Related papers: Error-prone polymerase activity causes multinucleo…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
Cancer cells evolve through random somatic mutations. "Beneficial" mutations which disrupt key pathways (e.g. cell cycle regulation) are subject to natural selection. Multiple mutations may lead to the same "beneficial" effect, in which…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Modelling gene-gene epistatic interactions when computing genetic risk scores is not a well-explored subfield of genetics and could have potential to improve risk stratification in practice. Though applications of machine learning (ML) show…
In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection,…
We study the following model for a diploid population of constant size $N$: Every individual carries a random number of (genetic) elements. Upon a reproduction event each of the two parents passes each element independently with probability…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
An important parameter in the study of population evolution is $\theta=4N\nu$, where $N$ is the effective population size and $\nu$ is the rate of mutation per locus per generation. Therefore, $\theta$ represents the mean number of…
Polygenic risk scores (PRS) estimate the genetic risk of an individual for a complex disease based on many genetic variants across the whole genome. In this study, we compared a series of computational models for estimation of breast cancer…
In this paper, a new mixture family of multivariate normal distributions, formed by mixing multivariate normal distribution and skewed distribution, is constructed. Some properties of this family, such as characteristic function, moment…
Clustering of gene expression time series gives insight into which genes may be coregulated, allowing us to discern the activity of pathways in a given microarray experiment. Of particular interest is how a given group of genes varies with…
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…
It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are…
I study a population model in which the reproduction rate lambda is inherited with mutation, favoring fast reproducers in the short term, but conflicting with a process that eliminates agglomerations of individuals. The model is a variant…
The subpopulationtion shift, characterized by a disparity in subpopulation distributibetween theween the training and target datasets, can significantly degrade the performance of machine learning models. Current solutions to subpopulation…
In this paper, we investigate a stochastic model describing the time evolution of a polymerization process. A polymer is a macro-molecule resulting from the aggregation of several elementary sub-units called monomers. Polymers can grow by…
Maintenance of sexual reproduction and genetic recombination imposes physiological costs when compared to parthenogenic reproduction, most prominently: for maintaining the corresponding (molecular) machinery, for finding a mating partner,…
The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for…