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Algorithms in Bioinformatics

14th International Workshop, WABI 2014, Wroclaw, Poland, September 8-10, 2014. Proceedings

  • Dan Brown
  • Burkhard Morgenstern
Conference proceedings WABI 2014

Part of the Lecture Notes in Computer Science book series (LNCS, volume 8701)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 8701)

Table of contents

  1. Front Matter
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  2. QCluster: Extending Alignment-Free Measures with Quality Values for Reads Clustering
    Matteo Comin, Andrea Leoni, Michele Schimd
    Pages 1-13
  3. Improved Approximation for the Maximum Duo-Preservation String Mapping Problem
    Nicolas Boria, Adam Kurpisz, Samuli Leppänen, Monaldo Mastrolilli
    Pages 14-25
  4. A Faster 1.375-Approximation Algorithm for Sorting by Transpositions
    Luís Felipe I. Cunha, Luis Antonio B. Kowada, Rodrigo de A. Hausen, Celina M. H. de Figueiredo
    Pages 26-37
  5. A Generalized Cost Model for DCJ-Indel Sorting
    Phillip E. C. Compeau
    Pages 38-51
  6. Efficient Local Alignment Discovery amongst Noisy Long Reads
    Gene Myers
    Pages 52-67
  7. Efficient Indexed Alignment of Contigs to Optical Maps
    Martin D. Muggli, Simon J. Puglisi, Christina Boucher
    Pages 68-81
  8. Navigating in a Sea of Repeats in RNA-seq without Drowning
    Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix
    Pages 82-96
  9. Linearization of Median Genomes under DCJ
    Shuai Jiang, Max A. Alekseyev
    Pages 97-106
  10. An LP-Rounding Algorithm for Degenerate Primer Design
    Yu-Ting Huang, Marek Chrobak
    Pages 107-121
  11. GAML: Genome Assembly by Maximum Likelihood
    Vladimír Boža, Broňa Brejová, Tomáš Vinař
    Pages 122-134
  12. A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems
    Sebastian Will, Peter F. Stadler
    Pages 135-147
  13. Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences
    Laxmi Parida, Cinzia Pizzi, Simona E. Rombo
    Pages 148-160
  14. Estimating Evolutionary Distances from Spaced-Word Matches
    Burkhard Morgenstern, Binyao Zhu, Sebastian Horwege, Chris-André Leimeister
    Pages 161-173
  15. On the Family-Free DCJ Distance
    Fábio V. Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye
    Pages 174-186
  16. New Algorithms for Computing Phylogenetic Biodiversity
    Constantinos Tsirogiannis, Brody Sandel, Adrija Kalvisa
    Pages 187-203
  17. The Divisible Load Balance Problem and Its Application to Phylogenetic Inference
    Kassian Kobert, Tomáš Flouri, Andre Aberer, Alexandros Stamatakis
    Pages 204-216
  18. Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality
    Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker
    Pages 217-231
  19. An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data
    Dominik Kopczynski, Sven Rahmann
    Pages 232-246
  20. Best-Fit in Linear Time for Non-generative Population Simulation
    Niina Haiminen, Claude Lebreton, Laxmi Parida
    Pages 247-262
  21. GDNorm: An Improved Poisson Regression Model for Reducing Biases in Hi-C Data
    Ei-Wen Yang, Tao Jiang
    Pages 263-280
  22. Pacemaker Partition Identification
    Sagi Snir
    Pages 281-295
  23. Manifold de Bruijn Graphs
    Yu Lin, Pavel A. Pevzner
    Pages 296-310
  24. Constructing String Graphs in External Memory
    Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
    Pages 311-325
  25. Topology-Driven Trajectory Synthesis with an Example on Retinal Cell Motions
    Chen Gu, Leonidas Guibas, Michael Kerber
    Pages 326-339
  26. A Graph Modification Approach for Finding Core–Periphery Structures in Protein Interaction Networks
    Sharon Bruckner, Falk Hüffner, Christian Komusiewicz
    Pages 340-351
  27. Interpretable Per Case Weighted Ensemble Method for Cancer Associations
    Adrin Jalali, Nico Pfeifer
    Pages 352-353
  28. Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures
    Iman Hajirasouliha, Benjamin J. Raphael
    Pages 354-367
  29. Back Matter
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About these proceedings

Introduction

This book constitutes the refereed proceedings of the 14th International Workshop on Algorithms in Bioinformatics, WABI 2014, held in Wroclaw, Poland, in September 2014. WABI 2014 was one of seven conferences that were organized as part of ALGO 2014. WABI is an annual conference series on all aspects of algorithms and data structure in molecular biology, genomics and phylogeny data analysis. The 26 full papers presented together with a short abstract were carefully reviewed and selected from 61 submissions. The selected papers cover a wide range of topics from sequence and genome analysis through phylogeny reconstruction and networks to mass spectrometry data analysis.

Keywords

bioinformatics complexity computational genomics data mining data structures design and analysis of algorithms discrete mathematics evolutionary dynamics genome assembly genomic sequences graph theory

Editors and affiliations

  • Dan Brown
    • 1
  • Burkhard Morgenstern
    • 2
  1. 1.David R. Cheriton School of Computer ScienceUniversity of WaterlooCanada
  2. 2.Institute of Microbiology and Genetics, Department of BioinformaticsUniversity of Göttingen, GermanyGöttingenGermany

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-662-44753-6
  • Copyright Information Springer-Verlag Berlin Heidelberg 2014
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-662-44752-9
  • Online ISBN 978-3-662-44753-6
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site