[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications

Y Wang, Y Zhao, A Bollas, Y Wang, KF Au - Nature biotechnology, 2021 - nature.com
Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …

Artificial intelligence aids in development of nanomedicines for cancer management

P Tan, X Chen, H Zhang, Q Wei, K Luo - Seminars in cancer biology, 2023 - Elsevier
Over the last decade, the nanomedicine has experienced unprecedented development in
diagnosis and management of diseases. A number of nanomedicines have been approved …

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps

X Wang, Y Luan, F Yue - Science Advances, 2022 - science.org
The Hi-C technique has been shown to be a promising method to detect structural variations
(SVs) in human genomes. However, algorithms that can use Hi-C data for a full-range SV …

Structural variation in the sequencing era

SS Ho, AE Urban, RE Mills - Nature Reviews Genetics, 2020 - nature.com
Identifying structural variation (SV) is essential for genome interpretation but has been
historically difficult due to limitations inherent to available genome technologies. Detection …

A survey of algorithms for the detection of genomic structural variants from long-read sequencing data

MU Ahsan, Q Liu, JE Perdomo, L Fang, K Wang - Nature Methods, 2023 - nature.com
As long-read sequencing technologies are becoming increasingly popular, a number of
methods have been developed for the discovery and analysis of structural variants (SVs) …

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

M Goel, H Sun, WB Jiao, K Schneeberger - Genome biology, 2019 - Springer
Genomic differences range from single nucleotide differences to complex structural
variations. Current methods typically annotate sequence differences ranging from SNPs to …

A roadmap for understanding the evolutionary significance of structural genomic variation

C Mérot, RA Oomen, A Tigano… - Trends in Ecology & …, 2020 - cell.com
Structural genomic variants (SVs) are ubiquitous and play a major role in adaptation and
speciation. Yet, comparative and population genomics have focused predominantly on gene …

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing

Y Che, Y Xia, L Liu, AD Li, Y Yang, T Zhang - Microbiome, 2019 - Springer
Abstract Background Wastewater treatment plants (WWTPs) are recognized as hotspots for
horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our …

A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome

S Perumal, CS Koh, L Jin, M Buchwaldt, EE Higgins… - Nature plants, 2020 - nature.com
It is only recently, with the advent of long-read sequencing technologies, that we are
beginning to uncover previously uncharted regions of complex and inherently recursive …

Current status of structural variation studies in plants

Y Yuan, PE Bayer, J Batley… - Plant Biotechnology …, 2021 - Wiley Online Library
Structural variations (SVs) including gene presence/absence variations and copy number
variations are a common feature of genomes in plants and, together with single nucleotide …