Genome Informatics Vol. 15, No. 1 (2004)

Presented at the Fourth International Workshop on Bioinformatics and Systems Biology
May 31 - June 3, 2004, the Palulu Plaza, Kyoto, Japan

Published as: H. Mamitsuka, T.F. Smith, H-G. Holzhütter, M. Kanehisa, C. DeLisi, R. Heinrich, and S. Miyano (eds.)
"Genome Informatics 2004"
Universal Academy Press, Tokyo, 2004

Preface by Hiroshi Mamitsuka, Temple F. Smith, and Hermann-Georg Holzhütter

Program Committee


Full Talk Papers

A Model of the Mammalian Circadian Oscillator Including the REV-ERBα Module
Sabine Becker-Weimann, Jana Wolf, Achim Kramer, Hanspeter Herzel
Genome Informatics 15(1): 3-12 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Interrelations between Dynamical Properties and Structural Characteristics of Signal Transduction Networks
Bernd Binder, Reinhart Heinrich
Genome Informatics 15(1): 13-23 (2004)
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Cytosolic Processing of Proteasomal Cleavage Products Can Enhance the Presentation Efficiency of MHC-1 Epitopes
Sascha Bulik, Björn Peters, Christian Ebeling, Hergo Holzhütter
Genome Informatics 15(1): 24-34 (2004)
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Structural Analysis of Expanding Metabolic Networks
Oliver Ebenhöh, Thomas Handorf, Reinhart Heinrich
Genome Informatics 15(1): 35-45 (2004)
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Collective Phenomena in Intracellular Processes
Erwin Frey, Andrea Parmeggiani, Thomas Franosch
Genome Informatics 15(1): 46-55 (2004)
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A Simple Method for Inferring Strengths of Protein-Protein Interactions
Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu
Genome Informatics 15(1): 56-68 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Extraction of Species-Specific Glycan Substructures
Yoshiyuki Hizukuri, Yoshihiro Yamanishi, Kosuke Hashimoto, Minoru Kanehisa
Genome Informatics 15(1): 69-81 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Markedly Reduced Evolutionary Rates of Transcription Factors and Cytoplasmic Ribosomal RNAs and Proteins in Higher Vertebrates and Their Evolutionary Implications
Daisuke Hoshiyama, Kei-ichi Kuma, Takashi Miyata
Genome Informatics 15(1): 82-92 (2004)
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Clustering of Database Sequences for Fast Homology Search Using Upper Bounds on Alignment Score
Masumi Itoh, Tatsuya Akutsu, Minoru Kanehisa
Genome Informatics 15(1): 93-104 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Neural Network Method for Identification of RNA-Interacting Residues in Protein
Euna Jeong, I-Fang Chung, Satoru Miyano
Genome Informatics 15(1): 105-116 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Prediction of Cis-Regulatory Elements of Coregulated Genes
Szymon M. Kielbasa, Nils Blüthgen, Christine Sers, Reinhold Schäfer, Hanspeter Herzel
Genome Informatics 15(1): 117-124 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Inferring Dynamic Properties of Biochemical Reaction Networks from Structural Knowledge
Edda Klipp, Wolfram Liebermeister, Christoph Wierling
Genome Informatics 15(1): 125-137 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Model Reduction and Analysis of Robustness for the Wnt/β-Catenin Signal Transduction Pathway
Roland Krüger, Reinhart Heinrich
Genome Informatics 15(1): 138-148 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Constructing Networks with Correlation Maximization Methods
Joseph C. Mellor, Jie Wu, Charles DeLisi
Genome Informatics 15(1): 149-159 (2004)
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Optimizing Protein Representations with Information Theory
Julian Mintseris, Zhiping Weng
Genome Informatics 15(1): 160-169 (2004)
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Detection of Inter-Spread Repeat Sequence in Genomic DNA Sequence
Hiroo Murakami, Nobuyoshi Sugaya, Makihiko Sato, Akira Imaizumi, Sachiyo Aburatani, Katsuhisa Horimoto
Genome Informatics 15(1): 170-179 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Versatile Petri Net Based Architecture for Modeling and Simulation of Complex Biological Processes
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 15(1): 180-197 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Peptide Binding at Class I Major Histocompatibility Complex Scored with Linear Functions and Support Vector Machines
Henning Riedesel, Björn Kolbeck, Oliver Schmetzer, Ernst-Walter Knapp
Genome Informatics 15(1): 198-212 (2004)
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ELISA: A Unified, Multidimensional View of the Protein Domain Universe
Boris E. Shakhnovich, John Max Harvey, Charles DeLisi
Genome Informatics 15(1): 213-220 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Comparisons of Predicted Genetic Modules: Identification of Co-Expressed Genes through Module Gene Flow
Boris E Shakhnovich, Timothy E Reddy, Kevin Galinsky, Joseph Mellor, Charles Delisi
Genome Informatics 15(1): 221-228 (2004)
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Causes for the Large Genome Size in a Cyanobacterium Anabaena sp. PCC7120
Nobuyoshi Sugaya, Makihiko Sato, Hiroo Murakami, Akira Imaizumi, Sachiyo Aburatani, Katsuhisa Horimoto
Genome Informatics 15(1): 229-238 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Gene Expression Module Discovery Using Gibbs Sampling
Chang-Jiun Wu, Yutao Fu, T. M. Murali, Simon Kasif
Genome Informatics 15(1): 239-248 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Extraction of Phylogenetic Network Modules from Prokayrote Metabolic Pathways
Takuji Yamada, Susumu Goto, Minoru Kanehisa
Genome Informatics 15(1): 249-258 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]