Genome Informatics Vol. 17, No. 2 (2006)

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Genome Informatics Vol. 17, No. 2 (2006)

Presented at the 17th International Conference on Genome Informatics
December 18-20, Yokohama Pacifico, Japan

Published as: Y. Sakakibara, Temple F. Smith, M. Kanehisa, S. Miyano, and T. Takagi (eds.)
"Genome Informatics 2006"
Universal Academy Press, Tokyo,

Preface by Yasubumi Sakakibara and Temple Smith

Program Committee

 


 

  • Full Talk Papers
  • Keynote Address
  •  


     

    Full Talk Papers

    Hybrid Gibbs-Sampling Algorithm for Challenging Motif Discovery: GibbsDST
    Kazuhito Shida
    Genome Informatics 17(2): 3-13 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Computational Annotation of Transcription Factor Binding Sites in D. Melanogaster Developmental Genes
    Vipin Narang, Wing-Kin Sung, Ankush Mittal
    Genome Informatics 17(2): 14-24 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Gram Distribution Kernel Applied to Glycan Classification and Motif Extraction
    Tetsuji Kuboyama, Kouichi Hirata, Kiyoko F. Aoki-Kinoshita, Hisashi Kashima, Hiroshi Yasuda
    Genome Informatics 17(2): 25-34 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Discovering Signal Transduction Networks Using Signaling Domain-Domain Interactions
    Thanh Phuong Nguyen, Tu Bao Ho
    Genome Informatics 17(2): 35-45 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Finding Conserved and Non-Conserved Reactions Using a Metabolic Pathway Alignment Algorithm
    José C. Clemente, Kenji Satou, Gabriel Valiente
    Genome Informatics 17(2): 46-56 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

    A Function-Centric Approach to the Biological Interpretation of Microarray Time-Series
    Pablo Minguez, Fátima Al-Shahrour, Joaquín Dopazo
    Genome Informatics 17(2): 57-66 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    RaPiDS: An Algorithm for Rapid Expression Profile Database Search
    Paul B. Horton, Larisa Kiseleva, Wataru Fujibuchi
    Genome Informatics 17(2): 67-76 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Development of an Approach for Ab Initio Estimation of Compound-Induced Liver Injury Based on Global Gene Transcriptional Profiles
    Xudong Dai, Yudong D. He, Hongyue Dai, Pek Y. Lum, Christopher J. Roberts, Jeffrey F. Waring, Roger G. Ulrich
    Genome Informatics 17(2): 77-88 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

    The Distribution and Deposition Algorithm for Multiple Oligo Nucleotide Arrays
    Kang Ning, Hon Wai Leong
    Genome Informatics 17(2): 89-99 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Detection and Restoration of Hybridization Problems in Affymetrix GeneChip Data by Parametric Scanning
    Tomokazu Konishi
    Genome Informatics 17(2): 100-109 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

    Gene Ontology Annotation by Density and Gravitation Models
    Wen-Juan Hou, Kevin Hsin-Yih Lin, Hsin-Hsi Chen
    Genome Informatics 17(2): 110-120 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Text Mining and Protein Annotations: the Construction and Use of Protein Description Sentences
    Martin Krallinger, Rainer Malik, Alfonso Valencia
    Genome Informatics 17(2): 121-130 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

    Assessing Clustering Results with Reference Taxonomies
    Gabriel Valiente
    Genome Informatics 17(2): 131-140 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Pairwise Alignment with Rearrangements
    Le Sy Vinh, Andrés Varón, Ward C. Wheeler
    Genome Informatics 17(2): 141-151 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Techniques for Multi-Genome Synteny Analysis to Overcome Assembly Limitations
    Arjun Bhutkar, Susan Russo, Temple F. Smith, William M. Gelbart
    Genome Informatics 17(2): 152-161 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Markov Chain Model for Haplotype Assembly from SNP Fragments
    Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen
    Genome Informatics 17(2): 162-171 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    MetaClustering: Discovery of The Different Sample Clusterings in Gene Expression Data
    David Venet, Hugues Bersini, Hitoshi Iba
    Genome Informatics 17(2): 172-183 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

    Biomarkers for Epithelial Ovarian Cancers
    Pritha Mahata
    Genome Informatics 17(2): 184-193 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    PepSOM: An Algorithm for Peptide Identification by Tandem Mass Spectrometry Based on SOM
    Kang Ning, Hoong Kee Ng, Hon Wai Leong
    Genome Informatics 17(2): 194-205 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    DAPID: A 3D-Domain Annotated Protein-Protein Interaction Database
    Yung-Chiang Chen, Heng-Chu Chen, Jinn-Moon Yang
    Genome Informatics 17(2): 206-215 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Method to Detect Important Residues Using Protein Binding Site Comparison
    Keunwan Park, Dongsup Kim
    Genome Informatics 17(2): 216-225 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Modeling and Estimation of Dynamic EGFR Pathway by Data Assimilation Approach Using Time Series Proteomic Data
    Shinya Tasaki, Masao Nagasaki, Masaaki Oyama, Hiroko Hata, Kazuko Ueno, Ryo Yoshida, Tomoyuki Higuchi, Sumio Sugano, Satoru Miyano
    Genome Informatics 17(2): 226-238 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

    A Large-Scale Computational Approach to Drug Repositioning
    Yvonne Y. Li, Jianghong An, Steven J.M. Jones
    Genome Informatics 17(2): 239-247 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Generalized Threading Model Using Integer Programming that Allows for Secondary Structure Element Deletion
    Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu
    Genome Informatics 17(2): 248-258 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Protein Topology Classification Using Two-Stage Support Vector Machines
    Jayavardhana Gubbi, Alistair Shilton, Michael Parker, Marimuthu Palaniswami
    Genome Informatics 17(2): 259-269 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Robotic Path Planning and Protein Complex Modeling Considering Low Frequency Intra-Molecular Loop and Domain Motions
    Carlos A. Del Carpio, Pei Qiang, Eiichiro Ichiishi, Hideyuki Tsuboi, Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Momoji Kubo, Akira Miyamoto
    Genome Informatics 17(2): 270-278 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Keynote Address

    RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
    Ivo L Hofacker
    Genome Informatics 17(2): 281-282 (2006)
    [Full-text HTML]   [Full-text PDF]

    The New Phase of Transcriptome Analysis
    Yoshihide Hayashizaki
    Genome Informatics 17(2): 283-283 (2006)
    [Full-text HTML]   [Full-text PDF]

    Increasing Confidence of Protein-Protein Interactomes
    Jin Chen, Hon Nian Chua, Wynne Hsu, Mong-Li Lee, See-Kiong Ng, Rintaro Saito, Wing-Kin Sung, Limsoon Wong
    Genome Informatics 17(2): 284-297 (2006)
    [Full-text HTML]   [Full-text PDF]