Algorithms in Bioinformatics

1. Front Matter

   Pages I-XVII

   PDF

2. Optimal Computation of Avoided Words

   • Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis et al.

   Pages 1-13

3. A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands

   • Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson

   Pages 14-26

4. An Efficient Branch and Cut Algorithm to Find Frequently Mutated Subnetworks in Cancer

   • Anna Bomersbach, Marco Chiarandini, Fabio Vandin

   Pages 27-39

5. Isometric Gene Tree Reconciliation Revisited

   • Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomáš Vinař

   Pages 40-51

6. Further Improvement in Approximating the Maximum Duo-Preservation String Mapping Problem

   • Brian Brubach

   Pages 52-64

7. SpecTrees: An Efficient Without a Priori Data Structure for MS/MS Spectra Identification

   • Matthieu David, Guillaume Fertin, Dominique Tessier

   Pages 65-76

8. Predicting Core Columns of Protein Multiple Sequence Alignments for Improved Parameter Advising

   • Dan DeBlasio, John Kececioglu

   Pages 77-89

9. Fast Compatibility Testing for Phylogenies with Nested Taxa

   • Yun Deng, David Fernández-Baca

   Pages 90-101

10. The Gene Family-Free Median of Three

    • Daniel Doerr, Pedro Feijão, Metin Balaban, Cedric Chauve

    Pages 102-120

11. Correction of Weighted Orthology and Paralogy Relations - Complexity and Algorithmic Results

    • Riccardo Dondi, Nadia El-Mabrouk, Manuel Lafond

    Pages 121-136

12. Copy-Number Evolution Problems: Complexity and Algorithms

    • Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi et al.

    Pages 137-149

13. Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support

    • Marius Erbert, Steffen Rechner, Matthias Müller-Hannemann

    Pages 150-161

14. Genome Rearrangements on Both Gene Order and Intergenic Regions

    • Guillaume Fertin, Géraldine Jean, Eric Tannier

    Pages 162-173

15. Better Identification of Repeats in Metagenomic Scaffolding

    • Jay Ghurye, Mihai Pop

    Pages 174-184

16. A Better Scoring Model for De Novo Peptide Sequencing: The Symmetric Difference Between Explained and Measured Masses

    • Ludovic Gillet, Simon Rösch, Thomas Tschager, Peter Widmayer

    Pages 185-196

17. StreAM- \(T_g\): Algorithms for Analyzing Coarse Grained RNA Dynamics Based on Markov Models of Connectivity-Graphs

    • Sven Jager, Benjamin Schiller, Thorsten Strufe, Kay Hamacher

    Pages 197-209

18. Solving Generalized Maximum-Weight Connected Subgraph Problem for Network Enrichment Analysis

    • Alexander A. Loboda, Maxim N. Artyomov, Alexey A. Sergushichev

    Pages 210-221

19. A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference

    • Sorina Maciuca, Carlos del Ojo Elias, Gil McVean, Zamin Iqbal

    Pages 222-233

20. Inferring Population Genetic Parameters: Particle Filtering, HMM, Ripley’s K-Function or Runs of Homozygosity?

    • Svend V. Nielsen, Simon Simonsen, Asger Hobolth

    Pages 234-245

This book constitutes the refereed proceedings of the 16th International Workshop on Algorithms in Bioinformatics, WABI 2016, held in Aarhus, Denmark. The 25 full papers  together with 2 invited talks presented were carefully reviewed and selected from 54 submissions.

The selected papers cover a wide range of topics from networks, to
phylogenetic studies, sequence and genome analysis, comparative genomics, and mass spectrometry data analysis. 

• bioinformatics
• complexity
• computational biology
• phylogenetics
• synthetic biology
• algorithm analysis and problem complexity

• AIST and University of Tokyo , Tokyo, Japan

  Martin Frith

• Aarhus University, Aarhus, Denmark

  Christian Nørgaard Storm Pedersen

Policies and ethics