RNA structure, binding, and coordination in Arabidopsis
Sign Up to like & getrecommendations! Published in 2017 at "Wiley Interdisciplinary Reviews: RNA"
DOI: 10.1002/wrna.1426
Abstract: From the moment of transcription, up through degradation, each RNA transcript is bound by an ever‐changing cohort of RNA binding proteins. The binding of these proteins is regulated by both the primary RNA sequence, as… read more here.
Keywords: rna secondary; rna; secondary structure; rna structure ... See more keywords
Predicting RNA Secondary Structure Using In Vitro and In Vivo Data.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1851-6_2
Abstract: The new flow of high-throughput RNA secondary structure data coming from different techniques allowed the further development of machine learning approaches. We developed CROSS and CROSSalive, two algorithms trained on experimental data able to predict… read more here.
Keywords: rna secondary; predicting rna; secondary structure; vitro vivo ... See more keywords
Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Plant"
DOI: 10.1016/j.molp.2018.01.008
Abstract: RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, we… read more here.
Keywords: rna secondary; rice; secondary structure; conservation ... See more keywords
RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure
Sign Up to like & getrecommendations! Published in 2017 at "Nature Communications"
DOI: 10.1038/s41467-017-01458-8
Abstract: Adenosine deaminase acting on RNA 1 (ADAR1) is the master RNA editor, catalyzing the deamination of adenosine to inosine. RNA editing is vital for preventing abnormal activation of cytosolic nucleic acid sensing pathways by self-double-stranded… read more here.
Keywords: rna secondary; adar1; rna; secondary structure ... See more keywords
R2DT is a framework for predicting and visualising RNA secondary structure using templates
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-23555-5
Abstract: Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and… read more here.
Keywords: framework predicting; rna secondary; r2dt framework; visualising rna ... See more keywords
Increasing the specificity of CRISPR systems with engineered RNA secondary structures
Sign Up to like & getrecommendations! Published in 2019 at "Nature biotechnology"
DOI: 10.1038/s41587-019-0095-1
Abstract: CRISPR (clustered regularly interspaced short palindromic repeat) systems have been broadly adopted for basic science, biotechnology, and gene and cell therapy. In some cases, these bacterial nucleases have demonstrated off-target activity. This creates a potential… read more here.
Keywords: rna secondary; crispr systems; crispr; increasing specificity ... See more keywords
Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad186
Abstract: Computational analysis of RNA sequences constitutes a crucial step in the field of RNA biology. As in other domains of the life sciences, the incorporation of artificial intelligence and machine learning techniques into RNA sequence… read more here.
Keywords: machine; machine learning; rna secondary; biology ... See more keywords
ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa147
Abstract: SUMMARY Current methods for comparing RNA secondary structures are based on tree representations and exploit edit distance or alignment algorithms. Most of them can only process structures without pseudoknots. To overcome this limitation we introduce… read more here.
Keywords: rna secondary; tool alignment; secondary structures; aspralign tool ... See more keywords
The super‐n‐motifs model: a novel alignment‐free approach for representing and comparing RNA secondary structures
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw773
Abstract: Motivation: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take… read more here.
Keywords: rna secondary; secondary structures; motifs model; alignment free ... See more keywords
Structurexplor: a platform for the exploration of structural features of RNA secondary structures
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx323
Abstract: Summary Discovering function-related structural features, such as the cloverleaf shape of transfer RNA secondary structures, is essential to understand RNA function. With this aim, we have developed a platform, named Structurexplor, to facilitate the exploration… read more here.
Keywords: rna secondary; secondary structures; structurexplor platform; structural features ... See more keywords
e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic acids research"
DOI: 10.1093/nar/gkad296
Abstract: e-RNA is a collection of web-servers for the prediction and visualisation of RNA secondary structures and their functional features, including in particular RNA-RNA interactions. In this updated version, we have added novel tools for RNA… read more here.
Keywords: structure; secondary structure; rna; visualisation ... See more keywords