Algorithms for Computational Biology

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 Induced Subgraphs 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.