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).

• Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

  PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

  Full-text index only

  DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

  genomic snp high-throughput decision

• A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

  PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

  Full-text index only

  A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

  genomic same synthetic invader pyrosequencing hplc

• Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

  PMID 31092189 · PMC6521551 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 7 setups

  Has reproduction · 45

  Graphtyper outperformed GATK and SAMtools in genotype concordance, non-reference sensitivity, and non-reference discrepancy compared to microarray genotypes

  original sire-son whole-genome multi-sample graph-based

• High-resolution, high-throughput HLA genotyping by next-generation sequencing.

  PMID 19845894 · PMC4205125 · Tissue antigens · 2009 · 7 claims · 5 setups

  Full-text index only

  Clonal 454 sequencing reads (>250 nt) are long enough to span HLA exons and set phase of linked polymorphisms, resolving ambiguities inherent to Sanger-based heterozygote sequencing.

  cell-line mixtures blood genomic flx amplicon pcr

• Nimbus: a design-driven analyses suite for amplicon-based NGS data.

  PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 5 setups

  Has reproduction · 64

  Nimbus tracks the source amplicon of reads throughout alignment and SNP/InDel calling

  blood na15510 twin haloplex haloplex spiked-in humanexome-12

• ATM variants 7271T>G and IVS10-6T>G among women with unilateral and bilateral breast cancer.

  PMID 14562025 · PMC2394328 · British journal of cancer · 2003 · 8 claims · 4 setups

  Full-text index only

  Women with bilateral breast cancer show greater genetic predisposition (higher family history prevalence) than women with unilateral breast cancer

  blood-derived blood random dhplc microsatellite duplicate

• High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

  PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

  genomic whole-genome same call snp technical genotype

• Minisequencing mitochondrial DNA pathogenic mutations.

  PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

  Full-text index only

  A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

  blood-derived same genomic pcr minisequencing automatic multiplex

• Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

  PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 8 setups

  Has reproduction · 88

  Among annotated HM450K GEO samples, about two-thirds were from blood, one-quarter from brain, and about one-third were from cancer patients.

  hm450k geo seven dnam beadarray regular-expression-based

• Multiplexed genetic analysis using an expanded genetic alphabet.

  PMID 15319316 · PMC1592527 · Clinical chemistry · 2004 · 7 claims · 6 setups

  Full-text index only

  MultiCode PLx is a three-step platform (PCR, target-specific extension, liquid chip decoding) performed in a single reaction vessel and completed in ~3 h

  genomic synthetic subset newborn multicode eracode automated

• Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

  PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

  Full-text index only

  About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

  genomic japanese reference snp concentration agarose

• Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

  PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

  tumor each rna-seq whole-genome targeted pcr-based

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

  Full-text index only

  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• The liver as an immunological barrier redefined by single-cell analysis.

  PMID 32176810 · PMC7218664 · Immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 100

  Emerging single-cell technologies have advanced or redefined understanding of the liver's immunological barrier function

  liver c57bl sorted pdgfrb-gfp scrna-seq single-molecule

• Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

  PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

  wga non-amplified archived serum-derived snp purification whole-genome

• Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

  PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

  Full-text index only

  TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

  genomic dbsnp tnt duplex bioinformatic

• Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

  PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

  Full-text index only

  BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

  serum-derived tumour serum ht29 arms sanger topo

• Developmental and genetic regulation of human surfactant protein B in vivo.

  PMID 18776725 · PMC2765709 · Neonatology · 2009 · 8 claims · 7 setups

  Full-text index only

  Pro-SP-B peptides are more common in developmentally less mature humans (amniotic fluid, neonatal tracheal aspirates) than in adults

  amniotic tracheal bronchoalveolar simultaneous immunoblotting reducing gene

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction