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).

• Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

  PMID 16916263 · PMC7121524 · Methods in molecular biology (Clifton, N.J.) · 2006 · 7 claims · 7 setups

  Full-text index only

  PCR-based amplification and direct sequencing of SARS-CoV genome fragments is feasible from uncultured clinical specimens (serum, nasopharyngeal aspirate, stool), avoiding culture-derived artifacts and biohazard risk.

  sars-cov extracted cdna pcr viral reverse real-time

• Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.

  PMID 42038409 · PMC13107125 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

  Has reproduction · 78

  Long-read shotgun metagenomic sequencing of eDNA can simultaneously detect and quantify organismal DNA from viruses to mammals in a single assay

  river edna extracted raw edna concentration quantitative

• Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

  PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

  Has reproduction · 86

  CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

  tissues predicted tss-enhancer cattle cage extraction coexpression

• Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.

  PMID 34498920 · PMC8428255 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

  Has reproduction · 78

  The complete genome sequence of Leishmania (Mundinia) orientalis, isolate LSCM4, strain LV768, was determined using combined short-read and long-read sequencing.

  leishmania orientalis culture extraction short-read

• SNP-specific extraction of haplotype-resolved targeted genomic regions.

  PMID 18611953 · PMC2528194 · Nucleic acids research · 2008 · 6 claims · 4 setups

  Full-text index only

  SNP-specific extraction isolates haploid genomic DNA flanking targeted SNPs by hybridizing an allele-specific oligo, enzymatically extending it with biotinylated nucleotides, and capturing the tagged allele with streptavidin-coated magnetic particles.

  genomic diploid quantitative sanger low

• Clinical and genetic analysis of Korean patients with Miyoshi myopathy: identification of three novel mutations in the DYSF gene.

  PMID 16891820 · PMC2729898 · Journal of Korean medical science · 2006 · 7 claims · 7 setups

  Full-text index only

  All three unrelated Korean MM patients carried compound heterozygous mutations in the DYSF gene.

  peripheral dysf chromosomes korean genomic pcr direct

• Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.

  PMID 16504056 · PMC1402321 · BMC genetics · 2006 · 7 claims · 8 setups

  Full-text index only

  No statistical evidence of a major association between T1D and any of the interferon or interferon-related genes tested (IFNA cluster, IFNB1, IFNW1, IFNG, ICSBP1)

  t1d european warren resequencing database tag

• Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

  PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups

  Has reproduction · 97

  The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)

  duvernoy's nigriceps rna-seq differential extraction

• De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.

  PMID 29451882 · PMC5815590 · PloS one · 2018 · 7 claims · 7 setups

  Has reproduction · 45

  This is the first de novo transcriptomic analysis of Cornus officinalis, providing fundamental gene and biosynthetic pathway information.

  cornus frozen high-quality officinalis bulk extraction novo

• RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

  PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.

  microbial reconstructed synthetic real shotgun ssu full-length

• EGFR mutation status in tumour-derived DNA from pleural effusion fluid is a practical basis for predicting the response to gefitinib.

  PMID 17060940 · PMC2360588 · British journal of cancer · 2006 · 7 claims · 4 setups

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  EGFR mutations can be detected by direct sequencing of DNA extracted from cell-free pleural effusion fluid supernatant in NSCLC patients

  cell-free pleural nsclc direct extraction clinical

• Genetic analysis of three Korean patients with clinical features of Ehlers-Danlos syndrome type IV.

  PMID 17728513 · PMC2693823 · Journal of Korean medical science · 2007 · 7 claims · 6 setups

  Full-text index only

  EDS type IV is genetically heterogeneous; not all clinically/biochemically diagnosed patients carry COL3A1 mutations

  genomic peripheral abdominal cerebral direct genomic angiography

• Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

  PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 6 setups

  Has reproduction

  Selective linkage disequilibrium pruning (SLDP) refines whole-genome SNP sets using GWAS prior information to improve genomic prediction accuracy.

  duroc 1000-individual real low-coverage genome-wide genomic

• Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

  PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups

  Has reproduction · 83

  AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

  stage patients tumour whole-tumour radiomics bulk cellular

• Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

  PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  A chromosome-level genome assembly of G. vermiculophylla was generated by combining DNBSeq short reads, Nanopore long reads, and Hi-C data.

  gracilaria whole-genome nanopore hi-c

• Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains.

  PMID 36003939 · PMC9393633 · Frontiers in microbiology · 2022 · 7 claims · 8 setups

  Has reproduction · 95

  Benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams along the lateral chronosequence

  benthic lyophilized streamwater 16s 18s flow

• Heterogeneity of p53 mutational status in intramucosal carcinoma of the colorectum.

  PMID 11223545 · PMC5926696 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 4 setups

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  p53 gene mutations occur and diverge at the intramucosal carcinoma stage, before submucosal invasion

  endoscopically same pcr-based immunohistochemistry histologic

• Advanced colorectal polyps with the molecular and morphological features of serrated polyps and adenomas: concept of a 'fusion' pathway to colorectal cancer.

  PMID 16879389 · PMC1619718 · Histopathology · 2006 · 8 claims · 5 setups

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  KRAS mutation occurs more frequently than BRAF mutation in conventional adenomas, especially those with villous architecture

  archival adenomas colorectal kras braf p53

• FGFR3 protein expression and its relationship to mutation status and prognostic variables in bladder cancer.

  PMID 17668422 · PMC2443273 · The Journal of pathology · 2007 · 8 claims · 4 setups

  Full-text index only

  FGFR3 mutations occur in 42% of primary urothelial carcinomas and are significantly associated with low tumour grade and stage

  urothelial tumour direct manual 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

  Full-text index only

  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