Genome Informatics Vol. 18 (2007)

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Genome Informatics Vol. 18 (2007)

Presented at the The Seventh Annual International Workshop on Bioinformatics and Systems Biology
July 31 - August 2, 2007, Institute of Medical Science, The University of Tokyo, Japan

Published as: S. Miyano, C. DeLisi, H.-G. Holzhütter, M. Kanehisa
"Genome Informatics Vol. 18"
Imperial College Press, London

Dedicated to Prof. Dr.Dr. hc. Reinhart Heinrich (1946 ∼ 2006)

Preface by Satoru Miyano, Charles DeLisi, Hermann-Georg Holzhütter and Minoru Kanehisa

Program Committee

 


 

Papers

Regulatory Elements of Marine Cyanobacteria
Szymon M. Kiełbasa, Hanspeter Herzel, Ilka M. Axmann
Genome Informatics 18: 1-11 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

Evolutionary Changes in Gene Regulation from a Comparative Analysis of Multiple Drosophila Species
Lan Hu, Daniel Segrè, Temple F. Smith
Genome Informatics 18: 12-21 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

A Structural Genomics Approach to the Regulation of Apoptosis: Chimp vs. Human
Jessica Ahmed, Stefan Günther, Friedrich Möller, Robert Preissner
Genome Informatics 18: 22-34 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

Gene Expansion in Trichomonas Vaginalis: A Case Study on Transmembrane Cyclases
Jike Cui, Temple F. Smith, John Samuelson
Genome Informatics 18: 35-43 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Statistical Properties and Information Content of Calcium Oscillations
Alexander Skupin, Martin Falcke
Genome Informatics 18: 44-53 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Minimal Circadian Clock Model
Ilka M. Axmann, Stefan Legewie, Hanspeter Herzel
Genome Informatics 18: 54-64 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Promoter Analysis of Mammalian Clock Controlled Genes
Katarzyna Bożek, Szymon M. Kiełbasa, Achim Kramer, Hanspeter Herzel
Genome Informatics 18: 65-74 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Modeling Development: Spikes of the Sea Urchin
Clemens Kühn, Alexander Kühn, Albert J. Poustka, Edda Klipp
Genome Informatics 18: 75-84 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

Insights into the Network Controlling the G1/S Transition in Budding Yeast
Matteo Barberis, Edda Klipp
Genome Informatics 18: 85-99 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Steady State Analysis of Signal Response in Receptor Trafficking Networks
Zhike Zi, Edda Klipp
Genome Informatics 18: 100-108 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Using Transcription Factor Binding Site Co-Occurrence to Predict Regulatory Regions
Holger Klein, Martin Vingron
Genome Informatics 18: 109-118 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Identification of Activated Transcription Factors from Microarray Gene Expression Data of Kampo Medicine-Treated Mice
Rui Yamaguchi, Masahiro Yamamoto, Seiya Imoto, Masao Nagasaki, Ryo Yoshida, Kenji Tsuiji, Atsushi Ishige, Hiroaki Asou, Kenji Watanabe, Satoru Miyano
Genome Informatics 18: 119-129 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Breast Cancer Stratification from Analysis of Micro-Array Data of Micro-Dissected Specimens
Gabriela Alexe, Gul S. Dalgin, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, Charles Delisi, Gyan Bhanot
Genome Informatics 18: 130-140 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks
Matthias E. Futschik, Anna Tschaut, Gautam Chaurasia, Hanspeter Herzel
Genome Informatics 18: 141-151 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

New Amino Acid Indices Based on Residue Network Topology
Jian Huang, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 18: 152-161 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Computational Analysis of Protein-Protein Interactions in Metabolic Networks of Escherichia Coli and Yeast
Carola Huthmacher, Christoph Gille, Hermann-Georg Holzhütter
Genome Informatics 18: 162-172 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Context Specific Protein Function Prediction
Naoki Nariai, Simon Kasif
Genome Informatics 18: 173-182 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Evaluation of Sequence Alignments of Distantly Related Sequence Pairs with Respect to Structural Similarity
Aysam Gürler, Ernst-Walter Knapp
Genome Informatics 18: 183-191 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Conformational Entropy of Biomolecules: Beyond the Quasi-Harmonic Approximation
Jorge Numata, Michael Wan, Ernst-Walter Knapp
Genome Informatics 18: 192-205 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Detecting Near-Native Docking Decoys by Monte Carlo Stability Analysis
Stephan Lorenzen
Genome Informatics 18: 206-214 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Automatically Generated Model of a Metabolic Network
Simon Borger, Wolfram Liebermeister, Jannis Uhlendorf, Edda Klipp
Genome Informatics 18: 215-224 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Conversion from BioPAX to CSO for System Dynamics and Visualization of Biological Pathway
Euna Jeong, Masao Nagasaki, Satoru Miyano
Genome Informatics 18: 225-236 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

An Improved Scoring Scheme for Predicting Glycan Structures from Gene Expression Data
Akitsugu Suga, Yoshihiro Yamanishi, Kosuke Hashimoto, Susumu Goto, Minoru Kanehisa
Genome Informatics 18: 237-246 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Comparison of Smoking-Induced Gene Expression on Affymetrix Exon and 3'-Based Expression Arrays
Xiaoling Zhang, Gang Liu, Marc E Lenburg, Avrum Spira
Genome Informatics 18: 247-257 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Clustering Samples Characterized by Time Course Gene Expression Profiles Using the Mixture of State Space Models
Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
Genome Informatics 18: 258-266 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

PURE: A PubMed Article Recommendation System Based on Content-Based Filtering
Takashi Yoneya, Hiroshi Mamitsuka
Genome Informatics 18: 267-276 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Performance Improvement in Protein N-Myristoyl Classification by BONSAI with Insignificant Indexing Symbol
Manabu Sugii, Ryo Okada, Hiroshi Matsuno, Satoru Miyano
Genome Informatics 18: 277-286 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Identification of Diverse Carbon Utilization Pathways in Shewanella oneidensis MR-1 via Expression Profiling
Michael E. Driscoll, Margie F. Romine, Frank S. Juhn, Margrethe H. Serres, Lee Anne Mccue, Alex S. Beliaev, James K. Fredrickson, Timothy S. Gardner
Genome Informatics 18: 287-298 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

Analysis of Common Substructures of Metabolic Compounds within the Different Organism Groups
Ai Muto, Masahiro Hattori, Minoru Kanehisa
Genome Informatics 18: 299-308 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Pruning Genome-Scale Metabolic Models to Consistent ad functionem Networks
Sabrina Hoffmann, Andreas Hoppe, Hermann-Georg Holzhütter
Genome Informatics 18: 309-320 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

Metabolic Synergy: Increasing Biosynthetic Capabilities by Network Cooperation
Nils Christian, Thomas Handorf, Oliver Ebenhöh
Genome Informatics 18: 321-330 (2007)
[Abstract]   [Full-text HTML]   [Full-text PDF]