Results 41 to 50 of about 64,518 (349)

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

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

Bridging the gap: Multi‐stakeholder perspectives of molecular diagnostics in oncology

Molecular Oncology, EarlyView.
Although molecular diagnostics is transforming cancer care, implementing novel technologies remains challenging. This study identifies unmet needs and technology requirements through a two‐step stakeholder involvement. Liquid biopsies for monitoring applications and predictive biomarker testing emerge as key unmet needs. Technology requirements vary by
Jorine Arnouts, Senada Koljenović, Elise Daems, Karolien De Wael, Marc Peeters, Léon C. van Kempen, Greetje Vanhoutte, Karen Zwaenepoel, Timon Vandamme   +8 more
wiley   +1 more source

Expanding applications for nanopore sequencing [PDF]

Nature Reviews Genetics, 2019
Two new studies report advances for nanopore-based long-read sequencing for characterizing complex human transcriptomes and for analysing human repetitive DNA regions.
openaire   +2 more sources

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

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

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

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

ATF4‐mediated stress response as a therapeutic vulnerability in chordoma

Molecular Oncology, EarlyView.
We screened 5 chordoma cell lines against 100+ inhibitors of epigenetic and metabolic pathways and kinases and identified halofuginone, a tRNA synthetase inhibitor. Mechanistically halofuginone induces an integrated stress response, with eIF2alpha phosphorylation, activation of ATF4 and its target genes CHOP, ASNS, INHBE leading to cell death ...
Lucia Cottone, James Dunford, Eleanor Calcutt, Vicki Gamble, Filiz Senbabaoglu Aksu, Lorena Ligammari, Georgina Wherry, Giorgia Gaeta, John C. Christianson, Adrienne M. Flanagan, Udo Oppermann, Adam P. Cribbs   +11 more
wiley   +1 more source

Nanopore-Based Target Sequence Detection

PLOS ONE, 2016
The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be
Trevor J Morin, Tyler Shropshire, Xu Liu, Kyle Briggs, Cindy Huynh, Vincent Tabard-Cossa, Hongyun Wang, William B Dunbar   +7 more
openaire   +4 more sources