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Principles of Computational Cell Biology: From Protein Complexes to Cellular Networks [Mīkstie vāki]

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Volkhard Helms

Formāts: Paperback / softback, 289 pages, height x width x depth: 240x171x15 mm, weight: 568 g
Izdošanas datums: 10-Jun-2008
Izdevniecība: Wiley-VCH Verlag GmbH
ISBN-10: 3527315551
ISBN-13: 9783527315550

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Cellular biology (cytology) - (Noliktavā: 1 punkts)

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Formāts: Paperback / softback, 289 pages, height x width x depth: 240x171x15 mm, weight: 568 g
Izdošanas datums: 10-Jun-2008
Izdevniecība: Wiley-VCH Verlag GmbH
ISBN-10: 3527315551
ISBN-13: 9783527315550

Citas grāmatas par šo tēmu:

Cellular biology (cytology) - (Noliktavā: 1 punkts)

Permanent link: https://www.kriso.lv/db/9783527315550.html

Keywords:

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 aspects of the topic while keeping maths to a minimum. In particular, the text focuses on a network-based approach to the study of cellular systems.

Recenzijas

A"This volume contains succinct, yet clear, descriptions of each of these topics and is best suited for readers who are delving into these concepts for the first time.A"( The Quarterly Review of Biology , 2009)

Preface

Networks in Biological Cells

(16)

Some Basics about Networks

(3)

Random Networks

(1)

Small-World Phenomenon

(1)

Scale-Free Network Model

(1)

Biological Background

(3)

Cellular Components

(1)

Spatial Organization of Eukaryotic Cells - Compartments

(1)

Cellular Organisms

(1)

Cellular Pathways

(5)

Biochemical Pathways

(1)

Enzymatic Reactions

(3)

Signal Transduction

(1)

Cell Cycle

(1)

Ontologies and Databases

(2)

Ontologies

(1)

Systems Biology Markup Language

(1)

KEGG

(1)

Brenda

(1)

Methods in Cellular Modeling

(3)

Algorithms on Mathematical Graphs

(22)

Primer on Mathematical Graphs

(1)

A Few Words about Algorithms and Computer Programs

(3)

Implementation of Algorithms

(1)

Classes of Algorithms

(1)

Data Structures for Graphs

(2)

Dijkstra's Algorithm

(6)

Description of the Algorithm

(2)

Pseudocode

(2)

Running Time

(1)

Minimum Spanning Tree

(2)

Kruskal's Algorithm

(1)

Graph Drawing

(8)

Protein-Protein Interaction Networks - Pairwise Connectivity

(28)

Principles of Protein-Protein Interactions

(1)

Experimental High-Throughput Methods for Detecting Protein-Protein Interactions

(9)

Gel Electrophoresis

(1)

Two-Dimensional Gel Electrophoresis

(1)

Affinity Chromatography

(1)

Yeast Two-Hybrid Screening

(2)

Synthetic Lethality

(1)

Gene Coexpression

(1)

Mass Spectroscopy

(1)

Databases for Interaction Networks

(1)

Overlap of Interactions

(2)

Criteria to Judge the Reliability of Interaction Data

(1)

How Many Protein-Protein Interactions can be Expected in Yeast?

(1)

Bioinformatic Prediction of Protein-Protein Interactions

(3)

Analysis of Gene Order

(1)

Phylogenetic Profiling/Coevolutionary Profiling

(1)

Coevolution

(1)

Bayesian Networks for Judging the Accuracy of Interactions

(7)

Bayes' Theorem

(1)

Bayesian Network

(1)

Application of Bayesian Networks to Protein-Protein Interaction Data

(1)

Measurement of reliability ``likelihood ratio''

(1)

Prior and posterior odds

(1)

A worked example: parameters of the naive Bayesian network for essentiality

(1)

Fully connected experimental network

(2)

Protein Domain Networks

(8)

Protein-Protein Interaction Networks - Structural Hierarchies

(32)

Protein Interaction Graph Networks

(4)

Degree Distribution

(1)

Clustering Coefficient

(2)

Finding Cliques

(1)

Random Graphs

(1)

Scale-Free Graphs

(2)

Detecting Communities in Networks

(7)

Divisive Algorithms for Mapping onto Tree

(4)

Modular Decomposition

(4)

Modular Decomposition of Graphs

(4)

Network Growth Mechanisms

(13)

Gene Regulatory Networks

(16)

Regulation of Gene Transcription at Promoters

100

(1)

Gene Regulatory Networks

101

(4)

Gene Regulatory Network of E. coli

101

(4)

Graph Theoretical Models

105

(1)

Coexpression Networks

105

(1)

Bayesian Networks

106

(1)

Dynamic Models

106

(5)

Boolean Networks

106

(1)

Reverse Engineering Boolean Networks

107

(3)

Differential Equations Models

110

(1)

Motifs

111

(4)

Feed-Forward Loop (FFL)

112

(1)

SIM Motif

112

(1)

Densely Overlapping Region (DOR)

112

(3)

Metabolic Networks

115

(40)

Introduction

115

(3)

Stoichiometric Matrix

118

(3)

Linear Algebra Primer

121

(4)

Matrices: Definitions and Notations

121

(1)

Adding, Subtracting and Multiplying Matrices

121

(1)

Linear Transformations, Ranks and Transpose

122

(1)

Square Matrices and Matrix Inversion

123

(1)

Eigenvalues of Matrices

124

(1)

System of Linear Equations

124

(1)

Flux Balance Analysis

125

(3)

Double Description Method

128

(5)

Extreme Pathways and Elementary Modes

133

(7)

Analysis of Eextreme Pathways

137

(2)

Elementary Flux Modes

139

(1)

Minimal Cut Sets

140

(6)

Applications of Minimal Cut Sets

144

(2)

High-Flux Backbone

146

(9)

Kinetic Modeling of Cellular Processes

155

(38)

Ordinary Differential Equation Models

155

(3)

Examples for ODEs

156

(2)

Modeling Cellular Feedback Loops by ODEs

158

(11)

Protein Synthesis and Degradation: Linear Response

159

(1)

Phosphorylation/Dephosphorylation - Hyperbolic Response

160

(2)

Phosphorylation/Dephosphorylation - Buzzer

162

(1)

Perfect Adaptation - Sniffer

163

(1)

Positive Feedback - One-Way Switch

164

(1)

Mutual Inhibition - Toggle Switch

165

(1)

Negative Feedback - Homeostasis

166

(1)

Negative Feedback: Oscillatory Response

166

(1)

Cell Cycle Control System

167

(2)

Partial Differential Equations

169

(3)

Spatial Gradients of Signaling Activities

170

(2)

Dynamic Monte Carlo (Gillespie Algorithm)

172

(1)

Basic Outline of the Gillespie Method

173

(1)

Stochastic Modeling of a Small Molecular Network

173

(9)

Model System: Bacterial Photosynthesis

174

(2)

Pools-and-Proteins Model

176

(1)

Evaluating the Binding and Unbinding Kinetics

177

(1)

Pools of the Chromatophore Vesicle

178

(1)

Results for the Steady-State Regimes of the Vesicle

179

(3)

Parameter Optimization with Genetic Algorithms

182

(11)

Structures of Protein Complexes and Subcellular Structures

193

(38)

Examples of Protein Complexes

193

(4)

Complexeome of S. cerevisiae

197

(2)

Experimental Determination of Three-dimensional Structures of Protein Complexes

199

(5)

X-ray Crystallography

199

(1)

NMR

200

(1)

Electron Crystallography/Electron Microscopy

201

(1)

Immuno-electron Microscopy

201

(1)

Fluorescence Resonance Energy Transfer

202

(2)

Density Fitting

204

(2)

Correlation-based Fitting

204

(2)

Fourier Transformation

206

(4)

Fourier Series

206

(1)

Continuous Fourier Transform

207

(1)

Discrete Fourier Transform

207

(1)

Convolution Theorem

208

(1)

Fast Fourier Transformation

208

(2)

Advanced Density Fitting

210

(6)

Laplacian Filter

211

(1)

Fitting Using Core Downweighting

212

(2)

Core-weighted Correlation Function

214

(1)

Surface Overlap Maximization (SOM)

215

(1)

FFT Protein-Protein Docking

216

(2)

Prediction of Assemblies from Pairwise Docking

218

(3)

Electron Tomography

221

(10)

Reconstruction of a Phantom Cell

222

(9)

Biomolecular Association and Binding

231

(30)

Modeling by Homology

231

(2)

Structural Properties of Protein-Protein Interfaces

233

(6)

Size and Shape

233

(2)

Hot Spots

235

(1)

An Experimental Model System: Human Growth Hormone and its Receptor

236

(3)

Bioinformatic Prediction of Protein-Protein Interfaces

239

(7)

Amino acid Composition of Protein Interfaces

239

(1)

Pairing Propensities

240

(1)

Interface Statistical Potentials

240

(1)

Conservation at Protein Interfaces

241

(2)

Correlated Mutations at Protein Interfaces

243

(2)

Classification of Protein Interfaces

245

(1)

Forces Important for Biomolecular Association

246

(3)

Protein-Protein Association

249

(5)

Brownian Dynamics Simulations

250

(4)

Assembly of Macromolecular Complexes: the Ribosome

254

(7)

Integrated Networks

261

(10)

Correlating Interactome and Gene Regulation

261

(2)

Response of Gene Regulatory Network to Outside Stimuli

263

(3)

Integrated Analysis of Metabolic and Regulatory Networks

266

(5)

Outlook

271

(2)

Index

273

Volkhard Helms has been Professor of Bioinformatics in the Center of Bioinformatics, Saarland University since 2003, where he heads the bioinformatics department. He worked for his PhD in the European Molecular Biology Laboratory in Heidelberg and carried out post-doctoral work at UC San Diego. He then went on to lead a research group in theoretical biophysics at the Max Plank Institute of Biophysics in Frankfurt. In 2001 he was selected as an EMBO Young Investigator, and since 2000 he has been a member of the "Faculty of 1000". His work focuses on experimental and computational approaches to the study of protein-protein interactions.

Principles of Computational Cell Biology: From Protein Complexes to Cellular Networks [Mīkstie vāki]

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