Published in Journal of theoretical biology
We introduce an alignment-free method, the Magnus Representation, to analyze genome sequences. The Magnus Representation captures higher-order information in genome sequences. We combine our approach with the idea of k-mers to define an effectively computable Mean Magnus Vector. We perform phylogenetic analysis on three datasets: mosquito-borne vir...
Published in Journal of theoretical biology
Essential proteins have vital functions, when they are destroyed in cells, the cells will die or stop reproducing. Therefore, it is very important to identify essential proteins from a large number of other proteins. Due to the time-consuming, expensive, and inefficient process in biological experimental methods, computational methods become more a...
Published in Journal of theoretical biology
The main purpose of this paper is to analyze a new dynamical model pertaining to bovine Babesiosis transmission, and investigate its consequent morphology. We present and study various ramifications of our mathematical model for bovine Babesiosis spread, given, firstly, by a temporal system of ordinary differential equations and, finally, by a spat...
Published in Journal of theoretical biology
This paper describes the behavior of binding and functional receptor systems where an antagonist of the receptor/G protein binding reaction is added as a blocker of agonist-induced receptor function. For agonist radioligands, the reduction of G protein receptor interaction leads to a possible change in the binding affinity of the agonist radioligan...
Published in Journal of theoretical biology
The existence of cooperation is problematic for those who view the world through an evolutionary lens. Although natural selection disfavors unconditional cooperation, cooperators who can distinguish cooperators from defectors and discontinue their interactions with the latter can be favored. Economic experiments have indicated that human beings ind...
Published in Journal of theoretical biology
Many bacterial species produce toxins that inhibit their competitors. We model this phenomenon by extending classic two-species Lotka-Volterra competition in one spatial dimension to incorporate toxin production by one species. Considering solutions comprising two adjacent single-species colonies, we show how the toxin inhibits the susceptible spec...
Published in Journal of theoretical biology
In nature, cooperation among individuals is often accompanied by competition among the same individuals for the cooperatively produced rewards. In such a situation, the evolution of cooperative and competitive investments influences each other, but previous theoretical studies mostly focused on either cooperation or competition. Here we consider a ...
Published in Journal of theoretical biology
Several mechanisms have been proposed to explain the spontaneous generation of self-organised patterns, hypothesised to play a role in the formation of many of the magnificent patterns observed in Nature. In several cases of interest, the system under scrutiny displays a homogeneous equilibrium, which is destabilised via a symmetry breaking instabi...
Published in Journal of theoretical biology
A range of gene drive systems have been proposed that are predicted to increase their frequency and that of associated desirable genetic material even if they confer a fitness cost on individuals carrying them. Engineered underdominance (UD) is such a system and, in one version, is based on the introduction of two independently segregating transgen...
Published in Journal of theoretical biology
We investigate the evolution of timidity in a prey species whose predator has cannibalistic tendencies. The ecological model is derived from individual-level processes, in which the prey seeks refuge after detecting a predator, and the predator cannibalises on the conspecific juveniles. Bifurcation analysis of the model reveals ecological bistabili...
