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).

• Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.

  PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 41

  A CPAN-index prognostic model built from 11 PANoptosis-related differentially expressed genes (CPAN_DEGs) stratifies CRC patients into high-risk and low-risk groups with distinct survival and immunophenotypes.

  crc merged hct116 bulk single-cell immune

• p53 mutations, protein expression and cell proliferation in squamous cell carcinomas of the head and neck.

  PMID 7710950 · PMC2033757 · British journal of cancer · 1995 · 6 claims · 4 setups

  Full-text index only

  There is a discrepancy between p53 immunoreactivity and p53 gene mutation status, with mutations found in similar proportions of immunopositive and immunonegative tumours.

  formalin-fixed extracted p53-immunonegative scchn immunohistochemistry pcr-single sequencing

• cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer.

  PMID 19671129 · PMC2731783 · BMC cancer · 2009 · 8 claims · 6 setups

  Full-text index only

  cDNA sequencing detects P53 missense mutations in colorectal cancer more frequently and reliably than DNA sequencing

  colorectal paired sequencing cdna real-time

• The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.

  PMID 33772001 · PMC7998036 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  AAMDC is an amplified/overexpressed oncogene in a subgroup of ER-positive breast cancers (IntClust2) associated with poor prognosis

  breast luminal sum52pe t-47d immunohistochemistry fluorescence qrt-pcr

• Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

  PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

  Has reproduction · 80

  DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

  transcripts platforms bacillus multi-subcellular simulated negative benchmark

• CHEK2 variants associate with hereditary prostate cancer.

  PMID 14612911 · PMC2394451 · British journal of cancer · 2003 · 8 claims · 6 setups

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  CHEK2 1100delC frameshift mutation is significantly more frequent in Finnish HPC patients than in population controls

  index hpc unselected affected sscp sequencing minisequencing

• ARSACS in the Dutch population: a frequent cause of early-onset cerebellar ataxia.

  PMID 18465152 · PMC2441586 · Neurogenetics · 2008 · 8 claims · 8 setups

  Full-text index only

  37% (16/43) of Dutch index patients with early-onset recessive cerebellar ataxia carry SACS mutations, indicating ARSACS is far more frequent than previously estimated

  genomic identified sacs-mutation-positive alleles pcr clinical brain

• Identification of recombinant human papillomavirus type 16 variants.

  PMID 19758676 · PMC2769496 · Virology · 2009 · 8 claims · 5 setups

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  Concurrent infection with 8 HPV16 variants (1 prototype/European, 6 recombinant clones, plus later African-2) was detected in a single woman via PCR-based cloning and sequencing

  cervical pcr-based recombinant-specific direct

• Expression of p73, a novel protein related to the p53 tumour suppressor p53, and apoptosis in cholangiocellular carcinoma of the liver.

  PMID 10362118 · PMC2363034 · British journal of cancer · 1999 · 7 claims · 6 setups

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  p73 protein is expressed (nuclear immunostaining) in a substantial subset of cholangiocellular carcinomas

  cholangiocellular ccc lysates immunohistochemistry direct western

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read

• SNP@Evolution: a hierarchical database of positive selection on the human genome.

  PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

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  SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

  hapmap autosomes simulated sliding snp sliding haplotype-based

• Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

  PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

  genes candidate simulated alzheimer's genome-wide term null-hypothesis

• Mutation of the p53 gene precedes aneuploid clonal divergence in colorectal carcinoma.

  PMID 7841032 · PMC2033599 · British journal of cancer · 1995 · 7 claims · 5 setups

  Full-text index only

  p53 mutation occurs as a single clonal event that precedes and may facilitate aneuploid clonal divergence in colorectal carcinoma

  tumour plpd-fixed frozen pcr-sscp dideoxy restriction

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

  Full-text index only

  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells.

  PMID 18847511 · PMC2571112 · BMC genomics · 2008 · 8 claims · 8 setups

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  [BF/S+L/Ep] butanol fraction from E. purpurea enhances maturation of human immature dendritic cells (increased CD83 expression)

  immature idcs [bf phytocompounds flow mtt lal

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

  PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

  Full-text index only

  A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

  gbs clinical bioinformatic eburst kinetic

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence