Constitutes the refereed proceedings of the Second International Bioinformatics Research and Development Conference, BIRD 2008, held in Vienna, Austria in July 2008. This work contains 30 papers that are organized in topical sections followed by 11 papers from the ALBIO workshop and 8 papers from the PETRIN workshop.

BIRD Conference.- A Tree Index to Support Clustering Based Exploratory Data Analysis.- XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data.- Clustering in a Fixed Manifold to Detect Groups of Genes with Similar Expression Patterns.- Families of FPGA-Based Accelerators for BLAST Algorithm with Multi-seeds Detection and Parallel Extension.- Fast Structured Motif Search in DNA Sequences.- A Discriminative Method for Protein Remote Homology Detection Based on N-nary Profiles.- Searching for Supermaximal Repeats in Large DNA Sequences.- Motif Location Prediction by Divide and Conquer.- Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics.- A Symmetry-Free Subspace for Ab initio Protein Folding Simulations.- Comparative Analysis of Disulfide Bond Determination Using Computational-Predictive Methods and Mass Spectrometry-Based Algorithmic Approach.- Exploration of Evolutionary Relations between Protein Structures.- Two Local Search Methods for Protein Folding Simulation in the HP and the MJ Lattice Models.- A Robust Class of Stable Proteins in the 2D HPC Model.- A Novel Adaptive Multiple Imputation Algorithm.- Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies.- Gene Expression Mining for Cohesive Pattern Discovery.- Identifying Subcellular Locations from Images of Unknown Resolution.- E-BioFlow: Different Perspectives on Scientific Workflows.- Knowledge Acquisition Focused Cooperative Development of Bio-ontologies – A Case Study with BIO2Me.- Nested q-Partial Graphs for Genetic Network Inference from ”Small n, Large p” Microarray Data.- A Computational Method for Reconstructing Gapless Metabolic Networks.- Finding FrequentSubgraphs in Biological Networks Via Maximal Item Sets.- Multi-functional Protein Clustering in PPI Networks.- Protein-Protein Interaction Network Querying by a “Focus and Zoom” Approach.- Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns.- Combining Molecular and Physiological Data of Complex Disorders.- Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins.- Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database.- Bayesian Phylogeny on Grid.- Comparison of Exact String Matching Algorithms for Biological Sequences.- A New Approximation Algorithm for the Minimum Fragment Removal Problem.- Indexing Factors in DNA/RNA Sequences.- Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model.- Suffix Tree Characterization of Maximal Motifs in Biological Sequences.- Efficient Seeding Techniques for Protein Similarity Search.- An Algorithm for Multiple and Global Alignments.- LASA: A Tool for Non-heuristic Alignment of Multiple Sequences.- SVM-Based Local Search for Gene Selection and Classification of Microarray Data.- GENFOCS – A Comparative Tool on Gene Finding with Sensitivity and Specificity.- Gene Machine© – A Hardware/Software Platform for Analyzing Genome Data.- Complex Representation of DNA Sequences.- Wavelet Analysis of Impulses in Axon Physiology.- Acquisition and Algorithms for Fluorescence Applications.- Control of the Lasers Dynamics by Pumping Modulation for Biophotonics Applications.- Quantum Well Lasers for Medical Industry.- Computational Model for the Study of the Fractal Parameters Characteristic for the Surface of Titanium Dental Implants.- VEMS-TM – A ManagementInfrastructure.- PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities.

This book constitutes the refereed proceedings of the Second International Bioinformatics Research and Development Conference, BIRD 2008, held in Vienna, Austria in July 2008. The 49 revised full papers presented were carefully reviewed and selected. 30 papers are organized in topical sections followed by 11 papers from the ALBIO workshop and 8 papers from the PETRIN workshop.

From the reviews: "This is a collection of 49 papers from the Bioinformatics Research and Development (BIRD) 2008 Conference … that covers a variety of interesting subfields of theoretical and applicative bioinformatics. Researchers, teachers, students, and the community of bioinformaticians need such a periodic review of the new developments and current trends in this exciting field at the border of biology, medicine, and informatics." (Adrian Pasculescu, ACM Computing Reviews, November, 2008)