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).

• 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

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• 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

• miRGen: a database for the study of animal microRNA genomic organization and function.

  PMID 17108354 · PMC1669779 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  miRGen is an integrated database combining Genomics, Targets, and Clusters interfaces to study miRNA genomic organization and function across 11 animal genomes

  animal genome mouse-human mirna genomic mirna cross-species

• 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

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger