Results 21 to 30 of about 37,057 (264)

High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies

Frontiers in Microbiology, 2020
Advances in nanopore-based sequencing techniques have enabled rapid characterization of genomes and transcriptomes. An emerging application of this sequencing technology is point-of-care characterization of pathogenic bacteria.
Jared T. Broddrick, Richard Szubin, Charles J. Norsigian, Jonathan M. Monk, Bernhard O. Palsson, Mary N. Parenteau   +5 more
doaj   +1 more source

De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing [version 2; referees: 1 approved, 3 approved with reservations]

F1000Research, 2018
Background: The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for de novo assembly of complex genomes without using other ...
Michael Liem, Hans J. Jansen, Ron P. Dirks, Christiaan V. Henkel, G. Paul H. van Heusden, Richard J.L.F. Lemmers, Trifa Omer, Shuai Shao, Peter J. Punt, Herman P. Spaink   +9 more
doaj   +1 more source

Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units

Frontiers in Public Health, 2021
Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and ...
Guilherme Marcelino Viana de Siqueira, Felipe Marcelo Pereira-dos-Santos, Rafael Silva-Rocha, María-Eugenia Guazzaroni   +3 more
doaj   +1 more source

MethPhaser: methylation-based long-read haplotype phasing of human genomes

Nature Communications
The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease.
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J. Treangen, Fritz J. Sedlazeck   +6 more
doaj   +1 more source

Liquid biopsy epigenetics: establishing a molecular profile based on cell‐free DNA

Molecular Oncology, EarlyView.
Cell‐free DNA (cfDNA) fragments in plasma from cancer patients carry epigenetic signatures reflecting their cells of origin. These epigenetic features include DNA methylation, nucleosome modifications, and variations in fragmentation. This review describes the biological properties of each feature and explores optimal strategies for harnessing cfDNA ...
Christoffer Trier Maansson, Anders Lade Nielsen, Boe Sandahl Sorensen   +2 more
wiley   +1 more source

Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection

Frontiers in Microbiology, 2023
In a previous study, Multiplex-nanopore-sequencing based whole genome sequencing (WGS) allowed for accurate in silico serotype prediction of Salmonella within one day for five multiplexed isolates, using both SISTR and SeqSero2.
Xingwen Wu, Hao Luo, Chongtao Ge, Feng Xu, Xiangyu Deng, Martin Wiedmann, Robert C. Baker, Abigail E. Stevenson, Guangtao Zhang, Silin Tang   +9 more
doaj   +1 more source

The impact of Hnrnpl deficiency on transcriptional patterns of developing muscle cells

FEBS Open Bio, EarlyView.
We performed nanopore whole‐transcriptome sequencing comparing RNA from Hnrnpl‐knockdown versus control C2C12 myoblasts to investigate the contributions of Hnrnpl to muscle development. Our results indicate that Hnrnpl regulates the expression of genes involved with Notch signaling and skeletal muscle, particularly splicing patterns of specific muscle ...
Hannah R. Littel, Mekala Gunasekaran, Audrey L. Daugherty, Natalya M. Wells, Johnnie Turner, Christine C. Bruels, Christina A. Pacak, Isabelle Draper, Peter B. Kang   +8 more
wiley   +1 more source

Transcriptome analysis of interna rootlets of the rhizocephalan Parasacculina sinensis reveals potential mechanisms of parasite host control

BMC Genomics
Background The endoparasitic rhizocephalan Parasacculina sinensis has a radically simplified morphology and primarily infests decapods crustaceans. Rhizocephalan barnacles usually absorb nutrients from the host through a complex rootlet system (the ...
Wenjie Li, Yiheng Feng, Haocheng Liu, Niklas Dreyer, Yue Him Wong   +4 more
doaj   +1 more source

Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis

BMC Pulmonary Medicine, 2023
Background To determine the diagnostic accuracy of a nanopore sequencing assay of PCR products from a M. tuberculosis complex-specific region for testing of bronchoalveolar lavage fluid (BALF) samples or sputum samples from suspected pulmonary ...
Zhifeng Liu, Yang Yang, Qingfeng Wang, Lei Wang, Wenjuan Nie, Naihui Chu   +5 more
doaj   +1 more source

Portable nanopore-sequencing technology: Trends in development and applications

Frontiers in Microbiology, 2023
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology.
Pin Chen, Zepeng Sun, Jiawei Wang, Xinlong Liu, Yun Bai, Jiang Chen, Anna Liu, Feng Qiao, Yang Chen, Chenyan Yuan, Jingjie Sha, Jinghui Zhang, Li-Qun Xu, Jian Li   +13 more
doaj   +1 more source