种群与进化
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
Black Sigatoka disease (BSD), also known as black leaf streak disease, is an airborne fungal infection caused by \textit{Pseudocercospora fijiensis} that severely impacts global banana and plantain production. Its persistence and resistance…
Mosquito vector competence is usually represented as a process in which once virus is detected in saliva, mosquitoes are assumed to remain infectious for life, implying an irreversible transition to the transmitting state. However, some…
Transfer RNAs (tRNAs) are essential components of the translational machinery. Their abundance and diversity shape decoding capacity and protein synthesis efficiency and accuracy. Because tRNA abundance is encoded in the genome through tDNA…
Gene drive alleles bias their own inheritance to offspring. They can fix in a wild-type population in spite of a fitness cost, and even lead to the eradication of the target population if the fitness cost is high. However, this outcome may…
Dengue virus transmission models commonly assume an exponential distribution for the mosquito extrinsic incubation period (EIP), potentially oversimplifying biological variability. We developed a stochastic mechanistic dengue transmission…
Tuberculosis (TB) is an airborne disease caused by the pathogen Mycobacterium tuberculosis. In 2023, according to the World Health Organization, it ''probably'' replaced COVID-19 as the leading cause of death from an infectious agent…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Compartmental epidemic models, grounded in mass-action kinetics, often assume homogeneous mixing. Although this neglects network structure, recent results show that for Poisson random graphs, the classical SIR model, especially the…
Different strains competing for a common pool of susceptible individuals is a key problem in mathematical epidemiology. To address this problem, we investigate a two-strain model within a Susceptible-Infected-Recovered (SIR) framework.…
Dengue remains a major global public health concern due to its high mortality and economic burden. Mathematical modeling is essential to understand its transmission mechanisms and for evaluating intervention strategies. In this paper, we…
We study the dominant eigenstructure of positive-kernel Fredholm operators arising in multi-state structured population models, including integral projection models and age-structured McKendrick-type equations. To obtain a determinant-free…
In temperate regions, respiratory virus epidemics recur on a yearly basis, primarily during the winter season. This is believed to be induced by seasonal forcing, where the rate at which the virus can be transmitted varies cyclically across…
Anti-viral therapies are typically designed to target only the current strains of a virus, a myopic response. However, therapy-induced selective pressures drive the emergence of new viral strains, against which the original myopic therapies…
In epistatic fitness landscapes, the fitness effect of a mutation depends on the genetic background and may even switch between deleterious and beneficial depending on the presence of another mutation. Epistatic interactions may cause both…
Due to climatic changes, excessive grazing, and deforestation, semi-arid and arid ecosystems are vulnerable to desertification and land degradation. As aridity increases, vegetation cover often self-organizes into spatial patterns before…
A much-cited 2022 paper by Pekar et al. claimed that Bayesian analysis of the molecular phylogeny of early SARS-CoV-2 cases indicated that it was more likely that two successful introductions to humans had occurred than that just one had.…
Mutational signatures describe the pattern of mutations over the different mutation types. Each mutation type is determined by a base substitution and the flanking nucleotides to the left and right of that base substitution. Due to the…
Recognizing individual animals over time is central to many ecological and conservation questions, including estimating abundance, survival, movement, and social structure. Recent advances in automated identification from images and even…
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new functions (i.e. emergence). Here, we…