We introduce a new method for detection of recombination hotspots from population genetic data. This method is based on (a) defining an (approximate) penalized likelihood for how recombination rate varies with physical position and (b) maximizing this penalized likelihood over possible sets of recombination hotspots. Simulation results suggest that this is a more powerful method for detection o...

RAG1 protein is one of the key component of RAG complex regulating the V(D)J recombination. There are only few studies for RAG1 concerning evolutionary history, detailed sequence and mutational hotspots. Herein, we present out datasets used for the recent comprehensive study of RAG1 based on sequence, phylogenetic and genetic variant analyses (Kumar et al., 2015) [1]. Protein sequence alignment...

BACKGROUND Hemorrhagic fever with renal syndrome (HFRS) is highly endemic in mainland China, and has extended from rural areas to cities recently. Beijing metropolis is a novel affected region, where the HFRS incidence seems to be diverse from place to place. METHODOLOGY/PRINCIPAL FINDINGS The spatial scan analysis based on geographical information system (GIS) identified three geo-spatial "h...

The contradiction between the long-term persistence of the chromosomal hotspots that initiate meiotic recombination and the self-destructive mechanism by which they act strongly suggests that our understanding of recombination is incomplete. This "hotspot paradox" has been reinforced by the finding that biased gene conversion also removes active hotspots from human sperm. To investigate the req...

In many organisms, meiotic recombination occurs preferentially at a limited number of sites in the genome known as hotspots. In the fission yeast Schizosaccharomyces pombe, simple sequence motifs determine the location of at least some, and possibly most or all, hotspots. Recently, we showed that a large number of different sequences can create hotspots. Among those sequences we identified some...

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 ...

In cancer genomics, recurrence of mutations in independent tumor samples is a strong indicator of functional impact. However, rare functional mutations can escape detection by recurrence analysis owing to lack of statistical power. We enhance statistical power by extending the notion of recurrence of mutations from single genes to gene families that share homologous protein domains. Domain muta...

Railway suicide is a significant public health problem. In addition to the loss of lives, these suicides occur in public space, causing traumatization among train drivers and passengers, and significant public transport delays. Prevention efforts depend upon accurate knowledge of clustering phenomena across the railway network, and spatial risk factors. Factors such as proximity to psychiatric ...

A range of different biodiversity-based selection methods for nature reserves has been tested for terrestrial environments, including those based on diversity hotspots, endemicity hotspots and complementarity. In this study, we investigate the utility of these approaches for a coral reef embayment. We compare coral and fish species richness in a random accumulation of reserve sites with (a) hot...