Computational Systems Biology 1st Edition by Andres Kriete, Roland Eils 0080459349 9780080459349

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ISBN 10: 0080459349 

ISBN 13: 9780080459349

Author:  Andres Kriete, Roland Eils 

Systems Biology is concerned with the quantitative study of complex biosystems at the molecular, cellular, tissue, and systems scales. Its focus is on the function of the system as a whole, rather than on individual parts.

Computational Systems Biology 1st Table of contents:

Chapter 1: Introducing Computational Systems Biology
Publisher Summary
I INTRODUCTION
II AREAS OF COMPUTATIONAL SYSTEMS BIOLOGY
III CHALLENGES IN COMPUTATIONAL SYSTEMS BIOLOGY
IV OUTLOOK
I: Enabling Information and Integration Technologies for Systems Biology
Chapter 2: Databases for Systems Biology
I INTRODUCTION
II A DATABASE SOLUTION FOR SYSTEMS BIOLOGY
III PROSPECTIVE APPLICATIONS: USAGE AND WORKFLOW
ACKNOWLEDGMENTS
Chapter 3: Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology
I INTRODUCTION
II ONTOLOGY-ENHANCED BIOMEDICAL LITERATURE MINING
III EXPERIMENT RESULTS
IV CONCLUSIONS
ACKNOWLEDGMENTS
Chapter 4: Integrated Imaging Informatics
I INTRODUCTION
II ARCHITECTURE
III INFORMATICS
IV QUANTITATIVE ANALYSIS
V APPLICATIONS
VI CONCLUSIONS
ACKNOWLEDGMENTS
Chapter 5: Simpathica: A Computational Systems Biology Tool Within the Valis Bioinformatics Environment
I INTRODUCTION
II VALIS AND SIMPATHICA SYSTEMS
III SIMPATHICA WITHIN VALIS
IV Wnt SIGNALING EXAMPLE
V CONCLUSIONS
ACKNOWLEDGMENTS
Chapter 6: Standards, Platforms, and Applications
I INTRODUCTION
II QUANTITATIVE APPROACHES
III PLATFORMS
IV APPLICATIONS
V CONCLUSIONS
ACKNOWLEDGMENTS
RESOURCES
II: Foundations of Biochemical Network Analysis and Modeling
Chapter 7: Introduction to Computational Models of Biochemical Reaction Networks
I INTRODUCTION
II ANALYSIS OF STRUCTURAL, REGULATORY, AND KINETIC MODELS
III SIMULATION METHODS FOR KINETIC MODELS
IV ANALYSIS OF REGULATION AND CONTROL OF SYSTEMIC PROPERTIES OF BIOCHEMICAL REACTION NETWORKS
V CONCLUSIONS
ACKNOWLDEGMENTS
INTERNET REFERENCES
Chapter 8: Biological Foundations of Signal Transduction and the Systems Biology Perspective
I INTRODUCTION
II CONCEPTS AND PRINCIPLES OF SIGNAL TRANSDUCTION
III SIGNALING PATHWAYS: FORMATION OF NETWORKS
IV CONCLUSIONS
ACKNOWLEDGMENTS
Chapter 9: Reconstruction of Metabolic Networks from Genome Information and Its Structural and Functional Analysis
I INTRODUCTION
II RECONSTRUCTION AND REPRESENTATION OF METABOLIC NETWORKS
III STRUCTURAL ANALYSIS OF METABOLIC NETWORKS
IV FROM NETWORK TO MODULES AND FUNCTIONAL ANALYSIS
V CONCLUSIONS
Chapter 10: Integrated Regulatory and Metabolic Models
I INTRODUCTION
II METABOLIC NETWORKS
III REGULATORY NETWORKS
IV EXPERIMENTAL AND COMPUTATIONAL DATA INTERPRETATION
V CONCLUSIONS
ACKNOWLEDGMENTS
III: Computer Simulations of Dyrlamis Networks
Chapter 11: Gene Networks: Estimation, Modeling, and Simulation
I INTRODUCTION
II GENE NETWORK ESTIMATION FROM MICROARRAY GENE EXPRESSION DATA
III ADVANCED METHODS FOR GENE NETWORK ESTIMATION
IV PETRI-NET-BASED MODELING OF GENE NETWORKS
V CONCLUSIONS
ACKNOWLEDGMENTS
RELATED INTERNET RESOURCES
Chapter 12: A Discrete Approach to Top-Down Modeling of Biochemical Networks
I INTRODUCTION
II TOP-DOWN MODELING
III DISCRETE MODELING METHODS
IV DATA DISCRETIZATION
V RELATIONSHIP BETWEEN DISCRETE AND CONTINUOUS MODELS
VI A MATHEMATICAL THEORY FOR DISCRETE MODELS
VII TOWARD A MATHEMATICAL THEORY OF BIOLOGICAL SYSTEM IDENTIFICATION
VIII CONCLUSIONS
ACKNOWLEDGMENTS
Chapter 13: Computational Models for Circadian Rhythms: Deterministic Versus Stochastic Approaches
I INTRODUCTION: THE COMPUTATIONAL BIOLOGY OF CIRCADIAN RHYTHMS
II MODELING THE DROSOPHILA CIRCADIAN CLOCK
III STOCHASTIC MODELS FOR CIRCADIAN RHYTHMS
IV MODELING THE MAMMALIAN CIRCADIAN CLOCK
V CONCLUSIONS
ACKNOWLEDGMENTS
IV: Multi-Scale Representations of Cells and Emerging Phenotypes
Chapter 14: Multistability and Multicellularity: Cell Fates as High-Dimensional Attractors of Gene Regulatory Networks
I INTRODUCTION
II GENE EXPRESSION PROFILES IN GENE EXPRESSION STATE SPACE
III CELL FATES AND CELL TYPES AS DYNAMIC ENTITIES IN MULTICELLULAR ORGANISMS
IV LIMITATIONS OF MOLECULAR PATHWAYS AS EXPLANATION OF CELL FATE BEHAVIOR
V CELL FATE DYNAMICS: CONSTRAINED BY THE GENE REGULATORY NETWORK
VI MULTISTABILITY IN A SMALL GENE CIRCUIT
VII CELL FATES AS ATTRACTORS
VIII THE BOOLEAN NETWORK FORMALISM
IX SMALL CIRCUITS VERSUS GENOME-WIDE NETWORKS: DIFFERENT PHILOSOPHIES
X DYNAMICS OF LARGE NETWORKS AND THE ENSEMBLE APPROACH
XI ARCHITECTURAL FEATURES OF LARGE NETWORKS AND THEIR DYNAMICS
XII REALITY CHECK: GENOME-SCALE NETWORK TOPOLOGY
XIII EXPERIMENTAL EVIDENCE FOR HIGH-DIMENSIONAL ATTRACTORS
XIV BROADER BIOLOGICAL IMPLICATIONS
XV CONCLUSIONS
Chapter 15: Spatiotemporal Systems Biology
I INTRODUCTION
II SPATIOTEMPORAL SYSTEMS BIOLOGY: THEORY
III CELLSIM: A CELLULAR SIMULATOR
IV SPATIOTEMPORAL IMAGING
V CONCLUSIONS
ACKNOWLEDGMENTS
RECOMMENDED RESOURCES
Chapter 16: Cytomics: From Cell States to Predictive Medicine
I INTRODUCTION
II COMPUTATIONAL IMAGING IN CYTOMICS
III DATA ANALYSIS
IV DISCUSSION
V CONCLUSIONS
Chapter 17: The IUPS Physiome Project: Progress and Plans
I INTRODUCTION
II ORGAN SYSTEMS: CURRENT PROGRESS AND FUTURE PLANS
III OPEN STANDARDS AND OPEN-SOURCE TOOLS FOR THE PHYSIOME PROJECT
IV DISCUSSION
V CONCLUSIONS
ACKNOWLEDGMENTS

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