ArticleBioinformatics (Oxford, England)2018
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
34 citing papers in PubMed.
- Copper-sensitive OsSPL9 TF regulates expression of indica rice domestication-associated miRNAs and phenotypes.Communications biology · 2026Article
- Technical considerations and review of urinary microRNAs as biomarkers for chronic kidney disease in dogs and cats.Veterinary clinical pathology · 2025Review
- Loss of function of chromatin remodeler OsCLSY4 leads to RdDM-mediated mis-expression of endosperm-specific genes affecting grain qualities.PLoS genetics · 2025Article
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler.Nature communications · 2024Article
- Identification of plant microRNAs using convolutional neural network.Frontiers in plant science · 2024Article
- Benchmarking of bioinformatics tools for NGS-based microRNA profiling with RT-qPCR method.Functional & integrative genomics · 2023Article
- RA-induced prominence-specific response resulted in distinctive regulation of Wnt and osteogenesis.Life science alliance · 2023Article
- Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.Genome research · 2023Article
- Dynamic Regulation of Grapevine's microRNAs in Response to Mycorrhizal Symbiosis and High Temperature.Plants (Basel, Switzerland) · 2023Article
- Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking.International journal of molecular sciences · 2023Article
- Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy.Frontiers in bioinformatics · 2023Article
- tiny-count: a counting tool for hierarchical classification and quantification of small RNA-seq reads with single-nucleotide precision.Bioinformatics advances · 2023Article
- Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain.Plant physiology · 2022Article
- A plant tethering system for the functional study of protein-RNA interactions in vivo.Plant methods · 2022Article
- Identification of Two Exosomal miRNAs in Circulating Blood of Cancer Patients by Using Integrative Transcriptome and Network Analysis.Non-coding RNA · 2022Article
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.The Plant cell · 2022Article
- MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.BMC bioinformatics · 2022Article
- CRISPR/Cas9-mediated fine-tuning of miRNA expression in tetraploid potato.Horticulture research · 2022Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Motivation: RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential. Results: We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses. Availability and implementation: The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk. The source code is available at: https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.