Algorithms in Bioinformatics

1. MSARC: Multiple Sequence Alignment by Residue Clustering

   • Michał Modzelewski, Norbert Dojer

   Pages 259-272

2. Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs

   • Limor Leibovich, Zohar Yakhini

   Pages 273-286

3. Probabilistic Approaches to Alignment with Tandem Repeats

   • Michal Nánási, Tomáš Vinař, Broňa Brejová

   Pages 287-299

4. Multiscale Identification of Topological Domains in Chromatin

   • Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford

   Pages 300-312

5. Modeling Intratumor Gene Copy Number Heterogeneity Using Fluorescence in Situ Hybridization Data

   • Charalampos E. Tsourakakis

   Pages 313-325

6. Phylogenetic Analysis of Cell Types Using Histone Modifications

   • Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret

   Pages 326-337

7. Detecting Superbubbles in Assembly Graphs

   • Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya

   Pages 338-348

8. Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads

   • Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna

   Pages 349-363

9. Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs

   • Kamil Salikhov, Gustavo Sacomoto, Gregory Kucherov

   Pages 364-376

10. Back Matter

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This book constitutes the refereed proceedings of the 13th International Workshop on Algorithms in Bioinformatics, WABI 2013, held in Sophia Antipolis, France, in September 2013. WABI 2013 is one of seven workshops which, along with the European Symposium on Algorithms (ESA), constitute the ALGO annual meeting and highlights research in algorithmic work for bioinformatics, computational biology and systems biology. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. The 27 full papers presented were carefully reviewed and selected from 61 submissions. The papers cover all aspects of algorithms in bioinformatics, computational biology and systems biology.

• complexity
• evolutionary dynamics
• genome assembly
• statistical methods
• topological domains
• algorithm analysis and problem complexity

• ithree institute,, University of Technology Sydney, Ultimo, Australia

  Aaron Darling

• Faculty of Technology, Bielefeld University, Bielefeld, Germany

  Jens Stoye

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