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).

• Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

  PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

  Full-text index only

  202 novel box H/ACA RNA-related sequences were identified in the human genome

  genome chimpanzee aca flanking megablast comparative sequence

• A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

  PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

  tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided

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

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

  Has reproduction · 95

  254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs) were detected in the P. ostreatus CCEF00389 genome assembly, the first genome-scale identification of sncRNAs for a basidiomycete.

  ostreatus ccef00389 genome bulk computational

• 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

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc