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).

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

  PMID 37444556 · PMC10340377 · Cancers · 2023 · 7 claims · 4 setups

  Has reproduction · 90

  Different EV isolation methods vary in reproducibility for isolating small RNAs and have characteristic effects on small RNA composition, with differential ultracentrifugation showing the highest variability/lowest replicability.

  evs plasma small isolation validation

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

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

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel

• 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

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

  PMID 31114926 · PMC6602500 · Nucleic acids research · 2019 · 8 claims · 3 setups

  Has reproduction

  sRNAtoolbox 2019 adds all major small RNA library preparation protocols (including UMI-based) to sRNAbench with automatic protocol-specific preprocessing.

  biological srp046046 ensembl small consensus genome

• Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

  PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 86

  RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

  peripheral demrnas blood thp-1 rna-seq annotation wgcna

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

  PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 8 claims · 2 setups

  Has reproduction · 78

  IsomiR Window is an integrated, user-friendly platform that systematically identifies, quantifies, and functionally explores isomiR expression in small-RNA-seq datasets without requiring computational skills

  simulated basal small-rna-seq

• DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

  PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 6 claims · 7 setups

  Has reproduction · 84

  DeepProg, an ensemble of deep-learning and machine-learning models, robustly predicts patient survival subtypes from multi-omics data and explicitly models survival as the objective while predicting new patient risks

  tcga breast metabric brca bulk mirna methylation

• miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.

  PMID 34637468 · PMC8509996 · PloS one · 2021 · 7 claims · 6 setups

  Has reproduction · 100

  RBPs beyond Drosha/DGCR8/Dicer are involved in regulating miRNA biogenesis and explain its spatio-temporal nature

  tissues computational rbps clip-seq rna-seq srna-seq

• Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

  PMID 37948380 · PMC10637681 · PloS one · 2023 · 6 claims · 7 setups

  Has reproduction · 90

  Three stem cell-related genes (ORC1L, KIF20A, DLGAP5) are differentially expressed in LUAD and correlate with altered immune infiltration and reduced patient survival.

  luad differentially bulk mirna-seq microarray

• MUTACLASH: identifying functional small RNA target sites using crosslinking-induced mutations.

  PMID 41330639 · PMC12810180 · RNA (New York, N.Y.) · 2026 · 8 claims · 4 setups

  Has reproduction · 30

  CIMs are present and enriched in PIWI (piRNA) and Argonaute (miRNA) CLASH data and serve as molecular footprints of Argonaute binding on target mRNAs.

  elegans clash iclip sequencing

• nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.

  PMID 36694127 · PMC9875403 · BMC bioinformatics · 2023 · 8 claims · 4 setups

  Has reproduction · 76

  Existing circRNA workflows are limited: none delineate circRNA-miRNA interactions and only one performs differential expression analysis, requiring users to supplement missing analysis types with in-house expertise

  paired-end rna-seq mature circrna read circrna mirna

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

  PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 6 claims · 5 setups

  Has reproduction

  miRge3.0 with 12 CPUs consistently has the best execution speed compared to miRge2.0, Chimira and sRNAbench

  sra synthetic qiagen small small umi differential

• Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.

  PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 6 claims · 7 setups

  Has reproduction · 91

  CEL (carboxyl ester lipase) is the real hub gene shared between CP and PDAC and is markedly downregulated in PDAC

  pancreatic gse143754 pdac tcga microarray wgcna differential

• Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

  PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 8 setups

  Has reproduction · 19

  Shared differentially expressed genes link glioblastoma with ischemic stroke and with moyamoya disease, revealing molecular associations among the diseases.

  glioblastoma ischemic moyamoya shared bulk microarray gene

• Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

  PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

  Has reproduction · 55

  RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

  amir-sul col 14-day-old arabidopsis small rna-seq gel

• 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

  PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

  Has reproduction · 93

  Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.

  aml bulk mutation copy

• Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

  PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

  Has reproduction · 50

  2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

  flower roots analysis parental high-throughput quantitative pcr

• Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.

  PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 3 setups

  Has reproduction · 89

  Graph Random Forest (GRF) embeds graph/network information directly into the decision-tree building process by splitting on features in the k-hop neighborhood of a data-driven head-splitting node.

  scale-free non-small embryonic simulation rna-seq

• Intergenic risk variant rs56258221 skews the fate of naive CD4(+) T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis.

  PMID 38901430 · PMC11293351 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 58

  rs56258221 (BACH2/MIR4464) associates with a distinct peripheral blood T cell immunophenotype in people with PSC

  peripheral liver facs-sorted cd4+ flow bulk cite-seq

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

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

  Has reproduction · 100

  34 lncRNA-associated loci are conserved between birds and mammals, and 12 of these were validated in chicken by RNA-seq.

  avian bird chicken covariance-model trna mirna