种群与进化
The basic reproduction number, $R_0$, is a well-known quantifier of epidemic spread. However, a class of existing methods for estimating $R_0$ from incidence data early in the epidemic can lead to an over-estimation of this quantity. In…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Despite its endemic nature as well as the recent outbreaks, information on the opportunistic DENV in Anambra state has been sparse. This study thus aimed to give seroepidemiological evidence of past dengue virus infection among HIV-infected…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
With a single circulating vector-borne virus, the basic reproduction number incorporates contributions from tick-to-tick (co-feeding), tick-to-host and host-to-tick transmission routes. With two different circulating vector-borne viral…
Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…
Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more…
The potential effects of conservation actions on threatened species can be predicted using ensemble ecosystem models by forecasting populations with and without intervention. These model ensembles commonly assume stable coexistence of…
Decisions to disperse from a habitat stand out among organismal behaviors as pivotal drivers of ecosystem dynamics across scales. Encounters with other species are an important component of adaptive decision-making in dispersal, resulting…
In this paper, we introduce a general numerical method to approximate the reproduction numbers of a large class of multi-group, age-structured, population models with a finite age span. To provide complete flexibility in the definition of…
How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for…
The Cartographic Assessment of Ecological Potential (CARPO) allows users to characterize the ecological context of a group of sites at several scales (its perimeter and surrounding area) and on the basis of 4 themes: biodiversity zonings,…
We study epidemic spreading in complex networks by a multiple random walker approach. Each walker performs an independent simple Markovian random walk on a complex undirected (ergodic) random graph where we focus on Barab\'asi-Albert (BA),…
This study focuses on the modeling, mathematical analysis, developing theories, and numerical simulation of Influenza virus transmission. We have proved the existence, uniqueness, positivity, and boundedness of the solutions. Also,…
Plasmodium vivax is one of the most geographically widespread malaria parasites in the world due to its ability to remain dormant in the human liver as hypnozoites and subsequently reactivate after the initial infection (i.e. relapse…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
B-cell repertoires are characterized by a diverse set of receptors of distinct specificities generated through two processes of somatic diversification: V(D)J recombination and somatic hypermutations. B cell clonal families stem from the…
Mathematical and simulation models are often used to predict the spread of a disease and estimate the impact of public health interventions, and many such models have been developed and used during the COVID-19 pandemic. This paper…
Evolutionary game theory examines how strategies spread and persist in populations through reproduction and imitation based on their fitness. Traditionally, models assume instantaneous dynamics where fitness depends on the current…
Diagnostic testing followed by isolation of identified cases with subsequent tracing and quarantine of close contacts - often referred to as test-trace-isolate-and-quarantine (TTIQ) strategy - is one of the cornerstone measures of…