Algorithms for Computational Biology

This book constitutes the refereed proceedings of the First International Conference, AlCoB 2014, held in July 2014 in Tarragona, Spain.

The 20 revised full papers were carefully reviewed and selected from 39 submissions. The scope of AlCoB includes topics of either theoretical or applied interest, namely: exact sequence analysis, approximate sequence analysis, pairwise sequence alignment, multiple sequence alignment, sequence assembly, genome rearrangement, regulatory motif finding, phylogeny reconstruction, phylogeny comparison, structure prediction, proteomics: molecular pathways, interaction networks, transcriptomics: splicing variants, isoform inference and quantification, differential analysis, next-generation sequencing: population genomics, metagenomics, metatranscriptomics, microbiome analysis, systems biology.

Inhalt

Comparative Genomics Approaches to Identifying Functionally Related Genes.- A Greedy Algorithm for Hierarchical Complete Linkage Clustering.- Vester's Sensitivity Model for Genetic Networks with Time-Discrete Dynamics.- Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem.- Heuristics for the Sorting by Length-Weighted Inversions Problem on Signed Permutations.- On Low Treewidth Graphs and Supertrees.- On Optimal Read Trimming in Next Generation Sequencing and Its Complexity.- On the Implementation of Quantitative Model Refinement.- HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads.- Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads.- Modeling the Geometry of the Endoplasmic Reticulum Network.- On Sorting of Signed Permutations by Prefix and Suffix Reversals and Transpositions.- On the Diameter of Rearrangement Problems.- Efficiently Enumerating All Connected InducedSubgraphs of a Large Molecular Network.- On Algorithmic Complexity of Biomolecular Sequence Assembly Problem.- A Closed-Form Solution for Transcription Factor Activity Estimation Using Network Component Analysis.- SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints.- Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures.- Inference of Boolean Networks from Gene Interaction Graphs Using a SAT Solver.- RRCA: Ultra-Fast Multiple In-species Genome Alignments.- Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric.