Computational Systems Biology
- 1st Edition - December 6, 2014
- Editors: Andres Kriete, Roland Eils
- Language: English
- Paperback ISBN:9 7 8 - 1 - 4 9 3 3 - 0 0 0 7 - 5
- eBook ISBN:9 7 8 - 0 - 0 8 - 0 4 5 9 3 4 - 9
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… Read more
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. This exciting new arena applies mathematical modeling and engineering methods to the study of biological systems. This book is the first of its kind to focus on the newly emerging field of systems biology with an emphasis on computational approaches. The work covers new concepts, methods for information storage, mining and knowledge extraction, reverse engineering of gene and metabolic networks, as well as modelling and simulation of multi-cellular systems. Central themes include strategies for predicting biological properties and methods for elucidating structure-function relationships.
Graduate students and researchers in Bioinformatics, Biocomputing, Theoretical Biology, Biochemistry/Biophysics, and Cell Biology.
CONTENT
1. Introducing Computational Systems Biology. A Kriete and R Eils
I. Enabling Information and Integration Technologies for Systems Biology:
2. Databases for Systems Biology. J Eils, C Lawerenz, K Astrahantseff, M Ginkel, and R Eils
Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology. X Hu
Integrated Imaging Informatics. B Parvin, G Fontenay, Q Yang, and MH Barcellos-Hoff
Simpathica: A Computational Systems Biology Tool within the Valis Bioinformatics Environment.
B Mishra, M Antoniotti, S Paxia and N Ugel
Standards, Platforms and Applications. HM Sauro
II. Foundations of Biochemical Network Analysis and Modeling
7. Introduction to Computational Models of Biochemical Reaction Networks.
FJ Bruggeman, BM Bakker, JJ Hornberg, and HV Westerhoff
8. Biological Foundations of Signal Transduction and the Systems Biology Perspective. U Klingmüller
9. Reconstruction of Metabolic Network from Genome Information and Its Structural and Functional Analysis.
H-W Ma and A-P Zeng
10. Integrated Regulatory and Metabolic Models. M.W. Covert
III. Computer Simulations of Dynamic Networks
11. A Discrete Approach to Network Modeling. R Laubenbacher and P Mendes
12. Gene Networks: Estimation, Modeling and Simulation. S Imoto, H Matsuno, and S Miyano
13. Computational models for circadian rhythms: Deterministic versus stochastic approaches.
J-C Leloup, D Gonze, and A Goldbeter
IV. Multi-Scale Representations of Cells and Emerging Phenotypes
14. Multistability and Multicellularity: Cell Fates as High-dimensional Attractors of Gene Regulatory Networks. S Huang
15. Spatio-Temporal Systems Biology. A Ghosh, D Miller, R Zou, B Sokhansanj,and A Kriete
16. Cytomics—from cell states to predictive medicine. G Valet, RF Murphy, JP Robinson, A Tárnok, A Kriete
17. The IUPS Physiome Project: Progress and Plans. P Hunter, K Burrowes, J Fernandez, P Nielsen,
N Smith, and M Tawhai
Subject Index
1. Introducing Computational Systems Biology. A Kriete and R Eils
I. Enabling Information and Integration Technologies for Systems Biology:
2. Databases for Systems Biology. J Eils, C Lawerenz, K Astrahantseff, M Ginkel, and R Eils
Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology. X Hu
Integrated Imaging Informatics. B Parvin, G Fontenay, Q Yang, and MH Barcellos-Hoff
Simpathica: A Computational Systems Biology Tool within the Valis Bioinformatics Environment.
B Mishra, M Antoniotti, S Paxia and N Ugel
Standards, Platforms and Applications. HM Sauro
II. Foundations of Biochemical Network Analysis and Modeling
7. Introduction to Computational Models of Biochemical Reaction Networks.
FJ Bruggeman, BM Bakker, JJ Hornberg, and HV Westerhoff
8. Biological Foundations of Signal Transduction and the Systems Biology Perspective. U Klingmüller
9. Reconstruction of Metabolic Network from Genome Information and Its Structural and Functional Analysis.
H-W Ma and A-P Zeng
10. Integrated Regulatory and Metabolic Models. M.W. Covert
III. Computer Simulations of Dynamic Networks
11. A Discrete Approach to Network Modeling. R Laubenbacher and P Mendes
12. Gene Networks: Estimation, Modeling and Simulation. S Imoto, H Matsuno, and S Miyano
13. Computational models for circadian rhythms: Deterministic versus stochastic approaches.
J-C Leloup, D Gonze, and A Goldbeter
IV. Multi-Scale Representations of Cells and Emerging Phenotypes
14. Multistability and Multicellularity: Cell Fates as High-dimensional Attractors of Gene Regulatory Networks. S Huang
15. Spatio-Temporal Systems Biology. A Ghosh, D Miller, R Zou, B Sokhansanj,and A Kriete
16. Cytomics—from cell states to predictive medicine. G Valet, RF Murphy, JP Robinson, A Tárnok, A Kriete
17. The IUPS Physiome Project: Progress and Plans. P Hunter, K Burrowes, J Fernandez, P Nielsen,
N Smith, and M Tawhai
Subject Index
- Edition: 1
- Published: December 6, 2014
- Language: English
AK
Andres Kriete
Associate Professor for Bioinformation Engineering at Drexel University, Philadelphia and Director of the Biocomputing Laboratory at the Coriell Institute for Medical Research
Affiliations and expertise
Drexel University, Philadelphia, PA and Coriell Institute for Medical Research, Camden, NJ, USARE
Roland Eils
Professor of Bioinformatics at the University of Heidelberg and Director of the Division of Theoretical Bioinformatics at the German Cancer Research Center (DKFZ) in Heidelberg
Affiliations and expertise
Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, and Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, GermanyRead Computational Systems Biology on ScienceDirect