Algorithms in Bioinformatics

Minimum Factorization Agreement of Spliced ESTs.- Annotating Fragmentation Patterns.- biRNA: Fast RNA-RNA Binding Sites Prediction.- Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks.- PMFastR: A New Approach to Multiple RNA Structure Alignment.- On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices.- Constructing Majority-Rule Supertrees.- SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy.- A Simple, Practical and Complete -Time Algorithm for RNA Folding Using the Four-Russians Speedup.- Back-Translation for Discovering Distant Protein Homologies.- A Markov Classification Model for Metabolic Pathways.- Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction.- Phylogenetic Comparative Assembly.- K-Partite RNA Secondary Structures.- Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes.- Predicting Gene Structures from Multiple RT-PCR Tests.- A Tree Based Method for the Rapid Screening of Chemical Fingerprints.- Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters.- Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes.- A General Framework for Local Pairwise Alignment Statistics with Gaps.- mpscan: Fast Localisation of Multiple Reads in Genomes.- Fast Prediction of RNA-RNA Interaction.- FlexSnap: Flexible Non-sequential Protein Structure Alignment.- A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures.- Exact Score Distribution Computation for Similarity Searches in Ontologies.- Linear-Time Protein 3-D Structure Searching with Insertions and Deletions.- Visualizing Phylogenetic Treespace Using Cartographic Projections.- A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen.- Aligning Biomolecular Networks Using Modular Graph Kernels.- MADMX: A Novel Strategy for Maximal Dense Motif Extraction.- Large-Scale Neighbor-Joining with NINJA.- A Unifying View on Approximation and FPT of Agreement Forests.- Structural Alignment of RNA with Complex Pseudoknot Structure.- Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models.