种群与进化
Infectious diseases continue to pose significant public health challenges worldwide, requiring effective prevention and control strategies to mitigate their negative impact. Infectious diseases can be broadly classified into two groups:…
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach…
Oncolytic virotherapy, utilizing genetically modified viruses to combat cancer and trigger anti-cancer immune responses, has garnered significant attention in recent years. In our previous work arXiv:2305.12386, we developed a stochastic…
The expected meeting time of two random walkers on an undirected graph of size $N$, where at each time step one walker moves and the process stops when they collide, satisfies a system of $\binom{N}{2}$ linear equations. Na\"{i}vely,…
Antibiotic resistance is a major threat to global health. It emerges in multispecies microbial communities under antibiotic exposure. This makes antibiotic spectrum -- a drug's distribution of effects across species -- a potential key…
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…
Fitness landscapes are mappings between genotypes, phenotypes, and fitness that shape evolution. In recent years, empirical work and theoretical models have greatly advanced our understanding of how populations navigate rugged fitness…
Tree-grass coexistence is a defining feature of savanna ecosystems, which play an important role in supporting biodiversity and human populations worldwide. While recent advances have clarified many of the underlying processes, how these…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…
(Im)balance indices can be used to quantify the (im)balance of trees by assigning numerical scores to them. An easy way to generate a new index is to construct a compound index, e.g., a linear combination of established indices. Two of the…
The spread of infectious disease is strongly influenced by social dynamics. In addition to infection risk, individuals vaccination decisions depend on prevailing social behavior: high infection levels and widespread vaccination can increase…
Scientists have long been fascinated by magnetoreception, the innate capacity of many animals to sense and use the Earth's magnetic field for navigation. In eusocial insects like honey bees, magnetoreception has been linked to communication…
Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
We study the random times between successive cases in a transmission chain of infectious diseases with asymptomatic carriers. We derive the probability distribution of this generation time (in days) from a discrete-time epidemic model with…
Ecological interactions can dramatically alter evolutionary outcomes in complex communities. Yet, the framework of population genetics largely neglects interactions from a species-rich community. Here, we bridge this gap by using dynamical…
Cancer cell populations often exhibit remarkably similar growth laws despite their heterogeneity. Explanations of universal cell population growth remain partly unresolved to this day. Here, we present a growth-law unification by…
We investigate the role of migration patterns on the spread of epidemics in complex networks. We enhance the SIS-diffusion model on metapopulations to a nonlinear diffusion. Specifically, individuals move randomly over the network but at a…
Cooperation is central to the organization of complex biological and social systems. Most theoretical models assume homogeneous environments; in reality, populations inhabit spatially varying landscapes in which the payoffs of cooperation…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…