Related papers: Identifying recombination hotspots using populatio…
Redescription mining is a data analysis technique that has found applications in diverse fields. The most used redescription mining approaches involve two phases: finding matching pairs among data attributes and extending the pairs. This…
The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator express phenotypic compounds necessary to carry out its genetic replication. For example, viruses…
The benefit of sexual recombination is one of the most fundamental questions both in population genetics and evolutionary computation. It is widely believed that recombination helps solving difficult optimization problems. We present the…
Background: Regions with copy number variations (in germline cells) or copy number alteration (in somatic cells) are of great interest for human disease gene mapping and cancer studies. They represent a new type of mutation and are…
In recent years, deep learning gained proliferating popularity in the cybersecurity application domain, since when being compared to traditional machine learning, it usually involves less human effort, produces better results, and provides…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
Hidden Markov Models (HMMs) are a commonly used tool for inference of transcription factor (TF) binding sites from DNA sequence data. We exploit the mathematical equivalence between HMMs for TF binding and the "inverse" statistical…
The paramount importance of replicating associations is well recognized in the genome-wide associaton (GWA) research community, yet methods for assessing replicability of associations are scarce. Published GWA studies often combine…
Genomic aberrations, such as somatic copy number alterations, are frequently observed in tumor tissue. Recurrent aberrations, occurring in the same region across multiple subjects, are of interest because they may highlight genes associated…
When a network is inferred from data, two types of errors can occur: false positive and false negative conclusions about the presence of links. We focus on the influence of local network characteristics on the probability $\alpha$ - of type…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
We study a family of selection-mutation models of a sexual population structured by a phenotypical trait. The main feature of these models is the asymmetric trait heredity or fecundity between the parents : we assume that each individual…
Large whole-genome sequencing projects have provided access to much of the rare variation in human populations, which is highly informative about population structure and recent demography. Here, we show how the age of rare variants can be…
In the high dimensional regression analysis when the number of predictors is much larger than the sample size, an important question is to select the important variable which are relevant to the response variable of interest. Variable…
Node similarity is a significant property driving the growth of real networks. In this paper, based on the observed spreading results we apply the node similarity metrics to reconstruct propagation networks. We find that the reconstruction…
To segment a sequence of independent random variables at an unknown number of change-points, we introduce new procedures that are based on thresholding the likelihood ratio statistic. We also study confidence regions based on the likelihood…
It has been a puzzling question why some organisms reproduce sexually. Fisher and Muller hypothesized that reproducing by sex can speed up the evolution. They explained that in the sexual reproduction, recombination can combine beneficial…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
We propose a flexible change-point model for inhomogeneous Poisson Processes, which arise naturally from next-generation DNA sequencing, and derive score and generalized likelihood statistics for shifts in intensity functions. We construct…
This paper addresses the challenge of efficiently capturing a high proportion of true signals for subsequent data analyses when sample sizes are relatively limited with respect to data dimension. We propose the signal missing rate as a new…