| 9:30 | Registration | |
| 10:00-10:10 | Opening Address Satoru Miyano | |
| Session 1 | Chair: Charles DeLisi | |
| 10:10-10:35 | "Regulatory Elements of Marine Cyanobacteria", Szymon M. Kiełbasa, Hanspeter Herzel, Ilka M. Axmann | |
| 10:35-11:00 | "Evolutionary Changes in Gene Regulation from a Comparative Analysis of Multiple Drosophila Species", Lan Hu, Daniel Segrè, Temple F. Smith | |
| 11:00-11:25 | "A Structural Genomics Approach to the Regulation of Apoptosis: Chimp vs. Human", Jessica Ahmed, Stefan Günther, Friedrich Möller, Robert Preissner | |
| 11:25-11:50 | "Gene Expansion in Trichomonas vaginalis: A Case Study on Transmembrane Cyclases", Jike Cui, Temple Smith, John Samuelson | |
| 11:50-13:30 | Lunch on your own | |
| Session 2 | Chair: Hermann-Georg Holzhütter | |
| 13:30-13:55 | "Exploring the Properties of Calcium Oscillations", Alexander Skupin, Martin Falcke | |
| 13:55-14:20 | "A Minimal Circadian Clock Model", Ilka M. Axmann, Stefan Legewie, Hanspeter Herzel | |
| 14:20-14:45 | "Promoter Analysis of Mammalian Clock Controlled Genes", Katarzyna Bożek, Szymon M. Kiełbasa, Achim Kramer, Hanspeter Herzel | |
| 14:45-15:10 | Break | |
| Session 3 | Chair: Brandon Xia | |
| 15:10-15:35 | "Modeling Development: Spikes of the Sea Urchin", Clemens Kuehn, Albert J. Poustka, Edda Klipp | |
| 15:35-16:00 | "Insights into the Network Controlling the G1/S Transition in Budding Yeast", Matteo Barberis, Edda Klipp | |
| 16:00-16:25 | "Steady State Analysis of Signal Response in Receptor Trafficking Networks", Zhike Zi, Edda Klipp | |
| 16:30-18:00 | Poster Session 1 at Amgen Hall (Snacks and drinks) 16:30-17:15 odd numbered posters 17:15-18:00 even numbered posters |
| Session 4 | Chair: Hiroshi Mamitsuka | |
| 9:30-9:55 | "Using Transcription Factor Binding Site Co-Occurrence to Predict Regulatory Regions", Holger Klein, Martin Vingron | |
| 9:55-10:20 | "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 | |
| 10:20-10:45 | "Breast Cancer Stratification from Analysis of Micro-array Data of Micro-dissected Specimens", Gabriela Alexe, Gul Dalgin, Daniel Scanfeld, Pablo Tamayo, Jill Mesirov, Shridar Ganesan, Gyan Bhanot, Charles DeLisi | |
| 10:50-12:00 | Poster Session 2 at Amgen Hall 10:50-11:25 even numbered posters 11:25-12:00 odd numbered posters | |
| 12:00-13:30 | Lunch on your own | |
| Session 5 | Chair: Seiya Imoto | |
| 13:30-13:55 | "Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks", Matthias E. Futschik, Gautam Chaurasia, Hanspeter Herzel | |
| 13:55-14:20 | "New Amino Acid Indices Based on Residue Network Topology", Jian Huang, Shuichi Kawashima, Minoru Kanehisa | |
| 14:20-14:45 | "Statistical Analysis of Protein-Protein Interactions in Metabolic Networks of Yeast and Escherichia coli ", Carola Huthmacher, Christoph Gille, Hermann-Georg Holzhütter | |
| 14:45-15:10 | "Context Specific Protein Function Prediction", Naoki Nariai, Simon Kasif | |
| 15:10-15:35 | Break | |
| Session 6 | Chair: Minoru Kanehisa | |
| 15:35-16:00 | "Evaluation of Sequence Alignments of Distantly Related Sequence Pairs with Respect to Structural Similarity", Aysam Gürler, Ernst-Walter Knapp | |
| 16:00-16:25 | "Conformational Entropy of Biomolecules: Beyond the Quasi-harmonic Approximation", Jorge Numata, Michael Wan, Ernst-Walter Knapp | |
| 16:25-16:50 | "Detecting Near-Native Docking Decoys by Monte Carlo Stability Analysis", Stephan Lorenzen | |
| 16:50-17:15 | Break | |
| Session 7 | Chair: Susumu Goto | |
| 17:15-17:40 | "Automatically Generated Model of a Metabolic Network", Simon Borger, Wolfram Liebermeister, Jannis Uhlendorf, Edda Klipp | |
| 17:40-18:05 | "Conversion from BioPAX to CSO for System Dynamics and Visualization of Biological Pathway", Euna Jeong, Masao Nagasaki, Satoru Miyano | |
| 18:20-20:00 | Buffet Style Banquet at Hospital 8F | |
| Session 8 | Chair: Oliver Ebenhöh | |
| 9:30-9:55 | "An Improved Scoring Scheme for Predicting Glycan Structures from Gene Expression Data", Akitsugu Suga, Yoshihiro Yamanishi, Kosuke Hashimoto, Susumu Goto, Minoru Kanehisa | |
| 9:55-10:20 | "Comparison of Smoking-Induced Gene Expression on Affymetrix Exon and 3'-Based Expression Arrays", Xiaoling Zhang, Gang Liu, Marc E Lenburg, Avrum Spira | |
| 10:20-10:45 | "Clustering with Time Course Gene Expression Profiles and the Mixture of State Space Models", Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano | |
| 10:45-11:05 | Break | |
| Session 9 | Chair: Nikolaus Rajewsky | |
| 11:05-11:30 | "PURE: A PubMed Article Recommendation System Based on Content-Based Filtering", Takashi Yoneya, Hiroshi Mamitsuka | |
| 11:30-11:55 | "Performance Improvement in Protein N-Myristoyl Classification by BONSAI with Insignificant Indexing Symbol", Manabu Sugii, Ryo Okada, Hiroshi Matsuno, Satoru Miyano | |
| 11:55-13:30 | Lunch on your own | |
| Session 10 | Chair: Satoru Miyano | |
| 13:30-13:55 | "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 | |
| 13:55-14:20 | "Analysis of Common Substructures of Metabolic Compounds within the Different Organism Groups", Ai Muto, Masahiro Hattori, Minoru Kanehisa | |
| 14:20-14:45 | "Pruning Genome-Scale Metabolic Models to Consistent ad Functionem networks", Sabrina Hoffmann, Andreas Hoppe, Hermann-Georg Holzhütter | |
| 14:45-15:10 | "Metabolic Synergy: Increasing Biosynthetic Capabilities by Network Cooperation", Nils Christian, Thomas Handorf, Oliver Ebenhöh | |
| 15:10-15:35 | "Detection of miRNA Genes Using Deep Sequencing Information", Marc Friedländer | |