vol.23 (2009): 106-116
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    The Prediction of Local Modular Structures in a Co-Expression Network Based on Gene Expression Datasets
    Yoshiyuki Ogata, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Kazuki Saito, Daisuke Shibata
    Genome Informatics Vol.23 (2009): 117-127
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Gradient-Based Optimization of Hyperparameters for Base-Pairing Profile Local Alignment Kernels
    Kengo Sato, Yutaka Saito, Yasubumi Sakakibara
    Genome Informatics Vol.23 (2009): 128-138
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Method for Efficient Execution of Bioinformatics Workflows
    Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    Genome Informatics Vol.23 (2009): 139-148
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Development of a New Meta-Score for Protein Structure Prediction from Seven All-Atom Distance Dependent Potentials Using Support Vector Regression
    Matsuyuki Shirota, Takashi Ishida, Kengo Kinoshita
    Genome Informatics Vol.23 (2009): 149-158
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Refining Markov Clustering for Protein Complex Prediction by Incorporating Core-Attachment Structure
    Sriganesh Srihari, Kang Ning, HonWai Leong
    Genome Informatics Vol.23 (2009): 159-168
    [Abstract]   [Full-text HTML]   [Full-text PDF] [Supplementary Data]

    An Assessment of Prediction Algorithms for Nucleosome Positioning
    Yoshiaki Tanaka, Kenta Nakai
    Genome Informatics Vol.23 (2009): 169-178
    [Abstract]   [Full-text HTML]   [Full-text PDF] [Supplementary Data]

    Cancer Classification Using Single Genes
    Xiaosheng Wang, Osamu Gotoh
    Genome Informatics Vol.23 (2009): 179-188
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    RECOUNT: Expectation Maximization Based Error Correction Tool for Next Generation Sequencing Data
    Edward Wijaya, Martin Frith, Yutaka Suzuki, Paul Horton
    Genome Informatics Vol.23 (2009): 189-201
    [Abstract]   [Full-text HTML]   [Full-text PDF] [Supplementary Data]

    Keynote Address

    A New Generation of Homology Search Tools Based on Probabilistic Inference
    Sean R. Eddy
    Genome Informatics Vol.23 (2009): 205-211
    [Full-text HTML]   [Full-text PDF]

    Representation and Analysis of Molecular Networks Involving Diseases and Drugs
    Minoru Kanehisa
    Genome Informatics Vol.23 (2009): 212-213
    [Full-text HTML]   [Full-text PDF]

    Systems Biotechnology
    Sang Yup Lee
    Genome Informatics Vol.23 (2009): 214-216
    [Full-text HTML]   [Full-text PDF]

    Strategies Toward CNS-Regeneration Using Induced Pluripotent Stem Cells
    Hideyuki Okano
    Genome Informatics Vol.23 (2009): 217-220
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Thinking Laterally About Genomes
    Mark A. Ragan
    Genome Informatics Vol.23 (2009): 221-222
    [Full-text HTML]   [Full-text PDF]