种群与进化
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with…
This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on…
Comparative studies of cancer-related genes allow us to gain novel information about the evolution and function of these genes, but also to understand cancer as a driving force in biological systems and species life histories. So far,…
The state of the art of epidemic modelling in terrestrial ecosystems is the compartmental SIR model and its extensions from the now classical work of Kermack-Mackendrick. In contrast, epidemic modelling of marine ecosystems is a bit behind,…
Computational models of infectious disease can be broadly categorized into two types: individual-based (Agent-based), or compartmental models. While compartmental models can be structured to separate distinct sectors of a population, they…
The basic reproduction number, $R_0$ is an important and widely used concept in the study of infectious diseases. We briefly review the recent trend of calculating the average of various $R_0$ estimates in systematic reviews aimed at…
The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for…
In this article, we propose a theory to explain the reduction in vaccine effectiveness (VE) against the Delta SARS-CoV-2 variant and decreasing VE over time reported in recent studies. Using a model illustration, we show that in-host viral…
We present artificial neural networks as a feasible replacement for a mechanistic model of mosquito abundance. We develop a feed-forward neural network, a long short-term memory recurrent neural network, and a gated recurrent unit network.…
Bacteria are ubiquitous in our daily lives, either as motile planktonic cells or as immobilized surface-attached biofilms. These different phenotypic states play key roles in agriculture, environment, industry, and medicine; hence, it is…
We consider the $SEIRS$ epidemiology model with such features of the COVID-19 outbreak as: abundance of unidentified infected individuals, limited time of immunity and a possibility of vaccination. Within a compartmental realization of this…
This article explores mathematical models for understanding the evolution of contagious diseases. The most widely known set of models are the compartmental ones, which are based on a set of differential equations. But these are not the only…
In contrast to the common assumption in epidemic models that the rate of infection between individuals is constant, in reality, an individual's viral load determines their infectiousness. We compare the average and individual reproductive…
The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…
We introduce a system of differential equations to assess the impact of (self-)quarantine of symptomatic infectious individuals on disease dynamics. To this end we depart from using the classic bilinear infection process, but remain still…
Broadly neutralizing antibodies (bNAbs) are promising targets for vaccination and therapy against HIV. Passive infusions of bNAbs have shown promise in clinical trials as a potential alternative for anti-retroviral therapy. A key challenge…
Marine ecosystem models are an important tool to assess the role of the ocean biota in climate change and to identify relevant biogeochemical processes by validating the model outputs against observational data. For the assessment of the…
This study focuses on open quasispecies systems with competition and death flow, described by modified Eigen and Crow-Kimura models. We examine the evolutionary adaptation process as a reaction to changes in rates. One of the fundamental…
A dynamical epidemic model optimized using genetic algorithm and cross validation method to overcome the overfitting problem is proposed. The cross validation procedure is applied so that available data are split into a training subset used…
We introduce a population-age-time (PAT) model which describes the temporal evolution of the population distribution in age. The surprising result is that the qualitative nature of the population distribution dynamics is robust with respect…