种群与进化
The COVID-19 epidemics, started in China in January 2020, was recognized to have reached Italy around February 20; recent estimates show that most probably the virus circulated in the country already in January, but was not recognized. Data…
Adoptive Cell Transfer therapy of cancer is currently in full development and mathematical modeling is playing a critical role in this area. We study a stochastic model developed by Baar et al. in 2015 for modeling immunotherapy against…
Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depend on the context and…
The set of T cells that express the same T cell receptor (TCR) sequence represents a T cell clone. The number of different naive T cell clones in an organism reflects the number of different T cell receptors (TCRs) arising from…
In agricultural landscapes, the composition and spatial configuration of cultivated and semi-natural elements strongly impact species dynamics, their interactions and habitat connectivity. To allow for landscape structural analysis and…
Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these…
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly…
Mathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for realism in addressing complex public health questions is…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
A reparametrized Dirichlet-multinomial distribution is introduced, and the covariance matrix, as well as, the algorithm for calculating the PDF for n species are provided. The distribution is suited for modelling the joint distribution of…
Objectives.--To estimate the basic reproduction number of the Wuhan novel coronavirus (2019-nCoV). Methods.--Based on the susceptible-exposed-infected-removed (SEIR) compartment model and the assumption that the infectious cases with…
Honest signals and cues have been observed as part of interspecific and intraspecific communication among animals. Recent theories suggest that existing signaling systems have evolved through natural selection imposed by predators. Honest…
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the…
Many vector-borne disease epidemic models neglect the fact that in modern human civilization, social awareness as well as self-defence system are overwhelming against advanced propagation of the disease. News are becoming more effortlessly…
We model the COVID-19 coronavirus epidemic in China. We use early reported case data to predict the cumulative number of reported cases to a final size. The key features of our model are the timing of implementation of major public policies…
The margins within the geographic range of species are often specific in terms of ecological and evolutionary processes, and can strongly influence the species' reaction to climate change. One of the frequently observed features at range…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Rock-paper-scissors games metaphorically model cyclic dominance in ecology and microbiology. In a static environment, these models are characterized by fixation probabilities obeying two different "laws" in large and small well-mixed…
Highly Pathogenic Avian Influenza A H5N6 is a mutated virus of Influenza A H5N1 and a new emerging infection that recently caused an outbreak in the Philippines. The 2017 H5N6 outbreak resulted in a depopulation of 667,184 domestic birds.…
The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient…