Invited Papers -- Differential Gene Expression in the Auditory System -- Searching for Non-coding RNA -- Cyberinfrastructure for PathoSystems Biology -- Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites -- Full Papers -- Perturbing Thermodynamically Unfeasible Metabolic Networks -- Protein Cellular Localization with Multiclass Support Vector Machines and Decision Trees -- Combining One-Class Classifiers for Robust Novelty Detection in Gene Expression Data -- Evaluation of the Contents of Partitions Obtained with Clustering Gene Expression Data -- Machine Learning Techniques for Predicting Bacillus subtilis Promoters -- An Improved Hidden Markov Model Methodology to Discover Prokaryotic Promoters -- Modeling and Property Verification of Lactose Operon Regulation -- YAMONES: A Computational Architecture for Molecular Network Simulation -- Structure Prediction and Docking Studies of Chorismate Synthase from Mycobacterium Tuberculosis -- Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction -- Tests of Automatic Annotation Using KOG Proteins and ESTs from 4 Eukariotic Organisms -- Diet as a Pressure on the Amino Acid Content of Proteomes -- A Method for Comparing Three Genomes -- Comparison of Genomic DNA to cDNA Alignment Methods -- Segmentation and Centromere Locating Methods Applied to Fish Chromosomes Images -- Extended Abstracts -- Sequence Motif Identification and Protein Family Classification Using Probabilistic Trees -- Prediction of Myotoxic and Neurotoxic Activities in Phospholipases A2 from Primary Sequence Analysis -- Genomics and Gene Expression Management Tools for the Schistosoma Mansoni cDNA Microarray Project -- SAM Method as an Approach to Select Candidates for Human Prostate Cancer Markers -- New EST Trimming Strategy -- A Modification of the Landau-Vishkin Algorithm Computing Longest Common Extensions via Suffix Arrays -- The BioPAUÁ Project: A Portal for Molecular Dynamics Using Grid Environment -- Analysis of Structure Prediction Tools in Mutated MeCP-2 -- Protein Loop Classification Using Artificial Neural Networks -- VIZ – A Graphical Open-Source Architecture for Use in Structural Bioinformatics -- Selection of Data Sets of Motifs as Attributes in the Process of Automating the Annotation of Proteins’ Keywords -- Bioinformatics Tools for HIV-1 Identification in Southern Brazilian States -- Fact and Task Oriented System for Genome Assembly and Annotation -- A Clustering Strategy to Find Similarities in Mycoplasma Promoters -- Gene Prediction by Syntenic Alignment -- Real Time Immersive Visualization and Manipulation of the Visible Human Data Set.