This book constitutes the refereed proceedings of the First International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2010, held in Bangkok, Thailand, in November 2010. The 19 revised full papers presented were carefully reviewed and selected from a total of 48 submissions. The papers cover a wide range of topics and are organized in five topical sections on modeling and simulation of biological processes, gene expression analysis, biological sequence analysis and network reconstruction, bio-data visualization and biological databases, as well as medical and biomedical informatics.
Author(s): Jonathan H. Chan, Yew-Soon Ong, Sung-Bae Cho
Edition: 1st Edition.
Publisher: Springer
Year: 2010
Language: English
Pages: 240
Cover
......Page 1
Preface......Page 6
Organization......Page 8
Table of Contents......Page 12
Introduction......Page 15
Continuous and Discrete Models......Page 17
Hybrid Modelling......Page 20
Construction of the Delays Constraints......Page 24
References......Page 26
Introduction......Page 28
Previous Work......Page 29
Agent-Based Model......Page 30
Parameter Optimisation......Page 32
Results......Page 33
Discussion......Page 36
Conclusions......Page 37
References......Page 38
Introduction......Page 40
Molecular Docking......Page 42
Molecular Docking of CYP2C9*1......Page 43
Molecular Dynamics Simulation of CYP2C9*1 and CYP2C9*13......Page 44
Pharmacophore Model of CYP2C9*1 and CYP2C9*13......Page 45
Discussion......Page 46
References......Page 47
Introduction......Page 50
Template-Based Modeling......Page 52
Secondary Structure of GLELOp Sequence......Page 53
Modeling......Page 55
References......Page 58
Introduction......Page 60
Data......Page 61
Existing Gene Signatures......Page 62
Feature Extraction......Page 63
Combining Feature Selection and Feature Extraction......Page 64
Analysis......Page 65
Discussion on Feature Extraction Methods......Page 67
References......Page 70
On Assigning Individuals from Cryptic Population Structures to Optimal Predicted Subpopulations: An Empirical Evaluation of Non-parametric Population Structure Analysis Techniques......Page 72
Introduction......Page 73
Dataset......Page 74
ipPCA Analysis......Page 76
AWclust Analysis......Page 78
Discussion......Page 82
References......Page 83
Introduction......Page 85
Microarray Data and Data Pre-Processing......Page 87
Data Discretization......Page 88
Constraint-Based Boolean Network Inference......Page 89
Data Discretization......Page 91
Genetic Network of Circadian Rhythms......Page 92
Network Evaluation......Page 94
References......Page 95
Introduction......Page 97
Materials and Methods......Page 98
Results......Page 101
Discussion......Page 103
References......Page 106
Introduction......Page 108
Model Quality Metrics......Page 110
Algorithm Description......Page 112
Data Preparation......Page 115
Experimental Discussions......Page 116
Conclusion......Page 117
References......Page 118
Introduction......Page 120
Materials and Methods......Page 121
Predicted ncRNA in S. Platensis Genome......Page 123
Classification of ncRNA Candidates......Page 124
Non-coding RNA Target Prediction......Page 127
Conclusion and Further Works......Page 129
References......Page 130
Introduction......Page 132
Data Resources......Page 134
Reference Pathway Formulation......Page 135
Sequence Similarity Search (BLASTn)......Page 138
Identification of the Enzymes in the Sucrose Metabolism and Starch Biosynthesis Pathway in Cassava via Similarity Search (BLASTn)......Page 139
Sucrose Metabolism and Starch Biosynthesis Pathway in Cassava......Page 140
Conclusion......Page 142
References......Page 143
Introduction......Page 144
Data Sources......Page 145
System Design......Page 146
Data Analysis......Page 147
Database Query......Page 150
Possible Uses of ThaiSNPdb......Page 151
References......Page 152
Introduction......Page 155
The Logic Tier......Page 156
The Genome Atlas Data Model......Page 158
Correlation between Growth Rate and the Properties of Chromosomes......Page 159
Zooming into Regions of Chromosomes......Page 161
Conclusion......Page 162
References......Page 163
Introduction......Page 165
Problem Definition......Page 166
Implementation......Page 167
Result......Page 175
Conclusions......Page 176
References......Page 177
Introduction......Page 179
Pan-Genomics......Page 181
Probe Selection for Target Genes......Page 182
Analysis Methods......Page 183
Validation of the Custom Arrays......Page 184
Discussion and Perspective......Page 190
References......Page 191
Introduction......Page 194
Mathematical Model of Two Compartment Model......Page 196
Proposed Control Schema......Page 197
Design Objectives and Goal Values......Page 198
Selection Method of Global Guide and Local Guide......Page 199
Implementation......Page 200
Validation and Results......Page 201
Comparative Performances......Page 204
References......Page 205
Introduction......Page 207
Protein Modeling......Page 209
Docking in AutoDock......Page 210
siRNA Design Specific to IgE......Page 211
Modeling Protein Structures......Page 212
AutoDock......Page 213
Discussion......Page 214
Conclusion......Page 216
References......Page 217
Introduction......Page 222
Informative Marker Selection......Page 223
Assigning Samples to Sub-populations......Page 226
Results and Discussion......Page 227
Conclusion......Page 229
References......Page 230
Introduction......Page 231
Methodology......Page 233
Linking $S. Typhi$ and Human Genes to Their Protein Signatures in Term of InterPro Accession Numbers......Page 234
Comparing Protein Signatures between $S. Typhi$ and $H. Sapiens$ via InterPro accession Numbers......Page 235
Mapping the List of Preliminary Drug Targets to Essential Genes from TraDis Experiment......Page 236
Discussion......Page 237
References......Page 238
Author Index
......Page 240
