Algorithms in Bioinformatics

Chapter 1 Extending the Reach of Phylogenetic Inference

Chapter 2 Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework

Chapter 3 Towards Reliable Automatic Protein Structure Alignment

Chapter 4 A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

Chapter 5 Faster Mass Decomposition

Chapter 6 On NP-Hardness of the Paired de Bruijn Sound Cycle Problem

Chapter 7 Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing

Chapter 8 A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths

Chapter 9 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

Chapter 10 Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

Chapter 11 Faster Algorithms for RNA-Folding Using the Four-Russians Method

Chapter 12 Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree

Chapter 13 The Generalized Robinson-Foulds Metric

Chapter 14 Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time

Chapter 15 Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs

Chapter 16 Unifying Parsimonious Tree Reconciliation

Chapter 18 On the Matrix Median Problem

Chapter 19 A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications

Chapter 20 MSARC: Multiple Sequence Alignment by Residue Clustering

Chapter 21 Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs

Chapter 22 Probabilistic Approaches to Alignment with Tandem Repeats

Chapter 23 Multiscale Identification of Topological Domains in Chromatin

Chapter 24 Modeling Intratumor Gene Copy Number Heterogeneity Using Fluorescence in Situ Hybridization Data

Chapter 25 Phylogenetic Analysis of Cell Types Using Histone Modifications

Chapter 26 Detecting Superbubbles in Assembly Graphs

Chapter 27 Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads

Chapter 28 Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs