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Important objectives in cancer research are the prediction of a patient's risk based on molecular measurements such as gene expression data and the identification of new prognostic biomarkers (e.g. genes). In clinical practice, this is…
The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. While standard methods…
We introduce a Bayesian sequential data assimilation method for COVID-19 forecasting. It is assumed that suitable transmission, epidemic and observation models are available and previously validated and the transmission and epidemic models…
Many medical decisions involve the use of dynamic information collected on individual patients toward predicting likely transitions in their future health status. If accurate predictions are developed, then a prognostic mode can identify…
Large-scale testing is considered key to assess the state of the current COVID-19 pandemic. Yet, the link between the reported case numbers and the true state of the pandemic remains elusive. We develop mathematical models based on…
The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…
Severe acute respiratory disease SARS-CoV-2 has had a found impact on public health systems and healthcare emergency response especially with respect to making decisions on the most effective measures to be taken at any given time. As…
In population genetics, extant samples are usually used for inference of past population genetic forces. With the Kingman coalescent and the backward diffusion equation, inference of the marginal likelihood proceeds from an extant sample…
Effective population size (Ne(t)) is a fundamental parameter in population genetics and phylodynamics that quantifies genetic diversity and reveals demographic history. Coalescent-based methods enable the inference of Ne(t) trajectories…
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…
This technical report describes a dynamic causal model of the spread of coronavirus through a population. The model is based upon ensemble or population dynamics that generate outcomes, like new cases and deaths over time. The purpose of…
Since the beginning of the COVID-19 pandemic, many dashboards have emerged as useful tools to monitor the evolution of the pandemic, inform the public, and assist governments in decision making. Our goal is to develop a globally applicable…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
Epidemiological forecasts are beset by uncertainties about the underlying epidemiological processes, and the surveillance process through which data are acquired. We present a Bayesian inference methodology that quantifies these…
Timely prediction of the COVID-19 progression is not possible without a comprehensive understanding of environmental factors that may affect the infection transmissibility. Studies addressing parameters that may influence COVID-19…
Studying how diverse human populations are related is of historical and anthropological interest, in addition to providing a realistic null model for testing for signatures of natural selection or disease associations. Furthermore,…
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies,…
The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial,…
Recruitment dynamics, or the distribution of the number of offspring among individuals, is central for understanding ecology and evolution. Sweepstakes reproduction (heavy right-tailed offspring number distribution) is central for…
We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially…