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 research and incidental findings.

  PMID 18547197 · PMC2570703 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 1 setups

  Full-text index only

  Incidental findings in genomic research (the 'incidentalome') create complex legal, ethical, and financial problems that most researchers are neither prepared for nor willing to address.

  bone genome-wide

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 4 setups

  Has reproduction · 87

  CoINcIDE is a novel framework for discovering patient subtypes across multiple datasets that requires no between-dataset transformations (e.g., batch correction)

  breast ovarian simulated gene consensus simulated

• Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

  PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 6 setups

  Has reproduction · 76

  DRW-GM evaluates gene topological importance by directed random walk on a global gene–metabolite pathway graph integrating gene expression and metabolomic profiles to infer pathway activities

  prostate matched gse8511 gene metabolomic pathway

• In vivo induction of activin A-producing alveolar macrophages supports the progression of lung cell carcinoma.

  PMID 36650150 · PMC9845242 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 96

  AMs accumulate in human lung cancer tissue and support cancer cell proliferation, contributing to unfavourable outcome

  normal llc lung c57bl immunohistochemistry count flow

• Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

  PMID 34911933 · PMC8674326 · Nature communications · 2021 · 8 claims · 7 setups

  Has reproduction · 79

  Low-grade (Gleason pattern 3) prostate cancer cells share chromatin accessibility features that are lost in high-grade (Gleason pattern 4) tumours

  flash-frozen tcga single differentially single-cell bulk topic

• Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.

  PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups

  Has reproduction · 89

  High pretreatment abundance of Lactobacillus (and Bifidobacterium) in gut microbiota correlates with absence of ACRIII in rectal cancer patients

  fecal bacterial whole-abdomen cecal metagenomic random fecal

• Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

  PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

  mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

  afb1 breast training candidate computational bulk weighted

• Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

  PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  The integrated stress response (ISR) induces CRC cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

  ht29-derived ht29 nod rna-seq faire-qpcr chip-seq

• stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

  PMID 41692960 · PMC12960910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  stDyer-image directly associates the image modality with predicted cluster labels rather than using images to enhance/impute gene expression data

  non-small morphology brain breast spatial image

• Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.

  PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  KCTD16, CD3D, and GSDMB were identified as prognostic succinylation-related genes in BLCA

  soochow-blca tcga-blca gse13507 gse135337 bulk scrna-seq somatic

• 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

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.

  PMID 35547750 · PMC9065207 · Theranostics · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  THBS2 is a tumor size-independent biomarker that robustly predicts post-surgical OS and RFS in multiple independent early-stage LUAD cohorts

  tcga paired thbs2+ scrna-seq wgcna scrna-seq gsea

• The application of basic science to translational cancer research.

  PMID 12620114 · PMC151297 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Sister-chromatid separation at anaphase is triggered by degradation of securin, releasing the protease separase to cleave the cohesin ring holding chromatids together

  yeast lamin tumor breast protease-cleavage rad53 brdu

• Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

  PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

  Full-text index only

  DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

  breast sars serum tumour microarray custom mass

• The promise of biomarkers in colorectal cancer detection.

  PMID 15322316 · PMC3839323 · Disease markers · 2004 · 8 claims · 8 setups

  Full-text index only

  A panel/combination of biomarkers is likely to provide better predictive value for early CRC detection than any single biomarker.

  stool specimens serum multi-target afb1-n7-guanine mutation

• Molecular tumor profiling: translating genomic insights into clinical advances.

  PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

  breast ovarian panel tumor gene-expression candidate-gene large-scale

• Constructing support vector machine ensembles for cancer classification based on proteomic profiling.

  PMID 16689692 · PMC5173238 · Genomics, proteomics & bioinformatics · 2005 · 7 claims · 4 setups

  Full-text index only

  CSVME, built by selecting a subset of base SVMs via SVM-RFE ranking and fusing them with a trained upper-layer SVM, achieves better classification performance than an ensemble of all base SVMs.

  serum computational seldi-tof svm-rfe-based 10-fold