This volume contains 18 peer-reviewed papers based on the presentations at the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) held at Kyoto University from July 26 to July 28, 2010. 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:Boston — Graduate Program in Bioinformatics, Boston University Berlin — The International Research Training Group (IRTG) “Genomics and Systems Biology of Molecular Networks”Kyoto — The JSPS International Training Program (ITP) “International Research and Training Program of Bioinformatics and Systems Biology”Tokyo — Global COE Program “Center of Education and Research for Advanced Genome-Based Medicine”Contents: Predicting Protein Complex Geometries with Linear Scoring Functions (O Demir-Kavuk et al.)Gene Regulatory Network Clustering for Graph Layout Based on Microarray Gene Expression Data (K Kojima et al.)FluxViz — Cytoscape Plug-In for Visualization of Flux Distributions (M König & H-G Holzhütter)Phylogenetic Analysis of Lipid Mediator GPCRs (S Mizutani et al.)Genome-Wide Analysis of Plant UGT Family Based on Sequence and Substrate Information (Y Nishimura et al.)Integer Programming-Based Method for Completing Signaling Pathways and Its Application to Analysis of Colorectal Cancer (T Tamura et al.)A Dynamic Programming Algorithm to Predict Synthesis Processes of Tree-Structured Compounds with Graph Grammar (Y Zhao et al.)and other papersReadership: Researchers and graduate students in bioinformatics and computational biology.