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Algorithms in Bioinformatics

4th International Workshop, WABI 2004, Bergen, Norway, September 17-21, 2004, Proceedings

  • Conference proceedings
  • © 2004

Overview

Editors:
  1. Inge Jonassen

    1. Department of Informatics and Computational Biology Unit, HIB, University of Bergen, Bergen, Norway

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    You can also search for this editor in PubMed   Google Scholar

  2. Junhyong Kim

    1. Department of Biology,, Penn Center for Bioinformatics, Penn Genomics Institute, Philadelphia, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Lecture Notes in Computer Science (LNCS, volume 3240)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: WABI 2004.

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Table of contents (39 papers)

  1. Front Matter

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  2. Papers

    1. Reversing Gene Erosion – Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data

      • Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M. E. Moret
      Pages 1-13

    2. Reconstructing Ancestral Gene Orders Using Conserved Intervals

      • Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cedric Chauve
      Pages 14-25

    3. Sorting by Reversals with Common Intervals

      • Martin Figeac, Jean-Stéphane Varré
      Pages 26-37

    4. A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns

      • Jens Gramm
      Pages 38-49

    5. A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals

      • Tzvika Hartman, Roded Sharan
      Pages 50-61

    6. Algorithms for Finding Maximal-Scoring Segment Sets

      • Miklós Csűrös
      Pages 62-73

    7. Gapped Local Similarity Search with Provable Guarantees

      • Manikandan Narayanan, Richard M. Karp
      Pages 74-86

    8. Monotone Scoring of Patterns with Mismatches

      • Alberto Apostolico, Cinzia Pizzi
      Pages 87-98

    9. Suboptimal Local Alignments Across Multiple Scoring Schemes

      • Morris Michael, Christoph Dieterich, Jens Stoye
      Pages 99-110

    10. A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statistic

      • Uri Keich, Niranjan Nagarajan
      Pages 111-122

    11. Adding Hidden Nodes to Gene Networks

      • Benny Chor, Tamir Tuller
      Pages 123-134

    12. Joint Analysis of DNA Copy Numbers and Gene Expression Levels

      • Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini
      Pages 135-146

    13. Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting

      • Daichi Shigemizu, Osamu Maruyama
      Pages 147-158

    14. Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation

      • Lev Soinov, Alexander Kanapin, Misha Kapushesky
      Pages 159-169

    15. Multiple Vector Seeds for Protein Alignment

      • Daniel G. Brown
      Pages 170-181

    16. Solving the Protein Threading Problem by Lagrangian Relaxation

      • Stefan Balev
      Pages 182-193

    17. Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations

      • Alexandra Shulman-Peleg, Shira Mintz, Ruth Nussinov, Haim J. Wolfson
      Pages 194-205

    18. ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences

      • Stanislav Angelov, Sanjeev Khanna, Li Li, Fernando Pereira
      Pages 206-217

    19. Local Search Heuristic for Rigid Protein Docking

      • Vicky Choi, Pankaj K. Agarwal, Herbert Edelsbrunner, Johannes Rudolph
      Pages 218-229
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  1. Algorithms in Bioinformatics

Keywords

Editors and Affiliations

  • Department of Informatics and Computational Biology Unit, HIB, University of Bergen, Bergen, Norway

    Inge Jonassen

  • Department of Biology,, Penn Center for Bioinformatics, Penn Genomics Institute, Philadelphia, USA

    Junhyong Kim

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