Algorithms in Bioinformatics - Info and Reading Options

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Intro -- Preface -- Organization -- Abstracts -- Reference-free Compression of High Throughput Sequencing Data with a Probabilistic de Bruijn Graph -- Genome Scaffolding with PE-Contaminated Mate-Pair Libraries -- Network Properties of the Ensemble of RNA Structures -- Contents -- BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules -- 1 Introduction -- 2 Background -- 3 Solution -- 3.1 Network Modules with Flexible Coherency -- 3.2 BicNET: Efficient Biclustering of Biological Networks -- 4 Results and Discussion -- 4.1 Results on Synthetic Data -- 4.2 Results on Real Data -- 5 Conclusions and Future Work -- References -- Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via WAVE -- 1 Introduction -- 1.1 Motivation -- 1.2 Related Work -- 1.3 Our Contributions and Significance -- 2 Methods -- 2.1 Data -- 2.2 Combining Topological and Sequence Information Within NCF -- 2.3 Evaluation of Alignment Quality -- 2.4 Our Methodology -- 3 Results and Discussion -- 3.1 Comparison of Edge-Weighted and Edge-Unweighted Versions of WAVE -- 3.2 Comparison of Different Parameter Values Within WAVE -- 3.3 Comparison of Five NCF-AS Methods -- 3.4 Comparison of WAVE with Very Recent Methods -- 4 Concluding Remarks -- A Appendix -- A.1 Appendix Figures -- References -- The Topological Profile of a Model of Protein Network Evolution Can Direct Model Improvement -- 1 Introduction -- 2 Methods -- 2.1 The Evolutionary Model -- 2.2 The Empirical Network -- 2.3 Topological Measures Assessed -- 3 Results -- 3.1 Success of Driving Properties Towards the Empirical Topology -- 3.2 Non-Optimized Topological Properties that Trend Towards Empirical Values -- 3.3 Variability of Topological Measures -- 3.4 Correlation Among Topological Characteristics -- 3.5 Improving the Evolutionary Model -- 4 Conclusion

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