Enterohaemorrhagic and other Shiga toxin‐producing Escherichia coli (STEC): Where are we now regarding diagnostics and control strategies?

DG Newell, RM La Ragione - Transboundary and emerging …, 2018 - Wiley Online Library
Escherichia coli comprises a highly diverse group of Gram‐negative bacteria and is a
common member of the intestinal microflora of humans and animals. Generally, such …

[HTML][HTML] The long reads ahead: de novo genome assembly using the MinION

C de Lannoy, D de Ridder, J Risse - F1000Research, 2017 - ncbi.nlm.nih.gov
Nanopore technology provides a novel approach to DNA sequencing that yields long, label-
free reads of constant quality. The first commercial implementation of this approach, the …

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

V Jayakumar, Y Sakakibara - Briefings in bioinformatics, 2019 - academic.oup.com
Long reads obtained from third-generation sequencing platforms can help overcome the
long-standing challenge of the de novo assembly of sequences for the genomic analysis of …

The effect of methodological considerations on the construction of gene-based plant pan-genomes

L Glick, I Mayrose - Genome Biology and Evolution, 2023 - academic.oup.com
Pan-genomics is an emerging approach for studying the genetic diversity within plant
populations. In contrast to common resequencing studies that compare whole genome …

The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of …

HA Safar, F Alatar, K Nasser, R Al-Ajmi, W Alfouzan… - BMC …, 2023 - Springer
Oxford Nanopore sequencing technology (ONT) is currently widely used due to its
affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation …

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources

M Hanussek, F Bartusch, J Krüger - PLoS Computational Biology, 2021 - journals.plos.org
The large amount of biological data available in the current times, makes it necessary to use
tools and applications based on sophisticated and efficient algorithms, developed in the …

Three rounds of read correction significantly improve eukaryotic protein detection in ONT reads

HA Safar, F Alatar, AS Mustafa - Microorganisms, 2024 - mdpi.com
Background: Eukaryotes' whole-genome sequencing is crucial for species identification,
gene detection, and protein annotation. Oxford Nanopore Technology (ONT) is an affordable …

A sequencer coming of age: de novo genome assembly using MinION reads

C de Lannoy, D de Ridder, J Risse - BioRxiv, 2017 - biorxiv.org
Nanopore technology provides a novel approach to DNA sequencing that yields long, label-
free reads of constant quality. The first commercial implementation of this approach, the …

Rapid and accurate sequencing of enterovirus genomes using MinION nanopore sequencer

W Ji, YH Ke, Y Zhang, KQ Huang, W Lei… - Biomedical and …, 2017 - Elsevier
Objective Knowledge of an enterovirus genome sequence is very important in
epidemiological investigation to identify transmission patterns and ascertain the extent of an …

Bioinformatic Resources for Plant Genomic Research

SK Valsala Sudarsanan, N Sreekumar - Current Bioinformatics, 2024 - ingentaconnect.com
Genome assembly and annotation are crucial steps in plant genomics research as they
provide valuable insights into plant genetic makeup, gene regulation, evolutionary history …