Algorithms in Bioinformatics

1. Front Matter

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2. Automated Segmentation of DNA Sequences with Complex Evolutionary Histories

   • Broňa Brejová, Michal Burger, Tomáš Vinař

   Pages 1-13

3. Towards a Practical O(n logn) Phylogeny Algorithm

   • Daniel G. Brown, Jakub Truszkowski

   Pages 14-25

4. A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding

   • Stefan Canzar, Mohammed El-Kebir

   Pages 26-38

5. Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph

   • Rayan Chikhi, Dominique Lavenier

   Pages 39-48

6. Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions

   • Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh

   Pages 49-60

7. Constructing Large Conservative Supertrees

   • Jianrong Dong, David Fernández-Baca

   Pages 61-72

8. PepCrawler: A Fast RRT–Like Algorithm for High–Resolution Refinement and Binding–Affinity Estimation of Peptide Inhibitors

   • Elad Donsky, Haim J. Wolfson

   Pages 73-75

9. Removing Noise from Gene Trees

   • Andrea Doroftei, Nadia El-Mabrouk

   Pages 76-91

10. Boosting Binding Sites Prediction Using Gene’s Positions

    • Mohamed Elati, Rim Fekih, Rémy Nicolle, Ivan Junier, Joan Hérisson, François Képès

    Pages 92-103

11. Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters

    • Rob Gysel, Fumei Lam, Dan Gusfield

    Pages 104-115

12. On a Conjecture about Compatibility of Multi-states Characters

    • Michel Habib, Thu-Hien To

    Pages 116-127

13. Learning Protein Functions from Bi-relational Graph of Proteins and Function Annotations

    • Jonathan Qiang Jiang

    Pages 128-138

14. Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems

    • Hans-Michael Kaltenbach, Simona Constantinescu, Justin Feigelman, Jörg Stelling

    Pages 139-150

15. Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping

    • Kouichi Kimura, Asako Koike, Kenta Nakai

    Pages 151-162

16. A Practical Algorithm for Ancestral Rearrangement Reconstruction

    • Jakub Kováč, Broňa Brejová, Tomáš Vinař

    Pages 163-174

17. Bootstrapping Phylogenies Inferred from Rearrangement Data

    • Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

    Pages 175-187

18. Speeding Up Bayesian HMM by the Four Russians Method

    • Md Pavel Mahmud, Alexander Schliep

    Pages 188-200

19. Using Dominances for Solving the Protein Family Identification Problem

    • Noel Malod-Dognin, Mathilde Le Boudic-Jamin, Pritish Kamath, Rumen Andonov

    Pages 201-212

20. Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data

    • Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion Mandoiu, Alex Zelikovsky

    Pages 213-224

This book constitutes the refereed proceedings of the 11th International Workshop on Algorithms in Bioinformatics, WABI 2011, held in Saarbrücken, Germany, in September 2011. The 30 papers presented were carefully reviewed and selected from 77 submissions. They cover aspects of algorithms in bioinformatics, computational biology and systems biology.

• DNA sequencing
• genetic interaction networks
• graph computations
• machine learning
• protein family identification
• proteonomics
• statistical analysis algorithms
• algorithm analysis and problem complexity
• data structures

• National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, USA

  Teresa M. Przytycka

• Institut National de Recherche en Informatique et en Automatique (INRIA) and Université Lyon 1 (UCBL), Villeurbanne cedex, France

  Marie-France Sagot

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