Page 3 - Cancer Systems Biology: Methods and Protocols

Contents
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PART IV SYSTEMS BIOLOGY OF METASTASIS AND TUMOR/
MICROENVIRONMENT INTERACTIONS

10 Stochastic and Deterministic Models for the Metastatic Emission Process:
Formalisms and Crosslinks............................................... 193
Christophe Gomez and Niklas Hartung
11 Mechanically Coupled Reaction-Diffusion Model to Predict Glioma
Growth: Methodological Details. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
David A. Hormuth II, Stephanie L. Eldridge, Jared A. Weis,
Michael I. Miga, and Thomas E. Yankeelo
12 Profiling Tumor Infiltrating Immune Cells with CIBERSORT . . . . . . . . . . . . . . . 243
Binbin Chen, Michael S. Khodadoust, Chih Long Liu,
Aaron M. Newman, and Ash A. Alizadeh
13 Systems Biology Approaches in Cancer Pathology . . . . . . . . . . . . . . . . . . . . . . . . . . 26l
Aaron De Ward and Rebecca J. Critchley-Thorne

PART V MODELING DRUG RESPONSES IN CANCER CELLS

14 Bioinformatics Approaches to Predict Drug Responses
from Genomic Sequencing............................................... 277
Neel S. Madhukar and Olivier Elemento
15 A Robust Optimization Approach to Cancer Treatment under Toxicity
Uncertainty............................................................ 297
Junfeng Zhu, Hamidreza Badri, and Kevin Leder
16 Modeling oflnteractions between Cancer Stem Cells
and their Microenvironment: Predicting Clinical Response................... 333
Mary E. Sehl and Max S. Wicha
17 Methods for High-throughput Drug Combination Screening
and Synergy Scoring .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 35l
Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister
Wennerberg, Tero Aittokallio, and Jing Tang

Index...................................................................... 399