Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs
Explore this paper's citation graph
Summary
A user’s guide for CoRAL (Classification of RNAs by Analysis of Length), a computational method for discriminating between different classes of RNA using high-throughput small RNA-sequencing data that can give biologists a glimpse into the characteristics of different RNA processing pathways and how these might differ between tissue types, biological conditions, or even different species.
- Type
- article
- Published
- 2013-10-18
- Cited by
- 16
- References
- 30
- Access
- Open access
- OpenAlex
- https://openalex.org/W1970757825
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:24070861
Keywords
Small nucleolar RNA, Small RNA, RNA, Biology, microRNA
References
- Fast folding and comparison of RNA secondary structures
- Antisense Transcription in the Mammalian Transcriptome
- A Major Epigenetic Programming Mechanism Guided by piRNAs
- DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments
- Identification of human miRNA precursors that resemble box C/D snoRNAs
- CoRAL: predicting non-coding RNAs from small RNA-sequencing data
- A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline
- Human miRNA Precursors with Box H/ACA snoRNA Features
- Cutadapt removes adapter sequences from high-throughput sequencing reads
- Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs
- tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA in Haloferax volcanii
- A novel class of small RNAs: tRNA-derived RNA fragments (tRFs).
- SAVoR: a server for sequencing annotation and visualization of RNA structures
- Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis.
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- The UCSC Genome Browser database: update 2011
- miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
- Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
- R: A language and environment for statistical computing.
- Random Forests
Cited by
- Predicting and classifying short non-coding RNAs using a multiclass evolutionary methodology
- Classification of RNA-Seq Data via Bagging Support Vector Machines
- Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi
- Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection
- A survey of software tools for microRNA discovery and characterization using RNA-seq
- Revisit of Machine Learning Supported Biological and Biomedical Studies.
- Tuning the Performance of Synthetic Riboswitches using Machine Learning.
- A systematic review of the application of machine learning in the detection and classification of transposable elements
- Altered non-coding RNA expression profile in F1 progeny 1 year after parental irradiation is linked to adverse effects in zebrafish
- Analyzing RNA-Seq Gene Expression Data Using Deep Learning Approaches for Cancer Classification
- Analyzing RNA-Seq Gene Expression Data for Cancer Classification Through ML Approach
- Epigenetic Biomarkers in Thrombophilia-Related Pregnancy Complications: Mechanisms, Diagnostic Potential, and Therapeutic Implications: A Narrative Review
- Using transfer learning approaches to predict RNA-Seq gene expression data for cancer classification
- Genomic approaches for studying transcriptional and post-transcriptional processes.
- Machine-Learning-Based Taxonomical Approach to Predict Circular RNA
- Machinesof RNA-Seq Data via Bagging Support Vector
Related papers
- Pseudouridines on Trypanosoma brucei spliceosomal small nuclear RNAs and their implication for RNA and protein interactions
- Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function
- SnoRNA guide activities: real and ambiguous
- Analysis of Snu13p mutations reveals differential interactions with the U4 snRNA and U3 snoRNA.
- Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk
- Beyond rRNA and snRNA: tRNA as a 2′-O-methylation target for nucleolar and Cajal body box C/D RNPs
- Identification of 13 novel human modification guide RNAs.
- Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis
- A Cajal body-specific pseudouridylation guide RNA is composed of two box H/ACA snoRNA-like domains.
- Regulation of small RNA stability: methylation and beyond