相关论文: Suffix Arrays for Spaced-SNP Databases
Much research has been devoted to optimizing algorithms of the Lempel-Ziv (LZ) 77 family, both in terms of speed and memory requirements. Binary search trees and suffix trees (ST) are data structures that have been often used for this…
The Suffix Array $SA_S[1\ldots n]$ of an $n$-length string $S$ is a lexicographically sorted array of the suffixes of $S$. The suffix array is one of the most well known and widely used data structures in string algorithms. We present a…
With the reduction of sequencing costs and the pervasiveness of computing devices, genomic data collection is continually growing. However, data collection is highly fragmented and the data is still siloed across different repositories.…
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…
Single nucleotide polymorphism (SNP) datasets are fundamental to genetic studies but pose significant privacy risks when shared. The correlation of SNPs with each other makes strong adversarial attacks such as masked-value reconstruction,…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a…
Genome wide association studies directly assay 10^6 single nucleotide polymorphisms (SNPs) across a study cohort. Probabilistic estimation of additional sites by genotype imputation can increase this set of variants by 10- to 40-fold. Even…
The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show…
The Suffix Array SA(S) of a string S[1 ... n] is an array containing all the suffixes of S sorted by lexicographic order. The suffix array is one of the most well known indexing data structures, and it functions as a key tool in many string…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…
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…
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…
In this paper we will describe a new approach on the well-known suffix-array algorithm using Big Table Data Technology. We will demonstrate how it is possible to refactor a well-known algorithm coupled by taking advantage of an…
The Suffix Array is a classic text index enabling on-line pattern matching queries via simple binary search. The main drawback of the Suffix Array is that it takes linear space in the text's length, even if the text itself is extremely…
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude larger than the number of training examples, making it difficult to avoid overfitting, even when…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
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…