Genome Informatics Vol. 16, No. 2 (2005)

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Genome Informatics Vol. 16, No. 2 (2005)

Presented at the Sixteenth International Conference on Genome Informatics
December 19-21, 2005, Yokohama Pacifico, Japan

Published as: R. Heinrich, H. Mamitsuka, M. Kanehisa, S. Miyano, and T. Takagi (eds.)
"Genome Informatics 2005"
Universal Academy Press, Tokyo, 2005

Preface by Reinhart Heinrich and Hiroshi Mamitsuka

Program Committee

 


 

  • Full Talk Papers
  • Keynote Address
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    Full Talk Papers

    Qualitatively Predicting Acetylation and Methylation Areas in DNA Sequences
    Tho Hoan Pham, Dang Hung Tran, Tu Bao Ho, Kenji Satou, Gabriel Valiente
    Genome Informatics 16(2): 3-11 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Knowledge-based Prediction of DNA Atomic Structure from Nucleic Sequence
    Marcos J. Araúzo-Bravo, Akinori Sarai
    Genome Informatics 16(2): 12-21 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Automatic Drawing of Biological Networks Using Cross Cost and Subcomponent Data
    Mitsuru Kato, Masao Nagasaki, Atsushi Doi, Satoru Miyano
    Genome Informatics 16(2): 22-31 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Supporting the Curation of Biological Databases with Reusable Text Mining
    Olivo Miotto, Tin Wee Tan, Vladimir Brusic
    Genome Informatics 16(2): 32-44 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Reconstruction of Phylogenetic Relationships from Metabolic Pathways Based on the Enzyme Hierarchy and the Gene Ontology
    José C. Clemente, Kenji Satou, Gabriel Valiente
    Genome Informatics 16(2): 45-55 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Mass Identification of Chloroplast Proteins of Endosymbiont Origin by Phylogenetic Profiling Based on Organism-Optimized Homologous Protein Groups
    Naoki Sato, Masayuki Ishikawa, Makoto Fujiwara, Kintake Sonoike
    Genome Informatics 16(2): 56-68 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Strategies for Genome Reduction in Microbial Genomes
    Kishore R. Sakharkar, Vincent T.K. Chow
    Genome Informatics 16(2): 69-75 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Reassembly and Interfacing Neural Models Registered on Biological Model Databases
    Mihoko Otake, Toshihisa Takagi
    Genome Informatics 16(2): 76-85 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Objective Measurement of Spindle Orientation in Early Caenorhabditis elegans Embryo
    Shugo Hamahashi, Shuichi Onami
    Genome Informatics 16(2): 86-93 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Evolution from Possible Primitive tRNA-Viroids to Early Poly-tRNA-Derived mRNAs: A New Approach from the Poly-tRNA Theory
    Koji Ohnishi, Madoka Ohshima, Naotaka Furuichi
    Genome Informatics 16(2): 94-103 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Study of Fragment-Based Protein Structure Prediction: Biased Fragment Replacement for Searching Low-Energy Conformation
    Sung-Joon Park
    Genome Informatics 16(2): 104-113 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Comparison of Protein Structures by Multi-Objective Optimization
    Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang, Shihua Zhang, Xiang-Sun Zhang
    Genome Informatics 16(2): 114-124 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Statistical Evaluation of a Bottom-Up Clustering for Single Particle Molecular Images
    Yutaka Ueno, Katsunori Isono, Katsutoshi Takahashi, Yukio Shimonohara, Kiyoshi Asai
    Genome Informatics 16(2): 125-135 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Inter-Species Validation for Domain Combination Based Protein-Protein Interaction Prediction Method
    Woo-Hyuk Jang, Dong-Soo Han, Hong-Soog Kim, Sung-Doke Lee
    Genome Informatics 16(2): 136-147 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Graph Theoretical Approach for Analysis of Protein Flexibility Change at Protein Complex Formation
    Carlos A. Del Carpio M., Abdul Rajjak Shaikh, Eichiro Ichiishi, Michihisa Koyama, Momoji Kubo, Kazumi Nishijima, Akira Miyamoto
    Genome Informatics 16(2): 148-160 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Fast Protein-Protein Docking Algorithm Using Series Expansion in Terms of Spherical Basis Functions
    Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
    Genome Informatics 16(2): 161-173 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Viewing the Proteome from Oligopeptides and Prediction of Protein Function
    Hisayuki Horai, Kouichi Doi, Hirofumi Doi
    Genome Informatics 16(2): 174-182 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Mass Distributed Clustering: A New Algorithm for Repeated Measurements in Gene Expression Data
    Shinya Matsumoto, Ken-ichi Aisaki, Jun Kanno
    Genome Informatics 16(2): 183-194 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Diagnosis of Early Relapse in Ovarian Cancer Using Serum Proteomic Profiling
    Jung Hun Oh, Jean Gao, Animesh Nandi, Prem Gurnani, Lynne Knowles, John Schorge, Kevin P. Rosenblatt
    Genome Informatics 16(2): 195-204 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Reverse Engineering Genetic Networks Using Evolutionary Computation
    Nasimul Noman, Hitoshi Iba
    Genome Informatics 16(2): 205-214 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Toward Integration of Systems Biology Formalism: The Gene Regulatory Networks Case
    Raffaella Gentilini
    Genome Informatics 16(2): 215-224 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Reconstruction of Gene Regulatory Networks under the Finite State Linear Model
    Dace Ruklisa, Alvis Brazma, Juris Viksna
    Genome Informatics 16(2): 225-236 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Space-Efficient Algorithm for the Constrained Pairwise Sequence Alignment Problem
    Dan He Abdullah N. Arslan
    Genome Informatics 16(2): 237-246 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Prediction of Functional Modules Based on Gene Distributions in Microbial Genomes
    Hongwei Wu, Fenglou Mao, Zhengchang Su, Victor Olman, Ying Xu
    Genome Informatics 16(2): 247-259 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Interaction Graph Mining for Protein Complexes Using Local Clique Merging
    Xiao-Li Li, Soon-Heng Tan, Chuan-Sheng Foo, See-Kiong Ng
    Genome Informatics 16(2): 260-269 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Topology of Mammalian Transcription Networks
    Anatolij P. Potapov, Nico Voss, Nicole Sasse, Edgar Wingender
    Genome Informatics 16(2): 270-278 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Keynote Address

    Chemoinformatics, Drug Design, and Systems Biology
    Pierre Baldi
    Genome Informatics 16(2): 281-285 (2005)
    [Full-text HTML]   [Full-text PDF]

    Membrane Proteins in Vivo and in Silico: Getting the Best of Two Worlds
    Gunnar von Heijne
    Genome Informatics 16(2): 286-286 (2005)
    [Full-text HTML]   [Full-text PDF]

    Cell-cell Interaction Network That Generates the Skin Pattern of Animal
    Shigeru Kondo
    Genome Informatics 16(2): 287-291 (2005)
    [Full-text HTML]   [Full-text PDF]