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Bioinformatics Research and Development

Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008 Proceedings

  • Conference proceedings
  • © 2008

Overview

Editors:
  1. Mourad Elloumi
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  2. Josef Küng
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  3. Michal Linial
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  4. Robert F. Murphy
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  5. Kristan Schneider
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  6. Cristian Toma
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Part of the book series: Communications in Computer and Information Science (CCIS, volume 13)

Included in the following conference series:

Conference proceedings info: BIRD 2008.

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Table of contents (49 papers)

  1. BIRD Conference

    1. Databases and Data Integration I

      1. Knowledge Acquisition Focused Cooperative Development of Bio-ontologies – A Case Study with BIO2Me
        • Dominic Mainz, Ingo Paulsen, Indra Mainz, Katrin Weller, Jochen Kohl, Arndt von Haeseler
        Pages 258-272

    2. Pathways, Networks, Systems Biology I

      1. Nested <i>q</i>-Partial Graphs for Genetic Network Inference from ”Small <i>n</i>, Large <i>p</i>” Microarray Data
        • Kevin Kontos, Gianluca Bontempi
        Pages 273-287
      2. A Computational Method for Reconstructing Gapless Metabolic Networks
        • Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen
        Pages 288-302
      3. Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets
        • Hans Zantema, Stefan Wagemans, Dragan Bošnački
        Pages 303-317
      4. Multi-functional Protein Clustering in PPI Networks
        • Clara Pizzuti, Simona E. Rombo
        Pages 318-330

    3. Pathways, Networks, Systems Biology II

      1. Protein-Protein Interaction Network Querying by a “Focus and Zoom” Approach
        • Valeria Fionda, Luigi Palopoli, Simona Panni, Simona E. Rombo
        Pages 331-346
      2. Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns
        • Jano van Hemert, Richard Baldock
        Pages 347-361
      3. Combining Molecular and Physiological Data of Complex Disorders
        • Emanuel Schwarz, F. Markus Leweke, Sabine Bahn, Pietro Liò
        Pages 362-376
      4. Combining Protein-Protein Interaction (PPI) Network and Sequence Attributes for Predicting Hypertension Related Proteins
        • Richard J. B. Dobson, Patricia B. Munroe, Charles A. Mein, Mark J. Caulfield, Mansoor A. S. Saqi
        Pages 377-391

    4. Databases and Data Integration II

      1. Genome Structure and Characterisation of an Endogenous Retrovirus from the Zebrafish Genome Project Database
        • Roziah Kambol, M. Faris Abtholuddin
        Pages 392-403
      2. Bayesian Phylogeny on Grid
        • Richard C. van der Wath, Elizabeth van der Wath, Antonio Carapelli, Francesco Nardi, Francesco Frati, Luciano Milanesi et al.
        Pages 404-416

    5. Workshop ALBIO

      1. Comparison of Exact String Matching Algorithms for Biological Sequences
        • Petri Kalsi, Hannu Peltola, Jorma Tarhio
        Pages 417-426
      2. A New Approximation Algorithm for the Minimum Fragment Removal Problem
        • Hatem Tahri, Mourad Elloumi
        Pages 427-435
      3. Indexing Factors in DNA/RNA Sequences
        • Tomáš Flouri, Costas Iliopoulos, M. Sohel Rahman, Ladislav Vagner, Michal Voráček
        Pages 436-445
      4. Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model
        • Pavlos Antoniou, Costas S. Iliopoulos, Inuka Jayasekera, M. Sohel Rahman
        Pages 446-455
      5. Suffix Tree Characterization of Maximal Motifs in Biological Sequences
        • Maria Federico, Nadia Pisanti
        Pages 456-465
      6. Efficient Seeding Techniques for Protein Similarity Search
        • Mikhail Roytberg, Anna Gambin, Laurent Noé, Sławomir Lasota, Eugenia Furletova, Ewa Szczurek et al.
        Pages 466-478
      7. An Algorithm for Multiple and Global Alignments
        • Mourad Elloumi, Ahmed Mokaddem
        Pages 479-488
      8. LASA: A Tool for Non-heuristic Alignment of Multiple Sequences
        • Ernst Althaus, Stefan Canzar
        Pages 489-498
      9. SVM-Based Local Search for Gene Selection and Classification of Microarray Data
        • Jose Crispin Hernandez Hernandez, Béatrice Duval, Jin-Kao Hao
        Pages 499-508
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  1. Bioinformatics Research and Development

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About this book

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.

Reviews

From the reviews:

"This is a collection of 49 papers from the Bioinformatics Research and Development (BIRD) 2008 Conference … that covers a variety of interesting subfields of theoretical and applicative bioinformatics. Researchers, teachers, students, and the community of bioinformaticians need such a periodic review of the new developments and current trends in this exciting field at the border of biology, medicine, and informatics." (Adrian Pasculescu, ACM Computing Reviews, November, 2008)

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