Related papers: Towards a core genome: pairwise similarity searche…
Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…
We showed in this paper that similarity network can be used as an powerful tools to study the relationship of tRNA genes. We constructed a network of 3719 tRNA gene sequences using simplest alignment and studied its topology, degree…
Comparative studies of cancer-related genes allow us to gain novel information about the evolution and function of these genes, but also to understand cancer as a driving force in biological systems and species life histories. So far,…
BRCA genes, comprising BRCA1 and BRCA2 play indispensable roles in preserving genomic stability and facilitating DNA repair mechanisms. The presence of germline mutations in these genes has been associated with increased susceptibility to…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
A series of results of evolution supervised by genetic algorithms with interest to agricultural and horticultural fields are reviewed. New obtained original results from the use of genetic algorithms on structure-activity relationships are…
Natural phenomenon of coevolution is the reciprocally induced evolutionary change between two or more species or population. Though this biological occurrence is a natural fact, there are only few attempts to use this as a simile in…
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,…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we relate conservation, essentiality and functional repertoire of a gene to the connectivity $k$ (i.e., the number of interaction…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
How to define and use the concept of inclusive fitness is a contentious topic in evolutionary theory. Inclusive fitness can be used to calculate selection on a focal gene, but it is also applied to whole organisms. Individuals are then…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…