Related papers: The infinitely many genes model with horizontal ge…

We introduce a notion of genus range as a set of values of genera over all surfaces into which a graph is embedded cellularly, and we study the genus ranges of a special family of four-regular graphs with rigid vertices that has been used…

We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…

Hypergraphs are powerful mathematical structures that can model complex, high-order relationships in various domains, including social networks, bioinformatics, and recommender systems. However, generating realistic and diverse hypergraphs…

Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…

To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a…

We investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution called dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial…

This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on…

Even closely related prokaryotes show an astounding diversity in their ability to grow in different nutritional environments. Mechanistically, this diversity arises predominantly through horizontal gene transfer, the exchange of DNA between…

Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…

Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…

When an infectious disease outbreak is of a relatively small size, describing the ancestry of a sample of infected individuals is difficult because most ancestral models assume large population sizes. Given a set of infected individuals, we…

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…

In the classical Erd\"os-R\'enyi random graph G(n,p) there are n vertices and each of the possible edges is independently present with probability p. The random graph G(n,p) is homogeneous in the sense that all vertices have the same…

With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the…

While network science has become an indispensable tool for studying complex systems, the conventional use of pairwise links often shows limitations in describing high-order interactions properly. Hypergraphs, where each edge can connect…

A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…

Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…

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…

The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…