Genome Informatics Vol. 17_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

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)
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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)
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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)
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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)
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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)
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SBMLmerge, a System for Combining Biochemical Network Models
Marvin Schulz, Jannis Uhlendorf, Edda Klipp, Wolfram Liebermeister
Genome Informatics 17(1): 62-71 (2006)
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Why Do Cells Cycle with a 24 Hour Period?
Samuel Bernard, Hanspeter Herzel
Genome Informatics 17(1): 72-79 (2006)
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Prediction of Enzyme Kinetic Parameters Based on Statistical Learning
Simon Borger, Wolfram Liebermeister, Edda Klipp
Genome Informatics 17(1): 80-87 (2006)
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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)
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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)
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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)
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Systematic Detection of Statistically Overrepresented DNA Motif Association Rules
Jane Marie Lin, Zhiping Weng
Genome Informatics 17(1): 124-133 (2006)
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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)
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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)
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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)
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Structural Analysis of Expressed Metabolic Subnetworks
Oliver Ebenhöh, Wolfram Liebermeister
Genome Informatics 17(1): 163-172 (2006)
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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)
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Metabolite Antigens and Pathway Incompatibility
Wataru Honda, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 17(1): 184-194 (2006)
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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)
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Patterns of Interactions of Reaction Pairs in Metabolic Networks
József Bruck, Oliver Ebenhöh, Reinhart Heinrich
Genome Informatics 17(1): 208-218 (2006)
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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)
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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)
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About the Interrelation of Evolutionary Rate and Protein Age
Hannes Luz, Eike Staub, Martin Vingron
Genome Informatics 17(1): 240-250 (2006)
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