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).

• Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

  PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

  Full-text index only

  RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

  tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic

• Detecting tipping points of complex diseases by network information entropy.

  PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 78

  NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

  real stringdb individual genes network background sample-specific

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.

  tcga gse72056 gse40419 gse103322 bulk single-cell rna-seq

• Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

  PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering

  tcga-nsclc geo bulk microarray unsupervised

• Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.

  PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.

  cervical als top yeast bulk stratified protein-protein

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.

  PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 7 setups

  Has reproduction

  CD4+ T cells and B cells independently and significantly contribute to MS GWAS heritability enrichment, distinct from a merely shared immune regulatory landscape.

  flow-sorted cd4+ hematopoietic gwas bulk atac-seq stratified

• Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

  PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

  aml hovon cancer tcga bulk consensus machine

• Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

  PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments

  tcga-blca famc1-3 differentially gse32894 bulk consensus gene

• A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

  PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 51

  An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73

  bladder tcga bulk univariate integrative

• Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

  PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration

  luad normal bulk wgcna tumor

• 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 · 7 setups

  Has reproduction · 49

  S100A3 shows consistent discriminatory performance across the training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort

  blood degs bulk single-gene gene

• 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

• Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.

  PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 40

  An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts

  bladder skin bulk integrative immune

• Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

  PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups

  Has reproduction · 100

  A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.

  metastatic pathway bulk gene elastic-net

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime

• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

  PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups

  Has reproduction · 74

  An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead

  ipsc-derived same top differentially bulk principal hierarchical

• Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.

  PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types

  bulk py2t mcf10a airway transcriptomic rna-seq single-cell

• A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

  PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

  Has reproduction · 85

  Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

  tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 8 setups

  Has reproduction · 83

  Disease-specific temporal (dynamic) gene expression and splicing signatures, distinct from fixed timepoint differential expression, can be derived from DSS and adoptive transfer colitis models to capture acute-chronic disease dynamics

  colon blood distal ibd bulk qpcr histopathology