Related papers: Late-replicating CNVs as a source of new genes
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder (NDD) that is caused by genetic, epigenetic, and environmental factors. Recent advances in genomic analysis have uncovered numerous candidate genes with common…
The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci, different loci affect each other's dynamics. This leads to…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
Replicating systems sustained by error-prone enzymatic amplification can undergo critical transitions between persistence and extinction. In RNA viruses, such transitions are classically governed by mutation rates and fitness landscapes,…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
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…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
Many life-history traits, like the age at maturity or adult longevity, are important determinants of the generation time. For instance, semelparous species whose adults reproduce once and die have shorter generation times than iteroparous…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum…
Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both…
Background: Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that…
Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population…
Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while…
Core collapse supernovae (CCSNe) impact many areas of astrophysics, including compact object formation and gravitational waves, but many uncertainties remain in our understanding of the evolution of their progenitors. We use the binary…
In this research, we present a generalized quasispecies model in which population growth is governed by an arbitrary nonlinear function incorporating time delays. We begin by demonstrating that, under the constant population constraint, the…
The present and future of evolutionary algorithms depends on the proper use of modern parallel and distributed computing infrastructures. Although still sequential approaches dominate the landscape, available multi-core, many-core and…