相关论文: Nonclassical phase diagram for virus bacterial co-…
The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a…
Cross-protection, which refers to a process whereby artificially inoculating a plant with a mild strain provides protection against a more aggressive isolate of the virus, is known to be an effective tool of disease control in plants. In…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
We investigate a discrete-time two-strain symbiotic epidemic model on complex networks with both random and long-range interactions. Our analysis examines how the co-infection recovery rate ($\mu$), the long-range decay exponent ($\alpha$),…
Marine viruses shape the structure of the microbial community. They are, thus, a key determinant of the most important biogeochemical cycles in the planet. Therefore, a correct description of the ecological and evolutionary behavior of…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection that precedes structural rearrangements by…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
We investigate a model of a parasite population invading spatially distributed immobile hosts on a graph, which is a modification of the frog model. Each host has an unbreakable immunity against infection with a certain probability $1-p$…
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical…
Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food…
Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In…
We present CRISP (COVID-19 Risk Score Prediction), a probabilistic graphical model for COVID-19 infection spread through a population based on the SEIR model where we assume access to (1) mutual contacts between pairs of individuals across…
In this paper, we develop a Bayesian calendar-time survival model motivated by infectious disease prevention studies occurring during an epidemic, when the risk of infection can change rapidly as the epidemic curve shifts. For studies in…
A certain class of viruses replicates inside a cell if they can enter the nucleus through one of many small target pores, before being permanently trapped or degraded. We adopt for viral motion a switching stochastic process model and we…
Cyclic dominant systems, like rock-paper-scissors game, are frequently used to explain biodiversity in nature, where mobility, reproduction and intransitive competition are on stage to provide the coexistence of competitors. A significantly…
Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the…
The growing threat of antibiotic resistance necessitates accurate differentiation between bacterial and viral infections for proper antibiotic administration. In this study, a Virus vs. Bacteria machine learning model was developed to…
This paper explores a number of questions regarding optimal strategies evolved by viruses upon entry into a vertebrate host. The infected cell life cycle consists of a non-productively infected stage in which it is producing virions but not…