Algorithms in Bioinformatics

Shotgun Protein Sequencing.- Locality Kernels for Protein Classification.- When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features.- Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps.- Bringing Folding Pathways into Strand Pairing Prediction.- A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage.- Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies.- Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity.- Haplotype Inference Via Hierarchical Genotype Parsing.- Seeded Tree Alignment and Planar Tanglegram Layout.- Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion.- An ?(n 2/logn) Speed-Up of Heuristics for the Gene-Duplication Problem.- Incremental Discovery of Irredundant Motif Bases in Time O(|?|n 2 logn).- A Graph Clustering Approach to Weak Motif Recognition.- Informative Motifs in Protein Family Alignments.- Topology Independent Protein Structural Alignment.- Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction.- Alignment-Free Local Structural Search by Writhe Decomposition.- Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment.- Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding.- Genomic Signatures in De Bruijn Chains.- Fast Kernel Methods for SVM Sequence Classifiers.- On-Line Viterbi Algorithm for Analysis of Long Biological Sequences.- Predicting Protein Folding Kinetics Via Temporal Logic Model Checking.- Efficient Algorithms to Explore Conformation Spaces of Flexible ProteinLoops.- Algorithms for the Extraction of Synteny Blocks from Comparative Maps.- Computability of Models for Sequence Assembly.- Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data.- RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound.- HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding.- Homology Search with Fragmented Nucleic Acid Sequence Patterns.- Fast Computation of Good Multiple Spaced Seeds.- Inverse Sequence Alignment from Partial Examples.- Novel Approaches in Psychiatric Genomics.- The Point Placement Problem on a Line - Improved Bounds for Pairwise Distance Queries.- Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach.- Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data.- A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence.- Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation.