[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications
Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …
molecules have led to substantial improvements in accuracy, read length and throughput …
Genomics in the long-read sequencing era
EL van Dijk, D Naquin, K Gorrichon, Y Jaszczyszyn… - Trends in Genetics, 2023 - cell.com
Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …
explore genomes. While in the early years these methods suffered technical limitations, they …
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore
PN Pratanwanich, F Yao, Y Chen, CWQ Koh… - Nature …, 2021 - nature.com
RNA modifications, such as N 6-methyladenosine (m6A), modulate functions of cellular RNA
species. However, quantifying differences in RNA modifications has been challenging. Here …
species. However, quantifying differences in RNA modifications has been challenging. Here …
Context-aware transcript quantification from long-read RNA-seq data with Bambu
Most approaches to transcript quantification rely on fixed reference annotations; however,
the transcriptome is dynamic and depending on the context, such static annotations contain …
the transcriptome is dynamic and depending on the context, such static annotations contain …
[HTML][HTML] Detection of m6A from direct RNA sequencing using a multiple instance learning framework
RNA modifications such as m6A methylation form an additional layer of complexity in the
transcriptome. Nanopore direct RNA sequencing can capture this information in the raw …
transcriptome. Nanopore direct RNA sequencing can capture this information in the raw …
The role of alternative splicing in adaptation and evolution
Regulation of gene expression plays a central role in adaptive divergence and evolution.
Although the role of gene regulation in microevolutionary processes is gaining wide …
Although the role of gene regulation in microevolutionary processes is gaining wide …
[HTML][HTML] Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data
Nanopore sequencing provides signal data corresponding to the nucleotide motifs
sequenced. Through machine learning-based methods, these signals are translated into …
sequenced. Through machine learning-based methods, these signals are translated into …
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures
The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare
the performance of existing long-read isoform detection and differential expression analysis …
the performance of existing long-read isoform detection and differential expression analysis …
PBSIM3: a simulator for all types of PacBio and ONT long reads
Long-read sequencers, such as Pacific Biosciences (PacBio) and Oxford Nanopore
Technologies (ONT) sequencers, have improved their read length and accuracy, thereby …
Technologies (ONT) sequencers, have improved their read length and accuracy, thereby …
[HTML][HTML] Isoform age-splice isoform profiling using long-read technologies
Alternative splicing (AS) of RNA is a key mechanism that results in the expression of multiple
transcript isoforms from single genes and leads to an increase in the complexity of both the …
transcript isoforms from single genes and leads to an increase in the complexity of both the …