相关论文: Matching reads to many genomes with the $r$-index

Within the field of instance segmentation, most of the state-of-the-art deep learning networks rely nowadays on cascade architectures, where multiple object detectors are trained sequentially, re-sampling the ground truth at each step. This…

With today's public data sets containing billions of data items, more and more companies are looking to integrate external data with their traditional enterprise data to improve business intelligence analysis. These distributed data sources…

We address the problem of building an index for a set $D$ of $n$ strings, where each string location is a subset of some finite integer alphabet of size $\sigma$, so that we can answer efficiently if a given simple query string (where each…

Btree and Rtree are two basic index structures; many different variants of them are proposed after them. Different variants are used in specific application for the performance optimization. In this paper different variants of Btree and…

Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…

Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment…

The automatic assignment of species information to the corresponding genes in a research article is a critically important step in the gene normalization task, whereby a gene mention is normalized and linked to a database record or…

The aim of this article is to introduce a reporting framework for reproducible, interactive research applied to Big Clinical Data, based on open source technologies. The framework is constituted by the following three axes: (i) data, (ii)…

Data compression is a powerful tool for managing massive but repetitive datasets, especially schemes such as grammar-based compression that support computation over the data without decompressing it. In the best case such a scheme takes a…

The ability to conduct reproducible research in Stata is often limited by the lack of version control for community-contributed packages. This article introduces the require command, a tool designed to ensure Stata package dependencies are…

Blini is a tool for quick lookup of nucleotide sequences in databases, and for quick dereplication of sequence collections. It is meant to help clean and characterize large collections of assembled contigs or long sequences that would…

The interlinking of datasets published in the Linked Data Cloud is a challenging problem and a key factor for the success of the Semantic Web. Manual rule-based methods are the most effective solution for the problem, but they require…

Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…

The $r$-index (Gagie et al., JACM 2020) represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude. Its space usage, $\mathcal{O}(r)$ where $r$ is the number of…

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 document describes an infra-structure provided by the R package performanceEstimation that allows to estimate the predictive performance of different approaches (workflows) to predictive tasks. The infra-structure is generic in the…

The root finding step of the Guruswami-Rudra list decoding algorithm for folded Reed-Solomon codes is considered. It is shown that a multivariate generalization of the Roth-Ruckenstein algorithm can be used to implement it. This leads to an…

This paper describes structuring data and constructing plots to explore forest classification models interactively. A forest classifier is an example of an ensemble, produced by bagging multiple trees. The process of bagging and combining…

Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…