6 papers
Gaussian process priors with Markov properties for effective reproduction number inference
Jessalyn N. Sebastian, Volodymyr M. Minin
Many quantities characterizing infectious disease outbreaks - like the effective reproduction number (), defined as the average number of secondary infections a newly infected…
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…
Phylogenetic least squares estimation without genetic distances
Peter B. Chi, Volodymyr M. Minin
Least squares estimation of phylogenies is an established family of methods with good statistical properties. State-of-the-art least squares phylogenetic estimation proceeds by fir…
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…
Fitting a stochastic model of intensive care occupancy to noisy hospitalization time series during the COVID-19 pandemic
Achal Awasthi, Volodymyr M. Minin, Jenny Huang +2
Intensive care occupancy is an important indicator of health care stress that has been used to guide policy decisions during the COVID-19 pandemic. Toward reliable decision-making…
Semi-parametric modeling of SARS-CoV-2 transmission using tests, cases, deaths, and seroprevalence data
Damon Bayer, Isaac Goldstein, Jonathan Fintzi +13
Mechanistic models fit to streaming surveillance data are critical to understanding the transmission dynamics of an outbreak as it unfolds in real-time. However, transmission model…