Computational detection of recombination hotspots from population polymorphism data is important both for understanding the nature of recombination and for applications such as association studies. We propose a new method for this task based on a multiple-hotspot model and an (approximate) log-likelihood ratio test. A truncated, weighted pairwise log-likelihood is introduced and applied to the ...

Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alle...

Several recent large clinical trials evaluated HIV vaccine candidates that were based on recombinant adenovirus serotype 5 (rAd-5) vectors expressing HIV-derived antigens. These vaccines primarily elicited T-cell responses, which are known to be critical for controlling HIV infection. In the current study, we present a meta-analysis of epitope mapping data from 177 participants in three clinica...

The regulation of protein function by modulating the surface charge status via sequence-locally enriched phosphorylation sites (P-sites) in so called phosphorylation "hotspots" has gained increased attention in recent years. We set out to identify P-hotspots in the model plant Arabidopsis thaliana. We analyzed the spacing of experimentally detected P-sites within peptide-covered regions along A...

Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected b...

As technology node shrinks down, hotspots, i.e. patterning failures on wafer after etching process, become an inevitable problem. The main cause of such hotspots is low contrast of aerial image. There are several methods that can improve aerial image contrast such as SRAF insertion and OPC. However, it is difficult to fix all hotspots by applying only SRAF and OPC in advanced technology node. T...

Meiotic recombination hotspots play important roles in life sciences, but the regulatory mechanism remain unclear. To predict DNA sequence motifs that regulate recombination hotspots, we designed an open source software tool called “LDsplit” that detects SNPs (single nucleotide polymorphisms) associated with meiotic recombination hotspots. The association is measured by the difference of histor...

Criminal activities are unevenly distributed over space. The concept of hotspots is widely used to analyze the spatial characters of crimes. But existing methods usually identify hotspots based on an arbitrary user-defined threshold with respect to the number of a target crime without considering underlying controlling factors. In this study we introduce a new data mining model – Hotspots Optim...

Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earth's land surface, more than half the world's plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southe...

Hotspots of crime localized in space and time are well documented. Previous mathematical models of urban crime have exhibited these hotspots but considered a static or otherwise suboptimal police response to them. We introduce a program of police response to hotspots of crime in which the police adapt dynamically to changing crime patterns. In particular, they choose their deployment to solve a...