Bioinformatics Research and Development: Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008 Proceedings (Communications in Computer and Information Science, 13)

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. Table of Contents......Page 14 A Tree Index to Support Clustering Based Exploratory Data Analysis......Page 19 XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data......Page 34 Clustering in a Fixed Manifold to Detect Groups of Genes with Similar Expression Patterns......Page 50 Families of FPGA-Based Accelerators for BLAST Algorithm with Multi-seeds Detection and Parallel Extension......Page 61 Fast Structured Motif Search in DNA Sequences......Page 76 A Discriminative Method for Protein Remote Homology Detection Based on N-nary Profiles......Page 92 Searching for Supermaximal Repeats in Large DNA Sequences......Page 105 Motif Location Prediction by Divide and Conquer......Page 120 Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics......Page 132 A Symmetry-Free Subspace for Ab initio Protein Folding Simulations......Page 146 Comparative Analysis of Disulfide Bond Determination Using Computational-Predictive Methods and Mass Spectrometry-Based Algorithmic Approach......Page 158 Exploration of Evolutionary Relations between Protein Structures......Page 172 Two Local Search Methods for Protein Folding Simulation in the HP and the MJ Lattice Models......Page 185 A Robust Class of Stable Proteins in the 2D HPC Model......Page 198 A Novel Adaptive Multiple Imputation Algorithm......Page 211 Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies......Page 225 Gene Expression Mining for Cohesive Pattern Discovery......Page 239 Identifying Subcellular Locations from Images of Unknown Resolution......Page 253 E-BioFlow: Different Perspectives on Scientific Workflows......Page 261 Knowledge Acquisition Focused Cooperative Development of Bio-ontologies – A Case Study with BIO2Me......Page 276 Nested q-Partial Graphs for Genetic Network Inference from "Small n, Large p" Microarray Data......Page 291 A Computational Method for Reconstructing Gapless Metabolic Networks......Page 306 Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets......Page 321 Multi-functional Protein Clustering in PPI Networks......Page 336 Protein-Protein Interaction Network Querying by a "Focus and Zoom" Approach......Page 349 Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns......Page 365 Combining Molecular and Physiological Data of Complex Disorders......Page 380 Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins......Page 395 Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database......Page 410 Bayesian Phylogeny on Grid......Page 422 Comparison of Exact String Matching Algorithms for Biological Sequences......Page 435 A New Approximation Algorithm for the Minimum Fragment Removal Problem......Page 445 Indexing Factors in DNA/RNA Sequences......Page 454 Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model......Page 464 Suffix Tree Characterization of Maximal Motifs in Biological Sequences......Page 474 Efficient Seeding Techniques for Protein Similarity Search......Page 484 An Algorithm for Multiple and Global Alignments......Page 497 LASA: A Tool for Non-heuristic Alignment of Multiple Sequences......Page 507 SVM-Based Local Search for Gene Selection and Classification of Microarray Data......Page 517 GENFOCS – A Comparative Tool on Gene Finding with Sensitivity and Specificity......Page 527 Gene Machine © – A Hardware/Software Platform for Analyzing Genome Data......Page 535 Complex Representation of DNA Sequences......Page 546 Wavelet Analysis of Impulses in Axon Physiology......Page 556 Acquisition and Algorithms for Fluorescence Applications......Page 564 Control of the Lasers Dynamics by Pumping Modulation for Biophotonics Applications......Page 574 Quantum Well Lasers for Medical Industry......Page 581 Computational Model for the Study of the Fractal Parameters Characteristic for the Surface of Titanium Dental Implants......Page 589 VEMS-TM – A Management Infrastructure......Page 599 PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities......Page 605 M......Page 612 Z......Page 613 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. 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.