Results 51 to 60 of about 5,800,592 (273)

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

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

Nature Communications, 2019
DNA modification generates unique electric signals in Oxford Nanopore sequencing data but the signals can be complicated to decipher. Here, the authors develop a deep learning framework, DeepMod, to detect DNA base modifications including 5mC and 6mA ...
Qian Liu, Li Fang, Guoliang Yu, Depeng Wang, Chuan-Le Xiao, Kai Wang   +5 more
doaj   +1 more source

Transformer‐based DNA methylation detection on ionic signals from Oxford Nanopore sequencing data

Quantitative Biology, 2023
Transformer is an algorithm that adopts self‐attention architecture in the neural networks and has been widely used in natural language processing. In the current study, we apply Transformer architecture to detect DNA methylation on ionic signals from ...
Xiuquan Wang, Mian Umair Ahsan, Yunyun Zhou, Kai Wang   +3 more
doaj   +1 more source

Gapless provides combined scaffolding, gap filling, and assembly correction with long reads

Life Science Alliance, 2023
gapless is a new tool for combined execution of correction, scaffolding and gap filling using PacBio or Oxford Nanopore reads. Continuity, correctness, and completeness of genome assemblies are important for many biological projects. Long reads represent
Stephan Schmeing, Mark D Robinson
doaj   +1 more source

Augmenting and Assaying Nav1.1 Protein Quantity for Dravet Syndrome Therapy

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Dravet Syndrome (DS) is a developmental and epileptic encephalopathy predominantly caused by heterozygous loss‐of‐function variants in SCN1A, which encodes Nav1.1. Conserved upstream open reading frames (uORFs) in SCN1A were validated to regulate translation in reporter assays, demonstrating the therapeutic viability of increasing Nav1.1 from ...
Aiswarya Saravanan, Jordan Safran, Anna Loughman, Grace Lin, Shivanshi Vaid, Dana Allababidi, Peter M. Tessier, Louis T. Dang   +7 more
wiley   +1 more source

Consistent ultra-long DNA sequencing with automated slow pipetting

BMC Genomics, 2021
Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome.
Trent M. Prall, Emma K. Neumann, Julie A. Karl, Cecilia G. Shortreed, David A. Baker, Hailey E. Bussan, Roger W. Wiseman, David H. O’Connor   +7 more
doaj   +1 more source

Confinement in Metal‐Organic Frameworks as a Route to Harnessing Liquid Barocalorics in the Solid‐State

Advanced Functional Materials, EarlyView.
Encapsulation of solid–liquid barocalorics (BC) within MOFs harnesses their colossal BC performance whilst allowing active control of BC properties through BC‐MOF interactions. ABSTRACT Barocaloric (BC) effects at liquid–vapor transitions in hydrofluorocarbons drive most commercial technologies used for heating and cooling in the heating, ventilation ...
Ming Zeng, Frederic Rendell‐Bhatti, Eamonn T. Connolly, Yang Wang, Clàudia Pérez‐Junyent, Josep‐Lluís Tamarit, Ross S. Forgan, Pol Lloveras, David Boldrin   +8 more
wiley   +1 more source

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Nature Communications
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes.
Marie C. Schoelmerich, Lynn Ly, Jacob West-Roberts, Ling-Dong Shi, Cong Shen, Nikhil S. Malvankar, Najwa Taib, Simonetta Gribaldo, Ben J. Woodcroft, Christopher W. Schadt, Basem Al-Shayeb, Xiaoguang Dai, Christopher Mozsary, Scott Hickey, Christine He, John Beaulaurier, Sissel Juul, Rohan Sachdeva, Jillian F. Banfield   +18 more
doaj   +1 more source

Site and Post-Excavation Data from an Excavation at Mansfield College, Love Lane, Oxford 2016

, 2021
This collection comprises reports, site photographs, CAD data, spreadsheets, and site records from an excavation carried out in January and February 2016 by Oxford Archaeology at the site of a proposed new residential block at the Love Lane site ...
Oxford Archaeology (South)
core   +1 more source

Iterative Selection of DNA Nanostructures for Cellular Uptake

Advanced Materials, EarlyView.
DNA nanostructures are promising cell targeting delivery vehicles for therapeutics, but the targeting behavior is not fully understood. In this study, libraries of DNA nanostructures that can be amplified and sequenced are combined with cellular uptake as a selection pressure to iteratively refine DNA structures taken up in cells to better understand ...
Anjali Rajwar, Lisa Eichhorn, Jakub Palacka, Sandra Ly, Erik Benson   +4 more
wiley   +1 more source