This volume contains the papers which were selected for presentation at the second Bio- formatics Research and Development (BIRD) conference held in Vienna, Austria during July 7-9, 2008. BIRD covers a wide range of topics related to bioinformatics. This year sequence analysis and alignment, pathways, networks, systems biology, protein and RNA structure and function, gene expression/regulation and microarrays, databases and data integration, machine learning and data analysis were the subjects of main interest. The decisions of the Program Committee are based on the recommendations of at least three, up to five, reviews for each paper. As a result, 30 of the 61 submitted c- tributions could be accepted for the conference. We were happy to have three invited talks presented by experienced researchers providing visitors with a good overview but also some very important insights into the fascinating domain of bioinformatics. Abstracts and more information on these talks are provided in the conference program as well as at the conference site. In the second part of this volume the selected contributions of the two workshops which were held in parallel to the main conference are presented: Workshop on - namical Aspects of Perturbation, Intervention and Transition in Biological Systems - PETRIN 2008 and Workshop on Algorithms in Molecular Biology - ALBIO 2008 Poster presentations of the BIRD conference are in the companion proceedings published by the Trauner Verlag, Linz.

This volume contains the papers which were selected for presentation at the second Bio- formatics Research and Development (BIRD) conference held in Vienna, Austria during July 7–9, 2008. BIRD covers a wide range of topics related to bioinformatics. This year sequence analysis and alignment, pathways, networks, systems biology, protein and RNA structure and function, gene expression/regulation and microarrays, databases and data integration, machine learning and data analysis were the subjects of main interest. The decisions of the Program Committee are based on the recommendations of at least three, up to five, reviews for each paper. As a result, 30 of the 61 submitted c- tributions could be accepted for the conference. We were happy to have three invited talks presented by experienced researchers providing visitors with a good overview but also some very important insights into the fascinating domain of bioinformatics. Abstracts and more information on these talks are provided in the conference program as well as at the conference site. In the second part of this volume the selected contributions of the two workshops which were held in parallel to the main conference are presented: Workshop on - namical Aspects of Perturbation, Intervention and Transition in Biological Systems – PETRIN 2008 and Workshop on Algorithms in Molecular Biology – ALBIO 2008 Poster presentations of the BIRD conference are in the companion proceedings published by the Trauner Verlag, Linz.

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 Frequent Subgraphs 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 Management Infrastructure.- PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities.

This volume contains the papers which were selected for presentation at the second Bio- formatics Research and Development (BIRD) conference held in Vienna, Austria during July 7–9, 2008. BIRD covers a wide range of topics related to bioinformatics. This year sequence analysis and alignment, pathways, networks, systems biology, protein and RNA structure and function, gene expression/regulation and microarrays, databases and data integration, machine learning and data analysis were the subjects of main interest. The decisions of the Program Committee are based on the recommendations of at least three, up to five, reviews for each paper. As a result, 30 of the 61 submitted c- tributions could be accepted for the conference. We were happy to have three invited talks presented by experienced researchers providing visitors with a good overview but also some very important insights into the fascinating domain of bioinformatics. Abstracts and more information on these talks are provided in the conference program as well as at the conference site. In the second part of this volume the selected contributions of the two workshops which were held in parallel to the main conference are presented: Workshop on - namical Aspects of Perturbation, Intervention and Transition in Biological Systems – PETRIN 2008 and Workshop on Algorithms in Molecular Biology – ALBIO 2008 Poster presentations of the BIRD conference are in the companion proceedings published by the Trauner Verlag, Linz.