Bioinformatics Research and Development: Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008 ProceedingsMourad Elloumi, Josef Küng, Michal Linial, Robert Murphy, Kristan Schneider, Cristian Toma 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. |
Contents
| 1 | |
| 16 | |
Clustering in a Fixed Manifold to Detect Groups of Genes with Similar Expression Patterns | 32 |
Families of FPGABased Accelerators for BLAST Algorithm with Multiseeds Detection and Parallel Extension | 43 |
Fast Structured Motif Search in DNA Sequences | 58 |
A Discriminative Method for Protein Remote Homology Detection Based on Nnary Profiles | 74 |
Searching for Supermaximal Repeats in Large DNA Sequences | 87 |
Motif Location Prediction by Divide and Conquer | 102 |
Combining Molecular and Physiological Data of Complex Disorders | 362 |
Combining ProteinProtein Interaction PPI Network and Sequence Attributes for Predicting Hypertension Related Proteins | 377 |
Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database | 392 |
Bayesian Phylogeny on Grid | 404 |
Comparison of Exact String Matching Algorithms for Biological Sequences | 417 |
A New Approximation Algorithm for the Minimum Fragment Removal Problem | 427 |
Indexing Factors in DNARNA Sequences | 436 |
Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model | 446 |
Improved Computation of RNARNA Binding Thermodynamics | 114 |
A SymmetryFree Subspace for Ab initio Protein Folding Simulations | 128 |
Comparative Analysis of Disulfide Bond Determination Using ComputationalPredictive Methods and Mass SpectrometryBased Algorithmic Approach | 140 |
Exploration of Evolutionary Relations between Protein Structures | 154 |
Two Local Search Methods for Protein Folding Simulation in the HP and the MJ Lattice Models | 167 |
A Robust Class of Stable Proteins in the 2D HPC Model | 180 |
A Novel Adaptive Multiple Imputation Algorithm | 193 |
Plasmid and NitrogenFixing Proteins Case Studies | 207 |
Gene Expression Mining for Cohesive Pattern Discovery | 221 |
Identifying Subcellular Locations from Images of Unknown Resolution | 235 |
Different Perspectives on Scientific Workflows | 243 |
Knowledge Acquisition Focused Cooperative Development of Bioontologies A Case Study with BIO2Me | 258 |
Nested qPartial Graphs for Genetic Network Inference from Small n Large p Microarray Data | 273 |
A Computational Method for Reconstructing Gapless Metabolic Networks | 288 |
Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets | 303 |
Multifunctional Protein Clustering in PPI Networks | 318 |
ProteinProtein Interaction Network Querying by a Focus and Zoom Approach | 331 |
Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns | 347 |
Suffix Tree Characterization of Maximal Motifs in Biological Sequences | 456 |
Efficient Seeding Techniques for Protein Similarity Search | 466 |
An Algorithm for Multiple and Global Alignments | 479 |
A Tool for Nonheuristic Alignment of Multiple Sequences | 489 |
SVMBased Local Search for Gene Selection and Classification of Microarray Data | 499 |
GENFOCS A Comparative Tool on Gene Finding with Sensitivity and Specificity | 509 |
Gene Machine A HardwareSoftware Platform for Analyzing Genome Data | 517 |
Complex Representation of DNA Sequences | 528 |
Wavelet Analysis of Impulses in Axon Physiology | 538 |
Acquisition and Algorithms for Fluorescence Applications | 546 |
Control of the Lasers Dynamics by Pumping Modulation for Biophotonics Applications | 556 |
Quantum Well Lasers for Medical Industry | 563 |
Computational Model for the Study of the Fractal Parameters Characteristic for the Surface of Titanium Dental Implants | 571 |
VEMSTM A Management Infrastructure | 581 |
PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities | 587 |
Author Index | 594 |
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Common terms and phrases
algorithm alphabet amino acid analysis applied approach approximate Berlin Heidelberg 2008 binding Bioinformatics biological CCIS 13 clustering clustering coefficient coefficients compared complex computational construction corresponding cysteine database dataset defined detection disulfide bond DNA sequences domain e-BioFlow edges Elloumi ESSM evaluation evolutionary experimental frequent subgraphs function gene expression Gene Ontology genetic genome graph HTd proteins implementation input interaction laser length match matrix maximal frequent metabolic network method microarray data missing value modulation Molecular multiple multiple sequence alignment node nucleotides obtained ontology output p-value pair parameters pathway pattern peptide performance perspective POL index prediction probes problem proposed protein folding protein sequence query random reaction score Section seeds selected sequence alignment similarity simple motif string structured motif subset substring Suffix Automaton suffix tree supermaximal repeats target tasks techniques threshold tion University vector wavelet workflow