Bioinformatics of Genome Regulation and Structure

Front Matter....Pages I-XV
Front Matter....Pages 1-1
Nucleosomal DNA Organization: An Integrated Information System....Pages 3-12
Using Change in Local DNA Sequence Complexity as a Pointer to the Mechanism of Mutagenesis in Inherited Disease....Pages 13-20
Properties of Insertion Regions of Drosophila LTR Retrotransposons....Pages 21-31
Compositional Asymmetries and Predicted Origins of Replication of the Saccharomyces Cerevisiae Genome....Pages 33-38
Revealing and Functional Analysis of Trna-Like Sequences in Various Genomes....Pages 39-46
Type-Specific Features of the Structure of the tRNA Gene Promoters....Pages 47-60
Mathematical Tools for Regulatory Signals Extraction....Pages 61-69
Argo_Viewer: A Package for Recognition and Analysis of Regulatory Elements in Eukaryotic Genes....Pages 71-80
Transcription Regulatory Regions Database (TRRD): Description of Transcription Regulation and the Main Capabilities of the Database....Pages 81-91
Sitecon—A Tool for Analysis of DNA Physicochemical and Conformational Properties: E2F/DP Transcription Factor Binding Site Analysis and Recognition....Pages 93-102
Local Secondary Structure May Be a Critical Characteristic Influencing Translation of Unicellular Organisms mRNA....Pages 103-114
Computer Analysis of miRNA-mRNA Duplexes and Its Application to Predicting Possible Target mRNAS of Arabidopsis ....Pages 115-124
Correlations between Sequence Features of Yeast Genes Functional Regions and the Level of Expression....Pages 125-132
Front Matter....Pages 133-133
Latent Periodicity of Many Domains in Protein Sequences Reflects Their Structure, Function, and Evolution....Pages 135-143
Logical Analysis of Data as a Predictor of Protein Secondary Structures....Pages 145-154
Structure-Specificity Relationship in Protein-DNA Recognition....Pages 155-161
Macromolecular Modeling as a Tool for Expanding Bioinformatics Databases....Pages 163-170
Graphic Representation of Equilibrium and Kinetics in Oligopeptides: Time-Dependent Free Energy Disconnectivity Graphs....Pages 171-178
Solvent Electrostatic Screening in Protein Simulations....Pages 179-184
PDBSiteScan: A Program Searching for Functional Sites in Protein 3D Structures....Pages 185-192
Front Matter....Pages 133-133
A Genetic Algorithm for the Inverse Folding of RNA....Pages 193-202
Signal Transduction Pathways Initiated Via Cell Surface Receptor CD150: In Silico and in Vitro Analysis....Pages 203-210
Front Matter....Pages 211-211
Study of the Specific Contextual Features of Translation Initiation and Termination Sites in Saccharomyces Cerevisiae ....Pages 213-222
Contribution of Coordinated Substitutions to the Constancy of Physicochemical Properties of ATP-Binding Loop in Protein Kinases....Pages 223-230
Sporadic Emergence of Latent Phenotype during Evolution....Pages 231-243
Similarity Analysis of Inversion Banding Sequences in Chromosomes of Chironomus Species (Breakpoint Phylogeny)....Pages 245-253
Front Matter....Pages 255-255
Integrative Analysis of Gene Networks Using Dynamic Process Pattern Modelling....Pages 257-264
Development and Analysis of Models of Genetic and Metabolic Networks and Signal Transduction Pathways in the GeneNet System....Pages 265-272
Extension of Cell Cycle Gene Network Description Based on Prediction of Potential Binding Sites for E2F Transcription Factor....Pages 273-282
Mathematical Simulation of Dynamics of Macrophage Gene Network Activated by Lipopolysaccharides and/or Interferon-g....Pages 283-292
Computer Dynamic Modeling of the Gene Network Controlling Intracellular Cholesterol Homeostasis....Pages 293-300
An Investigation of the Structural Stability of Drosophila Control Gene Subnetwork in Computer Experiments....Pages 301-309
Modeling Plant Development with Gene Regulation Networks Including Signaling and Cell Division....Pages 311-318
The Global Operation Modes of Gene Networks Determined by the Structure of Negative Feedbacks....Pages 319-329
Statistical Analysis of Microarray Data: Identification and Classification of Yeast Cell Cycle Genes....Pages 331-341
Back Matter....Pages 343-373