Genome Informatics Vol. 16, No. 1 (2005)

Presented at the Fifth International Workshop on Bioinformatics and Systems Biology
August 22-25, 2005, Humboldt University Berlin, Germany

Published as: R. Heinrich, C. DeLisi, M. Kanehisa, and S. Miyano (eds.)
"Genome Informatics 2005"
Universal Academy Press, Tokyo, 2005

Preface by Reinhart Heinrich, Charles Delisi, and Minoru Kanehisa

Program Committee


  • Full Talk Papers

  • Full Talk Papers

    Evaluating Distance Functions for Clustering Tandem Repeats
    Suyog Rao, Alfredo Rodriguez, Gary Benson
    Genome Informatics 16(1): 3-12 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Relationship between Segmental Duplications and Repeat Sequences in Human Chromosome 7
    Hiroo Murakami, Sachiyo Aburatani, Katsuhisa Horimoto
    Genome Informatics 16(1): 13-21 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Improvement in the Accuracy of Multiple Sequence Alignment Program MAFFT
    Kazutaka Katoh, Kei-ichi Kuma, Takashi Miyata, Hiroyuki Toh
    Genome Informatics 16(1): 22-33 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Gibbs Sampling Approach to Detection of Tree Motifs
    Lidio Marx Carvalho Meireles, Tatsuya Akutsu
    Genome Informatics 16(1): 34-43 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Antiviral Activity of Oligomerization-Deficient Stat1
    Uwe Vinkemeier, Thomas Meyer
    Genome Informatics 16(1): 44-48 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Identification of Conserved Structural Features at Sequentially Degenerate Locations in Transcription Factor Binding Sites
    Heather E. Burden, Zhiping Weng
    Genome Informatics 16(1): 49-58 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Assessing Transcription Factor Motif Drift from Noisy Decoy Sequences
    Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich
    Genome Informatics 16(1): 59-67 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Improvement of TRANSFAC Matrices Using Multiple Local Alignment of Transcription Factor Binding Site Sequences
    Yutao Fu, Zhiping Weng
    Genome Informatics 16(1): 68-72 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    On the Kinetic Design of Transcription
    Thomas Höfer, Malte J. Rasch
    Genome Informatics 16(1): 73-82 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Integrating Genomic Data to Predict Transcription Factor Binding
    Dustin T. Holloway, Mark Kon, Charles DeLisi
    Genome Informatics 16(1): 83-94 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Elucidation of the Relationships between LexA-Regulated Genes in the SOS Response
    Sachiyo Aburatani, Katsuhisa Horimoto
    Genome Informatics 16(1): 95-105 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Biological Profiling of Gene Groups utilizing Gene Ontology
    Nils Blüthgen, Karsten Brand, Branka Cajavec, Maciej Swat, Hanspeter Herzel, Dieter Beule
    Genome Informatics 16(1): 106-115 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Conservation of Gene Co-Regulation between Two Prokaryotes: Bacillus subtilis and Escherichia coli
    Shujiro Okuda, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa
    Genome Informatics 16(1): 116-124 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Comparative Analysis of Cell Cycle Regulated Genes in Eukaryotes
    Jerzy Dyczkowski, Martin Vingron
    Genome Informatics 16(1): 125-131 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Efficient Determination of Cluster Boundaries for Analysis of Gene Expression Profile Data Using Hierarchical Clustering and Wavelet Transform
    Harry Amri Moesa, Dukka Bahadur K.C., Tatsuya Akutsu
    Genome Informatics 16(1): 132-141 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Deciphering Protein Network Organization Using Phylogenetic Profile Groups
    Jie Wu, Joseph C. Mellor, Charles DeLisi
    Genome Informatics 16(1): 142-149 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Comprehensive Analysis and Prediction of Synthetic Lethality Using Subcellular Locations
    Takuji Yamada, Shuichi Kawashima, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa
    Genome Informatics 16(1): 150-158 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Lethality and Entropy of Protein Interaction Networks
    Thomas Manke, Lloyd Demetrius, Martin Vingron
    Genome Informatics 16(1): 159-163 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Structural and Dynamical Analyses of the Kinase Network Derived from the Transpath Database
    Bernd Binder, Reinhart Heinrich
    Genome Informatics 16(1): 164-173 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Comparative Analysis of DNA-Binding Proteins between Thermophilic and Mesophilic Bacteria
    Masashi Fujita, Minoru Kanehisa
    Genome Informatics 16(1): 174-181 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Identifying Drug Active Pathways from Gene Networks Estimated by Gene Expression Data
    Yoshinori Tamada, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
    Genome Informatics 16(1): 182-191 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Prediction of Debacle Points for Robustness of Biological Pathways by Using Recurrent Neural Networks
    Hironori Kitakaze, Hiroshi Matsuno, Nobuhiko Ikeda, Satoru Miyano
    Genome Informatics 16(1): 192-202 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Cross Species Comparison of Metabolic Network Functions
    Oliver Ebenhöh, Thomas Handorf, Reinhart Heinrich
    Genome Informatics 16(1): 203-213 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Global Representation of the Carbohydrate Structures: A Tool for the Analysis of Glycan
    Kosuke Hashimoto, Shin Kawano, Susumu Goto, Kiyoko F. Aoki-Kinoshita, Masayuki Kawashima, Minoru Kanehisa
    Genome Informatics 16(1): 214-222 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Combining Bioinformatics Resources for the Structural Modelling of Eukaryotic Metabolic Networks
    Christoph Gille, Sabrina Hoffmann, Hermann-Georg Holzhütter
    Genome Informatics 16(1): 223-232 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Robust Diagnosis of Non-Hodgkin Lymphoma Phenotypes Validated on Gene Expression Data from Different Laboratories
    Gyan Bhanot, Gabriela Alexe, Arnold J. Levine, Gustavo Stolovitzky
    Genome Informatics 16(1): 233-244 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Simple Discriminant Functions Identify Small Sets of Genes that Distinguish Cancer Phenotype from Normal
    Gul S. Dalgin, Charles DeLisi
    Genome Informatics 16(1): 245-253 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Selecting Stable Molecular Targets for Treatment and Prevention of AIDS
    Yaoyu E Wang, Chao Zhang, Jay Berzofsky, Charles DeLisi
    Genome Informatics 16(1): 254-261 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Aggregation in Huntington's Disease: Insights through Modelling
    Branka Cajavec, Samuel Bernard, Hanspeter Herzel
    Genome Informatics 16(1): 262-271 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Autoimmune Diseases and Peptide Variations
    Wataru Honda, Shuichi Kawashima, Minoru Kanehisa
    Genome Informatics 16(1): 272-280 (2005)
    [Abstract]   [Full-text HTML]   [Full-text PDF]