Related papers: Statistics of genome architecture
The margins within the geographic range of species are often specific in terms of ecological and evolutionary processes, and can strongly influence the species' reaction to climate change. One of the frequently observed features at range…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abundance on various phenomena, such as the size and repeat…
The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modelling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth…
A brief review of the search for variation of the fine structure constant in quasar absorption spectra is presented. Special consideration is given to the role of atomic calculations in the analysis of the observed data. A range of methods…
Observation of phenotypic diversity in a population of genetically identical cells is often linked to the stochastic nature of chemical reactions involved in gene regulatory networks. We investigate the distribution of population averaged…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
The format of graphing algorithms for genomic data has been a debate in recent biotechnology. In this paper, we discuss the construction of population graphs using said genomic data. We first examine the GENPOFAD distance measurement,…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
This paper develops a theory for characterisation of DNA sequences based on their measure representation. The measures are shown to be random cascades generated by an infinitely divisible distribution. This probability distribution is…
Good statistics for measuring large-scale structure in the Universe must be able to distinguish between different models of structure formation. In this paper, two and three dimensional ``counts in cell" statistics and a new ``discrete…
Large-scale white matter pathways crisscrossing the cortex create a complex pattern of connectivity that underlies human cognitive function. Generative mechanisms for this architecture have been difficult to identify in part because little…
This study elaborates some examples of a simple evolutionary stochastic rate process where the population rate of change depends on the distribution of properties--so different cohorts change at different rates. We investigate the effect on…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
We consider the challenging problem of statistical inference for exponential-family random graph models based on a single observation of a random graph with complex dependence. To facilitate statistical inference, we consider random graphs…
The diffusion and coalescence of individual atoms on a nanostructured surface are treated in a purely statistical way. From this, analytical formulas are derived which, from a known initial state, give the final cluster size distribution on…