Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Global and precise identification of functional miRNA targets in mESCs by integrative analysis.

  PMID 35899551 · PMC9442311 · EMBO reports · 2022 · 8 claims · 8 setups

  Has reproduction · 93

  Fewer than 10% of expressed genes are directly and functionally regulated by miRNAs in mESCs

  mirna_ko mescs drosha_ko escs bulk western ago2

• Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells.

  PMID 41526192 · PMC12863184 · Genome research · 2026 · 8 claims · 6 setups

  Full-text index only

  microRNAs form four distinct coexpression groups across single mESCs

  embryonic small-seq bulk smart-seq2

• bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

  PMID 41657247 · PMC12884093 · Nucleic acids research · 2026 · 8 claims · 6 setups

  Full-text index only

  bayesReact is a novel fully Bayesian generative model for inferring regulatory motif (e.g., miRNA) activity from bulk or single-cell expression data

  tcga gtex stem embryonic paired semi-synthetic single-cell

• IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.

  PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 7 claims · 3 setups

  Has reproduction · 78

  IsomiR Window is a novel integrated pipeline plus browser GUI that combines over ten third-party tools with a new algorithm capable of detecting all types of isomiRs (5' end, 3' end, tailings, SNP/editing, and fuzzy combinations)

  simulated basal isomir small-rna-seq mirna

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  An SVM-based novel miRNA detection model achieves an average MCC of 0.939 across 32 human cell datasets and outperforms miRDeep2 and miRAnalyzer on phylogenetic conservation of predicted miRNAs

  unmapped pooled colon adipose small novel a-to-i

• Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.

  PMID 37444556 · PMC10340377 · Cancers · 2023 · 8 claims · 6 setups

  Has reproduction · 90

  EV extraction methods vary in reproducibility for isolating small RNAs, with effects on small RNA composition

  evs matched plasma cell-line small differential adapter

• miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.

  PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction

  miRge3.0 is a Python 3-based small RNA-seq and tRF analysis pipeline that improves on miRge2.0 (which was Python 2.7-based)

  sra synthetic qiagen-processed same small umi mirna

• Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

  PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

  erwinia intergenic candidate wounded small northern race

• Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations.

  PMID 35186917 · PMC8851031 · Frontiers in cell and developmental biology · 2022 · 8 claims · 3 setups

  Has reproduction · 56

  SARS-CoV-2 viral preparations show selective enrichment of specific host tRNAs, tRNA fragments, and SRP RNA compared to uninfected VeroE6 cells

  veroe6 cell-free small large trna

• RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.

  PMID 34082707 · PMC8173825 · BMC bioinformatics · 2021 · 8 claims · 1 setups

  Has reproduction · 85

  RNAdetector is a free, cross-platform, user-friendly RNA-Seq analysis software usable locally (stand-alone) or in cloud environments via a GUI

  ncbi small

• sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

  PMID 31114926 · PMC6602500 · Nucleic acids research · 2019 · 8 claims · 1 setups

  Has reproduction

  sRNAtoolbox 2019 update adds automatic processing of the most used small RNA library preparation protocols, including UMI-based protocols, to sRNAbench

  srp046046 small

• DNA polymorphisms and N(6)-methyladenosine RNA methylation influencing microRNA expression and regulatory activity in plants.

  PMID 41792625 · PMC13077827 · BMC plant biology · 2026 · 7 claims · 8 setups

  Full-text index only

  Numerous miRNA precursors and mature miRNAs are differentially expressed between Col-0/NIP and other Arabidopsis accessions/rice varieties with distinct habitat parameters

  arabidopsis rice mirna rna-seq small degradome

• FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA.

  PMID 41704564 · PMC12907730 · NAR genomics and bioinformatics · 2026 · 6 claims · 1 setups

  Full-text index only

  FragmentFinder (FF) is a user-friendly, Windows-executable tool that identifies and characterizes short RNAs excised from any noncoding RNA precursor, requiring no computational background

  pancreatic sncrna

• MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases.

  PMID 41800385 · PMC12961272 · Bioinformatics advances · 2026 · 8 claims · 5 setups

  Full-text index only

  MIRit is a comprehensive, open-source R/Bioconductor framework for integrative miRNA–mRNA analysis that supports both paired and unpaired datasets using statistically appropriate methods.

  myocardial ccrcc brodmann synthetic mirna-seq microarray small

• Conservation and losses of non-coding RNAs in avian genomes.

  PMID 25822729 · PMC4378963 · PloS one · 2015 · 8 claims · 6 setups

  Has reproduction · 100

  Homology-based covariance model (Rfam CM) annotation, combined with tRNAscan-SE and miRBase-derived models, identifies ncRNA loci across 48 avian genomes

  avian bird chicken covariance trna microrna