Genome Informatics Vol. 16_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

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)
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Knowledge-based Prediction of DNA Atomic Structure from Nucleic Sequence
Marcos J. Araúzo-Bravo, Akinori Sarai
Genome Informatics 16(2): 12-21 (2005)
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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)
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Supporting the Curation of Biological Databases with Reusable Text Mining
Olivo Miotto, Tin Wee Tan, Vladimir Brusic
Genome Informatics 16(2): 32-44 (2005)
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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)
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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)
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Strategies for Genome Reduction in Microbial Genomes
Kishore R. Sakharkar, Vincent T.K. Chow
Genome Informatics 16(2): 69-75 (2005)
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Reassembly and Interfacing Neural Models Registered on Biological Model Databases
Mihoko Otake, Toshihisa Takagi
Genome Informatics 16(2): 76-85 (2005)
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Objective Measurement of Spindle Orientation in Early Caenorhabditis elegans Embryo
Shugo Hamahashi, Shuichi Onami
Genome Informatics 16(2): 86-93 (2005)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Viewing the Proteome from Oligopeptides and Prediction of Protein Function
Hisayuki Horai, Kouichi Doi, Hirofumi Doi
Genome Informatics 16(2): 174-182 (2005)
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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)
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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)
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Reverse Engineering Genetic Networks Using Evolutionary Computation
Nasimul Noman, Hitoshi Iba
Genome Informatics 16(2): 205-214 (2005)
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Toward Integration of Systems Biology Formalism: The Gene Regulatory Networks Case
Raffaella Gentilini
Genome Informatics 16(2): 215-224 (2005)
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Reconstruction of Gene Regulatory Networks under the Finite State Linear Model
Dace Ruklisa, Alvis Brazma, Juris Viksna
Genome Informatics 16(2): 225-236 (2005)
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A Space-Efficient Algorithm for the Constrained Pairwise Sequence Alignment Problem
Dan He Abdullah N. Arslan
Genome Informatics 16(2): 237-246 (2005)
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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)
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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)
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Topology of Mammalian Transcription Networks
Anatolij P. Potapov, Nico Voss, Nicole Sasse, Edgar Wingender
Genome Informatics 16(2): 270-278 (2005)
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Keynote Address

Chemoinformatics, Drug Design, and Systems Biology
Pierre Baldi
Genome Informatics 16(2): 281-285 (2005)
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Membrane Proteins in Vivo and in Silico: Getting the Best of Two Worlds
Gunnar von Heijne
Genome Informatics 16(2): 286-286 (2005)
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Cell-cell Interaction Network That Generates the Skin Pattern of Animal
Shigeru Kondo
Genome Informatics 16(2): 287-291 (2005)
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