Related papers: Nucleotide Distribution Patterns in Insect Genomes
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Insects as pollinators play a crucial role in ecosystem management and world food production. However, insect populations are declining, calling for efficient methods of insect monitoring. Existing methods analyze video or time-lapse images…
In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is…
No systematic method exists to derive intra-chromosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical…
We study the geometry of a random unicellular map which is uniformly distributed on the set of all unicellular maps whose genus size is proportional to the number of edges of the map. We prove that the distance between two uniformly…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
We investigate 738 complete genomes of viruses to detect the presence of short inverted repeats. The number of inverted repeats found is compared with the prediction obtained for a Bernoullian and for a Markovian control model. We find as a…
The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
Among all animals, mosquitoes are responsible for the most deaths worldwide. Interestingly, not all types of mosquitoes spread diseases, but rather, a select few alone are competent enough to do so. In the case of any disease outbreak, an…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Whole exome sequencing was performed on HLA-matched stem cell donors and transplant recipients to measure sequence variation contributing to minor histocompatibility antigen differences between the two. A large number of nonsynonymous…
In a short article submitted to ArXiv [1], Maddamsetti et al. argue that the variation in the neutral mutation rate among genes in Escherichia coli that we recently reported [2] might be explained by horizontal gene transfer (HGT). To…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
Many common diseases have a complex genetic basis in which large numbers of genetic variations combine with environmental and lifestyle factors to determine risk. However, quantifying such polygenic effects and their relationship to disease…
Cluster size distributions were investigated in case of different nozzle geometries in argon and xenon using Rayleigh scattering diagnostics. Different nozzle geometries result in different behaviour, therefore both spatial- and temporal…
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 mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…