Related papers: Towards a core genome: pairwise similarity searche…
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
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…
The aim of this study is to investigate the relation that can be found between the phylogeny of a large set of complete chloroplast genomes, and the evolution of gene content inside these sequences. Core and pan genomes have been computed…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
We identify a set of 575 human genes that are expressed in all conditions tested in a publicly available database of microarray results. Based on this common occurrence, the set is expected to be rich in "housekeeping" genes, showing…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
The theory of evolution states that the diversity of species can be explained by descent with modification. Therefore, all living beings are related through a common ancestor. This evolutionary process must have left traces in our molecular…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
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…
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…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…