Algorithms in Bioinformatics

Extending the Reach of Phylogenetic Inference.- Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework.- Towards Reliable Automatic Protein Structure Alignment.- A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions.- Faster mass decomposition.- On NP-Hardness of the Paired de Bruijn Sound Cycle Problem.- Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing.- A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths.- A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data.- Graph-Distance within RNA Secondary Structure Ensembles.- Faster Algorithms for RNA-folding using the Four-Russians method.- Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree.- The generalized Robinson-Foulds metric.- Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time.- Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs.- Unifying Parsimonious Tree.- Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes.- On the matrix median problem.- Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications.- MSARC: Multiple Sequence Alignment by Residue Clustering.- Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs.- Probabilistic Approaches to Alignment with Tandem Repeats.- Multiscale Identification of Topological Domains in Chromatin.- Modeling Intratumor Gene Copy Number Heterogeneity using Fluorescence in Situ Hybridization data.- Phylogenetic Analysis of Cell Types using Histone Modifications.- Detecting Superbubbles in Assembly Graphs.- A hybrid assembly using high throughput short and long.- Using cascading Bloom filters to improve the memory usage for de Bruijn graphs.