ArticleNucleic acids research2011
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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Who cites it
151 citing papers in PubMed.
- MicroRNAs in endometriosis: bioinformatics resources, machine learning strategies, and multi-omics perspectives.Journal of translational medicine · 2026Review
- FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA.NAR genomics and bioinformatics · 2026Article
- Screening for non-invasive rsRNA biomarkers to assess embryo quality utilizing ultra-sensitive pandora sequencing combined with machine learning.Journal of assisted reproduction and genetics · 2025Article
- MicroRNAs in plant-parasitic nematodes: what are they and why should we care?Journal of nematology · 2025Review
- Prenatal maternal stress in rats alters the epigenetic and transcriptomic landscape of the maternal-fetal interface across four generations.Communications biology · 2025Article
- A Review of the Application of Spatial Transcriptomics in Neuroscience.Interdisciplinary sciences, computational life sciences · 2024Review
- Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking.International journal of molecular sciences · 2023Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- The pale spear-nosed bat: A neuromolecular and transgenic model for vocal learning.Annals of the New York Academy of Sciences · 2022Article
- Differential miRNA expression profiling of highly pathogenic avian influenza virus H5N1 infected chicken lungs reveals critical microRNAs, biological pathways and genes involved in the molecular pathogenesis.Virologica Sinica · 2022Article
- ITAS: Integrated Transcript Annotation for Small RNA.Non-coding RNA · 2022Article
- Interrelationship between miRNA and splicing factors in pancreatic ductal adenocarcinoma.Epigenetics · 2022Review
- Analysis of the p53/microRNA Network in Cancer.Advances in experimental medicine and biology · 2022Review
- A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data.Frontiers in bioinformatics · 2022Article
- MicroRNA-mediated bioengineering for climate-resilience in crops.Bioengineered · 2021Review
- AASRA: an anchor alignment-based small RNA annotation pipeline†.Biology of reproduction · 2021Article
- RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.BMC bioinformatics · 2021Article
- Evaluation and application of tools for the identification of known microRNAs in plants.Applications in plant sciences · 2021Review
- Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing.Briefings in bioinformatics · 2021Article
91 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new version of miRanalyzer, a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features. Alignments are now based on the ultrafast short-read aligner Bowtie (granting also colour space support, allowing mismatches and improving speed) and 31 genomes, including 6 plant genomes, can now be analysed (previous version contained only 7). Differences between plant and animal microRNAs have been taken into account for the prediction models and differential expression of both, known and predicted microRNAs, between two conditions can be calculated. Additionally, consensus sequences of predicted mature and precursor microRNAs can be obtained from multiple samples, which increases the reliability of the predicted microRNAs. Finally, a stand-alone version of the miRanalyzer that is based on a local and easily customized database is also available; this allows the user to have more control on certain parameters as well as to use specific data such as unpublished assemblies or other libraries that are not available in the web server. miRanalyzer is available at http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php.
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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.