相关论文: Indexing Finite Language Representation of Populat…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…
Random Indexing is a simple implementation of Random Projections with a wide range of applications. It can solve a variety of problems with good accuracy without introducing much complexity. Here we use it for identifying the language of…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Inference of population structure from genetic data plays an important role in population and medical genetics studies. With the advancement and decreasing cost of sequencing technology, the increasingly available whole genome sequencing…
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…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Computational approaches in historical linguistics have been increasingly applied during the past decade and many new methods that implement parts of the traditional comparative method have been proposed. Despite these increased efforts,…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…
A model-assisted semiparametric method of estimating finite population totals is investigated to improve the precision of survey estimators by incorporating multivariate auxiliary information. The proposed superpopulation model is a…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
An index for a finite automaton is a powerful data structure that supports locating paths labeled with a query pattern, thus solving pattern matching on the underlying regular language. In this paper, we solve the long-standing problem of…