Part I: Systems Biology of the Cancer Genetic and Epigenetic Landscape
1. Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis
Hua Tan and Xiaobo Zhou
2. Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data
Amanda J. Kedaigle and Ernest Fraenkel
3. Analyzing DNA Methylation Patterns during Tumor Evolution
Heng 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 Panels
James Campbell, Colm J. Ryan, and Christopher J. Lord
Part II: Systems Analyses of Signaling Networks in Cancer Cells
6. Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells
Jakob Wirbel, Pedro Cutillas, and Julio Saez-Rodriguez
7. Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research
Stefka 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. Giskeødegård
Part III: Systems Biology of Metastasis and Tumor/ Microenvironment Interactions
10. Stochastic and Deterministic Models for the Metastatic Emission Process: Formalisms and Crosslinks
Christophe Gomez and Niklas Hartung
11. Mechanically Coupled Reaction-Diffusion Model to Predict Glioma Growth: Methodological Details
David 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 Pathology
Aaron 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 Uncertainty
Junfeng Zhu, Hamidreza Badri, and Kevin Leder
16. Modeling of Interactions between Cancer Stem Cells and their Microenvironment: Predicting Clinical Response
Mary E. Sehl and Max S. Wicha
17. Methods for High-throughput Drug Combination Screening and Synergy Scoring
Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, and Jing Tang
