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).

• Completing the map of human genetic variation.

  PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

  Full-text index only

  A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

  genomic fosmid full hapmap paired targeted genotyping

• SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

  PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

  Full-text index only

  EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

  genome affymetrix probe database microarray interactive

• Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

  PMID 19112531 · PMC2610290 · Molecular vision · 2008 · 8 claims · 4 setups

  Full-text index only

  A novel STRA6 missense variant (p.G217E, exon 8) and a novel STRA6 nonsense variant (p.Q592X, exon 18) were identified in one A/M subject and absent from 89 controls, implicating STRA6 in this subject's A/M phenotype.

  genomic stra6 direct variant

• Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

  PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups

  Full-text index only

  GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

  pools pcr genomic gs-flx massively sanger pcr

• Genetic variation in an individual human exome.

  PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

  Full-text index only

  The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

  huref genes subset whole-genome allele functional

• Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes.

  PMID 18648522 · PMC2480479 · Molecular vision · 2008 · 8 claims · 4 setups

  Full-text index only

  A rare CHX10 missense variant (c.728G>A, Gly243Asp) was identified in one PACG patient and absent in 215 controls, and is a possible disease-causing variant

  genomic same chx10 pacg pcr case-control cross-species

• Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

  PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

  Full-text index only

  Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

  aku hgd recombinant hgd missense splice

• Characterization of a natural mutator variant of human DNA polymerase lambda which promotes chromosomal instability by compromising NHEJ.

  PMID 19806195 · PMC2751832 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  The W438 hPolλ variant has reduced base substitution fidelity in vitro compared to wild-type R438

  normal recombinant hpolλ short pcr-sscp ber m13mp2

• Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant.

  PMID 19795481 · PMC3501199 · Human mutation · 2009 · 7 claims · 8 setups

  Full-text index only

  BRCA2 c.6853A>G (p.I2285V) co-occurs in trans with the deleterious founder mutation c.5946delT, supporting classification as a neutral variant

  lymphocytes brca2 brca2-null ashkenazi rt-pcr splicing allelic

• MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

  PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

  Full-text index only

  MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

  sporadic mitochondrial reported ataxia mitochondrial functional compensatory

• Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains.

  PMID 19750224 · PMC2735778 · PLoS pathogens · 2009 · 7 claims · 5 setups

  Full-text index only

  The IRGM −261TT genotype is negatively associated with (protective against) pulmonary TB caused by M. tuberculosis

  pulmonary tuberculosis reporter genotyped case-control gene spoligotyping

• The spectrum of ATM missense variants and their contribution to contralateral breast cancer.

  PMID 17393301 · PMC2137941 · Breast cancer research and treatment · 2008 · 6 claims · 3 setups

  Full-text index only

  ATM missense variant frequency does not differ significantly between CBC and UBC patients, indicating no major impact on overall CBC risk

  germline breast denaturing sanger case-control

• Surfactant protein B gene variations enhance susceptibility to squamous cell carcinoma of the lung in German patients.

  PMID 12107845 · PMC2376109 · British journal of cancer · 2002 · 8 claims · 1 setups

  Full-text index only

  The SP-B intron 4 gene variant is significantly more frequent in squamous cell lung carcinoma (SCC) patients (25.0%) than in matched controls, OR=3.2, P=0.016

  peripheral allele-specific

• The novel duplication HRAS c.186_206dup p.(Glu62_Arg68dup): clinical and functional aspects.

  PMID 32499600 · PMC7576819 · European journal of human genetics : EJHG · 2020 · 7 claims · 3 setups

  Has reproduction

  The novel HRAS c.186_206dup p.(Glu62_Arg68dup) variant was identified in an individual with hypertrophic cardiomyopathy, Chiari 1 malformation and ectodermal findings consistent with a RASopathy.

  hras expressing protein-protein phosphorylation growth

• Structural modeling and functional characterization of a novel gain-of-function TLR8 variant causing severe inflammatory syndrome.

  PMID 41729082 · PMC12956005 · JCI insight · 2026 · 8 claims · 8 setups

  Has reproduction · 89

  TLR8 A518T is a gain-of-function variant that enhances NF-κB activation and increases secretion of proinflammatory cytokines upon stimulation compared with WT TLR8

  plasma pbmcs expressing tlr8 targeted plasma quantitative

• Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

  PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

  gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 7 claims · 8 setups

  Has reproduction

  Tabular ML classifiers (TabNet, XGBoost, LightGBM) trained on tumor-only-derived features achieve state-of-the-art somatic vs germline classification, with AUC>94% on TCGA holdout and AUC>85% on metastatic melanoma.

  tcga metastatic tumor-only whole-exome wes copy-number

• Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

  PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

  Has reproduction · 50

  Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

  sars-cov-2 publicly simulated simulated amplicon-based variant

• A novel HRAS c.466C>T p.(Phe156Leu) variant in two patients with attenuated features of Costello syndrome.

  PMID 35764878 · PMC9437031 · European journal of human genetics : EJHG · 2022 · 8 claims · 6 setups

  Has reproduction

  HRAS c.466C>T p.(Phe156Leu) is a novel de novo pathogenic variant causing an attenuated Costello syndrome phenotype in two unrelated boys

  blood hek293t patients trio gst gap-binding

• Genetic polyploid phasing from low-depth progeny samples.

  PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 73

  WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

  solanum illumina pacbio wh-ppg