相关论文: Using sequencing coverage statistics to identify s…

Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…

Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…

Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…

The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…

Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…

The detection of echolocation clicks is key in understanding the intricate behaviors of cetaceans and monitoring their populations. Cetacean species relying on clicks for navigation, foraging and even communications are sperm whales…

Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…

Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…

Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…

Genomic data can be used to reconstruct population size over thousands of generations, using a new class of algorithms (SMC methods). These analyses often show a recent decline in $N_e$ (effective size), which at face value implies a…

Background: We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce…

Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…

We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…

For data represented by networks, the community structure of the underlying graph is of great interest. A classical clustering problem is to uncover the overall ``best'' partition of nodes in communities. Here, a more elaborate description…

The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…

Since the arrival of next-generation sequencing technologies the amount of genetic sequencing data has increased dramatically. This has has fueled an increase in human genetics research. At the same time, with the recent advent of…

Spatially resolved genetic data is increasingly used to reconstruct the migrational history of species. To assist such inference, we study, by means of simulations and analytical methods, the dynamics of neutral gene frequencies in a…

Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species: (i) the number…