Foreword Hiroaki Kitano, President, The Systems Biology Institute, Tokyo, Japan CANCER SYSTEMS BIOLOGY: CONCEPTS AND APPLICATIONS A Roadmap of Cancer Systems Biology Edwin Wang Network Biology, the Framework of Systems Biology Jing-Dong Han Reconstructing Gene Networks Using Gene Expression Profiles Mario Lauria and Diego di Bernardo Understanding Cancer Progression in Protein Interaction Networks Jinsheng Sun, Jie Li, and Edwin Wang From Tumor Genome Sequencing to Cancer Signaling Maps Cong Fu and Edwin Wang Ubiquitin-Mediated Regulation of Human Signaling Networks in Normal and Cancer Cells Cong Fu, Jie Li, and Edwin Wang microRNA Regulation of Networks of Normal and Cancer Cells Pradeep Kumar Shreenivasaiah, Do Han Kim, and Edwin Wang Network Model of Survival Signaling in T-Cell Large Granular Lymphocyte Leukemia Ranran Zhang, Thomas P. Loughran, Jr., and Reka Albert Cancer Metabolic Networks: Metabolic Pathways Modeling and Metabolomics in Cancer Research Miroslava Cuperlovic-Culf Warburg Revisited: Modeling Energy Metabolism for Cancer Systems Biology Mathieu Cloutier Cancer Gene Prediction Using a Network Approach Xuebing Wu and Shao Li CANCER BIOLOGY: BASIC CONCEPTS AND CUTTING-EDGE TOPICS Cancer Genomics to Cancer Biology Maria Luz Jaramillo and Chabane Tibiche Epithelial-to-Mesenchymal Transition (EMT): The Good, the Bad, and the Ugly Anne E.G. Lenferink Tumors and Their Microenvironments Nicholas R. Bertos and Morag Park Tumor Angiogenesis: Cell-Microenvironment Interactions Ally Pen, Danica B. Stanimirovic, Maria J. Moreno DATA RESOURCES AND SOFTWARE TOOLS FOR CANCER SYSTEMS BIOLOGY Modeling Tools for Cancer Systems Biology Wayne Materi and David S. Wishart Advanced Visualization, Analysis and Inference of Biological Networks Using VisANT Zhenjun Hu Gene Set and Pathway-Based Analysis for Cancer Omics Dougu Nam and Seon-Young Kim SH2 Domain Signaling Network and Cancer Shawn S.-C. Li and Thamara K.J. Dayarathna Data Sources and Computational Tools for Cancer Systems Biology Yun Ma, Pradeep Kumar Shreenivasaiah, and Edwin Wang