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).

• miRBase: tools for microRNA genomics.

  PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

  species utrs genomic chromosome genome-wide target transcription

• 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

• Developmental and genetic regulation of human surfactant protein B in vivo.

  PMID 18776725 · PMC2765709 · Neonatology · 2009 · 8 claims · 7 setups

  Full-text index only

  Pro-SP-B peptides are more common in developmentally less mature humans (amniotic fluid, neonatal tracheal aspirates) than in adults

  amniotic tracheal bronchoalveolar simultaneous immunoblotting reducing gene

• Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.

  PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 7 claims · 8 setups

  Has reproduction · 95

  Genome-scale identification detected 254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs, and other Rfam-classified sncRNAs) in the P. ostreatus CCEF00389 genome assembly

  pleurotus ostreatus ccef00389 sncrnas whole-genome rna-seq rfam

• An analysis of human microRNA and disease associations.

  PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

  literature-derived diseases mirnas mirna literature bipartite mirna

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

  Full-text index only

  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative