Related papers: Observations and perspectives on the prebiotic seq…
Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
The study of origins of life on Earth and the search for life on other planets are closely linked. Prebiotic chemical scenarios can help prioritize planets as targets for the search for life as we know it and can provide informative priors…
The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has…
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case,…
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 study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…
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…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
Natural selection explains how life has evolved over millions of years from more primitive forms. The speed at which this happens, however, has sometimes defied formal explanations when based on random (uniformly distributed) mutations.…
The rise of multicellularity in the early evolution of life represents a major challenge for evolutionary biology. Guidance for finding answers has emerged from disparate fields, from phylogenetics to modelling and synthetic biology, but…
Rearrangements of bacterial chromosomes can be studied mathematically at several levels, most prominently at a local, or sequence level, as well as at a topological level. The biological changes involved locally are inversions, deletions,…
By starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient subspaces of the…
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human…
We propose a scenario for the origin of life based on the coevolution of lipid bilayer vesicles and protein channels.
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…