Algorithms in Bioinformatics

1. Front Matter

   PDF

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

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.

• complexity
• evolutionary dynamics
• genome assembly
• statistical methods
• topological domains
• algorithm analysis and problem complexity

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

  Aaron Darling

• Faculty of Technology, Bielefeld University, Bielefeld, Germany

  Jens Stoye

Policies and ethics