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Algorithms in Bioinformatics

8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008, Proceedings

  • Conference proceedings
  • © 2008

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Editors:
  1. Keith A. Crandall
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  2. Jens Lagergren
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 5251)

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

Included in the following conference series:

Conference proceedings info: WABI 2008.

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Table of contents (32 papers)

  1. Front Matter

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  2. Multichromosomal Genome Median and Halving Problems

    • Eric Tannier, Chunfang Zheng, David Sankoff
    Pages 1-13

  3. A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem

    • Meng Zhang, William Arndt, Jijun Tang
    Pages 14-24

  4. Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem

    • Andrew Wei Xu, David Sankoff
    Pages 25-37

  5. Read Mapping Algorithms for Single Molecule Sequencing Data

    • Vladimir Yanovsky, Stephen M. Rumble, Michael Brudno
    Pages 38-49

  6. Exact Transcriptome Reconstruction from Short Sequence Reads

    • Vincent Lacroix, Michael Sammeth, Roderic Guigo, Anne Bergeron
    Pages 50-63

  7. Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments

    • Florian Battke, Carsten Müller-Tidow, Hubert Serve, Kay Nieselt
    Pages 64-75

  8. NAPX: A Polynomial Time Approximation Scheme for the Noah’s Ark Problem

    • Glenn Hickey, Paz Carmi, Anil Maheshwari, Norbert Zeh
    Pages 76-86

  9. Minimum Common String Partition Parameterized

    • Peter Damaschke
    Pages 87-98

  10. Hardness and Approximability of the Inverse Scope Problem

    • Zoran Nikoloski, Sergio Grimbs, Joachim Selbig, Oliver Ebenhöh
    Pages 99-112

  11. Rapid Neighbour-Joining

    • Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen
    Pages 113-122

  12. Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices

    • Seung-Jin Sul, Grant Brammer, Tiffani L. Williams
    Pages 123-134

  13. Efficient Genome Wide Tagging by Reduction to SAT

    • Arthur Choi, Noah Zaitlen, Buhm Han, Knot Pipatsrisawat, Adnan Darwiche, Eleazar Eskin
    Pages 135-147

  14. Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming

    • Serdar Bozdag, Timothy J Close, Stefano Lonardi
    Pages 148-161

  15. An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem

    • Rumen Andonov, Nicola Yanev, Noël Malod-Dognin
    Pages 162-173

  16. A Faster Algorithm for RNA Co-folding

    • Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir
    Pages 174-185

  17. An Automated Combination of Kernels for Predicting Protein Subcellular Localization

    • Cheng Soon Ong, Alexander Zien
    Pages 186-197

  18. Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach

    • Thomas Lingner, Peter Meinicke
    Pages 198-209

  19. Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles

    • Nico Pfeifer, Oliver Kohlbacher
    Pages 210-221

  20. An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks

    • Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan
    Pages 222-232
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Other volumes

  1. Algorithms in Bioinformatics

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About this book

This book constitutes the refereed proceedings of the 8th International Workshop on Algorithms in Bioinformatics, WABI 2008, held in Karlsruhe, Germany, in September 2008 as part of the ALGO 2008 meeting. The 32 revised full papers presented together with the abstract of a keynote talk were carefully reviewed and selected from 81 submissions. All current issues of algorithms in bioinformatics are addressed, reaching from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. The topics range in biological applicability from genome mapping, to sequence assembly, to microarray quality, to phylogenetic inference, to molecular modeling.

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