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).

• Prediction, syntax and semantic grounding in the brain and large language models.

  PMID 41807493 · PMC12979642 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 86

  Nouns show significant pre-onset (anticipatory) neural activity in ERPs/ERFs, suggesting enhanced anticipatory processing for this word class.

  healthy same llama-3.2-1b audio-book combined source cluster-based

• Visualization-based discovery and analysis of genomic aberrations in microarray data.

  PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

  saccharomyces breast yeast array gene

• Characterization of retrocopies in 663 individuals with esophageal squamous cell carcinoma.

  PMID 42058905 · PMC13122676 · iScience · 2026 · 8 claims · 7 setups

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  RIST, a new pipeline combined with GRIPper, refines retrocopy insertion site breakpoints and target-site duplication (TSD) detection, improving on existing tools (GRIPper2, sideRETRO)

  paired tool escc parent whole-genome nanopore sequencing

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp

• Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

  PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

  aspergillus circularized core orthologous mitogenome read organellar

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

  PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups

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  A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.

  sheep genome bac sequence randomization

• MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

  PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

  real combined pre-mirna training random independent repeated

• GRIP-Lung: Generative Model of Response to Drug-Induced Perturbation in Lung Cancer.

  PMID 41977443 · PMC13072768 · International journal of molecular sciences · 2026 · 8 claims · 7 setups

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  GRIP-Lung, a GAN framework embedding cell-line identity and drug conditions, predicts drug-induced gene expression profiles in lung cancer cell lines

  lung nsclc a549 nci-60 bulk five-fold differential