种群与进化
We present the phylogenetic quartet reconstruction method SAQ (Semi-algebraic quartet reconstruction). SAQ is consistent with the most general Markov model of nucleotide substitution and, in particular, it allows for rate heterogeneity…
Containment of epidemic outbreaks entails great societal and economic costs. Cost-effective containment strategies rely on efficiently identifying infected individuals, making the best possible use of the available testing resources.…
Macroscopic growth laws, solutions of mean field equations, describe in an effective way an underlying complex dynamics. They are applied to study the spreading of infections, as in the case of CoviD-19, where the counting of the cumulated…
Motivated with various responses of world governments to COVID-19, here we develop a toy model of the dependence epidemics spreading on the availability of tests for disease. Our model, that we call SUDR+K, is based on usual SIR model, but…
We propose a compartmental mathematical model for the spread of the COVID-19 disease, showing its usefulness with respect to the pandemic in Portugal, from the first recorded case in the country till the end of the three states of…
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…
SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 59 million infections and 1.4 million deaths in 11 months. Understanding the origin…
This technical report describes the rationale and technical details for the dynamic causal modelling of mitigated epidemiological outcomes based upon a variety of timeseries data. It details the structure of the underlying convolution or…
Recent studies have revealed effects of various tree species on soil physical and chemical properties. However, effects of various tree species on composition and activity of soil microbiota and the relevant controls remain poorly…
Consider a mathematical model of evolutionary adaptation of fitness landscape and mutation matrix as a reaction to population changes. As a basis, we use an open quasispecies model, which is modified to include explicit death flow. We…
Background. The paper concerns the SARS-CoV2 (COVID-19) pandemic that, starting from the end of February 2020, began spreading along the Italian peninsula, by first attacking small communities in north regions, and then extending to the…
We present modeling of the COVID-19 epidemic in Illinois, USA, capturing the implementation of a Stay-at-Home order and scenarios for its eventual release. We use a non-Markovian age-of-infection model that is capable of handling long and…
Whirling and swerving, a bacterium is swimming in a test tube, foraging for food. On the surface of a vibrating bath, a droplet starts walking. A certain similarity, but mostly dissimilarity, between the physical memory that emerges in…
Transients are fundamental to ecological systems with significant implications to management, conservation, and biological control. We uncover a type of transient synchronization behavior in spatial ecological networks whose local dynamics…
The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process commonly referred to as gastrulation. While substantial progress has been…
According to the current perception, symptomatic, presymptomatic, and asymptomatic infectious persons can infect the healthy population susceptible to the SARS-Cov-2. More importantly, various reports indicate that the number of…
Absent a drug or vaccine, containing epidemic outbreaks is achieved by means of social distancing, specifically mobility restrictions and lock-downs. Such measures impose a hurtful toll on the economy, and are difficult to sustain for…
Correlations between high life expectancy and low lifespan inequality are frequently observed. A recent article seeks to explain this phenomenon by proposing that a mortality improvement maps to life expectancy and relative lifespan…
In the current scenario of climate change, cold-adapted insects are among the most threatened organisms in high-altitude habitats of the Alps. Upslope shifts and changes in phenology are two of the most investigated responses to climate…
In the last months, due to the emergency of Covid-19, questions related to the fact of belonging or not to a particular class of individuals (`infected or not infected'), after being tagged as `positive' or `negative' by a test, have never…