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08/08/2022
Incorporating testing volume into estimation of effective reproduction number dynamics
Branching process inspired models are widely used to estimate the effect...
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12/06/2021
Statistical implications of relaxing the homogeneous mixing assumption in time series Susceptible-Infectious-Removed models
Infectious disease epidemiologists routinely fit stochastic epidemic mod...
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09/16/2021
How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
Bayesian inference is a popular and widely-used approach to infer phylog...
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09/06/2020
Using multiple data streams to estimate and forecast SARS-CoV-2 transmission dynamics, with application to the virus spread in Orange County, California
Near real-time monitoring of outbreak transmission dynamics and evaluati...
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01/15/2020
A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts
Stochastic epidemic models (SEMs) fit to incidence data are critical to ...
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06/27/2019
A Bayesian Phylogenetic Hidden Markov Model for B Cell Receptor Sequence Analysis
The human body is able to generate a diverse set of high affinity antibo...
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03/28/2019
Estimating effective population size changes from preferentially sampled genetic sequences
Coalescent theory combined with statistical modeling allows us to estima...
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02/24/2019
Fitting stochastic epidemic models to gene genealogies using linear noise approximation
Phylodynamics is a set of population genetics tools that aim at reconstr...
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11/28/2018
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
The marginal likelihood of a model is a key quantity for assessing the e...
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08/13/2018
Locally-adaptive Bayesian nonparametric inference for phylodynamics
Phylodynamics is an area of population genetics that uses genetic sequen...
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11/11/2017
Survival analysis of DNA mutation motifs with penalized proportional hazards
Antibodies, an essential part of our immune system, develop in an intric...
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11/01/2017