Related papers: Global divergence of microbial genome sequences me…
The ~4-Mbp basic genome shared by 32 independent isolates of E. coli representing considerable population diversity has been approximated by whole-genome multiple-alignment and computational filtering designed to remove mobile elements and…
We simulate a two dimensional model of self-propelled particles confined by a deformable boundary. The particles tend to accumulate near the boundary and the shape of the boundary deforms upon the collisions. We find that there are two…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
Models that invoke nonlinear wavefront propagation in a chemically excitable medium are rife in the biological literature. Indeed, the idea that wavefront propagation can serve as a signaling mechanism has often been invoked to explain…
We consider multiple diseases spreading in a static Configuration Model network. We make standard assumptions that infection transmits from neighbor to neighbor at a disease-specific rate and infected individuals recover at a…
Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…
We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for correlation across variants,…
A partial differential equation governing the global evolution of the joint probability distribution of an arbitrary number of local flow observations, drawn randomly from a control volume, is derived and applied to examples involving…
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…
Properties of reaction zones resulting from A+B -> C type reaction-diffusion processes are investigated by analytical and numerical methods. The reagents A and B are separated initially and, in addition, there is an initial macroscopic…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
We present a generic mechanism by which reproducing microorganisms, with a diffusivity that depends on the local population density, can form stable patterns. It is known that a decrease of swimming speed with density can promote separation…
This work describes a novel image analysis approach to characterize the uniformity of objects in agglomerates by using the propagation of normal wavefronts. The problem of width uniformity is discussed and its importance for the…
The ecological invasion problem in which a weaker exotic species invades an ecosystem inhabited by two strongly competing native species is modelled by a three-species competition-diffusion system. It is known that for a certain range of…
Genetic drift at the frontiers of two-dimensional range expansions of microorganisms can frustrate local cooperation between different genetic variants, demixing the population into distinct sectors. In a biological context, mutualistic or…
This paper is devoted to the study of the persistence versus extinction of species in the reaction-diffusion equation: \begin{equation} u_t-\Delta u=f(t,x_1-ct,y,u) \quad\quad t>0,\ x\in\Omega,\nonumber \end{equation} where $\Omega$ is of…
Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…
Motivated by experiments on cell segregation, we present a two-species model of interacting particles, aiming at a quantitative description of this phenomenon. Under precise scaling hypothesis, we derive from the microscopic model a…
Directed Percolation (DP) is a classic model for nonequilibrium phase transitions into a single absorbing state (fixation). It has been extensively studied by analytical and numerical techniques in diverse contexts. Recently, DP has…