Book description
Groundbreaking, long-ranging research in this emergent field that enables solutions to complex biological problems
Computational systems biology is an emerging discipline that is evolving quickly due to recent advances in biology such as genome sequencing, high-throughput technologies, and the recent development of sophisticated computational methodologies. Elements of Computational Systems Biology is a comprehensive reference covering the computational frameworks and techniques needed to help research scientists and professionals in computer science, biology, chemistry, pharmaceutical science, and physics solve complex biological problems. Written by leading experts in the field, this practical resource gives detailed descriptions of core subjects, including biological network modeling, analysis, and inference; presents a measured introduction to foundational topics like genomics; and describes state-of-the-art software tools for systems biology.
Offers a coordinated integrated systems view of defining and applying computational and mathematical tools and methods to solving problems in systems biology
Chapters provide a multidisciplinary approach and range from analysis, modeling, prediction, reasoning, inference, and exploration of biological systems to the implications of computational systems biology on drug design and medicine
Helps reduce the gap between mathematics and biology by presenting chapters on mathematical models of biological systems
Establishes solutions in computer science, biology, chemistry, and physics by presenting an in-depth description of computational methodologies for systems biology
Elements of Computational Systems Biology is intended for academic/industry researchers and scientists in computer science, biology, mathematics, chemistry, physics, biotechnology, and pharmaceutical science. It is also accessible to undergraduate and graduate students in machine learning, data mining, bioinformatics, computational biology, and systems biology courses.
Table of contents
- Cover Page
- Title Page
- Copyright
- CONTENTS
- PREFACE
- CONTRIBUTORS
- PART I: OVERVIEW
-
PART II: BIOLOGICAL NETWORK MODELING
- CHAPTER 2: MODELS IN SYSTEMS BIOLOGY: THE PARAMETER PROBLEM AND THE MEANINGS OF ROBUSTNESS
- CHAPTER 3: IN SILICO ANALYSIS OF COMBINED THERAPEUTICS STRATEGY FOR HEART FAILURE
- CHAPTER 4: RULE BASED MODELING AND MODEL REFINEMENT
- CHAPTER 5: A (NATURAL) COMPUTING PERSPECTIVE ON CELLULAR PROCESSES
- CHAPTER 6: SIMULATING FILAMENT DYNAMICS IN CELLULAR SYSTEMS
-
PART III: BIOLOGICAL NETWORK INFERENCE
- CHAPTER 7: RECONSTRUCTION OF BIOLOGICAL NETWORKS BY SUPERVISED MACHINE LEARNING APPROACHES
- CHAPTER 8: SUPERVISED INFERENCE OF METABOLIC NETWORKS FROM THE INTEGRATION OF GENOMIC DATA AND CHEMICAL INFORMATION
- CHAPTER 9: INTEGRATING ABDUCTION AND INDUCTION IN BIOLOGICAL INFERENCE USING CF-INDUCTION
- CHAPTER 10: ANALYSIS AND CONTROL OF DETERMINISTIC AND PROBABILISTIC BOOLEAN NETWORKS
-
CHAPTER 11: PROBABILISTIC METHODS AND RATE HETEROGENEITY
- 11.1 INTRODUCTION TO PROBABILISTIC METHODS
- 11.2 SEQUENCE EVOLUTION IS DESCRIBED USING MARKOV CHAINS
- 11.3 AMONG-SITE RATE VARIATION
- 11.4 DISTRIBUTION OF RATES ACROSS SITES
- 11.5 SITE-SPECIFIC RATE ESTIMATION
- 11.6 TREE RECONSTRUCTION USING AMONG-SITE RATE VARIATION MODELS
- 11.7 DEPENDENCIES OF EVOLUTIONARY RATES AMONG SITES
- 11.8 RELATED WORKS
- REFERENCES
-
PART IV: GENOMICS AND COMPUTATIONAL SYSTEMS BIOLOGY
- CHAPTER 12: FROM DNA MOTIFS TO GENE NETWORKS: A REVIEW OF PHYSICAL INTERACTION MODELS
- CHAPTER 13: THE IMPACT OF WHOLE GENOME IN SILICO SCREENING FOR NUCLEAR RECEPTOR-BINDING SITES IN SYSTEMS BIOLOGY
-
CHAPTER 14: ENVIRONMENTAL AND PHYSIOLOGICAL INSIGHTS FROM MICROBIAL GENOME SEQUENCES
- 14.1 SOME BACKGROUND, MOTIVATION, AND OPEN QUESTIONS
- 14.2 A FIRST STATISTICAL GLIMPSE TO GENOMIC SEQUENCES
- 14.3 AN AUTOMATIC DETECTION OF CODON BIAS IN GENES
- 14.4 GENOMIC SIGNATURES AND A SPACE OF GENOMES FOR GENOME COMPARISON
- 14.5 STUDY OF METABOLIC NETWORKS THROUGH SEQUENCE ANALYSIS AND TRANSCRIPTOMIC DATA
- 14.6 FROM GENOME SEQUENCES TO GENOME SYNTHESIS: MINIMAL GENE SETS AND ESSENTIAL GENES
- 14.7 A CHROMOSOMAL ORGANIZATION OF ESSENTIAL GENES
- 14.8 VIRAL ADAPTATION TO MICROBIAL HOSTS AND VIRAL ESSENTIAL GENES
- 14A.1 APPENDIX
- REFERENCES
- PART V: SOFTWARE TOOLS FOR SYSTEMS BIOLOGY
- INDEX
- WILEY SERIES ON BIOINFORMATICS: COMPUTATIONAL TECHNIQUES AND ENGINEERING
Product information
- Title: Elements of Computational Systems Biology
- Author(s):
- Release date: February 2010
- Publisher(s): Wiley
- ISBN: 9780470180938
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