Cancer Bioinformatics provides a comprehensive and up-to-date account of the enormous range of bioinformatics techniques now being developed for cancer research and therapy, from the laboratory to clinical trials.

Cancer Bioinformatics features a balanced range of topics, including both well-established techniques and emergent approaches in genomics, systems biology and e-science.

Each chapter delivers an overview of the topic, combined with more detailed technical descriptions of key aspects of informatics, biology and clinical science. Finally, three chapters on the ethical and legal implications of cancer bioinformatics provide an expanded view of these groundbreaking developments and how they may impact on patients and other health care stakeholders.

Contents

Section I: Cancer Systems

A Path to Knowledge: from Data to Complex Systems Models of Cancer

• Conceptual foundations: biological complexity
• A taxonomy of cancer complexity
• Modelling and simulation of cancer systems
• Data standards and integration
• Concluding remarks

Theory of Cancer Robustness

• Robustness: the fundamental organizational principle of biological systems
• Underlying mechanisms for robustness
• Intrinsic features of robust systems: Evolvability and trade-offs
• Cancer as a robust system
• Therapy strategies
• A proper index of treatment efficacy
• Computational Tools

Developing an Integrated Informatics Platform for Cancer Research

• Background
• The challenge
• The UK National Cancer Research Institute (NCRI) informatics platform
• Developing the informatics platform
• Benefits of the platform

Section II: In Silico Models

Mathematical Models of Cancer

• Growth models
• A very brief tour of cellular automata
• Angiogenesis models
• Treatment response models
• Dynamic pathways models
• Other models
• Simulations of complex biological systems

Some Mathematical Modelling Challenges and Approaches in Cancer

• Multiscale modelling
• Tumour vascular modelling
• Population models

Computer Simulation of Tumour Response to Therapy

• Tumour growth simulation
• Radiotherapy response simulation
• Chemotherapy response simulation
• Simulation of tumour response to other therapeutic modalities
• Simulation of normal tissue response to antineoplastic interventions
• Integration of molecular networks into tumour behaviour simulations

Structural Bioinformatics in Cancer

• Macromolecular crystallography
• Molecular modelling

Section III: In Vivo Models

The Mouse Tumor Biology Database: an Online Resource for Mouse Models of Human Cancer

• Background
• Database content
• Data acquisition
• Using the MTB database
• Connecting the MTB database with related databases

Bioinformatics Approaches to Integrate Cancer Models and Human Cancer Research

• Background
• The MMHCC Informatics at the outset of the programme
• Initial NCI bioinformatics infrastructure development
• Future directions for informatics support

Section IV: Data

The FAPESP/LICR Human Cancer Genome Project: Perspectives on Integration

• The FAPESP/LICR Human Cancer Genome Project
• An integrated view of the tumour transcriptome

Today's Science, Tomorrow's Patient: The Pivotal Role of Tissue, Clinical Data and Informatics in Modern Drug Development

• A new national strategy for the provision of tissue annotated with clinical information to meet current and future needs of academic researchers and industry
• The NCRI National Cancer Tissue Resource for cancer biology and treatment development
• A potential future world-class resource integrating research and health service information systems and bioinformatics for cancer diagnosis and treatment
• A proposed information system architecture that will meet the challenges and deliver the required functionality
• Consent and confidentiality: Ensuring that the NCTR is embedded in the UK?s legal and ethical framework
• Future challenges and opportunities

Section V: Ethics

Software Design Ethics for Biomedicine

• The problem: software and research
• Risk identification
• Biomedical software example
• Is an ethical risk analysis required?
• Details of SoDIS
• A SoDIS analysis of the biomedical software example

Ethical Issues of Electronic Patient Data and Informatics in Clinical Trial Settings

• Ethical aspects of using patient-identifiable health data
• Legislation and policies pertaining to patient-identifiable health data
• Using anonymized and pseudonymized data
• Protecting personal health data

Pharmacogenomics and Cancer: Ethical, Legal and Social Issues

• Getting pharmacogenomic tests and drugs to market
• Cost and coverage issues
• Ethical challenges of pharmacogenomics

Index

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