Search
Search Results
-
Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium
BackgroundVancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands,...
-
Isolation and whole genome sequencing of Pseudomonas aeruginosa strain RK1 and its biocontrol potential against phytopathogens of rice
Excessive use of chemical fungicides to control fungal diseases not only has a catastrophic impact on the environment, but also seriously affects...
-
Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes
BackgroundAlternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues....
-
Whole genome sequencing analysis of alpaca suggests TRPV3 as a candidate gene for the suri phenotype
BackgroundAlpaca is a domestic South American camelid probably arising from the domestication of two wild camelids, the vicugna and the guanaco. Two...
-
Isolation of High-Molecular-Weight (HMW ) DNA from Fusarium oxysporum for Long-Read Sequencing
In many instances Fusarium oxysporum genomes are complex and challenging to assemble mainly due to the increased number of repetitive elements and...
-
Genome Assembly of Tea Plants (Camellia spp.)
Tea plant [Camellia sinensis (L.) O. Kuntze (2n = 2x = 30)] is one of the most important nonalcoholic beverage crops and widely cultivated worldwide....
-
Genome-wide detection of short tandem repeat expansions by long-read sequencing
BackgroundShort tandem repeat (STR), or “microsatellite”, is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated...
-
Cyanobacterial Genome Sequencing, Annotation, and Bioinformatics
Cyanobacteria are collectively a globally important monophyletic phylum of bacteria. They have attracted a lot of attention, not only because they...
-
Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp.
BackgroundCampylobacter spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium...
-
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect...
-
Whole genome sequencing and functional analysis of a novel biofilm-eradicating strain Nocardiopsis lucentensis EMB25
The process of biofilm formation is intricate and multifaceted, requiring the individual cells to secrete extracellular polymeric substances (EPS)...
-
ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data
BackgroundA wide range of tools are available for the detection of copy number variants (CNVs) from whole-genome sequencing (WGS) data. However, none...
-
Whole genome sequencing reveals candidate genes involving in PAS resistance in M. Tuberculosis isolated from patients in Thailand
Para-amino salicylic acid (PAS) was first reported by Lehmann in 1946 and used for tuberculosis treatment. However, due to its adverse effects, it is...
-
Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences
Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally...
-
Long-read assembly of major histocompatibility complex and killer cell immunoglobulin-like receptor genome regions in cynomolgus macaque
BackgroundThe major histocompatibility complex (MHC) and the killer cell immunoglobulin-like receptors (KIR) are key regulators of immune responses....
-
A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing
BackgroundPosttranscriptional processing of precursor mRNAs contributes to transcriptome and protein diversity and gene regulatory mechanisms in...
-
Whole-genome sequencing and analysis of Streptomyces strains producing multiple antinematode drugs
BackgroundNematodes are parasitic animals that cause over 100 billion US dollars loss in agricultural business. The whole-genomes of two Streptomyces ...
-
-
Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing
Complete comprehension of clinically relevant variation among human genomes is likely only to come from sequencing platforms that are cost-efficient,...
-
SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data
BackgroundStructural variations (SVs) refer to variations in an organism’s chromosome structure that exceed a length of 50 base pairs. They play a...
