Systems Biology: A Disruptive Technology
By Ken Rubenstein, PhD
Chapter 1
INTRODUCTION
1.1. Scope and Content of This Report
1.2. Historical Perspective
1.3. Defining Systems Biology
Chapter 2
TECHNOLOGICAL ASPECTS OF SYSTEMS BIOLOGY
2.1. Bioanalytical Technologies
Academic Perspective: Institute for Systems Biology
Commercial Perspective: BG Medicine
2.2. Regulatory Mechanisms and Organization
DNA-Protein Binding: ChIP-on-Chip Analysis
DNA Methylation
MicroRNAs
2.3. Bioinformatics Technologies
Pathway Analysis
Databases
Commercial Software Systems
Cell and Disease Modeling
Genstruct
Entelos
Gene Network Sciences
2.4. Summary
Chapter 3
BASIC RESEARCH IN SYSTEMS BIOLOGY
3.1. Network-Based Models and Simulations
Types of Biological Networks
Transcriptomic/Genetic Variation Approach
Combination Drug Therapy
3.2. Protein Networks
Yeast Two-Hybrid and Related Technologies
Metabolic Interaction Networks
Databases
Systems Biology Research Approaches
3.3. An Emerging Paradigm for Viewing Health and Disease
Diseaseome
Genotyping/Gene Expression Combinations in Biological Network Construction
Implications of Systems Biology for Clinical Medicine
Systems Biology Approach for Cancer Research
Chapter 4
APPLIED RESEARCH IN SYSTEMS BIOLOGY
4.1. Impacts of Systems Biology on Specific Disease Areas
Cancer
Acceptance of Systems Biology by Big Pharma
Network-Based Cancer Research
Neurological Diseases
Cardiovascular Diseases
Metabolic Disorders
Chapter 5
MARKET DYNAMICS
5.1. Approaches of Small-Company Players X
Ariadne Genomics
BG Medicine
BioSeek
Connexios
Entelos
Gene Network Sciences
GeneGo
Genetics Squared
Genomatica
Genstruct
Ingenuity Systems
Optimata
Physiomics
Protein Lounge
5.2. Approaches of Selected Drug Discovery and Development Organizations
Cellicon Biotechnologies
CombinatoRx
e-Therapeutics
Merck
Merrimack Pharmaceuticals
Pfizer
SU Biomedicine
5.3. Systems Biology Deals
5.4. Insight Pharma Reports Systems Biology Survey: Results and Comments
Chapter 6
CONCLUSIONS AND FUTURE PROSPECTS
6.1. Challenges for Systems Biology in Drug Discovery
6.2. Possible Solutions to Advancing Medical and Pharmacological Knowledge via Systems Biology
6.3. Systems Biology as a Disruptive Technology
6.4. Future Prospects
Chapter 7
EXPERT INTERVIEWS
David de Graaf, PhD
Director of Systems Biology, Pfizer, Research Technology Center, Cambridge, MA
Brian Edmonds, PhD
Research Advisor, Integrative Biology and Global External Research, Lilly Research Laboratories, Indianapolis, IN
Colin Hill
CEO, President, Chairman, and Co-Founder, Gene Network Sciences, Cambridge, MA
David Lester, PhD
President and Founder, ITHW, Inc., Morristown, NJ
Stephen Naylor, PhD
Chairman, CEO, and Co-Founder, Predictive Physiology and Medicine (PPM), Bloomington, IN
References
Company Index with Web Addresses