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).

• 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

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• Reusable building blocks in biological systems.

  PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 4 setups

  Has reproduction · 82

  Biological systems can be decomposed into phenotypic building blocks (PBBs) via k-maximally reusable decompositions (k-MRD) that maximize average reusability across conditions.

  tissues conditions randomized est-based mirna randomization

• 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

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

  Full-text index only

  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence