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).

• A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.

  PMID 19941644 · PMC2789744 · BMC bioinformatics · 2009 · 7 claims · 4 setups

  Full-text index only

  Feature variability strongly influences breast cancer signature composition even when array platform and patient stratification are identical.

  breast preprocessed microarray two-color perturbation

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

  Full-text index only

  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

  Has reproduction · 86

  A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

  known tnbc unique unknown gene machine term

• STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.

  PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 7 claims · 6 setups

  Has reproduction · 50

  STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC and may serve as ancillary diagnostic biomarkers.

  hgsoc training independent paraffin-embedded transcriptome machine-learning diagnostic

• Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

  PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 55

  352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

  endometrial degs hub decidua microarray wgcna machine

• Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

  PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups

  Has reproduction · 80

  Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.

  peripheral overlapping asah drug-treatment microarray wgcna ppi

• A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.

  PMID 35619722 · PMC9128066 · Frontiers in immunology · 2022 · 6 claims · 6 setups

  Has reproduction · 90

  A random forest model trained solely on B-HOT panel genes (B-HOT Model) accurately classifies kidney transplant biopsies as NR, ABMR, or TCMR.

  kidney gene combined microarray machine sequential

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 69

  An ensemble feature selection method based on classifier consensus identifies a robust 100-miRNA signature from TCGA data.

  tcga geo 100-mirna mirna feature bibliographic

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).

  blood merged affymetrix-optimized gene feature out-of-sample

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

  Has reproduction · 83

  A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

  peripheral pbmcs blood normal gene-expression lymphocyte gene

• Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

  PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups

  Has reproduction · 48

  A hybrid signature combining the Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).

  metabric scan-b gene rna-seq feature

• Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

  PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  S100A3 is a robust candidate biomarker showing consistent discriminatory performance across the acute sleep deprivation training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort.

  peripheral blood normal integrated bulk interpretable immune

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• Optimality driven nearest centroid classification from genomic data.

  PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups

  Full-text index only

  A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).

  artificial simulated previously-published simulated simulation clinical

• Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets.

  PMID 35901020 · PMC9333302 · PloS one · 2022 · 7 claims · 3 setups

  Has reproduction · 83

  A Reproducibility Score, RS(D,BD), defined as the average Jaccard overlap between biomarker sets found by the same discovery process on comparable datasets from the same distribution, quantifies biomarker reproducibility on a 0-1 scale

  breast tcga-brca snp gene mrnaseq snp

• Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.

  PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance

  merged gse45827 superior differential feature comparative

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants

  infant merged individual pairwise whole-blood coconut gene-signature

• Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

  PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups

  Has reproduction · 78

  An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.

  proteins microarray ad-associated pahs target differential wgcna

• 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

  Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs

  afb1 breast training candidate computational bulk weighted

• Proteomics as a tool for biomarker discovery.

  PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

  Full-text index only

  A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

  serum laser ovarian seldi-tof two-dimensional gene