Related papers: Studying viral populations with tools from quantum…
A social (sexual) network is modeled by an extension of the configuration model to the situation where edges have weights, e.g. reflecting the number of sex-contacts between the individuals. An epidemic model is defined on the network such…
Quasispecies theory predicts that there is a critical mutation probability above which a viral population will go extinct. Above this threshold the virus loses the ability to replicate the best adapted genotype, leading to a population…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Morphologic diversity is observed across all families of viruses. Yet these supra-molecular assemblies are produced most of the time in a spontaneous way through complex molecular self-assembly scenarios. The modeling of these phenomena…
Viruses display striking diversity in structure, transmission mode, immune interaction, and evolutionary behavior. Despite this diversity, viral strategies are not unconstrained. Here we present a unifying framework that treats viral…
A simple, but ``classical``, stochastic model for epidemic spread in a finite, but large, population is studied. The progress of the epidemic can be divided into three different phases that requires different tools to analyse. Initially the…
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia…
Network models are increasingly used to study infectious disease spread. Exponential Random Graph models have a history in this area, with scalable inference methods now available. An alternative approach uses mechanistic network models.…
Inference of the reproduction number through time is of vital importance during an epidemic outbreak. Typically, epidemiologists tackle this using observed prevalence or incidence data. However, prevalence and incidence data alone is often…
Epidemiological models for the spread of pathogens in a population are usually only able to describe a single pathogen. This makes their application unrealistic in cases where multiple pathogens with similar symptoms are spreading…
Motivated by our intention to use SIR-type epidemiological models in the context of dynamic networks as provided by large-scale highly interacting inhomogeneous human crowds, we investigate in this framework possibilities to reduce the…
We study the problem of community detection in a general version of the block spin Ising model featuring M groups, a model inspired by the Curie-Weiss model of ferromagnetism in statistical mechanics. We solve the general problem of…
We investigate the long-time dynamics of a SIR epidemic model in the case of a population of pathogens infecting a homogeneous host population. The pathogen population is structured by a genotypic variable. When the initial mass of the…
Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the…
Based on the classical SIR model, we derive a simple modification for the dynamics of epidemics with a known incubation period of infection. The model is described by a system of integro-differential equations. Parameters of our model…
We study the problem of reconstructing the probability measure of the Curie-Weiss model from a sample of the voting behaviour of a subset of the population. While originally used to study phase transitions in statistical mechanics, the…
We reconsider the Eigen's quasi-species model for competing self-reproductive macromolecules in populations characterized by a single-peaked fitness landscape. The use of ideas and tools borrowed from polymers theory and statistical…
We propose a type-dependent branching model with mutation and competition for modeling phylogenies of a virus population. The competition kernel depends for any two virus particles on the particles' types, the total mass of the population…
Internal feedbacks are commonly present in biological populations and can play a crucial role in the emergence of collective behavior. We consider a generalization of Fisher-KPP equation to describe the temporal evolution of the…
Population dynamics and evolutionary genetics underly the structure of ecosystems, changing on the same timescale for interacting species with rapid turnover, such as virus (e.g. HIV) and immune response. Thus, an important problem in…