Bioinformatics of Genome Regulation and Structure

1. Computational Genomics.- Nucleosomal DNA Organization: An Integrated Information System.- Using Change in Local DNA Sequence Complexity as a Pointer to the Mechanism of Mutagenesis in Inherited Disease.- Properties of Insertion Regions of Drosophila LTR Retrotransposons.- Compositional Asymmetries and Predicted Origins of Replication of the SaccharomycesCerevisiae Genome.- Revealing and Functional Analysis of tRNA-Like Sequences in Various Genomes.- Type-Specific Features of the Structure of the tRNA Gene Promoters.- Mathematical Tools for Regulatory Signals Extraction.- Argo_Viewer: A Package for Recognition and Analysis of Regulatory Elements in Eukaryotic Genes.- Transcription Regulatory Regions Database (TRRD): Description of Transcription Regulation and the Main Capabilities of the Database.- Sitecon—A Tool for Analysis of DNA Physicochemical and Conformational Properties: E2F/DP Transcription Factor Binding Site Analysis and Recognition.- Local Secondary Structure May Be a Critical Characteristic Influencing Translation of Unicellular Organisms mRNA.- Computer Analysis of miRNA-mRNA Duplexes and Its Application to Predicting Possible Target mRNAS of Arabidopsis.- Correlations between Sequence Features of Yeast Genes Functional Regions and the Level of Expression.- 2. Computational Structural Biology.- Latent Periodicity of Many Domains in Protein Sequences Reflects Their Structure, Function, and Evolution.- Logical Analysis of Data as a Predictor of Protein Secondary Structures.- Structure-Specificity Relationship in Protein—DNA Recognition.- Macromolecular Modeling as a Tool for Expanding Bioinformatics Databases.- Graphic Representation of Equilibrium and Kinetics in Oligopeptides: Time-Dependent Free Energy Disconnectivity Graphs.- Solvent Electrostatic Screening in Protein Simulations.- Pdbsitescan: A Program Searching for Functional Sites in Protein 3D Structures.- A Genetic Algorithm for the Inverse Folding of RNA.- Signal Transduction Pathways Initiated via Cell Surface Receptor CD150: In Silico and in Vitro Analysis.- 3. Computational Evolutionary Biology.- Study of the Specific Contextual Features of Translation Initiation and Termination Sites in Saccharomyces Cerevisiae.- Contribution of Coordinated Substitutions to the Constancy of Physicochemical Properties of ATP-Binding Loop in Protein Kinases.- Sporadic Emergence of Latent Phenotype during Evolution.- Similarity Analysis of Inversion Banding Sequences in Chromosomes of Chironomus Species (Breakpoint Phylogeny).- 4. System Computational Biology.- Integrative Analysis of Gene Networks Using Dynamic Process Pattern Modelling.- Development and Analysis of Models of Genetic and Metabolic Networks and Signal Transduction Pathways in the Genenet System.- Extension of Cell Cycle Gene Network Description Based on Prediction of Potential Binding Sites for E2F Transcription Factor.- Mathematical Simulation of Dynamics of Macrophage Gene Network Activated by Lipopolysaccharides and/or Interferon-g.- Computer Dynamic Modeling of the Gene Network Controlling Intracellular Cholesterol Homeostasis.- An Investigation of the Structural Stability of Drosophila Control Gene Subnetwork in Computer Experiments.- Modeling Plant Development with Gene Regulation Networks Including Signaling and Cell Division.- The Global Operation Modes of Gene Networks Determined by the Structure of Negative Feedbacks.- Statistical Analysis of Microarray Data: Identification and Classification of Yeast Cell Cycle Genes.- References.