[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 …
[HTML][HTML] Opportunities and challenges in long-read sequencing data analysis
Long-read technologies are overcoming early limitations in accuracy and throughput,
broadening their application domains in genomics. Dedicated analysis tools that take into …
broadening their application domains in genomics. Dedicated analysis tools that take into …
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Y Perez-Riverol, A Csordas, J Bai… - Nucleic acids …, 2019 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www. ebi. ac. uk/pride/) is
the world's largest data repository of mass spectrometry-based proteomics data, and is one …
the world's largest data repository of mass spectrometry-based proteomics data, and is one …
[HTML][HTML] Transcriptome assembly from long-read RNA-seq alignments with StringTie2
RNA sequencing using the latest single-molecule sequencing instruments produces reads
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …
Nanopore native RNA sequencing of a human poly (A) transcriptome
High-throughput complementary DNA sequencing technologies have advanced our
understanding of transcriptome complexity and regulation. However, these methods lose …
understanding of transcriptome complexity and regulation. However, these methods lose …
[PDF][PDF] Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing
SK Leung, AR Jeffries, I Castanho, BT Jordan, K Moore… - Cell reports, 2021 - cell.com
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA
molecules from a single pre-mRNA with a prominent role in the development and function of …
molecules from a single pre-mRNA with a prominent role in the development and function of …
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Several new genomics technologies have become available that offer long-read sequencing
or long-range mapping with higher throughput and higher resolution analysis than ever …
or long-range mapping with higher throughput and higher resolution analysis than ever …
Transcriptome variation in human tissues revealed by long-read sequencing
DA Glinos, G Garborcauskas, P Hoffman, N Ehsan… - Nature, 2022 - nature.com
Regulation of transcript structure generates transcript diversity and plays an important role in
human disease,,,,,–. The advent of long-read sequencing technologies offers the opportunity …
human disease,,,,,–. The advent of long-read sequencing technologies offers the opportunity …
[HTML][HTML] Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
AD Tang, CM Soulette, MJ van Baren, K Hart… - Nature …, 2020 - nature.com
While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-
length isoform changes may better elucidate the functional consequences of these …
length isoform changes may better elucidate the functional consequences of these …
[HTML][HTML] High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing
ZX Shi, ZC Chen, JY Zhong, KH Hu, YF Zheng… - Nature …, 2023 - nature.com
Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative
RNA splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT …
RNA splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT …