Algorithms in Bioinformatics

Papers.- Reversing Gene Erosion – Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data.- Reconstructing Ancestral Gene Orders Using Conserved Intervals.- Sorting by Reversals with Common Intervals.- A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns.- A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals.- Algorithms for Finding Maximal-Scoring Segment Sets.- Gapped Local Similarity Search with Provable Guarantees.- Monotone Scoring of Patterns with Mismatches.- Suboptimal Local Alignments Across Multiple Scoring Schemes.- A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statistic.- Adding Hidden Nodes to Gene Networks.- Joint Analysis of DNA Copy Numbers and Gene Expression Levels.- Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting.- Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation.- Multiple Vector Seeds for Protein Alignment.- Solving the Protein Threading Problem by Lagrangian Relaxation.- Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations.- ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences.- Local Search Heuristic for Rigid Protein Docking.- Sequence Database Compression for Peptide Identification from Tandem Mass Spectra.- Linear Reduction for Haplotype Inference.- A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis.- Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction.- Approximation Algorithms for the Selection of Robust Tag SNPs.- The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approach.- A Faster and More Space-EfficientAlgorithm for Inferring Arc-Annotations of RNA Sequences Through Alignment.- New Algorithms for Multiple DNA Sequence Alignment.- Chaining Algorithms for Alignment of Draft Sequence.- Translation Initiation Sites Prediction with Mixture Gaussian Models.- Online Consensus and Agreement of Phylogenetic Trees.- Relation of Residues in the Variable Region of 16S rDNA Sequences and Their Relevance to Genus-Specificity.- Topological Rearrangements and Local Search Method for Tandem Duplication Trees.- Phylogenetic Super-networks from Partial Trees.- Genome Identification and Classification by Short Oligo Arrays.- Novel Tree Edit Operations for RNA Secondary Structure Comparison.- The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics.- Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding.- Finding Optimal Pairs of Patterns.- Finding Missing Patterns.