ArticleBioinformatics (Oxford, England)2015
Chimira: analysis of small RNA sequencing data and microRNA modifications.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
71 citing papers in PubMed, 116 citations in OpenAlex.
- MicroRNAs in endometriosis: bioinformatics resources, machine learning strategies, and multi-omics perspectives.Journal of translational medicine · 2026Review
- PymiRa: A rapid and accurate classification tool for small non-coding RNAs, including microRNAs.PLoS computational biology · 2026Article
- Deciphering miRNA signatures in axial spondyloarthritis: The link between miRNA-1-3p and pro-inflammatory cytokines.Heliyon · 2024Article
- Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes.RNA (New York, N.Y.) · 2024Article
- Pericardial Fluid Accumulates microRNAs That Regulate Heart Fibrosis after Myocardial Infarction.International journal of molecular sciences · 2024Article
- Role of myocardial microRNAs in the long-term ventricular remodelling of patients with aortic stenosis.European heart journal open · 2024Article
- Differential microRNA editing may drive target pathway switching in human temporal lobe epilepsy.Brain communications · 2024Article
- The Transcription Factor, α1ACT, Acts Through a MicroRNA Network to Regulate Neurogenesis and Cell Death During Neonatal Cerebellar Development.Cerebellum (London, England) · 2023Article
- miRNA Expression in Fibroblastic Foci within Idiopathic Pulmonary Fibrosis Lungs Reveals Novel Disease-Relevant Pathways.The American journal of pathology · 2023Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- Article
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type.RNA (New York, N.Y.) · 2022Article
- gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues.Scientific data · 2022Article
- The Lung Alveolar Cell (LAC) miRNome and Gene Expression Profile of the SP-A-KO Mice After Infection With and Without Rescue With Human Surfactant Protein-A2 (1AFrontiers in immunology · 2022Article
- Menopausal Transition: Prospective Study of Estrogen Status, Circulating MicroRNAs, and Biomarkers of Bone Metabolism.Frontiers in endocrinology · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm.Cellular and molecular life sciences : CMLS · 2021Review
- Urinary extracellular vesicles: Assessment of pre-analytical variables and development of a quality control with focus on transcriptomic biomarker research.Journal of extracellular vesicles · 2021Article
- Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements.Biology · 2021Review
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledChimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3'-modifications (e.g. uridylation, adenylation), 5'-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface. AVAILABILITY AND IMPLEMENTATION: Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira. CONTACT: aje@ebi.ac.uk 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.