Cancer Systems Biology

Part I: Systems Biology of the Cancer Genetic and Epigenetic Landscape1. Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity AnalysisHua Tan and Xiaobo Zhou 2. Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor DataAmanda J. Kedaigle and Ernest Fraenkel 3. Analyzing DNA Methylation Patterns during Tumor EvolutionHeng Pan and Olivier Elemento 4. MicroRNA Networks in Breast Cancer CellsAndliena Tahiri, and Miriam R. Aure, and Vessela N. Kristensen 5. Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line PanelsJames Campbell, Colm J. Ryan, and Christopher J. Lord Part II: Systems Analyses of Signaling Networks in Cancer Cells6. Phosphoproteomics-based Profiling of Kinase Activities in Cancer CellsJakob Wirbel, Pedro Cutillas, and Julio Saez-Rodriguez 7. Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer ResearchStefka Tyanova and Juergen Cox 8. Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastoma Tumors Hannah Johnson and Forest M White 9. Prediction of Clinical Endpoints in Breast Cancer using NMR Metabolic ProfilesLeslie R. Euceda, Tonje H. Haukaas, Tone F. Bathen, and Guro F. Giskeodegard Part III: Systems Biology of Metastasis and Tumor/ Microenvironment Interactions10. Stochastic and Deterministic Models for the Metastatic Emission Process: Formalisms and CrosslinksChristophe Gomez and Niklas Hartung 11. Mechanically Coupled Reaction-Diffusion Model to Predict Glioma Growth: Methodological DetailsDavid A. Hormuth II, Stephanie L. Eldridge, Jared A. Weis, Michael I. Miga, and Thomas E. Yankeelov 12. Profiling Tumor Infiltrating Immune Cells with CIBERSORTBinbin Chen, Michael S. Khodadoust, Chih Long Liu, Aaron M. Newman, and Ash A. Alizadeh 13. Systems Biology Approaches in Cancer PathologyAaron DeWard and Rebecca J. Critchley-Thorne Part IV: Modeling Drug Responses in Cancer Cells 14. Bioinformatics Approaches to Predict Drug Responses from Genomic SequencingNeel Madhukar and Olivier Elemento 15. A Robust Optimization Approach to Cancer Treatment under Toxicity UncertaintyJunfeng Zhu, Hamidreza Badri, and Kevin Leder 16. Modeling of Interactions between Cancer Stem Cells and their Microenvironment: Predicting Clinical ResponseMary E. Sehl and Max S. Wicha 17. Methods for High-throughput Drug Combination Screening and Synergy ScoringLiye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, and Jing Tang