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).

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

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

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  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

• Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

  PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

  p53 tp53 yeast-based sequence align-gvgd

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

  PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups

  Has reproduction · 85

  AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.

  gnomad alphafold2-predicted alphscore proteins machine secondary physicochemical

• Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

  PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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  FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

  armd dutch fibulin pef6-ssflag mutation computational site-directed

• Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

  PMID 16968793 · PMC1865081 · The Journal of clinical endocrinology and metabolism · 2006 · 8 claims · 7 setups

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  Homozygous StAR missense mutations Val187Met and Arg188Cys cause a novel, milder form of lipoid CAH ('non-classic lipoid CAH') presenting at 2-4 years of age rather than in infancy

  blood cos-1 bacteria mitochondria sequencing cell-based recombinant

• DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

  PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

  Has reproduction · 93

  Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

  homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic

• Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

  PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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  Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

  families genes individuals kidney genome-wide sanger resequencing

• Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

  PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

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  Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

  pancreatic computational targeted prevalence snp

• Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

  PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

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  The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

  genomic pcr-amplified case-control pon1 single-strand direct genetic

• Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

  PMID 20017903 · PMC2803168 · BMC medical genetics · 2009 · 6 claims · 5 setups

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  Only three nucleotide variations in ITGB1BP2 were found among 928 screened subjects, indicating a high degree of conservation of the gene in the populations analyzed

  genomic hela itgb1bp2 melusin direct minigene in-silico