Related papers: Discovering functional DNA elements using populati…
Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level…
Motivated by present activities in (statistical) physics directed towards biological evolution, we review the interplay of three evolutionary forces: mutation, selection, and genetic drift. The review addresses itself to physicists and…
The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed…
Recent advances in genomic sequencing technology have resulted in an abundance of genome sequence data. Despite the progress in interpreting those data, there remains a broad scope for their translation into clinical and societal benefits.…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Population dynamics provides a numerical tool allowing for the study of rare events by means of simulating a large number of copies of the system, supplemented with a selection rule that favours the rare trajectories of interest. The…
Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes.…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
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…
Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model…
Non-African populations have experienced major bottlenecks in the time since their split from West Africans, which has led to the hypothesis that natural selection to remove weakly deleterious mutations may have been less effective in…
This study analyzes rates and ways of data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on human ancient DNA published between 1988 and 2013. For the most part, data are available in…
Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function…
DNA methylation is a well-studied genetic modification that regulates gene transcription of Eukaryotes. Its alternations have been recognized as a significant component of cancer development. In this study, we use the DNA methylation 450k…
Motivation: Methods are needed to test pre-defined genomic regions such as promoters for differential methylation in genome-wide association studies, where the number of samples is limited and the data have large amounts of measurement…
Numerous genotypic diversity measures (GDMs) are available in the literature to assess the convergence status of an evolutionary algorithm (EA) or describe its search behavior. In a recent study, the authors of this paper drew attention to…
Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…