Chapter 1 BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules

Chapter 2 Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via WAVE

Chapter 3 The Topological Profile of a Model of Protein Network Evolution Can Direct Model Improvement

Chapter 4 Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns

Chapter 5 Orthology Relation and Gene Tree Correction: Complexity Results

Chapter 6 Finding a Perfect Phylogeny from Mixed Tumor Samples

Chapter 7 A Sub-quadratic Time and Space Complexity Solution for the Dated Tree Reconciliation Problem for Select Tree Topologies

Chapter 8 Maximum Parsimony Analysis of Gene Copy Number Changes

Chapter 9 Multiple-Ancestor Localization for Recently Admixed Individuals

Chapter 10 Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming

Chapter 11 Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data

Chapter 12 Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads

Chapter 13 Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches

Chapter 14 Optimizing Read Reversals for Sequence Compression

Chapter 15 Circular Sequence Comparison with q-grams

Chapter 16 Bloom Filter Trie – A Data Structure for Pan-Genome Storage

Chapter 17 A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches

Chapter 18 Models and Algorithms for Genome Rearrangement with Positional Constraints

Chapter 19 Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction

Chapter 20 A Sparsified Four-Russian Algorithm for RNA Folding

Chapter 22 Graph-Theoretic Modelling of the Domain Chaining Problem

Chapter 23 Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers