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).

• Optimisation of the core subset for the APY approximation of genomic relationships.

  PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

  Has reproduction · 85

  APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

  simulated real genotyped gblup population

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.

  cattle breed-pooled indian merged whole-genome snv template

• Iterative pruning PCA improves resolution of highly structured populations.

  PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups

  Full-text index only

  ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data

  simulated hapmap cattle shriver's simulated snp comparative

• Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

  PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

  bovine panel agresearch intact random gene northern

• A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts.

  PMID 18958306 · PMC2573734 · Molecular vision · 2008 · 8 claims · 7 setups

  Full-text index only

  The disease locus maps to chromosome 3q21-25, linked to markers D3S2322 and D3S1541

  four-generation bfsp2 wild-type microsatellite direct denaturing

• Mutation G61C in the CRYGD gene causing autosomal dominant congenital coralliform cataracts.

  PMID 18334953 · PMC2268897 · Molecular vision · 2008 · 8 claims · 6 setups

  Full-text index only

  A G61C (P.G61C) missense mutation in CRYGD causes autosomal dominant congenital coralliform cataracts in this family

  four-generation genomic crygd wild-type genotyping direct denaturing

• Discovering the phylodynamics of RNA viruses.

  PMID 19855824 · PMC2756585 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A comprehensive 'discovery phase' integrating ecological and evolutionary dynamics of RNA viruses across scales is needed to achieve a full phylodynamic understanding

  h3n2 influenza avian foot-and-mouth bayesian phylogenetic whole-genome