Related papers: A new integrated symmetrical table for genetic cod…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
In this paper, we study convolutional codes with a specific cyclic structure. By definition, these codes are left ideals in a certain skew polynomial ring. Using that the skew polynomial ring is isomorphic to a matrix ring we can describe…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
In our paper selected linguistic features of genomes to study the statistics of the gene codes are considered. We present the information theory from which it follows that if the system is described by distributions of hyperbolic type it…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
A key question in biological systems is whether genetic diversity persists in the long run under evolutionary competition or whether a single dominant genotype emerges. Classic work by Kalmus in 1945 has established that even in simple…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
The multidimensional convolutional codes are an extension of the notion of convolutional codes (CCs) to several dimensions of time. This paper explores the class of two-dimensional convolutional codes (2D CCs) and 2D tail-biting…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
We study standard monomial bases for Richardson varieties inside the flag variety. In general, writing down a standard monomial basis for a Richardson variety can be challenging, as it involves computing so-called defining chains or key…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…
The Kronecker family of the genetic matrices is investigated, which is based on the genetic matrix [C T; A G], where C, T, A, G are the letters of the genetic alphabet. The matrix [C T; A G] in the second Kronecker power is the (4*4)-matrix…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
A single-source network is said to be \textit{memory-free} if all of the internal nodes (those except the source and the sinks) do not employ memory but merely send linear combinations of the incoming symbols (received at their incoming…
Requiring stability of genetic code against translation errors, modelised by suitable mathematical operators in the crystal basis model of the genetic code, the main features of the organisation in multiplets of the mitochondrial and of the…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…