This volume contains 31 peer-reviewed papers based on the presentations at the 7th International Annual Workshop on Bioinformatics and Systems Biology (IBSB 2007) held at the Human Genome Center, Institute of Medical Science, University of Tokyo from July 31 to August 2, 2007. This workshop started in 2001 as an event for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following programs and partner institutions:

• Boston (Charles DeLisi) — Graduate Program in Bioinformatics, Boston University
• Berlin (Herman-Georg Holzhütter) — The International Research Training Group (IRTG) “Genomics and Systems Biology of Molecular Networks”
• Kyoto/Tokyo (Minoru Kanehisa/Satoru Miyano) — Joint Bioinformatics Education Program of Kyoto University and University of Tokyo.

This volume is dedicated to the memory of Prof. Dr. Dr. h.c. Reinhart Heinrich, a former Professor at Humboldt University Berlin and a co-founder of this workshop.

Contents:

• Regulatory Elements of Marine Cyanobacteria (S M Kielbasa et al.)
• A Structural Genomics Approach to the Regulation of Apoptosis: Chimp vs. Human (J Ahmed et al.)
• Promoter Analysis of Mammalian Clock-Controlled Genes (K Bozek et al.)
• Modeling Development: Spikes of the Sea Urchin (C Kühn et al.)
• Steady State Analysis of Signal Response in Receptor Trafficking Networks (Z Zi & E Klipp)
• Identification of Activated Transcription Factors from Microarray Gene Expression Data of Kampo Medicine-Treated Mice (R Yamaguchi et al.)
• Breast Cancer Stratification from Analysis of Micro-Array Data of Micro-Dissected Specimens (G Alexe et al.)
• New Amino Acid Indices Based on Residue Network Topology (J Huang et al.)
• Conformational Entropy of Biomolecules: Beyond the Quasi-Harmonic Approximation (J Numata et al.)
• Automatically Generated Model of a Metabolic Network (S Borger et al.)
• Comparison of Smoking-Induced Gene Expression on Affymetrix Exon and 3′-Based Expression Arrays (X Zhang et al.)
• PURE: A PubMed Article Recommendation System Based on Content-Based Filtering (T Yoneya & H Mamitsuka)
• Pruning Genome-Scale Metabolic Models to Consistent ad functionem Networks (S Hoffmann et al.)
• Metabolic Synergy: Increasing Biosynthetic Capabilities by Network Cooperation (N Christian et al.)
• and other papers