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.