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).

• PolyGenie: a reproducible Nextflow pipeline for phenome-wide association studies using polygenic risk scores.

  PMID 42272542 · PMC13247587 · NAR genomics and bioinformatics · 2026 · 7 claims · 6 setups

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  PolyGenie is an open-source Nextflow pipeline that takes precomputed PRS and phenotype data as input and performs scalable PheWAS analysis across binary and continuous outcomes

  gcat phewas genome-wide genotype

• Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

  PMID 17700570 · PMC2360390 · British journal of cancer · 2007 · 8 claims · 3 setups

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  Germline protein-truncating BRCA2 mutations confer an elevated relative risk (~7.8-fold) of early-onset prostate cancer in Caucasian men

  peripheral population-based same germline epidemiological genotype-phenotype

• Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

  PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 6 claims · 8 setups

  Has reproduction · 89

  STEC prevalence in surface water varies by watershed and by season in the Lower Mainland of British Columbia.

  surface sediment isolate presumptive hydrophobic stx monoplex

• Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

  PMID 15496254 · PMC3320417 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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  SFG Rickettsia infection prevalence in Maryland D. variabilis was 3.8% (15/392)

  dermacentor tick-derived glta field pcr single sequencing

• Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension.

  PMID 15661075 · PMC547905 · BMC medical genetics · 2005 · 8 claims · 7 setups

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  Heterozygous carriage of common βENaC/γENaC variants (G589S, i12-17CT, V546I) is significantly more prevalent in essential hypertension patients (9.2%) than in normotensive males (2.9%) or blood donors (3.0%)

  hypertensive lymphocytes βenac xenopus targeted pcr-rflp plasma

• Towards alignment independent quantitative assessment of homology detection.

  PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

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  The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

  curated homologene swiss-prot fruit signalp homologene-based fhom

• Advances in breast cancer: pathways to personalized medicine.

  PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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  Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

  population-based women breast high-risk germline genome-wide microarray

• An integrated genomic analysis of human glioblastoma multiforme.

  PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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  IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

  gbm additional missense exome targeted snp

• Population carrier frequency of hMSH2 and hMLH1 mutations.

  PMID 11104559 · PMC2363440 · British journal of cancer · 2000 · 6 claims · 6 setups

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  Population carrier frequency of hMSH2/hMLH1 mutations in people aged 15-74 years is estimated at 1:3139 (95% CI 1:1247-1:7626)

  peripheral scottish finnish baltimore cdna pedigree systematic

• MSI test to distinguish between HNPCC and other predisposing syndromes -- of value in tailored surveillance.

  PMID 15528791 · PMC3839337 · Disease markers · 2004 · 8 claims · 5 setups

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  MSI (or immunohistochemistry) testing applied to a pre-selected patient with a family history or early-onset colorectal cancer can distinguish HNPCC from unknown non-HNPCC colorectal cancer syndromes.

  population-based swedish colorectal hnpcc clinical histopathological microsatellite

• 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

• Bacillus Calmette-Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer.

  PMID 35311085 · PMC8930202 · Frontiers in oncology · 2022 · 8 claims · 8 setups

  Has reproduction · 30

  BCG therapy has bidirectional effects on tumor evolution and immune checkpoint landscape, with a significant reduction in neoantigen burden percentage in relapsed tumors

  tur matched nmibc relapsed whole-exome sequencing immune

• Environmental genome project: focusing on differences to understand the whole.

  PMID 12460813 · PMC1241127 · Environmental health perspectives · 2002 · 8 claims · 4 setups

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  The EGP has generated a working list of more than 550 environmentally responsive genes involved in pathways such as metabolism, DNA repair, and cell cycle control as candidates for SNP resequencing.

  environmentally comparative asthma specified resequencing transgenic genetic

• Genomics and the prevention and control of common chronic diseases: emerging priorities for public health action.

  PMID 15888216 · PMC1327699 · Preventing chronic disease · 2005 · 8 claims · 6 setups

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  Family history is the most consistent risk factor for almost all human diseases across the lifespan.

  adults care utah epidemiologic national observational population-based

• Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

  PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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  Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

  gastrointestinal ls174t pl3 msi gene rt-pcr rad51

• Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?

  PMID 18557994 · PMC2481495 · Breast cancer research : BCR · 2008 · 8 claims · 8 setups

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  Mutation frequencies in ATM, BRIP1, PALB2 and CHEK2 are many times higher in women with strong breast cancer family history (familial cases) than in population controls.

  women familial finnish unselected germline international statistical

• A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

  PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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  Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

  serum plasmids coli pcr oligonucleotide chip

• Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data.

  PMID 34503493 · PMC8428960 · BMC medicine · 2021 · 8 claims · 6 setups

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  Reopening all schools under lockdown-equivalent conditions would likely substantially increase the reproduction number of SARS-CoV-2

  general england studies longitudinal age-stratified next-generation

• Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.

  PMID 41772715 · PMC12983593 · Microbiome · 2026 · 8 claims · 8 setups

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  Quiescent prophages dominate gut viral metagenomes, consistent with 'piggyback-the-winner' dynamics

  fecal metagenomic custom subset shotgun viral kraken2-based

• Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

  PMID 42064353 · PMC13126010 · Wellcome open research · 2026 · 7 claims · 7 setups

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  Deformable gametocytes are immediately infectious upon release from the bone marrow into circulation.

  synchronized falciparum blood microsphere bulk exflagellation