List of Accepted Papers
Paper ID	Title and Authors
1	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
2	New Amino Acid Indices Based on Residue Network Topology
	Jian Huang, Shuichi Kawashima, Minoru Kanehisa
3	Metabolic Synergy: Increasing Biosynthetic Capabilities by Network Cooperation
	Nils Christian, Thomas Handorf, Oliver Ebenhöh
4	Promoter Analysis of Mammalian Clock Controlled Genes
	Katarzyna Bożek, Szymon M. Kiełbasa, Achim Kramer, Hanspeter Herzel
5	PURE: A PubMed Article Recommendation System Based on Content-Based Filtering
	Takashi Yoneya, Hiroshi Mamitsuka
7	Performance Improvement in Protein N-Myristoyl Classification by BONSAI with Insignificant Indexing Symbol
	Manabu Sugii, Ryo Okada, Hiroshi Matsuno, Satoru Miyano
8	Exploring the Properties of Calcium Oscillations
	Alexander Skupin, Martin Falcke
10	An Improved  Scoring Scheme for Predicting Glycan Structures from Gene Expression Data
	Akitsugu Suga, Yoshihiro Yamanishi, Kosuke Hashimoto, Susumu Goto, Minoru Kanehisa
11	Insights into the Network Controlling the G1/S Transition in Budding Yeast
	Matteo Barberis, Edda Klipp
12	Modeling Development: Spikes of the Sea Urchin
	Clemens Kuehn, Albert J. Poustka, Edda Klipp
14	Using Transcription Factor Binding Site Co-Occurrence to Predict Regulatory Regions
	Holger Klein, Martin Vingron
15	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
17	Steady State Analysis of Signal Response in Receptor Trafficking Networks
	Zhike Zi, Edda Klipp
18	A Minimal Circadian Clock Model
	Ilka M. Axmann, Stefan Legewie, Hanspeter Herzel
21	Regulatory Elements of Marine Cyanobacteria
	Szymon M. Kiełbasa, Hanspeter Herzel, Ilka M. Axmann
23	Evolutionary Changes in Gene Regulation from a Comparative Analysis of Multiple Drosophila Species
	Lan Hu, Daniel Segrè, Temple F. Smith
24	Conformational Entropy of Biomolecules: Beyond the Quasi-Harmonic Approximation
	Jorge Numata, Michael Wan, Ernst-Walter Knapp
26	Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks
	Matthias E. Futschik, Gautam Chaurasia, Hanspeter Herzel
27	Context Specific Protein Function Prediction
	Naoki Nariai, Simon Kasif
28	A Structural Genomics Approach to the Regulation of Apoptosis: Chimp vs. Human
	Jessica Ahmed, Stefan Günther, Friedrich Möller, Robert Preissner
29	Evaluation of Sequence Alignments of Distantly Related Sequence Pairs with Respect to Structural Similarity
	Aysam Gürler, Ernst-Walter Knapp
30	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
31	Detecting Near-Native Docking Decoys by Monte Carlo Stability Analysis
	Stephan Lorenzen
32	Analysis of Common Substructures of Metabolic Compounds within the Different Organism Groups
	Ai Muto, Masahiro Hattori, Minoru Kanehisa
34	Comparison of Smoking-Induced Gene Expression on Affymetrix Exon and 3'-Based Expression Arrays
	Xiaoling Zhang, Gang Liu, Marc E Lenburg, Avrum Spira
35	Gene Expansion in Trichomonas Vaginalis: A Case Study on Transmembrance Cyclases
	Jike Cui, Temple Smith, John Samuelson
36	Automatically Generated Model of a Metabolic Network
	Simon Borger, Wolfram Liebermeister, Jannis Uhlendorf, Edda Klipp
37	Conversion from BioPAX to CSO for System Dynamics and Visualization of Biological Pathway
	Euna Jeong, Masao Nagasaki, Satoru Miyano
38	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
39	Statistical Analysis of Protein-Protein Interactions in Metabolic Networks of Yeast and Escherichia coli
	Carola Huthmacher, Christoph Gille, Hermann-Georg Holzhütter
40	Pruning Genome-Scale Metabolic Models to Consistent ad Functionem Networks
	Sabrina Hoffmann, Andreas Hoppe, Hermann-Georg Holzhütter