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Algorithms in Bioinformatics

11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011, Proceedings

  • Conference proceedings
  • © 2011

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Editors:
  1. Teresa M. Przytycka

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

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  2. Marie-France Sagot

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

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 6833)

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

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Conference proceedings info: WABI 2011.

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About this book

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.

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Table of contents (30 papers)

  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
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Other volumes

  1. Algorithms in Bioinformatics

Editors and Affiliations

  • 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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