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 mammalian phenotype ontology: enabling robust annotation and comparative analysis.

  PMID 20052305 · PMC2801442 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 6 setups

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  The Mammalian Phenotype (MP) Ontology enables classification and organization of phenotypic data for mouse and other mammalian species in a computationally useful, standardized manner.

  genotypes neural inbred viable phenotype phylogenetic comparative

• Needles in the haystack: identifying individuals present in pooled genomic data.

  PMID 19798441 · PMC2747273 · PLoS genetics · 2009 · 8 claims · 7 setups

  Full-text index only

  The distribution of T for null samples (individuals not in F or G) deviates strongly from the assumed standard normal, in both location and width.

  cgems hapmap genetic-distance within-population snp-count

• Differentiating human from animal isolates of Cryptosporidium parvum.

  PMID 9866750 · PMC2640237 · Emerging infectious diseases · 1998 · 7 claims · 5 setups

  Full-text index only

  Two distinct genotypes of C. parvum (human/anthroponotic and bovine/zoonotic) exist, distinguishable by TRAP-C2 gene sequence differences at five nucleotide positions.

  parvum cloned aligned fecal pcr pcr-rflp sequencing

• Direct maximum parsimony phylogeny reconstruction from genotype data.

  PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

  simulated mitochondrial lipoprotein coalescent maximum sliding-window

• Imputation of missing genotypes: an empirical evaluation of IMPUTE.

  PMID 19077279 · PMC2636842 · BMC genetics · 2008 · 8 claims · 7 setups

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  IMPUTE achieves 97% median genotype imputation accuracy in Caucasian (NNC) subjects when <10% of SNPs are untyped

  caucasian african random thai genome-wide chromosome principal

• 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

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

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

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

  simulated same simulation random fisher

• Software for tag single nucleotide polymorphism selection.

  PMID 16004730 · PMC3525260 · Human genomics · 2005 · 8 claims · 3 setups

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  Pairwise R2 methods tend to pick more tagging SNPs than strictly needed because they miss redundancy where two or more tag SNPs jointly predict an untagged SNP with no single direct surrogate.

  tgfbr1 encode candidate tag haplotype

• Imputation-based analysis of association studies: candidate regions and quantitative traits.

  PMID 17676998 · PMC1934390 · PLoS genetics · 2007 · 8 claims · 2 setups

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  Imputation-based Bayesian regression increases power to detect association compared with standard single-SNP tests, even when the causal variant is directly typed

  study phenotyped genotype bayesian

• Genotypic analysis of two hypervariable human cytomegalovirus genes.

  PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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  UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

  hcmv clinical pcr ul146 pcr nested molecular

• Catechol-O-methyltransferase (COMT) gene variants: possible association of the Val158Met variant with opiate addiction in Hispanic women.

  PMID 18270997 · PMC2909109 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 8 claims · 5 setups

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  The G/A and A/A genotypes of G472A (Val158Met) are point-wise significantly associated with opiate addiction in Hispanic women but not men (P=0.049)

  genomic opioid-dependent subjects direct taqman statistical

• Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits.

  PMID 39901160 · PMC11789355 · Genome biology · 2025 · 8 claims · 2 setups

  Has reproduction · 86

  Multi-INTACT achieves higher power than existing single-gene-product methods while maintaining calibrated false discovery rates in simulations.

  simulated plasma multi-snp twas

• QTLs for heat-induced stomatal anatomy underpin gas exchange variation in field-grown wheat.

  PMID 42231893 · PMC13223016 · Frontiers in plant science · 2026 · 8 claims · 6 setups

  Has reproduction · 100

  Heat stress via delayed sowing reduces stomatal conductance (gs) and gas exchange efficiency (gse) despite unchanged theoretical maximum anatomical conductance (gsmax), revealing a decoupling of structural potential and physiological performance under stress.

  field-grown microscope wheat field stomatal in-field deep

• Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.

  PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome

• CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

  PMID 15507145 · PMC526769 · BMC medical genetics · 2004 · 8 claims · 7 setups

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  PCR amplification and sequencing of CLC-2 revealed 1 SNP in the promoter, 4 SNPs in intron 1, and none in exon 20

  nasal genomic ib3-1 western pcr fisher's

• Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

  PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

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  Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

  individuals mother-father-child transcribed snp quantitative multiplex

• Impact of RTS,S/AS02(A) and RTS,S/AS01(B) on genotypes of P. falciparum in adults participating in a malaria vaccine clinical trial.

  PMID 19924281 · PMC2773849 · PloS one · 2009 · 7 claims · 4 setups

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  Both RTS,S/AS02A and RTS,S/AS01B vaccines reduce multiplicity of infection (MOI) of breakthrough P. falciparum infections

  falciparum malaria-experienced blood csp msp-1 randomized

• Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

  PMID 19896990 · PMC3529174 · Virus research · 2010 · 7 claims · 5 setups

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  Both HCV-1a and HCV-1b show abundant slightly deleterious nonsynonymous variants subject to ongoing purifying selection across the polyprotein.

  hcv-1a phylogenetic sequence nucleotide

• Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

  PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

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  145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

  complete mutation sars-cov spike sequence phylogenetic selection

• Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

  PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups

  Has reproduction · 75

  rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases

  saccharomyces model ribose-seq emriboseq rhii-hyden-seq