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Coalescent Inference for Epidemics with Latent Periods
Isaac H. Goldstein, Julia A. Palacios
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent para…
The signal is not flushed away: Inferring the effective reproduction number from wastewater data in small populations
Isaac H. Goldstein, Daniel M. Parker, Sunny Jiang +2
The effective reproduction number is an important descriptor of an infectious disease epidemic. In small populations, ideally we would estimate the effective reproduction number us…
Semiparametric inference of effective reproduction number dynamics from wastewater pathogen surveillance data
Isaac H. Goldstein, Daniel M. Parker, Sunny Jiang +1
Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising…
Incorporating testing volume into estimation of effective reproduction number dynamics
Isaac H. Goldstein, Jon Wakefield, Volodymyr M. Minin
Branching process inspired models are widely used to estimate the effective reproduction number -- a useful summary statistic describing an infectious disease outbreak -- using cou…