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).

• 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

  LUAD samples cluster into IRG-high and IRG-low groups, with the IRG-high group showing significantly better survival and greater immune cell infiltration.

  luad geo degs immunotherapy-treated bulk weighted ppi

• 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 · 8 claims · 7 setups

  Has reproduction · 50

  STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC with strong diagnostic performance in the training cohort (AUC 0.908 and 0.842).

  hgsoc dirgs hub stat1 bulk functional protein-protein

• Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

  PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 8 claims · 8 setups

  Has reproduction · 48

  A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates

  tcga-coad ncbi-geo tisidb gepia rna-seq tumor-infiltrating 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

• Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

  PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

  Has reproduction

  Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

  thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics

• Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

  PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 6 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is a misleading measure of replicability for assessing differential expression, because it is dominated by gene-specific dynamic ranges rather than condition-dependent variation.

  liver encode publicly co-expressed rna-seq meta-analysis computational

• 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

• 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

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk