Scalable Genome Assembly through Parallel de Bruijn Graph Construction for Multiple k-mers
Sign Up to like & getrecommendations! Published in 2019 at "Scientific Reports"
DOI: 10.1038/s41598-019-51284-9
Abstract: Remarkable advancements in high-throughput gene sequencing technologies have led to an exponential growth in the number of sequenced genomes. However, unavailability of highly parallel and scalable de novo assembly algorithms have hindered biologists attempting to… read more here.
Keywords: bruijn graph; scalable genome; bruijn; construction ... See more keywords
A reinforcement learning approach to effective forecasting of pediatric hypoglycemia in diabetes I patients using an extended de Bruijn graph
Sign Up to like & getrecommendations! Published in 2024 at "Scientific Reports"
DOI: 10.1038/s41598-024-82649-4
Abstract: Pediatric diabetes I is an endemic and an especially difficult disease; indeed, at this point, there does not exist a cure, but only careful management that relies on anticipating hypoglycemia. The changing physiology of children… read more here.
Keywords: bruijn graph; approach; reinforcement; hypoglycemia ... See more keywords
The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs
Sign Up to like & getrecommendations! Published in 2024 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbae627
Abstract: Abstract Noncoding RNA refers to RNA that does not encode proteins. The lncRNA and miRNA it contains play crucial regulatory roles in organisms, and their aberrant expression is closely related to various diseases. Traditional experimental… read more here.
Keywords: multitask learning; improved bruijn; subcellular localization; bruijn graph ... See more keywords
Inference of viral quasispecies with a paired de Bruijn graph
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa782
Abstract: MOTIVATION RNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterise the quasispecies… read more here.
Keywords: bruijn graph; paired bruijn; graph based; viral quasispecies ... See more keywords
FastEtch: A Fast Sketch-Based Assembler for Genomes
Sign Up to like & getrecommendations! Published in 2019 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2017.2737999
Abstract: De novo genome assembly describes the process of reconstructing an unknown genome from a large collection of short (or long) reads sequenced from the genome. A single run of a Next-Generation Sequencing (NGS) technology can… read more here.
Keywords: bruijn graph; memory; fastetch fast; sketch ... See more keywords
HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly
Sign Up to like & getrecommendations! Published in 2017 at "International Journal of Genomics"
DOI: 10.1155/2017/6120980
Abstract: Background The rapid advancement of sequencing technologies has made it possible to regularly produce millions of high-quality reads from the DNA samples in the sequencing laboratories. To this end, the de Bruijn graph is a… read more here.
Keywords: bruijn graph; graph; graph construction; genome assembly ... See more keywords
The De Bruijn graph of non-sequential pattern repetitions in DNA strings
Sign Up to like & getrecommendations! Published in 2024 at "Indonesian Journal of Electrical Engineering and Computer Science"
DOI: 10.11591/ijeecs.v35.i2.pp787-794
Abstract: In molecular biology, constructing a genome based on substantially many reads from multitudes of deoxyribonucleic acid (DNA) strings has become an insurmountable task; one which has been continuously addressed by the introduction of various assembly… read more here.
Keywords: non sequential; sequential pattern; assembly algorithms; bruijn graph ... See more keywords