Related papers: An algebraic view of bacterial genome evolution
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary history. Our contribution is to show, in a very general…
Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
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…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
This dissertation presents a multifaceted look into the structural decomposition of permutation classes. The theory of permutation patterns is a rich and varied field, and is a prime example of how an accessible and intuitive definition…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
We consider an evolution algebra which corresponds to a bisexual population with a set of females partitioned into finitely many different types and the males having only one type. We study basic properties of the algebra. This algebra is…
An algebraic deformation theory of module-algebras over a bialgebra is constructed. The cases of module-coalgebras, comodule-algebras, and comodule-coalgebras are also considered.
The mitosis process of an eukaryotic cell can be represented by the structure constants of an evolution algebra. Any isotopism of the latter corresponds to a mutation of genotypes of the former. This paper uses Computational Algebraic…
We consider evolution algebras and their related substructures: evolution ideals and evolution subalgebras. After exposing some of the concepts related to them in the literature, we explore the order structures that arise in the sets of…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…