Related papers: Predicting sub-population specific viral evolution
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
We study the spread of susceptible-infected-recovered (SIR) infectious diseases where an individual's infectiousness and probability of recovery depend on his/her "age" of infection. We focus first on early outbreak stages when stochastic…
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…
Epidemiological models describe the spread of an infectious disease within a population. They capture microscopic details on how the disease is passed on among individuals in various different ways, while making predictions about the state…
Since 1927, until recently, models describing the spread of disease have mostly been of the SIR-compartmental type, based on the assumption that populations are homogeneous and well-mixed. The focus of these models have typically been on…
The propagations of diseases, behaviors and information in real systems are rarely independent of each other, but they are coevolving with strong interactions. To uncover the dynamical mechanisms, the evolving spatiotemporal patterns and…
We investigate a model for spatial epidemics explicitly taking into account bi-directional movements between base and destination locations on individual mobility networks. We provide a systematic analysis of generic dynamical features of…
The fundamental models of epidemiology describe the progression of an infectious disease through a population using compartmentalized differential equations, but do not incorporate population-level heterogeneity in infection susceptibility.…
The accurate estimation of time-varying transmission rates is fundamental for understanding infectious disease dynamics and implementing effective public health interventions. To this end, we propose an improved inverse method for…
Although previous infection and vaccination provide protection against SARS-CoV-2 infection, both reinfection and breakthrough infection are possible events whose occurrence would increase with time after first exposure to the antigen and…
Predicting the spread of vector-borne diseases in response to incursions requires knowledge of both host and vector demographics in advance of an outbreak. Whereas host population data is typically available, for novel disease introductions…
This work aims to assess the risks of Covid-19 disease spread in diverse daily-life situations (referred to as scenarios) involving crowds of maskless pedestrians, mostly outdoors. More concretely, we develop a method to infer the global…
The COVID-19 pandemic and its multiple outbreaks have challenged governments around the world. Much of the epidemiological modeling was based on pre-pandemic contact information of the population, which changed drastically due to…
Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and…
Cities have long served as nucleating centers for human development and advancement. Cities have facilitated the spread of both human creativity and human disease, and at the same time, efforts to minimize the spread of disease have…
Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of…
The problem of adaptive sampling for estimating probability mass functions (pmf) uniformly well is considered. Performance of the sampling strategy is measured in terms of the worst-case mean squared error. A Bayesian variant of the…
A previously established multiscale population genetics model states that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal…
In this paper, we propose a new real-time differential virus transmission model, which can give more accurate and robust short-term predictions of COVID-19 transmitted infectious disease with benefits of near-term trend projection.…