Computational Intelligence Methods for Bioinformatics and Biostatistics - Info and Reading Options

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Intro -- Preface -- Organization -- Contents -- An Open-Source Tool for Managing Time-Evolving Variant Annotation -- 1 Scientific Background -- 2 Materials and Methods -- 3 Results -- 4 Conclusion -- References -- Extracting Few Representative Reconciliations with Host Switches -- 1 Scientific Background -- 2 Equivalent Reconciliations -- 2.1 Equivalence 1 -- 2.2 Equivalence 2 -- 3 Results -- 4 Perspectives -- References -- A Quantitative and Qualitative Characterization of k-mer Based Alignment-Free Phylogeny Construction -- 1 Introduction -- 2 Methods and Materials -- 2.1 Datasets -- 3 Quantification of the Information Carried by k-mer -- 3.1 Distances -- 4 Results and Discussion -- 5 Conclusion -- References -- Cancer Mutational Signatures Identification with Sparse Dictionary Learning -- 1 Scientific Background -- 1.1 DNA Somatic Mutations -- 2 Materials and Methods -- 2.1 Learning Methods -- 2.2 Pipelines Description -- 3 Results -- 4 Conclusion -- References -- Icing: Large-Scale Inference of Immunoglobulin Clonotypes -- 1 Scientific Background -- 2 Icing -- 3 Materials and Methods -- 3.1 Synthetic Data Generation -- 3.2 Preprocessing -- 3.3 Clonotype Identification -- 3.4 Performance Assessment -- 3.5 Computing Architecture -- 4 Results -- 4.1 Performance Evaluation -- 4.2 Expected Clonotypes -- 5 Conclusion -- References -- Adenine: A HPC-Oriented Tool for Biological Data Exploration -- 1 Scientific Background -- 2 Adenine -- 3 Gene Expression Data -- 4 Usage Example -- 5 Results -- 6 Conclusions -- References -- Disease-Genes Must Guide Data Source Integration in the Gene Prioritization Process -- 1 Background -- 2 Materials -- 3 Methods -- 3.1 UNIPred -- 3.2 Constructing the Integrated Network -- 3.3 Inferring the Gene Prioritization List -- 4 Results -- 5 Conclusion -- References

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