相关论文: Eight-cluster structure of chloroplast genomes dif…

We studied the structuredness in a chloroplast genome of Siberian larch. The clusters in 63-dimensional space were identified with elastic map technique, where the objects to be clusterized are the different fragments of the genome. A…

Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…

In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…

The aim of this study is to investigate the relation that can be found between the phylogeny of a large set of complete chloroplast genomes, and the evolution of gene content inside these sequences. Core and pan genomes have been computed…

The structure of nanoclusters is complex to describe due to their noncrystallinity, even though bonding and packing constraints limit the local atomic arrangements to only a few types. A computational scheme is presented to extract…

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…

Clusters of galaxies are often embedded in larger-scale superclusters with dimensions of tens or perhaps even hundreds of Mpc. Observational and theoretical evidence suggest an important connection between cluster properties and their…

Chloroplasts regulate their growth to optimize photosynthesis. Quantitative data shows that the ratio of total chloroplast area to mesophyll cell area is constant across different cells within a single species, and also across species.…

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…

The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…

In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a…

This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…

The study of the internal structure of star clusters provides important clues concerning their formation mechanism and dynamical evolution. There are both observational and numerical evidences indicating that open clusters evolve from an…

We use two high resolution CDM simulations to show that (i) when clusters of galaxies form the infall pattern of matter is not random but shows clear features which are correlated in time; (ii) in addition, the infall patterns are…

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…

It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…

An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…

Clustering is typically measured by the ratio of triangles to all triples, open or closed. Generating clustered networks, and how clustering affects dynamics on networks, is reasonably well understood for certain classes of networks…