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 …

Third generation sequencing transforming plant genome research: Current trends and challenges

U Medhi, C Chaliha, A Singh, BK Nath, E Kalita - Gene, 2024 - Elsevier
In recent years, third-generation sequencing (TGS) technologies have transformed
genomics and transcriptomics research, providing novel opportunities for significant …

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 …

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 …

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 …

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 …

AAVolve: Concatenated long-read deep sequencing enables whole capsid tracking during shuffled AAV library selection

S Scott, A Westhaus, D Nazareth… - … Therapy Methods & …, 2024 - cell.com
Gene therapies using recombinant adeno-associated virus (AAV) vectors have
demonstrated considerable clinical success in the treatment of genetic disorders. Improved …

A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world's tallest trees

S Ferguson, YD Bar-Ness, J Borevitz, A Jones - BMC genomics, 2024 - Springer
Abstract Background Eucalyptus regnans (Mountain Ash) is an Australian native giant tree
species which form forests that are among the highest known carbon-dense biomasses in …

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 …