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

Evaluating Distance Functions for Clustering Tandem Repeats
Suyog Rao, Alfredo Rodriguez, Gary Benson
Genome Informatics 16(1): 3-12 (2005)
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Relationship between Segmental Duplications and Repeat Sequences in Human Chromosome 7
Hiroo Murakami, Sachiyo Aburatani, Katsuhisa Horimoto
Genome Informatics 16(1): 13-21 (2005)
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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)
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A Gibbs Sampling Approach to Detection of Tree Motifs
Lidio Marx Carvalho Meireles, Tatsuya Akutsu
Genome Informatics 16(1): 34-43 (2005)
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Antiviral Activity of Oligomerization-Deficient Stat1
Uwe Vinkemeier, Thomas Meyer
Genome Informatics 16(1): 44-48 (2005)
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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)
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Assessing Transcription Factor Motif Drift from Noisy Decoy Sequences
Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich
Genome Informatics 16(1): 59-67 (2005)
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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)
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On the Kinetic Design of Transcription
Thomas Höfer, Malte J. Rasch
Genome Informatics 16(1): 73-82 (2005)
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Integrating Genomic Data to Predict Transcription Factor Binding
Dustin T. Holloway, Mark Kon, Charles DeLisi
Genome Informatics 16(1): 83-94 (2005)
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Elucidation of the Relationships between LexA-Regulated Genes in the SOS Response
Sachiyo Aburatani, Katsuhisa Horimoto
Genome Informatics 16(1): 95-105 (2005)
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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)
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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)
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Comparative Analysis of Cell Cycle Regulated Genes in Eukaryotes
Jerzy Dyczkowski, Martin Vingron
Genome Informatics 16(1): 125-131 (2005)
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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)
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Deciphering Protein Network Organization Using Phylogenetic Profile Groups
Jie Wu, Joseph C. Mellor, Charles DeLisi
Genome Informatics 16(1): 142-149 (2005)
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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)
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Lethality and Entropy of Protein Interaction Networks
Thomas Manke, Lloyd Demetrius, Martin Vingron
Genome Informatics 16(1): 159-163 (2005)
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Structural and Dynamical Analyses of the Kinase Network Derived from the Transpath Database
Bernd Binder, Reinhart Heinrich
Genome Informatics 16(1): 164-173 (2005)
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Comparative Analysis of DNA-Binding Proteins between Thermophilic and Mesophilic Bacteria
Masashi Fujita, Minoru Kanehisa
Genome Informatics 16(1): 174-181 (2005)
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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)
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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)
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A Cross Species Comparison of Metabolic Network Functions
Oliver Ebenhöh, Thomas Handorf, Reinhart Heinrich
Genome Informatics 16(1): 203-213 (2005)
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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)
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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)
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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)
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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)
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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)
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Aggregation in Huntington's Disease: Insights through Modelling
Branka Cajavec, Samuel Bernard, Hanspeter Herzel
Genome Informatics 16(1): 262-271 (2005)
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Autoimmune Diseases and Peptide Variations
Wataru Honda, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 16(1): 272-280 (2005)
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