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Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study
(2019)BMJ OpenIntroduction Urban transmission patterns of influenza viruses are complex and poorly understood, and multiple factors may play a critical role in modifying transmission. Whole genome sequencing (WGS) allows the description of patient-to-patient transmissions at highest resolution. The aim of this study is to explore urban transmission patterns of influenza viruses in high detail by combining geographical, epidemiological and immunological ...Journal Article -
Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations
(2019)Virus EvolutionPopulation dynamics can be inferred from genetic sequence data by using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume migration rates and effective population sizes to be constant through time in structured populations. When considering rates to vary through time in structured populations, the number of parameters to infer increases rapidly and the available data might not be ...Journal Article -
Exploring the power of Bayesian birth‐death skyline models to detect mass extinction events from phylogenies with only extant taxa
(2019)EvolutionMass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth‐death models has made it possible to detect their signature based on extant‐taxa phylogenies. Most birth‐death models consider MEEs ...Journal Article