Related papers: Universal pacemaker of genome evolution
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
We investigate a driven particle system, a multilane asymmetric exclusion process, where the particle number in every lane is conserved, and stationary state is fully uncorrelated. The phase space has, starting from three lanes and more, an…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
One of the major characteristics of living organisms is metabolic rate, which is the amount of energy produced per unit of time. When the mass of organisms increases, the metabolic rate also increases (usually as a power function of mass),…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
Cell migration is crucial to many physiological and pathological processes. During migration, a cell adapts its morphology, including the overall morphology and nucleus morphology, in response to various cues in complex microenvironments,…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…
We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…
Metabolism of living organisms is a foundation of life. The metabolic rate (energy production per unit time) increases slower than organisms' mass. When this phenomenon is considered across different species, it is called interspecific…