Related papers: An algebraic view of bacterial genome evolution
The study of common heritability, or co-heritability, among multiple traits has been widely established in quantitative and molecular genetics. However, in bacteria, genome-based estimation of heritability has only been considered very…
We introduce a new Baxterisation for R-matrices that depend separately on two spectral parameters. The Baxterisation is based on a new algebra, close to but different from the braid group. This allows us to recover the R-matrix of the…
We aim at studying collections of algebraic structures defined over a commutative ring and investigating the complexity of significant constructions carried out on these objects. The assignment of measures of size, via a multiplicity…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
We study evolution algebras of arbitrary dimension. We analyze in deep the notions of evolution subalgebras, ideals and non-degeneracy and describe the ideals generated by one element and characterize the simple evolution algebras. We also…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
In the last quarter of a century, algebraic statistics has established itself as an expanding field which uses multilinear algebra, commutative algebra, computational algebra, geometry, and combinatorics to tackle problems in mathematical…
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…
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…
Evolution algebras are non-associative algebras inspired from biological phenomena, with applications to or connections with different mathematical fields. There are two natural ways to define an evolution algebra associated to a given…
Motivation: Gene blocks are genes co-located on the chromosome. In many cases, genes blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain,…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
Language theory, symbolic dynamics, modelisation of viral insertion into the genetic code of a host cell motivate the introduction of new types of bialgebras whose coalgebra parts are not necessarily coassociative. One of the aim of this…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…
The remarkable range of biological forms in and around us, such as the undulating shape of a leaf or flower in the garden, the coils in our gut, or the folds in our brain, raise a number of questions at the interface of biology, physics and…