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Algorithms in Bioinformatics

13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings

  • Conference proceedings
  • © 2013

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Editors:
  1. Aaron Darling

    1. ithree institute,, University of Technology Sydney, Ultimo, Australia

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  2. Jens Stoye

    1. Faculty of Technology, Bielefeld University, Bielefeld, Germany

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 8126)

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

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Conference proceedings info: WABI 2013.

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Table of contents (28 papers)

  1. Front Matter

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  2. Extending the Reach of Phylogenetic Inference

    • Bernard M. E. Moret
    Pages 1-2

  3. Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework

    • Ramanuja Simha, Hagit Shatkay
    Pages 3-17

  4. Towards Reliable Automatic Protein Structure Alignment

    • Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li
    Pages 18-32

  5. A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

    • Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan
    Pages 33-44

  6. Faster Mass Decomposition

    • Kai Dührkop, Marcus Ludwig, Marvin Meusel, Sebastian Böcker
    Pages 45-58

  7. On NP-Hardness of the Paired de Bruijn Sound Cycle Problem

    • Evgeny Kapun, Fedor Tsarev
    Pages 59-69

  8. Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing

    • Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert et al.
    Pages 70-84

  9. A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths

    • Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
    Pages 85-98

  10. A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data

    • Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot
    Pages 99-111

  11. Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

    • Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler
    Pages 112-125

  12. Faster Algorithms for RNA-Folding Using the Four-Russians Method

    • Balaji Venkatachalam, Dan Gusfield, Yelena Frid
    Pages 126-140

  13. Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree

    • Jesper Jansson, Chuanqi Shen, Wing-Kin Sung
    Pages 141-155

  14. The Generalized Robinson-Foulds Metric

    • Sebastian Böcker, Stefan Canzar, Gunnar W. Klau
    Pages 156-169

  15. Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time

    • Constantinos Tsirogiannis, Brody Sandel
    Pages 170-184

  16. Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs

    • Sudheer Vakati, David Fernández-Baca
    Pages 185-199

  17. Unifying Parsimonious Tree Reconciliation

    • Nicolas Wieseke, Matthias Bernt, Martin Middendorf
    Pages 200-214

  18. Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes

    • Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham
    Pages 215-229

  19. On the Matrix Median Problem

    • João Paulo Pereira Zanetti, Priscila Biller, João Meidanis
    Pages 230-243

  20. A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications

    • Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, Irena Rusu
    Pages 244-258
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Other volumes

  1. Algorithms in Bioinformatics

Keywords

About this book

This book constitutes the refereed proceedings of the 13th International Workshop on Algorithms in Bioinformatics, WABI 2013, held in Sophia Antipolis, France, in September 2013. WABI 2013 is one of seven workshops which, along with the European Symposium on Algorithms (ESA), constitute the ALGO annual meeting and highlights research in algorithmic work for bioinformatics, computational biology and systems biology. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. The 27 full papers presented were carefully reviewed and selected from 61 submissions. The papers cover all aspects of algorithms in bioinformatics, computational biology and systems biology.

Editors and Affiliations

  • ithree institute,, University of Technology Sydney, Ultimo, Australia

    Aaron Darling

  • Faculty of Technology, Bielefeld University, Bielefeld, Germany

    Jens Stoye

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