Bioinformatics Research and Development: Second International Conference, Bird 2008 Vienna, Austria, July 7-9, 2008 Proceedings

by Elloumi, Mourad; Kung, Josef; Linial, Michal; Murphy, Robert; Schneider, Kristan

• ISBN13: 9783540705987
• ISBN10: 3540705988
• Format: Paperback
• Copyright: 2008-10-04
• Publisher: Springer-Verlag New York Inc

Summary

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

BIRD Conference
Gene Expression/Regulation and Micro Arrays
A Tree Index to Support Clustering Based Exploratory Data Analysis	p. 1
XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data	p. 16
Clustering in a Fixed Manifold to Detect Groups of Genes with Similar Expression Patterns	p. 32
Sequence Analysis and Alignment I
Families of FPGA-Based Accelerators for BLAST Algorithm with Multi-seeds Detection and Parallel Extension	p. 43
Fast Structured Motif Search in DNA Sequences	p. 58
A Discriminative Method for Protein Remote Homology Detection Based on N-nary Profiles	p. 74
Sequence Analysis and Alignment II
Searching for Supermaximal Repeats in Large DNA Sequences	p. 87
Motif Location Prediction by Divide and Conquer	p. 102
Protein and RNA Structure and Function I
Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics	p. 114
A Symmetry-Free Subspace for Ab initio Protein Folding Simulations	p. 128
Protein and RNA Structure and Function II
Comparative Analysis of Disulfide Bond Determination Using Computational-Predictive Methods and Mass Spectrometry-Based Algorithmic Approach	p. 140
Exploration of Evolutionary Relations between Protein Structures	p. 154
Two Local Search Methods for Protein Folding Simulation in the HP and the MJ Lattice Models	p. 167
A Robust Class of Stable Proteins in the 2D HPC Model	p. 180
Machine Learning and Data Analysis
A Novel Adaptive Multiple Imputation Algorithm	p. 193
Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies	p. 207
Gene Expression Mining for Cohesive Pattern Discovery	p. 221
Databases and Data Integration I
Identifying Subcellular Locations from Images of Unknown Resolution	p. 235
E-BioFlow: Different Perspectives on Scientific Workflows	p. 243
Knowledge Acquisition Focused Cooperative Development of Bio-ontologies - A Case Study with BIO2Me	p. 258
Pathways, Networks, Systems Biology I
Nested q-Partial Graphs for Genetic Network Inference from "Small n, Large p" Microarray Data	p. 273
A Computational Method for Reconstructing Gapless Metabolic Networks	p. 288
Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets	p. 303
Multi-functional Protein Clustering in PPI Networks	p. 318
Pathways, Networks, Systems Biology II
Protein-Protein Interaction Network Querying by a "Focus and Zoom" Aproach	p. 331
Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns	p. 347
Combining Molecular and Physiological Data of Complex Disorders	p. 362
Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins	p. 377
Databases and Data Integration II
Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database	p. 392
Bayesian Phylogeny on Grid	p. 404
Workshop ALBIO
Comparison of Exact String Matching Algorithms for Biological Sequences	p. 417
A New Approximation Algorithm for the Minimum Fragment Removal Problem	p. 427
Indexing Factors in DNA/RNA Sequences	p. 436
Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model	p. 446
Suffix Tree Characterization of Maximal Motifs in Biological Sequences	p. 456
Efficient Seeding Techniques for Protein Similarity Search	p. 466
An Algorithm for Multiple and Global Alignments	p. 479
LASA: A Tool for Non-heuristic Alignment of Multiple Sequences	p. 489
SVM-Based Local Search for Gene Selection and Classification of Microarray Data	p. 499
GENFOCS - A Comparative Tool on Gene Finding with Sensitivity and Specificity	p. 509
Gene Machine[copy] - A Hardware/Software Platform for Analyzing Genome Data	p. 517
Workshop PETRIN
Complex Representation of DNA Sequences	p. 528
Wavelet Analysis of Impulses in Axon Physiology	p. 538
Acquisition and Algorithms for Fluorescence Applications	p. 546
Control of the Lasers Dynamics by Pumping Modulation for Biophotonics Applications	p. 556
Quantum Well Lasers for Medical Industry	p. 563
Computational Model for the Study of the Fractal Parameters Characteristic for the Surface of Titanium Dental Implants	p. 571
VEMS-TM - A Management Infrastructure	p. 581
PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities	p. 587
Author Index	p. 595
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