Comparative Genomics

Chapter 1 A Cubic Algorithm for the Generalized Rank Median of Three Genomes

Chapter 2 The Rooted SCJ Median with Single Gene Duplications

Chapter 3 A General Framework for Genome Rearrangement with Biological Constraints

Chapter 4 Estimation of the True Evolutionary Distance Under the INFER Model

Chapter 5 On the Hardness of Approximating Linearization of Scaffolds Sharing Repeated Contigs

Chapter 6 Detecting Large Indels Using Optical Map Data

Chapter 8 Speciation and Rate Variation in a Birth-and-Death Account of WGD and Fractionation; the Case of Solanaceae

Chapter 9 Detecting Introgression in Anopheles Mosquito Genomes Using a Reconciliation-Based Approach

Chapter 10 Reconstructing the History of Syntenies Through Super-Reconciliation

Chapter 11 On the Variance of Internode Distance Under the Multispecies Coalescent

Chapter 12 Linear-Time Algorithms for Some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance

Chapter 13 Multi-SpaM : A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees

Chapter 14 FastNet: Fast and Accurate Statistical Inference of Phylogenetic Networks Using Large-Scale Genomic Sequence Data

Chapter 15 NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees

Chapter 16 On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem

Chapter 17 Non-parametric and Semi-parametric Support Estimation Using SEquential RESampling Random Walks on Biomolecular Sequences

Chapter 18 Linear-Time Tree Containment in Phylogenetic Networks