Genome Informatics Vol. 17, No. 1 (2006)

Presented at the Sixth International Workshop on Bioinformatics and Systems Biology
July 24-26, 2006, Boston University, USA

Published as: C. DeLisi, M. Kanehisa, R. Heinrich and S. Miyano (eds.)
"Genome Informatics 2006"
Universal Academy Press, Tokyo, 2006

Preface by Charles DeLisi, Minoru Kenehisa and Reinhart Heinrich

Program Committee

  • Full Talk Papers

  • Full Talk Papers

    Multiple Methods for Protein Side Chain Packing Using Maximum Weight Cliques
    J.B. Brown, Dukka Bahadur K.C., Etsuji Tomita, Tatsuya Akutsu
    Genome Informatics 17(1): 3-12 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Computational Methods for Functional Site Identification Suggest a Substrate Access Channel in Transaldolase
    Michael Silberstein, Melissa R. Landon, Yaoyu E. Wang, Andras Perl, Sandor Vajda
    Genome Informatics 17(1): 13-22 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Inferring Protein-Protein Interactions in Viral Proteins by Co-Evolution of Conserved Side Chains
    Yaoyu E Wang, Charles DeLisi
    Genome Informatics 17(1): 23-35 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Systematic Functional Assessment of Human Protein-Protein Interaction Maps
    Gautam Chaurasia, Hanspeter Herzel, Erich E. Wanker, Matthias E. Futschik
    Genome Informatics 17(1): 36-45 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Genomic Data Assimilation for Estimating Hybrid Functional Petri Net from Time-Course Gene Expression Data
    Masao Nagasaki, Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Atsushi Doi, Yoshinori Tamada, Hiroshi Matsuno, Satoru Miyano, Tomoyuki Higuchi
    Genome Informatics 17(1): 46-61 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    SBMLmerge, a System for Combining Biochemical Network Models
    Marvin Schulz, Jannis Uhlendorf, Edda Klipp, Wolfram Liebermeister
    Genome Informatics 17(1): 62-71 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Why Do Cells Cycle with a 24 Hour Period?
    Samuel Bernard, Hanspeter Herzel
    Genome Informatics 17(1): 72-79 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Prediction of Enzyme Kinetic Parameters Based on Statistical Learning
    Simon Borger, Wolfram Liebermeister, Edda Klipp
    Genome Informatics 17(1): 80-87 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Statistical Framework for Genome-Wide Discovery of Biomarker Splice Variations with GeneChip Human Exon 1.0 ST Arrays
    Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano
    Genome Informatics 17(1): 88-99 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Cell Fate Simulation Model of Gustatory Neurons with MicroRNAs Double-Negative Feedback Loop by Hybrid Functional Petri Net with Extension
    Ayumu Saito, Masao Nagasaki, Atushi Doi, Kazuko Ueno, Satoru Miyano
    Genome Informatics 17(1): 100-111 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Combined Pathway to Simulate CDK-Dependent Phosphorylation and ARF-Dependent Stabilization for p53 Transcriptional Activity
    Atsushi Doi, Masao Nagasaki, Kazuko Ueno, Hiroshi Matsuno, Satoru Miyano
    Genome Informatics 17(1): 112-123 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Systematic Detection of Statistically Overrepresented DNA Motif Association Rules
    Jane Marie Lin, Zhiping Weng
    Genome Informatics 17(1): 124-133 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A New Statistical Model to Select Target Sequences Bound by Transcription Factors
    Utz J. Pape, Steffen Grossmann, Stefanie Hammer, Silke Sperling, Martin Vingron
    Genome Informatics 17(1): 134-140 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Design and Biological Evaluation of Photo-Switchable Inhibitors
    Melanie Füllbeck, Elke Michalsky, Ines Stephanie Jaeger, Peter Henklein, Hartmut Kuhn, Karola Rück-Braun, Robert Preissner
    Genome Informatics 17(1): 141-151 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Control of Signal Transduction Cycles: General Results and Application to the Jak-Stat Pathway
    Stephan Beirer, Thomas Höfer
    Genome Informatics 17(1): 152-162 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Structural Analysis of Expressed Metabolic Subnetworks
    Oliver Ebenhöh, Wolfram Liebermeister
    Genome Informatics 17(1): 163-172 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    The Repertoire of Desaturases for Unsaturated Fatty Acid Synthesis in 397 Genomes
    Kosuke Hashimoto, Akiyasu C. Yoshizawa, Koichi Saito, Takuji Yamada, Minoru Kanehisa
    Genome Informatics 17(1): 173-183 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Metabolite Antigens and Pathway Incompatibility
    Wataru Honda, Shuichi Kawashima, Minoru Kanehisa
    Genome Informatics 17(1): 184-194 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Composition of Metabolic Flux Distributions by Functionally Interpretable Minimal Flux Modes (MinModes)
    Sabrina Hoffmann, Andreas Hoppe, Hermann-Georg Holzhütter
    Genome Informatics 17(1): 195-207 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Patterns of Interactions of Reaction Pairs in Metabolic Networks
    József Bruck, Oliver Ebenhöh, Reinhart Heinrich
    Genome Informatics 17(1): 208-218 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A High Percentage of Introns in Human Genes Were Present Early in Animal Evolution: Evidence from the Basal Metazoan Nematostella vectensis
    James C. Sullivan, Adam M. Reitzel, John R. Finnerty
    Genome Informatics 17(1): 219-229 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Analysis of the Differences in Metabolic Network Expansion between Prokaryotes and Eukaryotes
    Michihiro Tanaka Takuji Yamada Masumi Itoh, Shujiro Okuda Susumu Goto Minoru Kanehisa
    Genome Informatics 17(1): 230-239 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    About the Interrelation of Evolutionary Rate and Protein Age
    Hannes Luz, Eike Staub, Martin Vingron
    Genome Informatics 17(1): 240-250 (2006)
    [Abstract]   [Full-text HTML]   [Full-text PDF]