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Principles of Computational Cell Biology: from protein complexes to cellur Networks.
This first textbook of its kind provides an ideal introduction to the field for students of biology and bioinformatics. Carefully designed study exercises -- with corresponding answers -- offer excellent support for those preparing for exams in these subjects, and help introduce the more technical a...
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| Format: | Printed Book |
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Weinheim
Wiley-VCH
2008
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Table of Contents:
- Networks in biological cells. Some basics about networks ; Biological background ; Cellular pathways ; Ontologies and databases ; Methods in cellular modeling
- Algorithms on mathematical graphs. Primer on mathematical graphs ; A few words about algorithms and computer programs ; Data structures for graphs ; Dijkstra's algorithm ; Minimum spanning tree ; Graph drawing
- Protein-protein interaction networks : pairwise connectivity. Principles of protein-protein interactions ; Experimental high-throughput methods of detecting ; Bioinformatic prediction of protein-protein interactions ; Bayesian networks for judging the accuracy of interactions ; Bayesian networks for judging the accuracy of interactions ; Protein domain networks
- Protein-protein interaction networks : structural hierarchies. Protein interaction graph networks ; Finding cliques ; Random graphs ; Scale-free graphs ; Detecting communities in networks ; Modular decomposition ; Network growth mechanisms
- Gene regulatory networks. Regulation of gene transcription at promoters ; Gene regulatory networks ; Graph theoretical models ; Dynamic models ; Motifs
- Metabolic networks. Introduction ; Stoichiometric matrix ; Linear algebra primer ; Flux balance analysis ; Double description method ; Extreme pathways and elementary modes ; Minimal cut sets ; High-flux backbone
- Kinetic modeling of cellular processes. Ordinary differential equation models. Modeling cellular feedback loops by ODEs ; Partial differential equations ; Dynamic Monte Carlo (Gillespie algorithm) ; Stochastic modeling of a small molecular network ; Parameter optimization with generic algorithms
- Structures of protein complexes and subcellular structures. Examples of protein complexes ; Complexeome of S. cerevisiae ; Experimental determination of three-dimensional structures of protein complexes ; Density fitting ; Fourier transformation ; Advanced density fitting ; FFT protein-protein docking ; Prediction of assemblies from pairwise docking ; Electron tomography
- Biomolecular association and binding. Modeling by homology ; Structural properties of protein-protein interfaces ; Bioinformatic prediction of protein-protein interfaces ; Forces important for biomolecular association ; Protein-protein association ; Assembly of macromolecular complexes : the ribosome
- Integrated network. Correlating interactome and gene regulation ; Response of Gene regulatory network to outside stimuli ; Integrated analysis of metabolic and regulatory networks
- Outlook.