edited by Charles DeLisi (Boston University, USA), Minoru Kanehisa (Kyoto University, Japan), Edda Klipp (Humboldt-Universität zu Berlin, Germany), Satoru Miyano (University of Tokyo, Japan), Scott Mohr (Boston University, USA), & Iwona Wallach (Charité – Universitätsmedizin Berlin, Germany)

This volume contains 17 peer-reviewed papers based on the presentations at the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2009) held at the Life Science Engineering Building of Boston University from July 27 to 29, 2009. This workshop started in 2001 as a platform 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 institutions and programs:

• Boston University Graduate Program in Bioinformatics
• Charité – Universitätsmedizin Berlin
• Freie Universität Berlin
• Global COE Program — Center of Education and Research for Advanced Genome-Based Medicine, University of Tokyo
• The International Research Training Group (IRTG) Genomics and Systems Biology of Molecular Networks
• International Research and Training Program on Bioinformatics and Systems Biology, Kyoto University Bioinformatics Center
• Max-Delbrück Center for Molecular Medicine in Berlin
• Max Planck Institute for Molecular Genetics in Berlin
• Max Planck Institute of Molecular Plant Physiology in Potsdam

• Structural Features and Evolution of Protein-Protein Interactions (J von Eichborn et al.)
• Strategies of Non-Sequential Protein Structure Alignments (A Guerler & E-W Knapp)
• Active Pathway Identification and Classification with Probabilistic Ensembles (T Hancock & H Mamitsuka)
• The Importance of Compartmentalization in Metabolic Flux Models: Yeast as an Ecosystem of Organelles (N Klitgord & D Segrè)
• Formal Representation of the High Osmolarity Glycerol Pathway in Yeast (C Kühn et al.)
• Prediction of Regulatory Transcription Factors in T Helper Cell Differentiation and Maintenance (Y-H Lee et al.)
• A Novel Meta-Analysis Approach of Cancer Transcriptomes Reveals Prevailing Transcriptional Networks in Cancer Cells (A Niida et al.)
• Efficient and Detailed Model of the Local Ca²⁺ Release Unit in the Ventricular Cardiac Myocyte (T Schendel & M Falcke)
• Co-Evolution of Metabolism and Protein Sequences (M Schütte et al.)
• Analysis and Prediction of Nutritional Requirements Using Structural Properties of Metabolic Networks and Support Vector Machines (T Tamura et al.)
• Analysis of a Lipid Biosynthesis Protein Family and Phospholipid Structural Variations (M Tanaka et al.)
• and other papers