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).

• Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts.

  PMID 39959292 · PMC11825298 · Bio-protocol · 2025 · 7 claims · 6 setups

  Has reproduction · 90

  Mapping adapter-trimmed reads first to the pathogen genome recovers more pathogen reads than the traditional host-first mapping approach.

  monocyte-derived raw same trimmed dual fastqc adapter

• Screening large-scale association study data: exploiting interactions using random forests.

  PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups

  Full-text index only

  Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.

  simulated same simulation random fisher

• A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

  PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 75

  Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.

  pure enriched stec-negative extracted ont real-time artificial

• Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.

  PMID 18793462 · PMC2537568 · BMC bioinformatics · 2008 · 8 claims · 4 setups

  Full-text index only

  Batch size affects genotype calling results (call rate and concordance) and the resulting lists of significantly associated SNPs.

  hapmap genotype genotype raw case-control

• Accurate whole human genome sequencing using reversible terminator chemistry.

  PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups

  Full-text index only

  A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.

  bac flow-sorted same yoruba reversible snp targeted

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

  PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

  Full-text index only

  2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

  simulated same snp type two-locus 2lomb benchmark

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman