ArticleNucleic acids research2019
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
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Who cites it
113 citing papers in PubMed, 192 citations in OpenAlex.
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- FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA.NAR genomics and bioinformatics · 2026Article
- Advancing Extracellular Vesicle Research: A Review of Systems Biology and Multiomics Perspectives.Proteomics · 2026Review
- Sperm RNA landscape during sexual maturation in Duroc boars.BMC genomics · 2026Article
- Dysregulation of miRNAs in Sicilian Patients with Autism Spectrum Disorder.Biomedicines · 2026Article
- Isolation of Red Beet Plant-Derived Nanovesicles, and Characterization of Their Molecular Content and Biological Activities in Human Cells.International journal of molecular sciences · 2025Article
- MicroRNA bioinformatics in precision oncology: an integrated pipeline from NGS to AI-based target discovery.Journal of applied genetics · 2025Review
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- Common and distinct circulating microRNAs in four neurovascular disorders.Biochemistry and biophysics reports · 2025Article
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- Insights into the Regulatory Roles of miRNAs in the Salivary Glands of the Soft TicksPathogens (Basel, Switzerland) · 2025Article
- RLSuccSite: succinylation sites prediction based on reinforcement learning dynamic with balanced reward mechanism and three-peaks enhanced method for physicochemical property scores.Journal of cheminformatics · 2025Article
- Comprehensive sequencing profile and functional analysis of IsomiRs in human pancreatic islets and beta cells.Diabetologia · 2025Article
- The Small RNA Landscape in Azoospermia: Implications for Male Infertility and Sperm Retrieval-A Preliminary Study.International journal of molecular sciences · 2025Article
- miRNA profiling of hiPSC-derived neurons from monozygotic twins discordant for schizophrenia.Schizophrenia (Heidelberg, Germany) · 2025Article
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- Blood-derived APLP1Science advances · 2025Article
53 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.
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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.