Related papers: Clustering of SNPs along a chromosome: can the neu…
About 2% of human genetic polymorphisms have been hypothesized to arise via multinucleotide mutations (MNMs), complex events that generate SNPs at multiple sites in a single generation. MNMs have the potential to accelerate the pace at…
Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the…
Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing…
Single-nucleotide polymorphisms (SNPs) account for most variations between human genomes. We show how, if the genomes in a database differ only by a reasonable number of SNPs and the substrings between those SNPs are unique, then we can…
Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are two kinds of commonly used markers in Y chromosome studies of forensic and population genetics. There has been increasing interest in the cost saving strategy by…
Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…
Deleterious genetic variants can be evaluated as quantitative traits using information theory-based sequence analysis of recognition sites. To assess the effect of such variants, fitness and genetic load of SNPs which alter binding site…
We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…
Integration of data from genome-wide single nucleotide polymorphism (SNP) association studies of different traits should allow researchers to disentangle the genetics of potentially related traits within individually associated regions.…
In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
Biometric data is often highly sensitive, and a leak of this data can lead to serious privacy breaches. Some of the most sensitive of this type of data relates to the usage of DNA data on individuals. A leak of this type of data without…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…
Single nucleotide polymorphisms (SNPs) are variations at specific locations in DNA. Sequence responsible for marking genes associated with diseases or tracking inherited diseases within The family. These variations in the Rb1 gene can cause…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with trait diversity and disease susceptibility, yet the functional properties of many genetic variants and their molecular…
The ~4-Mbp basic genome shared by 32 independent isolates of E. coli representing considerable population diversity has been approximated by whole-genome multiple-alignment and computational filtering designed to remove mobile elements and…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
Classic concepts of genetic (gene) diversity (heterozygosity) such as Nei (1973: PNAS) and Nei and Li (1979: PNAS) nucleotide diversity were defined within the context of populations. Although variations are often measured in population…