Related papers: Maximum principle and mutation thresholds for four…
In an evolutionary system in which the rules of mutation are local in nature, the number of possible outcomes after $m$ mutations is an exponential function of $m$ but with a rate that depends only on the set of rules and not the size of…
The transition from a normal to cancerous cell requires a number of highly specific mutations that affect cell cycle regulation, apoptosis, differentiation, and many other cell functions. One hallmark of cancerous genomes is genomic…
A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the…
Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to converge to the true value in the independent-sample case, we…
Among the wide variety of evolutionary computing models, Finite State Machines (FSMs) have several attractions for fundamental research. They are easy to understand in concept and can be visualised clearly in simple cases. They have a ready…
The evolution model with parallel mutation-selection scheme is solved for the case when selection is accompanied by base substitutions, insertions, and deletions. The fitness is assumed to be either a single-peak function (i.e., having one…
We explore how the asymptotic structure of a random permutation of $[n]$ with $m$ inversions evolves, as $m$ increases, establishing thresholds for the appearance and disappearance of any classical, consecutive or vincular pattern. The…
A bit-string model for the evolution of a population of haploid organisms, subject to competition, reproduction with mutation and selection is studied, using mean field theory and Monte Carlo simulations. We show that, depending on…
We present a mechanistic formalism for the study of evolutionary dynamics models based on the diffusion approximation described by the Kimura Equation. In this formalism, the central component is the fitness potential, from which we obtain…
When genetic algorithms are used to evolve decision trees, key tree quality parameters can be recursively computed and re-used across generations of partially similar decision trees. Simply storing instance indices at leaves is enough for…
In Tri-clustering, a sub-matrix is being created, which exhibit highly similar behavior with respect to genes, conditions and time-points. In this technique, genes with same expression values are discovered across some fragment of time…
In this Letter, we extend the semiconservative quasispecies equations to incorporate imperfect DNA lesion repair. We study the equilibrium behavior of this model in the limit of infinite sequence length and population size, using a…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
We consider a population evolving due to mutation, selection and recombination, where selection includes single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). We further consider the problem of inferring…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
A general stochastic maximum principle is proved for optimal controls of semilinear stochastic evolution equations. Stochastic evolution operators, and the control with values in a general set enter into both drift and diffusion terms.
The configuration model is a cornerstone of statistical assessment of network structure. While the Chung-Lu model is among the most widely used configuration models, it systematically oversamples edges between large-degree nodes, leading to…
We consider a model of a population of fixed size $N$ undergoing selection. Each individual acquires beneficial mutations at rate $\mu_N$, and each beneficial mutation increases the individual's fitness by $s_N$. Each individual dies at…
Moments are expectation values of products of powers of position and momentum, taken over quantum states (or averages over a set of classical particles). For free particles, the evolution in the quantum case is closely related to that of a…