Related papers: A Model-Based Analysis of GC-Biased Gene Conversio…
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…
Interlocus gene conversion (IGC) homogenizes paralogs. Little is known regarding the mutation events that cause IGC and even less is known about the IGC mutations that experience fixation. To disentangle the rates of fixed IGC mutations…
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,…
GC-content, the ratio of guanine and cytosine bases in an entire nucleotide sequence, and palindromic sequences are unique for every organism due to genomic evolution. The goals of our research was to establish a correlation between…
Identifying transcription factor binding sites (TFBS) is crucial for understanding gene regulation, as these sites enable transcription factors (TFs) to bind to DNA and modulate gene expression. Despite advances in high-throughput…
A model is presented relating the evolution of genomic GC content over time to AT$\rightarrow$GC and GC$\rightarrow$AT mutation rates. By employing It\^o calculus it is shown that if mutation rates in asexually reproducing organisms are…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…
Gene conversion is a mechanism by which a double-strand break in a DNA molecule is repaired using a homologous DNA molecule as a template. As a result, one gene is 'copied and pasted' onto the other gene. It was recently reported that the…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Until recently, the use of Bayesian inference in population genetics was limited to a few cases because for many realistic population genetic models the likelihood function cannot be calculated analytically . The situation changed with the…
In genome-wide prediction, independence of marker allele substitution effects is typically assumed; however, since early stages of this technology it has been known that nature points to correlated effects. In statistics, graphical models…
Globular clusters (GCs) are sensitive tracers of galaxy assembly histories but interpreting the information they encode is challenging because mergers are thought to promote both the formation and disruption of GCs. We use simulations with…
Approximate Bayesian computation (ABC) can be used for model fitting when the likelihood function is intractable but simulating from the model is feasible. However, even a single evaluation of a complex model may take several hours,…
The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving…
We use atomistic simulations to investigate grain boundary (GB) phase transitions in el- emental body-centered cubic (bcc) metal tungsten. Motivated by recent modeling study of grain boundary phase transitions in [100] symmetric tilt…
The accumulation of beneficial mutations on many competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the…
In the analysis of complex traits, genetic effects are frequently modelled as either fixed or random effects. Such assumptions serve as a foundation of defining heritability and relatedness using genome-wide single nucleotide polymorphism…
Deep clustering as an important branch of unsupervised representation learning focuses on embedding semantically similar samples into the identical feature space. This core demand inspires the exploration of contrastive learning and…
The rapid evolution of generative AI, from GANs to modern diffusion models, has resulted in increasingly subtle discriminative clues. These fine-grained signals are often overshadowed by dominant, high-fidelity image content (e.g., the main…