A first course in systems biology:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
New York ; London
Garland Science
[2018]
|
| Edition: | Second edition |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xi, 468 Seiten Illustrationen |
| ISBN: | 9780815345688 |
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| 245 | 1 | 0 | |a A first course in systems biology |c Eberhard O. Voit |
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Record in the Search Index
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|---|---|
| adam_text | Contents
Chapter 1: Biological Systems
Reductionism and Systems Biology
Even Simple Systems Can Confuse Us
Why Now?
Communicating Systems Biology
The Task Before Us
Exercises
References
Further Reading
Chapter 2: Introduction to
Mathematical Modeling
Goals, Inputs, and Initial Exploration
2.1 Questions of Scale
2.2 Data Availability
Model Selection and Design
2.3 Model Structure
2.4 System Components
2.5 Model Equations
2.6 Parameter Estimation
Model Analysis and Diagnosis
2.7 Consistency and Robustness
2.8 Exploration and Validation of
Dynamical Features
Model Use and Applications
2.9 Model Extensions and Refinements
2.10 Large-Scale Model Assessments
2.11 Questions of Design
2.12 Simplicity versus Complexity
Exercises
References
Further Reading
Chapter 3: Static Network Models
Strategies of Analysis
Interaction Graphs
3.1 Properties of Graphs
3.2 Small-World Networks Si;
Dependencies Among Network
Components 62
3.3 Causality Analysis 62
3.4 Mutual Information 62
Bayesian Reconstruction of Interaction
Networks 63
3.5 Application to Signaling Networks 66
3.6 Applications to Other Biological
Networks 69
Static Metabolic Networks and Their Analysis 69
3.7 Stoichiometric Networks 70
3.8 Variants of Stoichiometric Analysis 73
3.9 Metabolic Network Reconstruction 73
3.10 Metabolic Control Analysis 74
Exercises 78
References 80
Further Reading 82
Chapter 4: The Mathematics of
Biological Systems 83
Discrete Linear Systems Models 85
4.1 Recursive Deterministic Models 85
4.2 Recursive Stochastic Models 88
Discrete Nonlinear Systems 91
Continuous Linear Systems 93
4.3 Linear Differential Equations 94
4.4 Linearized Models 95
Continuous Nonlinear Systems 100
4.5 Ad hoc Models 101
4.6 Canonical Models 102
4.7 More Complicated Dynamical
Systems Descriptions 110
Standard Analyses of Biological
Systems Models 110
4.8 Steady-State Analysis 110
4.9 Stability Analysis 115
4.10 Parameter Sensitivity 118
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CONTENTS
ix
4.11 Analysis of Systems Dynamics 119
Other Attractors 122
4.12 Limit Cycles 123
4.13 Chaotic Attractors 126
Exercises 128
References 132
Further Reading 133
Chapters: Parameter Estimation 135
Parameter Estimation for Linear Systems 136
5.1 Linear Regression Involving a
Single Variable 136
5.2 Linear Regression Involving Several
Variables 138
Parameter Estimation for Nonlinear Systems 141
5.3 Comprehensive Grid Search 143
5.4 Nonlinear Regression 145
5.5 Genetic Algorithms 146
5.6 Other Stochastic Algorithms 148
5.7 Typical Challenges 149
Parameter Estimation for Systems of
Differential Equations 153
Structure Identification 160
Exercises 161
References 166
Further Reading 167
Chapter 6: Gene Systems 169
The Central Dogma 169
Key Properties of DNA and RNA 171
6.1 Chemical and Physical Features 171
6.2 Size and Organization of DNA 174
6.3 Genes and Noncoding DNA 175
6.4 Eukaryotic DNA Packing 178
6.5 Epigenetics 178
RNA 178
6.6 Messenger RNA (mRNA) 179
6.7 Transfer RNA (tRNA) 182
6.8 Ribosomal RNA (rRNA) 182
6.9 Small RNAs 183
6.10 RNA Viruses 184
Gene Regulation 185
6.11 TheZocOperon 186
6.12 Modes of Regulation 187
6.13 Transcription Factors 188
6.14 Models of Gene Regulation 190
Measuring Gene Expression 191
Localization of Gene Expression 194
Outlook 196
Exercises 196
References 198
Further Reading 200
Chapter 7: Protein Systems 201
Chemical and Physical Features of Proteins 202
7.1 Experimental Protein Structure
Determination and Visualization 206
An Incomplete Survey of the Roles and
Functions of Proteins 208
7.2 Enzymes 209
7.3 Transporters and Carriers 211
7.4 Signaling and Messenger Proteins 214
7.5 Proteins of the Immune System 215
7.6 Structure Proteins 216
Current Challenges in Protein Research 218
7.7 Proteomics 218
7.8 Structure and Function Prediction 220
7.9 Localization 222
7.10 Protein Activity and Dynamics 224
Exercises 226
References 228
Further Reading 230
Chapter 8: Metabolic Systems 231
Biochemical Reactions 232
8.1 Background 232
8.2 Mathematical Formulation of
Elementary Reactions 234
8.3 Rate Laws 235
Pathways and Pathway Systems 240
8.4 Biochemistry and Metabolomics 240
8.5 Resources for Computational
Pathway Analysis 241
8.6 Control of Pathway Systems 244
Methods of Metabolomic Data Generation 246
8.7 Sampling, Extraction, and
Separation Methods 247
8.8 Detection Methods 247
8.9 Flux Analysis 249
X
CONTENTS
From Data to Systems Models 250
8.10 Case Study 1: Analyzing Metabolism
in an Incompletely Characterized
Organism 250
8.11 Case Study 2: Metabolic Network
Analysis 251
8.12 Case Study 3: Extraction of Dynamic
Models from Experimental Data 251
Exercises 252
References 254
Further Reading 255
Chapter 9: Signaling Systems 257
Static Models of Signal Transduction
Networks 259
9.1 Boolean Networks 259
9.2 Network Inference 261
Signal Transduction Systems Modeled with
Differential Equations 261
9.3 Bistability and Hysteresis 261
9.4 Two-Component Signaling Systems 266
9.5 Mitogen-Activated Protein Kinase
Cascades 270
9.6 Adaptation 273
9.7 Other Signaling Systems 274
Exercises 278
References 279
Further reading 281
Chapter 10: Population Systems 283
Population Growth 283
10.1 Traditional Models of
Population Growth 284
10.2 More Complex Growth Phenomena 286
Population Dynamics Under External
Perturbations 288
Analysis of Subpopulations 289
Interacting Populations 292
10.3 General Modeling Strategy 292
10.4 Phase-Plane Analysis 292
10.5 More Complex Models of
Population Dynamics 297
Exercises 299
References 301
Further reading 302
Chapter 11: Integrative Analysis of
Genome, Protein, and
Metabolite Data: A Case
Study in Yeast 303
On the Origin of Models 304
A Brief Review of the Heat Stress
Response in Yeast 306
11.1 The Trehalose Cycle 308
Modeling Analysis of the Trehalose Cycle 310
11.2 Design and Diagnosis of a Metabolic
Pathway Model 310
11.3 Analysis of Heat Stress 312
11.4 Accounting for Glucose Dynamics 314
11.5 Gene Expression 315
Multiscale Analysis 318
11.6 In Vivo NMR Profiles 318
11.7 Multiscale Model Design 320
11.8 The Trehalase Puzzle 324
Concluding Comments 327
Exercises 328
References 329
Further reading 330
Chapter 12: Physiological Modeling:
The Heart as an Example 331
Hierarchy of Scales and Modeling Approaches 332
12.1 Basics of Heart Anatomy 333
12.2 Modeling Targets at the Organ Level 334
12.3 Modeling Targets at the Tissue Level 335
12.4 Modeling Targets at the Cell Level 337
Simple Models of Oscillations 339
12.5 Black-Box Models of Oscillations 339
12.6 Summary of Black-Box Oscillation
Models 342
12.7 From a Black Box to Meaningful
Models 343
Electrochemistry in Cardiomyocytes 345
12.8 Biophysical Description of
Electrochemical Processes at the
Membrane of Cardiomyocytes 347
12.9 Resting Potentials and Action
Potentials 348
12.10 Models of Action Potentials 350
12.11 Repeated Heartbeats 354
Issues of a Failing Heart 355
CONTENTS
xi
12.12 Modeling Heart Function and Failure
Based on Molecular Events 356
Outlook for Physiological Multiscale
Modeling 361
Exercises 362
References 365
Further Reading 366
Chapter 13: Systems Biology in Medicine
and Drug Development 369
Are you Unique? 369
13.1 Biological Variability and Disease 369
13.2 Modeling Variability and Disease 370
Personalized Medicine and Predictive Health 372
13.3 Data Needs and Biomarkers 373
13.4 Personalizing Mathematical Models 374
The Drug Development Process 378
The Role of Systems Biology in
Drug Development 380
13.5 Computational Target and Lead
Identification 381
13.6 Receptor Dynamics 382
13.7 Pharmacokinetic Modeling 385
13.8 Pathway Screening with Dynamic
Models 390
13.9 Emerging Roles of Systems Biology
in Drug Development 393
Exercises 394
References 395
Further Reading 396
Chapter 14: Design of Biological Systems 399
Natural Design of Biological Systems 400
14.1 The Search for Structural Patterns 400
14.2 Network Motifs 402
14.3 Design Principles 404
14.4 Operating Principles 406
Goal-Oriented Manipulations and Synthetic
Design of Biological Systems 407
14.5 Metabolic Engineering 407
14.6 Synthetic Biology 408
Case Studies of Synthetic Biological
Systems Designs 411
14.7 Elementary Mode Analysis in
Metabolic Engineering 411
14.8 Drug Development 414
14.9 Gene Circuits 415
The Future Has Begun 419
Exercises 419
References 421
Further Reading 423
Chapter 15: Emerging Topics in
Systems Biology 425
Emerging Applications 426
15.1 From Neurons to Brains 426
15.2 Complex Diseases, Inflammation,
and Trauma 428
15.3 Organisms and their Interactions
with the Environment 432
Modeling Needs 435
15.4 Multiscale Modeling 436
15.5 A Data-Modeling Pipeline 437
Toward a Theory of Biology... or Several
Theories? 439
References 441
Further Reading 443
Glossary 445
Index 459
|
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| language | English |
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| spelling | Voit, Eberhard O. Verfasser (DE-588)1037877950 aut A first course in systems biology Eberhard O. Voit Second edition New York ; London Garland Science [2018] xi, 468 Seiten Illustrationen txt rdacontent n rdamedia nc rdacarrier Biochemie (DE-588)4006777-4 gnd rswk-swf Systembiologie (DE-588)4809615-5 gnd rswk-swf Mathematische Modellierung (DE-588)7651795-0 gnd rswk-swf Systembiologie (DE-588)4809615-5 s Mathematische Modellierung (DE-588)7651795-0 s Biochemie (DE-588)4006777-4 s DE-604 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029797417&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Voit, Eberhard O. A first course in systems biology Biochemie (DE-588)4006777-4 gnd Systembiologie (DE-588)4809615-5 gnd Mathematische Modellierung (DE-588)7651795-0 gnd |
| subject_GND | (DE-588)4006777-4 (DE-588)4809615-5 (DE-588)7651795-0 |
| title | A first course in systems biology |
| title_auth | A first course in systems biology |
| title_exact_search | A first course in systems biology |
| title_full | A first course in systems biology Eberhard O. Voit |
| title_fullStr | A first course in systems biology Eberhard O. Voit |
| title_full_unstemmed | A first course in systems biology Eberhard O. Voit |
| title_short | A first course in systems biology |
| title_sort | a first course in systems biology |
| topic | Biochemie (DE-588)4006777-4 gnd Systembiologie (DE-588)4809615-5 gnd Mathematische Modellierung (DE-588)7651795-0 gnd |
| topic_facet | Biochemie Systembiologie Mathematische Modellierung |
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