Related papers: Comparative genomics study of inverted repeats in …
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…
Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
We explore the probabilistic structure of DNA in a number of bacterial genomes and conclude that a form of Markovianness is present at the boundaries between coding and non-coding regions, that is, the sequence of START and STOP codons…
We consider the enumeration of pattern-avoiding involutions, focusing in particular on sets defined by avoiding a single pattern of length 4. As we demonstrate, the numerical data for these problems demonstrates some surprising behavior.…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
Radical shifts in the genetic composition of large cell populations are rare events with quite low probabilities, which direct numerical simulations generally fail to evaluate accurately. In this paper, we develop a theoretical large…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
Bacteria commonly inhabit porous environments such as host tissues, soil, and marine sediments, where complex geometries constrain and redirect their motion. Although bacterial motility has been studied in porous media, the roles of cell…
The present paper is devoted to the study of the combinatorics of 216 maximal $C^3$ circular codes --- a particular type of structure arising in the analysis of genomic sequences. Their circularity property is believed to be intimately…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual…
Various rod-shaped bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant,…
Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA…
CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against foreign genetic elements. Genetic templates acquired during past infection events enable DNA-interacting enzymes to recognize foreign DNA for destruction. Due to…