Bioinformatics Research and Development : second international conference, Bird 2008 Vienna, Austria, July 7-9, 2008 proceedings

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
• Gene Expression/Regulation and Micro Arrays
• A Tree Index to Support Clustering Based Exploratory Data Analysis p. 1 Christian Martin and Tim W. Nattkemper
• XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data p. 16 Ben Dalziel and Hui Yang and Rahul Singh and Matthew Gormley and Susan Fisher
• Clustering in a Fixed Manifold to Detect Groups of Genes with Similar Expression Patterns p. 32 N.M. Phuong and H.D. Tuan
• Sequence Analysis and Alignment I
• Families of FPGA-Based Accelerators for BLAST Algorithm with Multi-seeds Detection and Parallel Extension p. 43 Fei Xia and Yong Dou and Jiaqing Xu
• Fast Structured Motif Search in DNA Sequences p. 58 Mihail Halachev and Nematollaah Shiri
• A Discriminative Method for Protein Remote Homology Detection Based on N-nary Profiles p. 74 Bin Liu and Lei Lin and Xiaolong Wang and Qiwen Dong and Xuan Wang
• Sequence Analysis and Alignment II
• Searching for Supermaximal Repeats in Large DNA Sequences p. 87 Chen Na Lian and Mihail Halachev and Nematollaah Shiri
• Motif Location Prediction by Divide and Conquer p. 102 Mohammed Alshalalfa and Reda Alhajj
• Protein and RNA Structure and Function I
• Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics p. 114 Ulrike Muckstein and Hakim Tafer and Stephan H. Bernhart and Maribel Hernandez-Rosales and Jorg Vogel and Peter F. Stadler and Ivo L. Hofacker
• A Symmetry-Free Subspace for Ab initio Protein Folding Simulations p. 128 Xiangchao Gan and Leonidas Kapsokalivas and Andreas A. Albrecht and Kathleen Steinhofel
• 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 Timothy Lee and Rahul Singh
• Exploration of Evolutionary Relations between Protein Structures p. 154 Natalja Kurbatova and Juris Viksna
• Two Local Search Methods for Protein Folding Simulation in the HP and the MJ Lattice Models p. 167 L. Kapsokalivas and X. Gan and A. Albrecht and K. Steinhofel
• A Robust Class of Stable Proteins in the 2D HPC Model p. 180 Alireza Hadj Khodabakhshi and Jan Manuch and Arash Rafiey and Arvind Gupta
• Machine Learning and Data Analysis
• A Novel Adaptive Multiple Imputation Algorithm p. 193 Veselka Boeva and Elena Tsiporkova
• Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies p. 207 Pietro Lio and Matteo Brilli and Renato Fani
• Gene Expression Mining for Cohesive Pattern Discovery p. 221 Ramkishore Bhattacharyya and Balaram Bhattacharyya
• Databases and Data Integration I
• Identifying Subcellular Locations from Images of Unknown Resolution p. 235 Luis Pedro Coelho and Robert F. Murphy
• E-BioFlow: Different Perspectives on Scientific Workflows p. 243 Ingo Wassink and Han Rauwerda and Paul van der Vet and Timo Breit and Anton Nijholt
• Knowledge Acquisition Focused Cooperative Development of Bio-ontologies - A Case Study with BIO2Me p. 258 Dominic Mainz and Ingo Paulsen and Indra Mainz and Katrin Weller and Jochen Kohl and Arndt von Haeseler
• Pathways, Networks, Systems Biology I
• Nested q-Partial Graphs for Genetic Network Inference from "Small n, Large p" Microarray Data p. 273 Kevin Kontos and Gianluca Bontempi
• A Computational Method for Reconstructing Gapless Metabolic Networks p. 288 Esa Pitkanen and Ari Rantanen and Juho Rousu and Esko Ukkonen
• Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets p. 303 Hans Zantema and Stefan Wagemans and Dragan Bosnacki
• Multi-functional Protein Clustering in PPI Networks p. 318 Clara Pizzuti and Simona E. Rombo
• Pathways, Networks, Systems Biology II
• Protein-Protein Interaction Network Querying by a "Focus and Zoom" Aproach p. 331 Valeria Fionda and Luigi Palopoli and Simona Panni and Simona E. Rombo
• Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns p. 347 Jano van Hemert and Richard Baldock
• Combining Molecular and Physiological Data of Complex Disorders p. 362 Emanuel Schwarz and F. Markus Leweke and Sabine Bahn and Pietro Lio
• Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins p. 377 Richard J.B. Dobson and Patricia B. Munroe and Charles A. Mein and Mark J. Caulfield and Mansoor A.S. Saqi
• Databases and Data Integration II
• Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database p. 392 Roziah Kambol and M. Faris Abtholuddin
• Bayesian Phylogeny on Grid p. 404 Richard C. van der Wath and Elizabeth van der Wath and Antonio Carapelli and Francesco Nardi and Francesco Frati and Luciano Milanesi and Pietro Lio
• Workshop ALBIO
• Comparison of Exact String Matching Algorithms for Biological Sequences p. 417 Petri Kalsi and Hannu Peltola and Jorma Tarhio
• A New Approximation Algorithm for the Minimum Fragment Removal Problem p. 427 Hatem Tahri and Mourad Elloumi
• Indexing Factors in DNA/RNA Sequences p. 436 Tomas Flouri and Costas Iliopoulos and M. Sohel Rahman and Ladislav Vagner and Michael Voracek
• Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model p. 446 Pavlos Antoniou and Costas S. Iliopoulos and Inuka Jayasekera and M. Sohel Rahman
• Suffix Tree Characterization of Maximal Motifs in Biological Sequences p. 456 Maria Federico and Nadia Pisanti
• Efficient Seeding Techniques for Protein Similarity Search p. 466 Mikhail Roytberg and Anna Gambin and Laurent Noe and Slawomir Lasota and Eugenia Furletova and Ewa Szczurek and Gregory Kucherov
• An Algorithm for Multiple and Global Alignments p. 479 Mourad Elloumi and Ahmed Mokaddem
• LASA: A Tool for Non-heuristic Alignment of Multiple Sequences p. 489 Ernst Althaus and Stefan Canzar
• SVM-Based Local Search for Gene Selection and Classification of Microarray Data p. 499 Jose Crispin Hernandez Hernandez and Beatrice Duval and Jin-Kao Hao
• GENFOCS - A Comparative Tool on Gene Finding with Sensitivity and Specificity p. 509 M.A. Lijo Anto and G. Gopakumar and Achuthsankar S. Nair and Indira Ghosh
• Gene Machine[copy] - A Hardware/Software Platform for Analyzing Genome Data p. 517 Roger Marshall
• Workshop PETRIN
• Complex Representation of DNA Sequences p. 528 Carlo Cattani
• Wavelet Analysis of Impulses in Axon Physiology p. 538 Carlo Cattani and Massimo Scalia
• Acquisition and Algorithms for Fluorescence Applications p. 546 Elena Mocanu and Paul Sterian
• Control of the Lasers Dynamics by Pumping Modulation for Biophotonics Applications p. 556 Paul Sterian and Octavian Marin and Valerica Ninulescu
• Quantum Well Lasers for Medical Industry p. 563 Valerica Ninulescu and Vladut-Bogdan Nicolae and Andreea Sterian
• Computational Model for the Study of the Fractal Parameters Characteristic for the Surface of Titanium Dental Implants p. 571 Stefan Pusca and Theodora Toma
• VEMS-TM - A Management Infrastructure p. 581 Trandafir Moisa and Cristian Morarescu
• PTF Model for Evaluating the Relationships between the VAC and Antimicrobial Resistance in Human Communities p. 587 Irina Codita and Stefan Pusca
• Author Index p. 595