Analysis of biological networks:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Hoboken, NJ
Wiley-Interscience
2008
|
| Schriftenreihe: | Wiley series on bioinformatics : Computational techniques and engineering
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XX, 346 S. Ill., graph. Darst. |
| ISBN: | 9780470041444 0470041447 |
Internformat
MARC
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| 245 | 1 | 0 | |a Analysis of biological networks |c ed. by Björn H. Junker ... |
| 264 | 1 | |a Hoboken, NJ |b Wiley-Interscience |c 2008 | |
| 300 | |a XX, 346 S. |b Ill., graph. Darst. | ||
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| 490 | 0 | |a Wiley series on bioinformatics : Computational techniques and engineering | |
| 650 | 4 | |a Algorithms | |
| 650 | 4 | |a Biological models | |
| 650 | 4 | |a Computational Biology | |
| 650 | 4 | |a Computational biology | |
| 650 | 4 | |a Models, Biological | |
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Datensatz im Suchindex
| _version_ | 1804138010626752512 |
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| adam_text | * * * * * * * * * * ********* * * * * * * * * ************* ***** * * *
* * * * * * * * * * * * * * ********* *** * * * * * * * * BJOERN H.
JUNKER 1.1* INTRODUCTION 1.2* BIOLOGY 101* 1.2.1 BIOCHEMISTRY AND
MOLECULAR BIOLOGY 1.2.2 CELL BIOLOGY 1.2.3 ECOLOGY AND EVOLUTION 1.3*
SYSTEMS BIOLOGY 1.4* PROPERTIES OF BIOLOGICAL NETWORKS 1.4.1 NETWORKS ON
A MICROSEOPIE SCALE 1.4.2 NETWORKS ON A MACROSCOPIC SCALE 1.4.3 OTHER
BIOLOGICAL NETWORKS 1.5* SUMMARY 1.6* EXERCISES* REFERENCES* X I I I *
XV* X I X * 1* 3* 3* 4* 4* 6* 7* 8* 8* 9* 11* 11* 12* 12* 12* V*
VI* 2 GRAPH THEORY FALK SCHREIBER 2.1* INTRODUCTION 2.2* BASIC NOTATION
2.2.1* SETS 2.2.2* GRAPHS 2.2.3* GRAPH ATTRIBUTES 2.3* SPECIAL GRAPHS
2.3.1* UNDIRECTED, DIRECTED, MIXED, AND MULTIGRAPHS 2.3.2* HYPERGRAPHS
AND BIPARTITE GRAPHS 2.3.3* TREES 2.4* GRAPH REPRESENTATION 2.4.1*
ADJACENCY MATRIX 2.4.2* ADJACENCY LIST 2.5* GRAPH ALGORITHMS 2.5.1*
RUNNING TIMES OF A1GORITHMS 2.5.2* TRAVERSAL 2.6* SUMMARY 2.7*
EXERCISES* REFERENCES* PART II NETWORK ANALYSIS 3 GLOBAL NETWORK
PROPERTIES RALF STEUER AND GORKA ZAMORA L6PEZ 3.1* INTRODUCTION 3.2*
GLOBAL PROPERTIES OF COMPLEX NETWORKS 3.2.1* DISTANCE, AVERAGE PATH
LENGTH, AND DIAMETER 3.2.2* SIX DEGREES OF SEPARATION: CONCEPTS OF A
SMALL WORLD 3.2.3* THE DEGREE DISTRIBUTION 3.2.4* ASSORTATIVE MIXING AND
DEGREE CORRELATIONS 3.2.5* THE CLUSTERING COEFFICIENT 3.2.6* THE
MATCHING INDEX 3.2.7* NETWORK CENTRALITIES 3.2.8* EIGENVALUES AND
SPECTRAL PROPERTIES OF NETWORKS 3.3* MODELS OF COMPLEX NETWORKS 3.3.1*
THE ERDOES-R6NYI MODEL 3.3.2* THE WATTS-STROGATZ MODEL 3.3.3* THE
BARABASI-ALBERT MODEL 3.3.4* EXTENSIONS OF THE BA MODEL 3.4* ADDITIONAL
PROPERTIES OF COMPLEX NETWORKS 3.4.1 STRUCTURAL ROBUSTNESS AND ATTACK
TOLERANCE CONTENTS 15* 15* 16* 16* 16* 19* 19* 19* 20* 21* 23* 23* 23*
24* 24* 25* 27* 27* 28* 29* 31* 31* 33* 33* 35* 35* 38* 39* 41* 42* 43*
43* 44* 45* 46* 48* 48* 49* CONTENTS* VII 3.4.2* MODU1ARITY, COMMUNITY
STRUCTURES AND HIERARCHIES 50 3.4.3* SUBGRAPHS AND MOTIFS IN NETWORKS 51
3.5 STATISTICAL TESTING OF NETWORK PROPERTIES* 52 3.5.1* GENERATING
NETWORKS AND NULL MODELS 53 3.5.2* THE CONCEPTUALIZATION OF CELLU1AR
NETWORKS 54 3.5.3* BIPARTITE GRAPHS 55 3.5.4* CORRE1ATION NETWORKS 57
3.6* SUMMARY 57 3.7* EXERCISES 58 REFERENCES 59 4 NETWORK CENTRALITIES*
65 DIRK KOSCHUETZKI 4.1* INTRODUCTION 65 4.2* CENTRALITY DEFINITION AND
FUNDAMENTAL PROPERTIES 67 4.2.1* COMPARISON OF CENTRA1ITY VA1UES 68
4.2.2* DISCONNECTED NETWORKS 68 4.3 DEGREE AND SHORTEST PATH-BASED
CENTRA1ITIES* 69 4.3.1* DEGREE CENTRALITY 69 4.3.2* ECCENTRICITY
CENTRALITY 71 4.3.3* C10SENESS CENTRALITY 72 4.3.4* SHORTEST PATH
BETWEENNESS CENTRALITY 73 4.3.5* ALGORITHMS 74 4.3.6* EXAMP1E 76 4.4
FEEDBACK-BASED CENTRALITIES* 77 4.4.1* KATZ S STATUS INDEX 77 4.4.2*
BONACICH S EIGENVECTOR CENTRA1ITY 78 4.4.3* PAGERANK 79 4.5* TOO1S 80
4.6* SUMMARY 80 4.7* EXERCISES 81 REFERENCES 81 5 NETWORK MOTIFS* 85
HENNING SCHWAEBBERMEYER 5.1* INTRODUCTION 85 5.2* DEFINITIONS AND BASIC
CONCEPTS 86 5.2.1* DEFINITIONS 86 5.2.2* MODELING OF BIO1OGICA1 NETWORKS
88 5.2.3* CONCEPTS OF MOTIF FREQUENCY 88 5.3 MOTIF STATISTICS AND
MOTIF-BASED NETWORK DISTANCE* 89 5.3.1* DETERMINATION OF STATISTICA1
SIGNIFICANCE OF NETWORK MOTIFS 89 VIII* CONTENTS 5.3.2* RANDOMIZATION
ALGORITHM FOR GENERATION OF NULL MODEL NETWORKS 90 5.3.3* INFLUENCE OF
THE NULL MODEL ON MOTIF SIGNIFICANCE 91 5.3.4* LIMITATIONS OF THE NULL
MODEL ON MOTIF DETECTION 91 5.3.5* MEASURES OF MOTIF SIGNIFICANCE AND
FOR NETWORK COMPARISON 91 5.4* COMPLEXITY OF NETWORK MOTIF DETECTION 94
5.4.1* ASPECTS AFFECTING THE COMPLEXITY OF NETWORK MOTIF DETECTION 94
5.4.2* FREQUENCY ESTIMATION BY MOTIF SAMPLING 96 5.5* METHODS AND TOOLS
FOR NETWORK MOTIF ANALYSIS 96 5.5.1* PAJEK 96 5.5.2* MFINDER 96 5.5.3*
MAVISTO 97 5.5.4* FANMOD 97 5.6* ANALYSES AND APPLICATIONS OF NETWORK
MOTIFS 97 5.6.1* NETWORK MOTIFS IN COMPLEX NETWORKS 97 5.6.2* DYNAMIC
PROPERTIES OF NETWORK MOTIFS 98 5.6.3* HIGHER ORDER STRUCTURES FORMED BY
NETWORK MOTIFS 102 5.6.4* NETWORK COMPARISON BASED ON NETWORK MOTIFS 104
5.6.5* EVOLUTIONARY ORIGIN OF NETWORK MOTIFS 106 5.7* SUMMARY 106 5.8*
EXERCISES 108 REFERENCES 108 6 NETWORK CLUSTERING* 113 BALABHASKAR
BALASUNDARAM AND SERGIY BUTENKO 6.1* INTRODUCTION 113 6.2* NOTATIONS AND
DEFINITIONS 115 6.3* NETWORK CLUSTERING PROBLEM 118 6.4* CLIQUE-BASED
CLUSTERING 119 6.4.1* MINIMUM CLIQUE PARTITIONING 120 6.4.2* MIN-MAX
K-CLUSTERING 122 6.5* CENTER-BASED CLUSTERING 125 6.5.1* CLUSTERING WITH
DOMINATING SETS 126 6.5.2* K-CENTER CLUSTERING 129 6.6* CONC1USION 131
6.7* SUMMARY 133 6.8* EXERCISES 133 REFERENCES 134 7 PETRI NETS* 139 [NA
KOCH AND MONIKA HEINER 7.1* INTRODUCTION 139 IX CONTENTS 7.2 QUALITATIVE
MODELING* 141 7.2.1 THE MODEL* 141 7.2.2 THE BEHAVIORAL PROPERTIES* 148
7.3 QUALITATIVE ANALYSIS* 152 7.3.1 STRUCTURAL ANALYSIS* 152 7.3.2
INVARIANT ANALYSIS* 155 7.3.3 MCT-SETS* 162 7.3.4 DYNAMIC ANALYSIS OF
GENERAL PROPERTIES* 164 7.3.5 DYNAMIC ANALYSIS OF SPECIAL PROPERTIES*
166 7.3.6 MODEL VALIDATION CRITERIA* 168 7.4 QUANTITATIVE MODELING AND
ANALYSIS* 169 7.5* TOOL SUPPORT 171 7.6* CASE STUDIES 172 7.7* SUMMARY
174 7.8* EXERCISES 175 REFERENCES 177 PART III BIOLOGICAL NETWORKS* 181
8 SIGNAL TRANSDUCTION AND GENE REGULATION NETWORKS* 183 ANATOLIJ P.
POTAPOV 8.1* INTRODUCTION 183 8.2* DECISIVE ROLE OF REGULATORY NETWORKS
IN THE EVOLUTION AND EXISTENCE OF ORGANISMS 184 8.3* GENE REGULATORY
NETWORK AS A SYSTEM OF MANY SUBNETWORKS 186 8.4* DATABASES ON GENE
REGULATION AND SOFTWARE TOOLS FOR NETWORK ANALYSIS 187 8.5*
PECULIARITIES OF SIGNAL TRANSDUCTION NETWORKS 188 8.6* TOPOLOGY OF
SIGNAL TRANSDUCTION NETWORKS 190 8.7* TOPOLOGY OF TRANSCRIPTION NETWORKS
191 8.8* LNTERCELLULAR MOLECULAR REGULATORY NETWORKS 198 8.9* SUMMARY
200 8.10* EXERCISES 201 REFERENCES 202 9 PROTEIN INTERACTION NETWORKS*
207 FREDERIK BOEMKE 9.1* INTRODUCTION 207 9.2* DETECTING PROTEIN
INTERACTIONS 209 9.2.1 THE YEAST TWO-HYBRID SYSTEM* 211 9.2.2 AFFINITY
CAPTURE OF PROTEIN COMPLEXES* 216 9.2.3 COMPUTATIONAL METHODS TO PREDICT
PROTEIN INTERACTIONS 218 X* CONTENTS 9.2.4* OTHER WAYS TO IDENTIFY
PROTEIN INTERAETIONS 219 9.3 ESTABLISHING PROTEIN INTERAETION NETWORKS*
220 9.3.1* DATA STORAGE AND NETWORK GENERATION 220 9.3.2* BENEHMARKING
HIGH-THROUGHPUT INTERAETION DATA 222 9.4 ANALYZING PROTEIN INTERAETION
NETWORKS* 223 9.4.1* NETWORK TOPOLOGY AND FUNETIONAL IMPLIEATIONS 223
9.4.2* FUNETIONAL MODULES IN PROTEIN INTERAETION NETWORKS 223 9.4.3*
EVOLUTION OF PROTEIN INTERAETION NETWORKS 224 9.4.4* COMPARATIVE
INTERAETOMIES 225 9.5* SUMMARY 225 9.6* EXEREISES 226 REFERENEES 227 10
METABOLIE NETWORKS* 233 MARCIO ROSA DA SILVA, JIBIN SUN, HONGWU MA, FENG
HE,* AND AN-PING ZENG* 10.1* INTRODUETION 233 10.2 VISUALIZATION AND
GRAPH REPRESENTATION* 234 10.3* REEONSTRUETION OF GENOME-SEALE METABOLIE
NETWORKS 234 10.4* CONNEETIVITY AND CENTRALITY IN METABOLIE NETWORKS 239
10.5* MODULARITY AND DEEOMPOSITION OF METABOLIE NETWORKS 242 10.5.1*
MODULARITY COEFFIEIENT 244 10.5.2 MODULARITY-BASED DEEOMPOSITION* 245
10.6* ELEMENTARY FLUX MODES AND EXTREME PATHWAYS 246 10.7* SUMMARY 249
10.8* EXEREISES 249 REFERENEES 251 11 PHYLOGENETIC NETWORKS* 255 BIRGIT
GEMEINHOLZER 11.1* INTRODUETION 255 11.2 CHARAETER SELEETION, CHARAETER
CODING, AND MATRIEES FOR PHYLOGENETIE REEONSTRUETION 257 11.3* TREE
REEONSTRUETION METHODOLOGIES 260 11.4* PHYLOGENETIE NETWORKS 264 11.4.1*
GALLED TREES 266 11.4.2 STATISTIEAL PARSIMONY* 267 11.4.3* MEDIAN
NETWORK 269 11.4.4 MEDIAN-JOINING NETWORKS* 270 11.4.5* PYRAMIDS 271
11.4.6 EXAMPLE OF A PYRAMIDAL CLUSTERING MODEL* 271 11.4.7 SPLIT
DEEOMPOSITION* 274 CONTENTS* XI 11.5* SUMMARY 276 11.6 EXERCISES* 276
REFERENCES 277 12 ECOLOGICAL NETWORKS* 283 URSULA GAEDKE 12.1*
INTRODUCTION 283 12.2* BINARY FOOD WEBS 289 12.2.1* INTRODUCTION AND
DEFINITIONS 289 12.2.2 DESCRIPTORS OF THE NETWORK* 289 12.2.3*
OPERATIONAL PROBLEMS 291 12.2.4 AIMS AND RESULTS* 291 12.2.5 CONCLUSION*
293 12.3 QUANTITATIVE TROPHIC FOOD WEBS* 293 12.3.1* INTRODUCTION,
DEFINITIONS, AND DATABASE 293 12.3.2 MULTIPLE COMMODITIES* 295 12.3.3*
DESCRIPTORS OF THE NETWORK AND INFORMATION TO BE GAINED 295 12.3.4
CONCLUSION* 298 12.4 ECOLOGICAL INFORMATION NETWORKS* 298 12.5* SUMMARY
300 12.6 EXERCISES* 301 REFERENCES 301 13 CORRELATION NETWORKS* 305 DIRK
STEINHAUSER; LEONARD KRALL, CARSTEN MUESSIG, DIRK BUESSIS,* AND BJOEM
USADEI* 13.1* INTRODUCTION 305 13.2 GENERAL REMARKS* 306 13.3* BASIC
NOTATION 307 13.3.1* DATA, UNIT, VARIABLE, AND OBSERVATION 307 13.3.2
SAMPIE, PROFILES, AND REPLICA SET* 308 13.3.3* MEASURES OF ASSOCIATION
309 13.3.4 SIMPLE CORRELATION MEASURES* 310 13.3.5 COMPLEX CORRELATION
AND ASSOCIATION MEASURES 311 13.3.6 PROBABILITY, CONFIDENCE, AND POWER*
313 13.3.7 MATRICES* 314 13.4 CONSTRUCTION AND ANALYSES OF CORRELATION
NETWORKS 314 13.4.1* DATA AND PROFILES 315 13.4.2 DATA SET AND MATRIX*
316 13.4.3 CORRELATION MATRIX* 318 13.4.4 NETWORK MATRIX* 318 13.4.5
CORRELATION NETWORK ANALYSIS* 319 XII 13.4.6 INTERPRETATION AND
VALIDATION 13.5* BIOLOGICAL USE OF CORRELATION NETWORKS 13.5.1 THE
GLOBAL ANALYSIS APPROACH 13.5.2 THE GUIDE GENE APPROACH 13.5.3 A SIMPLE
COREGULATION TEST: PHOTOSYNTHESIS 13.5.4 A COMPLEX COREGULATION TEST:
BRASSINOSTEROIDS 13.6* SUMMARY 13.7* EXERCISES* REFERENCES* INDEX
CONTENTS 321* 321* 321* 322* 324* 327* 328* 329* 330* 335*
|
| adam_txt |
* * * * * * * * * * ********* * * * * * * * * ************* ***** * * *
* * * * * * * * * * * * * * ********* *** * * * * * * * * BJOERN H.
JUNKER 1.1* INTRODUCTION 1.2* BIOLOGY 101* 1.2.1 BIOCHEMISTRY AND
MOLECULAR BIOLOGY 1.2.2 CELL BIOLOGY 1.2.3 ECOLOGY AND EVOLUTION 1.3*
SYSTEMS BIOLOGY 1.4* PROPERTIES OF BIOLOGICAL NETWORKS 1.4.1 NETWORKS ON
A MICROSEOPIE SCALE 1.4.2 NETWORKS ON A MACROSCOPIC SCALE 1.4.3 OTHER
BIOLOGICAL NETWORKS 1.5* SUMMARY 1.6* EXERCISES* REFERENCES* X I I I *
XV* X I X * 1* 3* 3* 4* 4* 6* 7* 8* 8* 9* 11* 11* 12* 12* 12* V*
VI* 2 GRAPH THEORY FALK SCHREIBER 2.1* INTRODUCTION 2.2* BASIC NOTATION
2.2.1* SETS 2.2.2* GRAPHS 2.2.3* GRAPH ATTRIBUTES 2.3* SPECIAL GRAPHS
2.3.1* UNDIRECTED, DIRECTED, MIXED, AND MULTIGRAPHS 2.3.2* HYPERGRAPHS
AND BIPARTITE GRAPHS 2.3.3* TREES 2.4* GRAPH REPRESENTATION 2.4.1*
ADJACENCY MATRIX 2.4.2* ADJACENCY LIST 2.5* GRAPH ALGORITHMS 2.5.1*
RUNNING TIMES OF A1GORITHMS 2.5.2* TRAVERSAL 2.6* SUMMARY 2.7*
EXERCISES* REFERENCES* PART II NETWORK ANALYSIS 3 GLOBAL NETWORK
PROPERTIES RALF STEUER AND GORKA ZAMORA L6PEZ 3.1* INTRODUCTION 3.2*
GLOBAL PROPERTIES OF COMPLEX NETWORKS 3.2.1* DISTANCE, AVERAGE PATH
LENGTH, AND DIAMETER 3.2.2* SIX DEGREES OF SEPARATION: CONCEPTS OF A
SMALL WORLD 3.2.3* THE DEGREE DISTRIBUTION 3.2.4* ASSORTATIVE MIXING AND
DEGREE CORRELATIONS 3.2.5* THE CLUSTERING COEFFICIENT 3.2.6* THE
MATCHING INDEX 3.2.7* NETWORK CENTRALITIES 3.2.8* EIGENVALUES AND
SPECTRAL PROPERTIES OF NETWORKS 3.3* MODELS OF COMPLEX NETWORKS 3.3.1*
THE ERDOES-R6NYI MODEL 3.3.2* THE WATTS-STROGATZ MODEL 3.3.3* THE
BARABASI-ALBERT MODEL 3.3.4* EXTENSIONS OF THE BA MODEL 3.4* ADDITIONAL
PROPERTIES OF COMPLEX NETWORKS 3.4.1 STRUCTURAL ROBUSTNESS AND ATTACK
TOLERANCE CONTENTS 15* 15* 16* 16* 16* 19* 19* 19* 20* 21* 23* 23* 23*
24* 24* 25* 27* 27* 28* 29* 31* 31* 33* 33* 35* 35* 38* 39* 41* 42* 43*
43* 44* 45* 46* 48* 48* 49* CONTENTS* VII 3.4.2* MODU1ARITY, COMMUNITY
STRUCTURES AND HIERARCHIES 50 3.4.3* SUBGRAPHS AND MOTIFS IN NETWORKS 51
3.5 STATISTICAL TESTING OF NETWORK PROPERTIES* 52 3.5.1* GENERATING
NETWORKS AND NULL MODELS 53 3.5.2* THE CONCEPTUALIZATION OF CELLU1AR
NETWORKS 54 3.5.3* BIPARTITE GRAPHS 55 3.5.4* CORRE1ATION NETWORKS 57
3.6* SUMMARY 57 3.7* EXERCISES 58 REFERENCES 59 4 NETWORK CENTRALITIES*
65 DIRK KOSCHUETZKI 4.1* INTRODUCTION 65 4.2* CENTRALITY DEFINITION AND
FUNDAMENTAL PROPERTIES 67 4.2.1* COMPARISON OF CENTRA1ITY VA1UES 68
4.2.2* DISCONNECTED NETWORKS 68 4.3 DEGREE AND SHORTEST PATH-BASED
CENTRA1ITIES* 69 4.3.1* DEGREE CENTRALITY 69 4.3.2* ECCENTRICITY
CENTRALITY 71 4.3.3* C10SENESS CENTRALITY 72 4.3.4* SHORTEST PATH
BETWEENNESS CENTRALITY 73 4.3.5* ALGORITHMS 74 4.3.6* EXAMP1E 76 4.4
FEEDBACK-BASED CENTRALITIES* 77 4.4.1* KATZ'S STATUS INDEX 77 4.4.2*
BONACICH'S EIGENVECTOR CENTRA1ITY 78 4.4.3* PAGERANK 79 4.5* TOO1S 80
4.6* SUMMARY 80 4.7* EXERCISES 81 REFERENCES 81 5 NETWORK MOTIFS* 85
HENNING SCHWAEBBERMEYER 5.1* INTRODUCTION 85 5.2* DEFINITIONS AND BASIC
CONCEPTS 86 5.2.1* DEFINITIONS 86 5.2.2* MODELING OF BIO1OGICA1 NETWORKS
88 5.2.3* CONCEPTS OF MOTIF FREQUENCY 88 5.3 MOTIF STATISTICS AND
MOTIF-BASED NETWORK DISTANCE* 89 5.3.1* DETERMINATION OF STATISTICA1
SIGNIFICANCE OF NETWORK MOTIFS 89 VIII* CONTENTS 5.3.2* RANDOMIZATION
ALGORITHM FOR GENERATION OF NULL MODEL NETWORKS 90 5.3.3* INFLUENCE OF
THE NULL MODEL ON MOTIF SIGNIFICANCE 91 5.3.4* LIMITATIONS OF THE NULL
MODEL ON MOTIF DETECTION 91 5.3.5* MEASURES OF MOTIF SIGNIFICANCE AND
FOR NETWORK COMPARISON 91 5.4* COMPLEXITY OF NETWORK MOTIF DETECTION 94
5.4.1* ASPECTS AFFECTING THE COMPLEXITY OF NETWORK MOTIF DETECTION 94
5.4.2* FREQUENCY ESTIMATION BY MOTIF SAMPLING 96 5.5* METHODS AND TOOLS
FOR NETWORK MOTIF ANALYSIS 96 5.5.1* PAJEK 96 5.5.2* MFINDER 96 5.5.3*
MAVISTO 97 5.5.4* FANMOD 97 5.6* ANALYSES AND APPLICATIONS OF NETWORK
MOTIFS 97 5.6.1* NETWORK MOTIFS IN COMPLEX NETWORKS 97 5.6.2* DYNAMIC
PROPERTIES OF NETWORK MOTIFS 98 5.6.3* HIGHER ORDER STRUCTURES FORMED BY
NETWORK MOTIFS 102 5.6.4* NETWORK COMPARISON BASED ON NETWORK MOTIFS 104
5.6.5* EVOLUTIONARY ORIGIN OF NETWORK MOTIFS 106 5.7* SUMMARY 106 5.8*
EXERCISES 108 REFERENCES 108 6 NETWORK CLUSTERING* 113 BALABHASKAR
BALASUNDARAM AND SERGIY BUTENKO 6.1* INTRODUCTION 113 6.2* NOTATIONS AND
DEFINITIONS 115 6.3* NETWORK CLUSTERING PROBLEM 118 6.4* CLIQUE-BASED
CLUSTERING 119 6.4.1* MINIMUM CLIQUE PARTITIONING 120 6.4.2* MIN-MAX
K-CLUSTERING 122 6.5* CENTER-BASED CLUSTERING 125 6.5.1* CLUSTERING WITH
DOMINATING SETS 126 6.5.2* K-CENTER CLUSTERING 129 6.6* CONC1USION 131
6.7* SUMMARY 133 6.8* EXERCISES 133 REFERENCES 134 7 PETRI NETS* 139 [NA
KOCH AND MONIKA HEINER 7.1* INTRODUCTION 139 IX CONTENTS 7.2 QUALITATIVE
MODELING* 141 7.2.1 THE MODEL* 141 7.2.2 THE BEHAVIORAL PROPERTIES* 148
7.3 QUALITATIVE ANALYSIS* 152 7.3.1 STRUCTURAL ANALYSIS* 152 7.3.2
INVARIANT ANALYSIS* 155 7.3.3 MCT-SETS* 162 7.3.4 DYNAMIC ANALYSIS OF
GENERAL PROPERTIES* 164 7.3.5 DYNAMIC ANALYSIS OF SPECIAL PROPERTIES*
166 7.3.6 MODEL VALIDATION CRITERIA* 168 7.4 QUANTITATIVE MODELING AND
ANALYSIS* 169 7.5* TOOL SUPPORT 171 7.6* CASE STUDIES 172 7.7* SUMMARY
174 7.8* EXERCISES 175 REFERENCES 177 PART III BIOLOGICAL NETWORKS* 181
8 SIGNAL TRANSDUCTION AND GENE REGULATION NETWORKS* 183 ANATOLIJ P.
POTAPOV 8.1* INTRODUCTION 183 8.2* DECISIVE ROLE OF REGULATORY NETWORKS
IN THE EVOLUTION AND EXISTENCE OF ORGANISMS 184 8.3* GENE REGULATORY
NETWORK AS A SYSTEM OF MANY SUBNETWORKS 186 8.4* DATABASES ON GENE
REGULATION AND SOFTWARE TOOLS FOR NETWORK ANALYSIS 187 8.5*
PECULIARITIES OF SIGNAL TRANSDUCTION NETWORKS 188 8.6* TOPOLOGY OF
SIGNAL TRANSDUCTION NETWORKS 190 8.7* TOPOLOGY OF TRANSCRIPTION NETWORKS
191 8.8* LNTERCELLULAR MOLECULAR REGULATORY NETWORKS 198 8.9* SUMMARY
200 8.10* EXERCISES 201 REFERENCES 202 9 PROTEIN INTERACTION NETWORKS*
207 FREDERIK BOEMKE 9.1* INTRODUCTION 207 9.2* DETECTING PROTEIN
INTERACTIONS 209 9.2.1 THE YEAST TWO-HYBRID SYSTEM* 211 9.2.2 AFFINITY
CAPTURE OF PROTEIN COMPLEXES* 216 9.2.3 COMPUTATIONAL METHODS TO PREDICT
PROTEIN INTERACTIONS 218 X* CONTENTS 9.2.4* OTHER WAYS TO IDENTIFY
PROTEIN INTERAETIONS 219 9.3 ESTABLISHING PROTEIN INTERAETION NETWORKS*
220 9.3.1* DATA STORAGE AND NETWORK GENERATION 220 9.3.2* BENEHMARKING
HIGH-THROUGHPUT INTERAETION DATA 222 9.4 ANALYZING PROTEIN INTERAETION
NETWORKS* 223 9.4.1* NETWORK TOPOLOGY AND FUNETIONAL IMPLIEATIONS 223
9.4.2* FUNETIONAL MODULES IN PROTEIN INTERAETION NETWORKS 223 9.4.3*
EVOLUTION OF PROTEIN INTERAETION NETWORKS 224 9.4.4* COMPARATIVE
INTERAETOMIES 225 9.5* SUMMARY 225 9.6* EXEREISES 226 REFERENEES 227 10
METABOLIE NETWORKS* 233 MARCIO ROSA DA SILVA, JIBIN SUN, HONGWU MA, FENG
HE,* AND AN-PING ZENG* 10.1* INTRODUETION 233 10.2 VISUALIZATION AND
GRAPH REPRESENTATION* 234 10.3* REEONSTRUETION OF GENOME-SEALE METABOLIE
NETWORKS 234 10.4* CONNEETIVITY AND CENTRALITY IN METABOLIE NETWORKS 239
10.5* MODULARITY AND DEEOMPOSITION OF METABOLIE NETWORKS 242 10.5.1*
MODULARITY COEFFIEIENT 244 10.5.2 MODULARITY-BASED DEEOMPOSITION* 245
10.6* ELEMENTARY FLUX MODES AND EXTREME PATHWAYS 246 10.7* SUMMARY 249
10.8* EXEREISES 249 REFERENEES 251 11 PHYLOGENETIC NETWORKS* 255 BIRGIT
GEMEINHOLZER 11.1* INTRODUETION 255 11.2 CHARAETER SELEETION, CHARAETER
CODING, AND MATRIEES FOR PHYLOGENETIE REEONSTRUETION 257 11.3* TREE
REEONSTRUETION METHODOLOGIES 260 11.4* PHYLOGENETIE NETWORKS 264 11.4.1*
GALLED TREES 266 11.4.2 STATISTIEAL PARSIMONY* 267 11.4.3* MEDIAN
NETWORK 269 11.4.4 MEDIAN-JOINING NETWORKS* 270 11.4.5* PYRAMIDS 271
11.4.6 EXAMPLE OF A PYRAMIDAL CLUSTERING MODEL* 271 11.4.7 SPLIT
DEEOMPOSITION* 274 CONTENTS* XI 11.5* SUMMARY 276 11.6 EXERCISES* 276
REFERENCES 277 12 ECOLOGICAL NETWORKS* 283 URSULA GAEDKE 12.1*
INTRODUCTION 283 12.2* BINARY FOOD WEBS 289 12.2.1* INTRODUCTION AND
DEFINITIONS 289 12.2.2 DESCRIPTORS OF THE NETWORK* 289 12.2.3*
OPERATIONAL PROBLEMS 291 12.2.4 AIMS AND RESULTS* 291 12.2.5 CONCLUSION*
293 12.3 QUANTITATIVE TROPHIC FOOD WEBS* 293 12.3.1* INTRODUCTION,
DEFINITIONS, AND DATABASE 293 12.3.2 MULTIPLE COMMODITIES* 295 12.3.3*
DESCRIPTORS OF THE NETWORK AND INFORMATION TO BE GAINED 295 12.3.4
CONCLUSION* 298 12.4 ECOLOGICAL INFORMATION NETWORKS* 298 12.5* SUMMARY
300 12.6 EXERCISES* 301 REFERENCES 301 13 CORRELATION NETWORKS* 305 DIRK
STEINHAUSER; LEONARD KRALL, CARSTEN MUESSIG, DIRK BUESSIS,* AND BJOEM
USADEI* 13.1* INTRODUCTION 305 13.2 GENERAL REMARKS* 306 13.3* BASIC
NOTATION 307 13.3.1* DATA, UNIT, VARIABLE, AND OBSERVATION 307 13.3.2
SAMPIE, PROFILES, AND REPLICA SET* 308 13.3.3* MEASURES OF ASSOCIATION
309 13.3.4 SIMPLE CORRELATION MEASURES* 310 13.3.5 COMPLEX CORRELATION
AND ASSOCIATION MEASURES 311 13.3.6 PROBABILITY, CONFIDENCE, AND POWER*
313 13.3.7 MATRICES* 314 13.4 CONSTRUCTION AND ANALYSES OF CORRELATION
NETWORKS 314 13.4.1* DATA AND PROFILES 315 13.4.2 DATA SET AND MATRIX*
316 13.4.3 CORRELATION MATRIX* 318 13.4.4 NETWORK MATRIX* 318 13.4.5
CORRELATION NETWORK ANALYSIS* 319 XII 13.4.6 INTERPRETATION AND
VALIDATION 13.5* BIOLOGICAL USE OF CORRELATION NETWORKS 13.5.1 THE
GLOBAL ANALYSIS APPROACH 13.5.2 THE GUIDE GENE APPROACH 13.5.3 A SIMPLE
COREGULATION TEST: PHOTOSYNTHESIS 13.5.4 A COMPLEX COREGULATION TEST:
BRASSINOSTEROIDS 13.6* SUMMARY 13.7* EXERCISES* REFERENCES* INDEX
CONTENTS 321* 321* 321* 322* 324* 327* 328* 329* 330* 335* |
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| id | DE-604.BV035064766 |
| illustrated | Illustrated |
| index_date | 2024-07-02T22:01:52Z |
| indexdate | 2024-07-09T21:21:23Z |
| institution | BVB |
| isbn | 9780470041444 0470041447 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016733237 |
| oclc_num | 166454234 |
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| owner_facet | DE-20 DE-355 DE-BY-UBR DE-11 DE-188 |
| physical | XX, 346 S. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
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| publisher | Wiley-Interscience |
| record_format | marc |
| series2 | Wiley series on bioinformatics : Computational techniques and engineering |
| spelling | Analysis of biological networks ed. by Björn H. Junker ... Hoboken, NJ Wiley-Interscience 2008 XX, 346 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wiley series on bioinformatics : Computational techniques and engineering Algorithms Biological models Computational Biology Computational biology Models, Biological Biologie (DE-588)4006851-1 gnd rswk-swf Analyse (DE-588)4122795-5 gnd rswk-swf Netzwerk (DE-588)4171529-9 gnd rswk-swf Biologisches Modell (DE-588)4726968-6 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Biologisches Modell (DE-588)4726968-6 s Bioinformatik (DE-588)4611085-9 s DE-604 Netzwerk (DE-588)4171529-9 s Biologie (DE-588)4006851-1 s Analyse (DE-588)4122795-5 s b DE-604 Junker, Björn H. 1976- Sonstige (DE-588)12972114X oth OEBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016733237&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Analysis of biological networks Algorithms Biological models Computational Biology Computational biology Models, Biological Biologie (DE-588)4006851-1 gnd Analyse (DE-588)4122795-5 gnd Netzwerk (DE-588)4171529-9 gnd Biologisches Modell (DE-588)4726968-6 gnd Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4006851-1 (DE-588)4122795-5 (DE-588)4171529-9 (DE-588)4726968-6 (DE-588)4611085-9 |
| title | Analysis of biological networks |
| title_auth | Analysis of biological networks |
| title_exact_search | Analysis of biological networks |
| title_exact_search_txtP | Analysis of biological networks |
| title_full | Analysis of biological networks ed. by Björn H. Junker ... |
| title_fullStr | Analysis of biological networks ed. by Björn H. Junker ... |
| title_full_unstemmed | Analysis of biological networks ed. by Björn H. Junker ... |
| title_short | Analysis of biological networks |
| title_sort | analysis of biological networks |
| topic | Algorithms Biological models Computational Biology Computational biology Models, Biological Biologie (DE-588)4006851-1 gnd Analyse (DE-588)4122795-5 gnd Netzwerk (DE-588)4171529-9 gnd Biologisches Modell (DE-588)4726968-6 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Algorithms Biological models Computational Biology Computational biology Models, Biological Biologie Analyse Netzwerk Biologisches Modell Bioinformatik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016733237&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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