种群与进化
The concept of individual admixture (IA) assumes that the genome of individuals is composed of alleles inherited from $K$ ancestral populations. Each copy of each allele has the same chance $q_k$ to originate from population $k$, and…
The reduction of the computational effort is desirable for the simulation of marine ecosystem models. Using a marine ecosystem model, the assessment and the validation of annual periodic solutions (i.e., steady annual cycles) against…
We analyzed the first 255 PCR-confirmed cases of monkeypox occurred in Italy in 2022. Preliminary estimates indicate: mean incubation period of 9.1 days (95%CI of the mean: 6.5-10.9); mean generation time of 12.5 days (95%CI of the mean:…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
COVID-19 pandemic is one of the major disasters that humanity has ever faced. In this paper, we try to model the effect of vaccination in controlling the pandemic, particularly in context to the third wave which is predicted to hit…
In this paper, we investigate the existence of stability-changing bifurcations in epidemiological models used to study the spread of zombiism through a human population. These bifurcations show that although linear instability of…
Plasmodium (P.) falciparum and P. vivax are the two most common causes of malaria. While the majority of deaths and severe morbidity are due to P. falciparum, P. vivax poses a greater challenge to eliminating malaria outside of Africa due…
Certain defense mechanisms of phages against the immune system of their bacterial host rely on cooperation of phages. Motivated by this example we analyse invasion probabilities of cooperative parasites in host populations that are…
The identification of the transmission parameters of a virus is fundamental to identify the optimal public health strategy. These parameters can present significant changes over time caused by genetic mutations or viral recombination,…
The surprisingly mercurial Covid-19 pandemic has highlighted the need to not only accelerate research on infectious disease, but to also study them using novel techniques and perspectives. A major contributor to the difficulty of containing…
Cooperation among individuals has been key to sustaining societies. However, natural selection favors defection over cooperation. Cooperation can be favored when the mobility of individuals allows cooperators to form a cluster (or group).…
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, as well as antigenic changes that reduce the cross-immunity…
The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…
Testing for infection with SARS-CoV-2 is an important intervention in reducing onwards transmission of COVID-19, particularly when combined with the isolation and contact-tracing of positive cases. Many countries with the capacity to do so…
We propose to use the mean time between infections (MTBI) metric as obtained from a recently introduced non-homogeneous Markov stochastic model. Different types of parameter calibration are performed. We estimate the MTBI using data from…
The origin of life is shrouded in mystery, with few surviving clues, obscured by evolutionary competition. Previous reviews have touched on the complementary approaches of top-down and bottom-up synthetic biology to augment our…
A hypercycle equation with infinitely many types of macromolecules is formulated and studied both analytically and numerically. The resulting model is given by an integro-differential equation of the mixed type. Sufficient conditions for…
The prevention of biodiversity loss in agricultural landscapes to protect ecosystem stability and functions is of major importance in itself and for the maintenance of associated ecosystem services. Intense agriculture leads to a loss in…
This work provides an overview on deterministic and stochastic models that have previously been proposed by us to study the transmission dynamics of the Coronavirus Disease 2019 (COVID-19) in Europe and USA. Briefly, we describe realistic…