Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates
A Nunn, I Rodríguez‐Arévalo… - Plant biotechnology …, 2022 - Wiley Online Library
Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop
capable of improving ecosystems and intensifying agricultural productivity without …
capable of improving ecosystems and intensifying agricultural productivity without …
Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows
O Al-Dossary, A Furtado, A KharabianMasouleh… - Plant Methods, 2023 - Springer
Background Long read sequencing allows the analysis of full-length transcripts in plants
without the challenges of reliable transcriptome assembly. Long read sequencing of …
without the challenges of reliable transcriptome assembly. Long read sequencing of …
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to
acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio …
acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio …
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in
well-annotated organisms. However, assessing the accuracy of different methods in …
well-annotated organisms. However, assessing the accuracy of different methods in …
HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript
T Vo, T Brownmiller, K Hall, TL Jones… - Nucleic Acids …, 2022 - academic.oup.com
In the presence of physiological monovalent cations, thousands of RNA G-rich sequences
can form parallel G-quadruplexes (G4s) unless RNA-binding proteins inhibit, destabilize, or …
can form parallel G-quadruplexes (G4s) unless RNA-binding proteins inhibit, destabilize, or …
Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection
While genetic variants are known to be associated with overall gene abundance in
stimulated immune cells, less is known about their effects on alternative isoform usage. By …
stimulated immune cells, less is known about their effects on alternative isoform usage. By …
Isoform sequencing and state-of-art applications for unravelling complexity of plant transcriptomes
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-
generation sequencing (TGS), offers longer reads than the second-generation sequencing …
generation sequencing (TGS), offers longer reads than the second-generation sequencing …
long-read-tools. org: an interactive catalogue of analysis methods for long-read sequencing data
Background The data produced by long-read third-generation sequencers have unique
characteristics compared to short-read sequencing data, often requiring tailored analysis …
characteristics compared to short-read sequencing data, often requiring tailored analysis …
Accurate spliced alignment of long RNA sequencing reads
Motivation Long-read RNA sequencing technologies are establishing themselves as the
primary techniques to detect novel isoforms, and many such analyses are dependent on …
primary techniques to detect novel isoforms, and many such analyses are dependent on …
Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon
A significant portion of genes in vertebrate genomes belongs to multigene families, with
each family containing several gene copies whose presence/absence, as well as isoform …
each family containing several gene copies whose presence/absence, as well as isoform …