Cancer Systems Biology

Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis.- Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data.- Analyzing DNA Methylation Patterns during Tumor Evolution.- MicroRNA Networks in Breast Cancer Cells.- Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels.- Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells.- Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research.- Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastoma Tumors.- Prediction of Clinical Endpoints in Breast Cancer using NMR Metabolic Profiles.- Stochastic and Deterministic Models for the Metastatic Emission Process: Formalisms and Crosslinks.- Mechanically Coupled Reaction-Diffusion Model to Predict Glioma Growth: Methodological Details.- Profiling Tumor Infiltrating Immune Cells with CIBERSORT.- Systems Biology Approaches in Cancer Pathology.- Bioinformatics Approaches to Predict Drug Responses from Genomic Sequencing.- A Robust Optimization Approach to Cancer Treatment under Toxicity Uncertainty.- Modeling of Interactions between Cancer Stem Cells and their Microenvironment: Predicting Clinical Response.- Methods for High-throughput Drug Combination Screening and Synergy Scoring.