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).

• The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

  PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

  Full-text index only

  P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

  sequences orthomcl yeast orthomcl jaccard phylogenetic

• DupyliCate: mining, classifying, and characterizing gene duplications.

  PMID 42209743 · PMC13219399 · Scientific reports · 2026 · 8 claims · 8 setups

  Full-text index only

  DupyliCate is a Python tool for identifying and classifying gene duplication arrays, using BUSCO-based species-specific thresholds and offering integrated expression divergence and Ka/Ks analysis.

  arabidopsis thaliana brassicales phytozome sequence duplication runtime

• Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

  PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

  Full-text index only

  The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

  cerevisiae mitocarta mitochondrial tissues comparative subcellular gene

• Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

  PMID 41327045 · PMC12763953 · BMC plant biology · 2025 · 8 claims · 7 setups

  Has reproduction · 58

  Genome-wide identification revealed 102 GLPs in B. juncea, 51 in B. nigra, and 48 in B. rapa

  juncea promoter duplicated super genome-wide phylogenetic synteny

• Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

  PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

  stricta long-read short-read hi-c