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Algorithms in Bioinformatics

12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings

  • Conference proceedings
  • © 2012

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Editors:
  1. Ben Raphael

    1. Department of Computer Science, Brown University, Providence, USA

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  2. Jijun Tang

    1. Department of Computer Science and Engineering, University of South Carolina, Columbia, USA

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 7534)

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

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Conference proceedings info: WABI 2012.

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Table of contents (35 papers)

  1. Front Matter

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  2. Preserving Inversion Phylogeny Reconstruction

    • Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier
    Pages 1-13

  3. Fast Phylogenetic Tree Reconstruction Using Locality-Sensitive Hashing

    • Daniel G. Brown, Jakub Truszkowski
    Pages 14-29

  4. Efficient Computation of Popular Phylogenetic Tree Measures

    • Constantinos Tsirogiannis, Brody Sandel, Dimitris Cheliotis
    Pages 30-43

  5. SibJoin: A Fast Heuristic for Half-Sibling Reconstruction

    • Daniel G. Brown, Daniel Dexter
    Pages 44-56

  6. Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models

    • Yun Zhu, Luay Nakhleh
    Pages 57-68

  7. Estimating Population Size via Line Graph Reconstruction

    • Bjarni V. Halldórsson, Dima Blokh, Roded Sharan
    Pages 69-80

  8. Extracting Conflict-Free Information from Multi-labeled Trees

    • Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
    Pages 81-92

  9. Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs

    • Rob Gysel, Kristian Stevens, Dan Gusfield
    Pages 93-105

  10. An Optimal Reconciliation Algorithm for Gene Trees with Polytomies

    • Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk
    Pages 106-122

  11. Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference

    • Thi Hau Nguyen, Jean-Philippe Doyon, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Vincent Ranwez, Vincent Berry
    Pages 123-134

  12. RNA Tree Comparisons via Unrooted Unordered Alignments

    • Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson
    Pages 135-148

  13. Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots

    • Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise
    Pages 149-164

  14. δ-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data

    • Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Edgar Wingender
    Pages 165-177

  15. CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population

    • Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk et al.
    Pages 178-189

  16. Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters

    • Brad Shutters, Sudheer Vakati, David Fernández-Baca
    Pages 190-200

  17. Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches

    • Yasuo Tabei
    Pages 201-213

  18. Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes

    • Anthony J. Cox, Tobias Jakobi, Giovanna Rosone, Ole B. Schulz-Trieglaff
    Pages 214-224

  19. Succinct de Bruijn Graphs

    • Alexander Bowe, Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya
    Pages 225-235

  20. Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter

    • Rayan Chikhi, Guillaume Rizk
    Pages 236-248
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Other volumes

  1. Algorithms in Bioinformatics

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About this book

This book constitutes the refereed proceedings of the 12th International Workshop on Algorithms in Bioinformatics, WABI 2012, held in Ljubljana, Slovenia, in September 2012. WABI 2012 is one of six workshops which, along with the European Symposium on Algorithms (ESA), constitute the ALGO annual meeting and focuses on algorithmic advances in bioinformatics, computational biology, and systems biology with a particular emphasis on discrete algorithms and machine-learning methods that address important problems in molecular biology. The 35 full papers presented were carefully reviewed and selected from 92 submissions. The papers include algorithms for a variety of biological problems including phylogeny, DNA and RNA sequencing and analysis, protein structure, and others.

Editors and Affiliations

  • Department of Computer Science, Brown University, Providence, USA

    Ben Raphael

  • Department of Computer Science and Engineering, University of South Carolina, Columbia, USA

    Jijun Tang

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