Probabilistic boolean networks: the modeling and control of gene regulatory networks
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| Main Authors: | , |
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| Format: | Book |
| Language: | English |
| Published: |
Philadelphia
SIAM
2010
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| Subjects: | |
| Online Access: | Autorenbiografie Verlagsmeldung Inhaltsverzeichnis Inhaltsverzeichnis |
| Physical Description: | XIII, 267 S. graph. Darst. |
| ISBN: | 9780898716924 |
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Record in the Search Index
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| adam_text | IMAGE 1
PROBABILISTIC BOOLEAN NETWORKS
THE MODELING AND CONTROL OF GENE REGULATORY NETWORKS
ILYA SHMULEVICH INSTITUTE FOR SYSTEMS BIOLOGY SEATTLE, WASHINGTON
EDWARD R. DOUGHERTY
TEXAS A&M UNIVERSITY COLLEGE STATION, TEXAS
TRANSLATIONAL GENOMICS RESEARCH INSTITUTE PHOENIX, ARIZONA
SIAIIL * SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS * PHILADELPHIA
IMAGE 2
CONTENTS
PREFACE XI
1 BOOLEAN NETWORKS 1
1.1 CELL TYPES AND CELLULAR FUNCTIONAL STATES 5
1.2 RELEVANT NODES 6
1.3 NETWORK PROPERTIES AND DYNAMICS 8
1.4 BOOLEAN MODELS OF BIOLOGICAL NETWORKS 15
1.4.1 THE SEGMENT POLARITY NETWORK OF THE FRUIT FLY 16
1.4.2 CONTROL OF THE CELL CYCLE 16
1.4.3 T-CELL RECEPTOR SIGNALING 20
1.5 DISCRETIZATION 21
1.5.1 COEFFICIENT OF DETERMINATION 23
2 STRUCTURE AND DYNAMICS OF PROBABILISTIC BOOLEAN NETWORKS 27
2.1 MARKOV CHAINS AS MODELS OF BIOLOGICAL REGULATION 27
2.2 DEFINITION OF PROBABILISTIC BOOLEAN NETWORKS 31
2.3 DYNAMICS: STATE TRANSITION PROBABILITIES 34
2.4 THE EXISTENCE OF STEADY-STATE DISTRIBUTIONS 38
2.5 STEADY-STATE ANALYSIS OF PBNS 40
2.5.1 STEADY-STATE ANALYSIS VIA SIMULATION 44
2.5.2 STEADY-STATE PROBABILITIES OF ATTRACTORS AND BASINS 48
2.6 RELATIONSHIPS OF PBNS TO BAYESIAN NETWORKS 58
2.6.1 BAYESIAN NETWORKS 58
2.6.2 INDEPENDENT PBNS AND DBNS 63
2.7 MAPPINGS BETWEEN PBNS 68
3 INFERENCE OF MODEL STRUCTURE 81
3.1 CONSISTENT AND BEST-FIT EXTENSIONS 81
3.1.1 SENSITIVITY REGULARIZATION 85
3.2 COEFFICIENT OF DETERMINATION AS AN INFERENTIAL TOOL 89
3.3 DESIGN OF NETWORKS UNDER DATA CONSISTENCY REQUIREMENTS 95 3.3.1
CONTEXTUAL DATA CONSISTENCY 100
3.3.2 OPTIMIZATION OF CONSISTENCY-BASED DESIGN 108
3.4 INFORMATION THEORETIC APPROACHES 115
VII
IMAGE 3
VIII CONTENTS
3.4.1 MINIMUM DESCRIPTION LENGTH-BASED NETWORK INFERENCE FROM TIME
SERIES DATA 116
3.5 INFERENCE OF PBNS FROM TIME SERIES DATA 119
3.5.1 SPLITTING THE TEMPORAL DATA SEQUENCE INTO PURE SUBSEQUENCES . ..
120 3.5.2 ESTIMATION OF SWITCHING, SELECTION, AND PERTURBATION
PROBABILITIES . 121 3.6 VALIDATION OF NETWORK INFERENCE PROCEDURES 122
4 STRUCTURAL INTERVENTION 125
4.1 IMPACT OF FUNCTION PERTURBATION ON STATE TRANSITIONS 126
4.1.1 IDENTIFYING FUNCTION PERTURBATIONS 129
4.2 INTERVENTION VIA CONSTRUCTIVE FUNCTION PERTURBATION 131
4.2.1 CONCEPT OF STRUCTURAL INTERVENTION 131
4.2.2 METHOD FOR CONSTRUCTIVE FUNCTION-BASED INTERVENTION 133 4.2.3
INTERVENTION IN A WNT5A NETWORK 134
4.3 IMPACT OF STRUCTURAL PERTURBATION ON THE STEADY-STATE DISTRIBUTION .
. . .136 4.3.1 RANK-ONE PERTURBATIONS 138
4.3.2 PERTURBATION IN THE SAME ROW 142
4.3.3 EXTENSION TO MULTIPLE ROWS BY ITERATIVE COMPUTATION 143 4.3.4
APPLICATION TO PBNS 143
4.4 STRUCTURAL INTERVENTION VIA MARKOV CHAIN PERTURBATION THEORY 145
4.4.1 AWNT5ABN 146
4.5 LONG-RUN SENSITIVITY 148
4.5.1 LONG-RUN SENSITIVITY WITH RESPECT TO PROBABILISTIC PARAMETERS . ..
148 4.5.2 LONG-RUN SENSITIVITY WITH RESPECT TO REGULATORY FUNCTIONS 150
4.5.3 ONE-PREDICTOR FUNCTION PERTURBATIONS 151
4.5.4 ONE-BIT FUNCTION PERTURBATIONS 153
4.5.5 FUNCTION PERTURBATIONS CONSIDERING ONE-GENE REGULATION 153 4.5.6
PROPERTIES OF LONG-RUN SENSITIVITY 154
4.5.7 SENSITIVITY AND ROBUSTNESS OF CONTROL 155
4.5.8 SENSITIVITY IN A MAMMALIAN CELL-CYCLE NETWORK 156
5 EXTERNAL CONTROL 161
5.1 INTERVENTION VIA ONE-TIME GENE PERTURBATION 161
5.2 FINITE-HORIZON CONTROL 165
5.2.1 CONTROL PROBLEM 165
5.2.2 SOLUTION BY DYNAMIC PROGRAMMING 167
5.2.3 ILLUSTRATIVE EXAMPLE 168
5.2.4 FINITE-HORIZON CONTROL IN A MELANOMA NETWORK 170
5.3 INFINITE-HORIZON CONTROL 171
5.3.1 OPTIMAL CONTROL SOLUTION: DISCOUNTED AND BOUNDED COST PER STAGE
173 5.3.2 OPTIMAL CONTROL SOLUTION: AVERAGE COST PER STAGE 178
5.3.3 INFINITE-HORIZON CONTROL FOR A WNT5A NETWORK 181
5.4 APPROXIMATION 183
5.4.1 A LINEAR MODEL 183
5.4.2 INTERVENTION IN A FAMILY OF BNS 184
IMAGE 4
CONTENTS IX
5.4.3 IMPERFECT INFORMATION 185
5.4.4 REDUCTION OF A CONTEXT-SENSITIVE PBN 187
5.4.5 REINFORCEMENT LEARNING 191
5.5 CONSTRAINED INTERVENTION 194
5.5.1 CONSTRAINED INTERVENTION IN A MAMMALIAN CELL-CYCLE NETWORK . .
.199 5.5.2 CYCLIC INTERVENTION 204
5.6 ROBUST CONTROL 205
5.6.1 PERTURBATION BOUNDS 206
5:6.2 MINIMAX ROBUST CONTROL 208
5.6.3 BAYESIAN ROBUST CONTROL 211
5.6.4 UNCERTAINTY IN THE SWITCHING PROBABILITIES 212
5.7 ADAPTIVE INFINITE-HORIZON CONTROL 215
5.8 MEAN-FIRST-PASSAGE-TIME STATIONARY CONTROL 216
5.8.1 MODEL-FREE INTERVENTION 218
5.9 STEADY-STATE-BASED CONTROL POLICIES 221
5.9.1 STEADY-STATE-DISTRIBUTION GREEDY CONTROL POLICY 221
5.9.2 CONSERVATIVE STEADY-STATE-DISTRIBUTION CONTROL POLICY 222 5.9.3
PERFORMANCE COMPARISON 224
6 ASYNCHRONOUS NETWORKS 227
6.1 ASYNCHRONOUS PBNS 227
6.1.1 DETERMINISTIC ASYNCHRONOUS PBNS 227
6.1.2 SEMI-MARKOV ASYNCHRONOUS PBNS 229
6.2 INTERVENTION IN ASYNCHRONOUS NETWORKS 232
6.2.1 INTERVENTION IN DA-PBNS 232
6.2.2 INTERVENTION IN SMA-PBNS 234
6.2.3 SOLUTION FOR THREE INTERTRANSITION INTERVAL DISTRIBUTIONS 238
6.2.4 INTERVENTION IN A MUTATED MAMMALIAN CELL-CYCLE SMA-PBN . . . 239
BIBLIOGRAPHY 243
INDEX 261
|
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| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.8/65 |
| dewey-search | 572.8/65 |
| dewey-sort | 3572.8 265 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Mathematik |
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| id | DE-604.BV036880491 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:50:03Z |
| institution | BVB |
| isbn | 9780898716924 |
| language | English |
| lccn | 2009034643 |
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| physical | XIII, 267 S. graph. Darst. |
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| spelling | Shmulevich, Ilya Verfasser aut Probabilistic boolean networks the modeling and control of gene regulatory networks Ilya Shmulevich ; Edward R. Dougherty Philadelphia SIAM 2010 XIII, 267 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Genetic regulation Computer simulation Gene Regulatory Networks Models, Genetic Models, Statistical Genregulation (DE-588)4122166-7 gnd rswk-swf Stochastisches Modell (DE-588)4057633-4 gnd rswk-swf Mathematische Modellierung (DE-588)7651795-0 gnd rswk-swf Boolesches Netzwerk (DE-588)4620007-1 gnd rswk-swf Genregulation (DE-588)4122166-7 s Mathematische Modellierung (DE-588)7651795-0 s Boolesches Netzwerk (DE-588)4620007-1 s DE-604 Stochastisches Modell (DE-588)4057633-4 s b DE-604 Dougherty, Edward R. 1945- Verfasser (DE-588)172047439 aut http://www.loc.gov/catdir/enhancements/fy1007/2009034643-b.html Autorenbiografie http://www.loc.gov/catdir/enhancements/fy1007/2009034643-d.html Verlagsmeldung http://www.loc.gov/catdir/enhancements/fy1007/2009034643-t.html Inhaltsverzeichnis HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020795885&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Shmulevich, Ilya Dougherty, Edward R. 1945- Probabilistic boolean networks the modeling and control of gene regulatory networks Genetic regulation Computer simulation Gene Regulatory Networks Models, Genetic Models, Statistical Genregulation (DE-588)4122166-7 gnd Stochastisches Modell (DE-588)4057633-4 gnd Mathematische Modellierung (DE-588)7651795-0 gnd Boolesches Netzwerk (DE-588)4620007-1 gnd |
| subject_GND | (DE-588)4122166-7 (DE-588)4057633-4 (DE-588)7651795-0 (DE-588)4620007-1 |
| title | Probabilistic boolean networks the modeling and control of gene regulatory networks |
| title_auth | Probabilistic boolean networks the modeling and control of gene regulatory networks |
| title_exact_search | Probabilistic boolean networks the modeling and control of gene regulatory networks |
| title_full | Probabilistic boolean networks the modeling and control of gene regulatory networks Ilya Shmulevich ; Edward R. Dougherty |
| title_fullStr | Probabilistic boolean networks the modeling and control of gene regulatory networks Ilya Shmulevich ; Edward R. Dougherty |
| title_full_unstemmed | Probabilistic boolean networks the modeling and control of gene regulatory networks Ilya Shmulevich ; Edward R. Dougherty |
| title_short | Probabilistic boolean networks |
| title_sort | probabilistic boolean networks the modeling and control of gene regulatory networks |
| title_sub | the modeling and control of gene regulatory networks |
| topic | Genetic regulation Computer simulation Gene Regulatory Networks Models, Genetic Models, Statistical Genregulation (DE-588)4122166-7 gnd Stochastisches Modell (DE-588)4057633-4 gnd Mathematische Modellierung (DE-588)7651795-0 gnd Boolesches Netzwerk (DE-588)4620007-1 gnd |
| topic_facet | Genetic regulation Computer simulation Gene Regulatory Networks Models, Genetic Models, Statistical Genregulation Stochastisches Modell Mathematische Modellierung Boolesches Netzwerk |
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