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).

• pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.

  PMID 16381926 · PMC1347407 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  pSTIING is a publicly accessible web-based knowledgebase integrating protein-protein, protein-lipid, protein-small molecule interactions, transcriptional regulatory associations, ligand-receptor-cell type information, and signal transduction modules, with a focus on inflammation, cell migration and cancer.

  model gene molecular sequence clustering literature

• Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq.

  PMID 33441952 · PMC7806779 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 47

  Carcinoma cell profiles are distinct for each patient, while diverse microenvironmental (nonmalignant) subsets are shared across different patients.

  tumour single differentially seurat-identified single-cell differential gene

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

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  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• The continuing search for cancer-causing somatic mutations.

  PMID 17319975 · PMC1851399 · Breast cancer research : BCR · 2007 · 8 claims · 3 setups

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  A screen of 91 breast cancers uncovered 87 somatic variants spread across 16 of the 21 genes examined

  breast limited targeted gene temporal

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups

  Has reproduction · 72

  edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

  ffpe same nanostring tnbc nanostring immunohistochemistry differential

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Genomic Landscape Analysis of Canine Pulmonary Adenocarcinoma Reveals Candidate Targetable Gene Fusions.

  PMID 41914575 · PMC13161739 · Veterinary and comparative oncology · 2026 · 8 claims · 7 setups

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  STAR-Fusion identified 26 gene fusions in 19 of 36 (53%) cPAC tumours with RNA-seq data

  cpac matched sdc4 rna-seq whole-genome whole-exome

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• Tumour-brain crosstalk restrains cancer immunity via a sensory-sympathetic axis.

  PMID 41639447 · PMC12935554 · Nature · 2026 · 8 claims · 8 setups

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  Lung adenocarcinoma (LUAD) induces increased innervation and functional/transcriptional engagement of vagal sensory neurons (VSNs)

  kras-g12d tumour-bearing vagal npy2r-ires-cre whole-mount aav neurite

• COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

  PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

  cancer tumour manual semi-automated candidate

• Evaluation of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 genes in familial colorectal cancer predisposition.

  PMID 17029639 · PMC1624846 · BMC cancer · 2006 · 6 claims · 4 setups

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  Coding sequences and intron-exon boundaries of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 were screened in 94 familial CRC cases with known genes excluded

  genomic predicted archival mutation targeted functional

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• High frequency of mitochondrial genome instability in human endometrial carcinomas.

  PMID 12915881 · PMC2376924 · British journal of cancer · 2003 · 7 claims · 3 setups

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  56% (28 out of 50) of endometrial carcinoma cases carry one or more somatic mtDNA changes (deletion, point mutation, or mtMSI) compared with matched normal tissue

  endometrial paraffin-embedded long-range pcr polyacrylamide

• Alterations of E-cadherin and beta-catenin in gastric cancer.

  PMID 11747475 · PMC60969 · BMC cancer · 2001 · 8 claims · 5 setups

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  High frequency (75%) of loss of heterozygosity (LOH) at 16q22.1, the E-cadherin locus, occurs in primary gastric tumours

  gastric normal paraffin-embedded loh mutation a592t

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• Dynamic changes of the immune microenvironment in ovarian cancer following neoadjuvant chemotherapy.

  PMID 41872134 · PMC13039919 · Cell death discovery · 2026 · 8 claims · 8 setups

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  Prostaglandin-mediated immunosuppressive microenvironment formation is a critical contributor to chemotherapy resistance following cisplatin treatment

  high-grade hgsoc bone bmdms scrna-seq cell-cell tensor

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical and molecular data according to user-defined terms

  pubmed invasive geo genes semantic computational gene

• 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

• Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability.

  PMID 15778432 · PMC1067522 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Dinucleotide microsatellite alterations in human cancer fall into two distinct modes: Type A (length changes ≤6 bp) and Type B (changes ≥8 bp)

  msh2− mlh1− lymphomas colorectal fluorescent sequencing immunohistochemistry

• Next-generation sequencing.

  PMID 20030863 · PMC2797692 · Breast cancer research : BCR · 2009 · 8 claims · 7 setups

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  Massively parallel sequencing can simultaneously capture base-pair mutations, copy number aberrations and somatic rearrangements of a cancer genome in a single experiment

  individuals metastatic acute oestrogen whole-exome whole-genome large-scale