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).

• miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

  PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

  major tissues conserved predicted quantitative bead-based microarray

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag

• The D2 dopamine receptor gene and nicotine dependence among bladder cancer patients and controls.

  PMID 19842028 · PMC3719969 · Behavior genetics · 2010 · 8 claims · 5 setups

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  Among ever-smoking controls, A1 and B1 genotypes were associated with greater smoking intensity and younger age at smoking initiation than A2A2/B2B2

  peripheral bladder current genotype pcr-rflp structured fagerström

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 99

  Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.

  coli lymphoblastoid na12878 mixture nanopore cas9-targeted whole-genome

• Mutations in the ST7/RAY1/HELG locus rarely occur in primary colorectal, gastric, and hepatocellular carcinomas.

  PMID 12799635 · PMC2741100 · British journal of cancer · 2003 · 7 claims · 4 setups

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  ST7 gene mutations are rare in primary colorectal, gastric, and hepatocellular carcinomas

  colorectal pcr same clinicopathological pcr-single-strand direct microsatellite

• Mutations in transglutaminase 1 gene in autosomal recessive congenital ichthyosis in Egyptian families.

  PMID 15665393 · PMC3839340 · Disease markers · 2004 · 8 claims · 4 setups

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  An intron-5/exon-6 splice acceptor mutation in TGM1, detectable by MspI digestion, was identified in two Egyptian families at a frequency of 9.6% (5/52 alleles)

  genomic arci pcr clinical pedigree

• Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

  PMID 16969349 · PMC2360724 · British journal of cancer · 2006 · 8 claims · 8 setups

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  K-Ras codon 12 mutations are significantly associated with metastatic (M+) CRC

  crc 202-patient pcr-rflp sscp immunohistochemistry

• Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

  PMID 17626639 · PMC1952070 · BMC cancer · 2007 · 7 claims · 4 setups

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  EGFR mutations (exon 19 deletions, exon 21 L858R) did not correlate with gefitinib response in this cohort

  microdissected formalin-fixed archival clinical pcr fluorescence laser

• Oncogenic mutations in GNAQ occur early in uveal melanoma.

  PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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  Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

  uveal peripheral normal well-characterized pcr sequencing array-based

• Coxiella burnetii genotyping.

  PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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  Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

  coxiella burnetii matrix sequence pcr molecular pcr-based

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• The spectrum of NF1 mutations in Korean patients with neurofibromatosis type 1.

  PMID 16479075 · PMC2733956 · Journal of Korean medical science · 2006 · 7 claims · 5 setups

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  NF1 mutations in Korean patients show a wide spectrum distributed across exon 3 to intron 47 with no mutational hot spots

  blood-derived lymphocytes blood unrelated genomic rt-pcr microsatellite

• Association of DRD4 uVNTR and TP53 codon 72 polymorphisms with schizophrenia: a case-control study.

  PMID 20040103 · PMC2808306 · BMC medical genetics · 2009 · 6 claims · 5 setups

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  Long form DRD4 uVNTR alleles (≥5 repeats) are associated with increased risk of schizophrenia

  blood-derived case-control pcr-rflp direct pcr-based

• Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

  PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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  Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

  msi-h computational rb1cc1 normal pcr nonlinear real-time

• Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

  PMID 19793394 · PMC2765450 · BMC genetics · 2009 · 8 claims · 4 setups

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  The three-locus TaqI B-TaqI D-TaqI A haplotype at DRD2 constitutes a powerful genetic marker reflecting the most ancient dispersal of anatomically modern humans

  genomic genotype rflp haplotype pcr-rflp hardy-weinberg pairwise

• Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand.

  PMID 19643205 · PMC2790030 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2009 · 8 claims · 6 setups

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  The domain II loop of PvAMA-1 is almost completely conserved at the amino acid level, consistent with strong purifying selection.

  plasmodium pvama-1 vivax pcr molecular merozoite

• Allelotype of squamous cell carcinoma of the head and neck: fractional allele loss correlates with survival.

  PMID 7577465 · PMC2033926 · British journal of cancer · 1995 · 7 claims · 4 setups

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  Allelic imbalance/LOH occurs most frequently on chromosome arms 3p, 9p, 17p and 18q (>45% LOH) in SCCHN

  scchn subset microsatellite fractional survival

• Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America.

  PMID 10081674 · PMC2627704 · Emerging infectious diseases · 1999 · 8 claims · 5 setups

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  SNV-like hantaviruses are widely distributed in Peromyscus species rodents throughout North America

  hantavirus-infected aligned phylogenetic archival rt-pcr maximum bootstrap

• p53 mutations in urinary bladder cancer.

  PMID 11384101 · PMC2363660 · British journal of cancer · 2001 · 6 claims · 5 setups

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  p53 mutations are strongly associated with high-grade/high-stage bladder tumors and are nearly absent in lowly malignant tumors (Ta, G1-G2a)

  urinary tumor patients single multiplex-pcr dyedeoxy loss