相关论文: Accounting for reporting delays in real-time phylo…

Bayesian adaptive designs have gained popularity in all phases of clinical trials with numerous new developments in the past few decades. During the COVID-19 pandemic, the need to establish evidence for the effectiveness of vaccines,…

The coronavirus pandemic has rapidly evolved into an unprecedented crisis. The susceptible-infectious-removed (SIR) model and its variants have been used for modeling the pandemic. However, time-independent parameters in the classical…

We identify a new natural coalescent structure, which we call the seed-bank coalescent, that describes the gene genealogy of populations under the influence of a strong seed-bank effect, where "dormant forms" of individuals (such as seeds…

Compared to a neutral model, purifying selection distorts the structure of genealogies and hence alters the patterns of sampled genetic variation. Although these distortions may be common in nature, our understanding of how we expect…

Phylodynamics is used to estimate epidemic dynamics from phylogenetic trees or genomic sequences of pathogens, but the likelihood calculations needed can be challenging for complex models. We present a neural Bayes estimator (NBE) for key…

Confronting the pandemic of COVID-19, is nowadays one of the most prominent challenges of the human species. A key factor in slowing down the virus propagation is the rapid diagnosis and isolation of infected patients. The standard method…

The COVID-19 pandemic has impacted lives and economies across the globe, leading to many deaths. While vaccination is an important intervention, its roll-out is slow and unequal across the globe. Therefore, extensive testing still remains…

In this study, we address three important challenges related to disease transmissions such as the COVID-19 pandemic, namely, (a) providing an early warning to likely exposed individuals, (b) identifying individuals who are asymptomatic, and…

Traditionally, frequency dependent evolutionary dynamics is described by deterministic replicator dynamics assuming implicitly infinite population sizes. Only recently have stochastic processes been introduced to study evolutionary dynamics…

The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best…

We argue that frequent sampling of the fraction of infected people (either by random testing or by analysis of sewage water), is central to managing the COVID-19 pandemic because it both measures in real time the key variable controlled by…

Forecasting infectious disease outbreaks is hard. Forecasting emerging infectious diseases with limited historical data is even harder. In this paper, we investigate ways to improve emerging infectious disease forecasting under operational…

We provide a predictive analysis of the spread of COVID-19, also known as SARS-CoV-2, using the dataset made publicly available online by the Johns Hopkins University. Our main objective is to provide predictions of the number of infected…

One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…

The global spread of COVID-19 had severe consequences for public health and the world economy. The quick onset of the pandemic highlighted the potential benefits of cheap and deployable pre-screening methods to monitor the prevalence of the…

Evolution occurs in populations of reproducing individuals. The structure of a biological population affects which traits evolve. Understanding evolutionary game dynamics in structured populations is difficult. Precise results have been…

Near-real time estimations of the effective reproduction number are among the most important tools to track the progression of a pandemic and to inform policy makers and the general public. However, these estimations rely on reported case…

We present a unifying, tractable approach for studying the spread of viruses causing complex diseases requiring to be modeled using a large number of types (e.g., infective stage, clinical state, risk factor class). We show that recording…

During the course of an epidemic, one of the most challenging tasks for authorities is to decide what kind of restrictive measures to introduce and when these should be enforced. In order to take informed decisions in a fully rational…

We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…