种群与进化
Broad mobility restrictions can help control infectious disease spread, but their socioeconomic costs and the variation in transmission risks by mobility purpose, age group, and spatial connectivity highlight the need for targeted…
Mathematical models of biological populations commonly use discrete structure classes to capture trait variation among individuals (e.g. age, size, phenotype, intracellular state). Upscaling these discrete models into continuum descriptions…
West Nile virus (WNV) is a mosquito-borne virus in the genus Flavivirus that circulates between mosquitoes and birds, whereas humans, equids, and other mammals are dead-end hosts. Since its emergence in Germany in 2018, the virus has spread…
West Nile virus (WNV) is a climate-sensitive mosquito-borne arbovirus circulating between mosquitoes of the genus Culex and birds, with a potential spillover to humans and other mammals. Recent trends in climatic change, characterized by…
Complex systems, such as life and languages, are governed by principles of evolution. The analogy and comparison between biology and linguistics\cite{alphafold2, RoseTTAFold, lang_virus, cell language, faculty1, language of gene, Protein…
We develop a generally covariant description of evolutionary dynamics that operates consistently in both genotype and phenotype spaces. We show that the maximum entropy principle yields a fundamental identification between the inverse…
Microbial communities harbor extensive fine-scale diversity: closely-related strains of the same species coexist alongside many distantly-related taxa. Yet strain coexistence remains poorly understood, largely because most studies neglect…
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) and Acinetobacter baumannii (CRAB) represent a major clinical and epidemiological challenge and pose a growing threat to public health and the environment. Accordingly, CRPA and CRAB were…
We show how biological grouping-particularly species formation-can emerge from interactions among populations governed by number-theoretic structure. In our framework, a species is identified with a $p$-Sylow subgroup of a community…
Wildlife-vehicle collisions (WVC) threaten both biodiversity and human safety worldwide. Despite empirical efforts to characterize the major determinants of WVC risk and optimize mitigation strategies, we still lack a theoretical framework…
Evolutionary accumulation models (EvAMs) are an emerging class of machine learning methods designed to infer the evolutionary pathways by which features are acquired. Applications include cancer evolution (accumulation of mutations),…
How do competing populations convert a spatial advantage into macroscopic dominance? We introduce a stochastic model for resource competition that decouples the transient discovery phase from monopolization. Initial symmetry breaking is…
Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…
Due to its ability to summarise 'real-time' epidemic behaviour, the time-dependent reproduction number, Rt, is a useful metric for tracking pathogen transmission and quantifying the effects of interventions during infectious disease…
Since early 2024, highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.3.4.4b has spilled over from wild birds to dairy cattle in the United States (U.S.), spreading to more than 1000 herds and threatening both animal and public…
Classical reaction-diffusion models of the 14th-century Black Death fail to explain the rapid genetic radiation of \textit{Yersinia pestis} and the anomalous emergence of vast, untouched geographic safe zones, such as Central Europe. In…
Frogeye Leaf Spot (FLS), caused by Cercospora sojina, poses a significant threat to soybean production, with yield losses of 30-60%. Traditional mass-action models assume homogeneous mixing, which rarely holds in real fields and limits…
This study simulated the introduction of Foot-and-mouth disease (FMD) into Mato Grosso do Sul, Brazil, to evaluate the effectiveness of outbreak control strategies. Our susceptible-exposed-infected-recovered model generated a range of…
We study a multitype SIR epidemic model where individuals are categorized into different types, and where infection spread is characterized by a next-generation matrix $M=\{m_{ij}\}$ with community fractions $\{\pi_j\}$ for the different…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…