相关论文: Shotgun DNA sequencing for human identification: D…

Many forensic genetic trace samples are of too low quality to obtain short tandem repeat (STR) DNA profiles as the nuclear DNA they contain is highly degraded (e.g., telogen hairs). Instead, performing shotgun DNA sequencing of such samples…

High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…

DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…

Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…

One of the basic tasks in bioinformatics is localizing a short subsequence $S$, read while sequencing, in a long reference sequence $R$, like the human geneome. A natural rapid approach would be finding a hash value for $S$ and compare it…

Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…

DNA fingerprinting is a cornerstone for human identification in forensics, where the sequence of highly polymorphic short tandem repeats (STRs) from an individual is compared against a DNA database. This presents significant privacy risks…

Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both…

Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…

This paper presents a new framework for analysing forensic DNA samples using probabilistic genotyping. Specifically it presents a mathematical framework for specifying and combining the steps in producing forensic casework electropherograms…

Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…

In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…

DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation…

The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…

Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced…

A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…

After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…

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…

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…

Identifying disease-associated genes enables the development of precision medicine and the understanding of biological processes. Genome-wide association studies (GWAS), gene expression data, biological pathway analysis, and protein network…