Bioinformatics of Genome Regulation and Structure II

Computational Structural, Functional and Evolutionary Genomics.- Recognition of Coding Regions in Genome Alignment.- Predicting sRNA Genes in the Genome of E. Coli by the Promoter-Search Algorithm PlatProm.- Content Sensors Based on Codon Structure and DNA Methylation for Gene Finding in Vertebrate Genomes.- The Sitega Tool for Recognition and Context Analysis of Transcription Factor Binding Sites: Significant Dinucleotide Features Besides the Canonical Consensus Exemplified By SF-1 Binding Site.- Transcription Regulatory Regions Database (TRRD): A Source of Experimentally Confirmed Data on Transcription Regulatory Regions of Eukaryotic Genes.- Artsite Database: Comparison of In Vitro Selected and Natural Binding Sites of Eukaryotic Transcription Factors.- Comparative Analysis of Electrostatic Patterns for Promoter and Nonpromoter DNA in E. Coli Genome.- Analysis of Nucleosome Formation Potential and Conformational Properties of Human J1-J2 and D2-D1 Type Alpha Satellite DNA.- VMM: A Variable Memory Markov Model Prediction of Nucleosome Formation Sites.- DNA Nucleosome Organization of the Promoter Gene Regions.- A Toolbox for Analysis of RNA Secondary Structure Based on Genetic Algorithm.- Comparative Genomics and Evolution of Bacterial Regulatory Systems.- Comparative Whole Genome Sequence Analysis of Corynebacteria.- New LTR Retrotransposable Elements from Eukaryotic Genomes.- A Genome-Wide Identification of Mitochondrial DNA Topoisomerase I in Arabidopsis.- Change in CpG Context is a Leading Cause of Correlation between the Rates of Non-Synonymous and Synonymous Substitutions in Rodents.- Universal Seven-Cluster Structure of Genome Fragment Distribution: Basic Symmetry in Triplet Frequencies.- New Methods to Infer DNA Function from Sequence Information.- Revelation and Classification of Dinucleotide Periodicity of Bacterial Genomes Using the Method of Information Decomposition.- Algorithms to Reconstruct Evolutionary Events at Molecular Level and Infer Species Phylogeny.- Computational Structural and Functional Proteomics.- Mining from Complete Proteomes to Identify Adhesins and Adhesin-Like Proteins: A Rapid Aid to Experimental Researchers.- Central Moments Based Statistical Analysis for the Determination of Functional Sites in Proteins with Thematics.- Amino Acids Surface Patterns in Protein Domain Functionality Analysis.- Computer Simulations of Anionic Unsaturated Lipid Bilayer—A Suitable Model to Study Membrane Interactions with A Cell-Penetrating Peptide.- The Role of Water in Homeodomain-DNA Interaction.- Molecular Modeling of Human MT1 and MT2 Melatonin Receptors.- Molecular Dynamics of Small Peptides Using Ergodic Trajectories.- A Periodical Nature of 94 Protein Families.- Prediction of Contact Numbers of Amino Acid Residues Using a Neural Network Model.- Fastprot: A Computational Workbench for Recognition of the Structural and Functional Determinants in Protein Tertiary Structures.- A Markov Model for Protein Sequences.- Proteome Complexity Measures Based on Counting of Domain-to-Protein Links for Replicative and Non-Replicative Domains.- Computational System Biology.- A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project.- Prediction and Alignment of Metabolic Pathways.- General Principles of Organization and Laws of Functioning in Governing Gene Networks.- From Gradients to Stripes: A Logical Analysis of Drosophila Segmentation Genetic Network.- Self-Oscillations in Hypothetical Gene Networks.- Periodic Trajectories and Andronov-Hopf Bifurcations in Models of Gene Networks.- On the Problem of Search for Stationary Points in Regulatory Circuits of Gene Networks.- Modeling of Gene Expression by the Delay Equation.- AGNS—A Database on Expression of Arabidopsis Genes.- Study of the Interactions between Viral and Human Genomes During Transformation of B Cells with Epstein-Barr Virus.- Probing Gene Expression: Sequence-Specific Hybridization on Microarrays.- Determination of the Developmental Age of a Drosophila Embryo from Confocal Images of its Segmentation Gene Expression Patterns.- Biomolecular Data and Processes Analysis.- Topical Clustering of Biomedical Abstracts by Self-Organizing Maps.- Software for Analysis of Gene Regulatory Sequences by Knowledge Discovery Methods.- A Mathematical Model of the Discontinuous Genetic Structures Fixation Process.