Related papers: Predicting evolution from the shape of genealogica…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…
Global mobility flow data are at the heart of spatial epidemiological models used to predict infectious disease behavior but this wealth of data on human mobility has been largely neglected by reconstructions of pathogen evolutionary…
Motivated by the cyclic pattern of reproductive regimes observed in some species of green flies (``{\it aphids}''), we simulate the evolution of a population enduring harsh seasonal conditions for survival. The reproductive regime of each…
We study the evolution of large but finite asexual populations evolving in fitness landscapes in which all mutations are either neutral or strongly deleterious. We demonstrate that despite the absence of higher fitness genotypes, adaptation…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
We consider a neutral haploid population whose generations are not overlapping and whose size is large and constantly of $N$ individuals. Any generation is replaced by a new one and any individual has a single parent. We do not choose the…
The spread of infectious disease in a human community or the proliferation of fake news on social media can be modeled as a randomly growing tree-shaped graph. The history of the random growth process is often unobserved but contains…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
We predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes. In 2016-2017, our model predicts 19% efficacy compared to…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
Rapidly evolving viruses use antigenic drift as a key mechanism to evade host immunity and persist in real populations. While traditional models of antigenic drift and epidemic spread rely on low-dimensional antigenic spaces, genomic…
Seasonal influenza presents an ongoing challenge to public health. The rapid evolution of the flu virus necessitates annual vaccination campaigns, but the decision to get vaccinated or not in a given year is largely voluntary, at least in…
When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can…
We consider an asexual population under strong selection-weak mutation conditions evolving on rugged fitness landscapes with many local fitness peaks. Unlike the previous studies in which the initial fitness of the population is assumed to…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
Diagnosing an inherited disease often requires identifying the pattern of inheritance in a patient's family. We represent family trees with genetic patterns of inheritance using hypergraphs and latent state space models to provide…
Many pathogens spread primarily via direct contact between infected and susceptible hosts. Thus, the patterns of contacts or contact network of a population fundamentally shapes the course of epidemics. While there is a robust and growing…
Consider a birth and death chain to model the number of types of a given virus. Each type gives birth to a new type at rate $\lambda$ and dies at rate 1. Each type is also assigned a fitness. When a death occurs either the least fit type…