[HTML][HTML] Best practices in microbial experimental evolution: using reporters and long-read sequencing to identify copy number variation in experimental evolution

P Spealman, T De, JN Chuong, D Gresham - Journal of Molecular …, 2023 - Springer
Copy number variants (CNVs), comprising gene amplifications and deletions, are a
pervasive class of heritable variation. CNVs play a key role in rapid adaptation in both …

Advances of high-throughput sequencing for unraveling biotechnological potential of microalgal-bacterial communities

PA Zaytsev, VA Rodin, AA Zaytseva, MI Zvereva… - Journal of Applied …, 2024 - Springer
Although established biotechnological applications of microalgae eg, the production of high-
value metabolites is based on axenic cultures, exploitation of the mutualistic consortia of …

[HTML][HTML] Sequencing accuracy and systematic errors of nanopore direct RNA sequencing

W Liu-Wei, W van der Toorn, P Bohn, M Hölzer… - BMC genomics, 2024 - Springer
Abstract Background Direct RNA sequencing (dRNA-seq) on the Oxford Nanopore
Technologies (ONT) platforms can produce reads covering up to full-length gene transcripts …

[HTML][HTML] Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater

D Garcia-Pedemonte, A Carcereny, J Gregori… - International Journal of …, 2023 - mdpi.com
Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented
sewage sentinel systems to monitor the circulation of the virus in the population. A …

[HTML][HTML] Evaluating the potential of (epi) genotype-by-low pass nanopore sequencing in dairy cattle: a study on direct genomic value and methylation analysis

O González-Recio, A López-Catalina… - Journal of Animal …, 2023 - Springer
Background Genotype-by-sequencing has been proposed as an alternative to SNP
genotyping arrays in genomic selection to obtain a high density of markers along the …

[HTML][HTML] HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing

R Han, J Qi, Y Xue, X Sun, F Zhang, X Gao, G Li - Genome biology, 2023 - Springer
DNA barcodes enable Oxford Nanopore sequencing to sequence multiple barcoded DNA
samples on a single flow cell. DNA sequences with the same barcode need to be grouped …

Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus

S Ferguson, A Jones, K Murray, RL Andrew… - …, 2024 - academic.oup.com
Structural variations (SVs) play a significant role in speciation and adaptation in many
species, yet few studies have explored the prevalence and impact of different categories of …

Streamlining remote nanopore data access with slow5curl

B Wong, JM Ferguson, JY Do, H Gamaarachchi… - …, 2024 - academic.oup.com
Background As adoption of nanopore sequencing technology continues to advance, the
need to maintain large volumes of raw current signal data for reanalysis with updated …

Dwell Time Prolongation and Identification of Single Nucleotides Passing through a Solid-State Nanopore by Using Ammonium Sulfate Aqueous Solution

I Yanagi, R Akahori, K Takeda - ACS omega, 2023 - ACS Publications
The ionic current blockades when poly (dT) 60 or dNTPs passed through SiN nanopores in
an aqueous solution containing (NH4) 2SO4 were investigated. The dwell time of poly (dT) …

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence.

S Ferguson, A Jones, KD Murray, RL Andrew… - bioRxiv, 2023 - biorxiv.org
Structural variants (SVs) play a significant role in speciation and adaptation in many species,
yet few studies have explored the prevalence and impact of different categories of SVs. We …