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).

• Structural modeling and functional characterization of a novel gain-of-function TLR8 variant causing severe inflammatory syndrome.

  PMID 41729082 · PMC12956005 · JCI insight · 2026 · 8 claims · 8 setups

  Has reproduction · 89

  TLR8 A518T is a gain-of-function variant that enhances NF-κB activation and increases secretion of proinflammatory cytokines upon stimulation compared with WT TLR8

  plasma pbmcs expressing tlr8 targeted plasma quantitative

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

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 6 setups

  Has reproduction · 87

  CoINcIDE is a methodological framework that discovers replicable patient subtypes (meta-clusters) across multiple datasets by finding consensus across dataset-specific clusterings, requiring no between-dataset transformations.

  breast ovarian simulated gene semi-supervised novo

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.

  surgically mammary menopaused integrated single-cell scrna-seq mammary

• Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

  PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 76

  FOXM1 and RHNO1 are head-to-head bidirectional genes co-amplified and co-expressed in HGSC, regulated by a shared bidirectional promoter (F/R-BDP).

  tcga ft282 fte hgsc copy expression rt-qpcr

• Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.

  PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 7 claims · 6 setups

  Has reproduction

  A 10 immune-related gene signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) was constructed via WGCNA combined with LASSO-Cox and predicts overall survival in gastric cancer

  gastric tcga-stad microarray rna-seq immune

• Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.

  PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 6 claims · 7 setups

  Has reproduction · 91

  CEL (carboxyl ester lipase) is the real hub gene shared between CP and PDAC and is markedly downregulated in PDAC

  pancreatic gse143754 pdac tcga microarray wgcna differential

• M6A-mediated molecular patterns and tumor microenvironment infiltration characterization in nasopharyngeal carcinoma.

  PMID 38532632 · PMC10978033 · Cancer biology & therapy · 2024 · 8 claims · 8 setups

  Has reproduction · 76

  NPC samples can be divided into two distinct m6A-related molecular subclasses based on prognostic m6A regulators

  npc reep2 bulk genome immune

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

  PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 44

  The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

  spinal brown sci microarray functional protein-protein

• Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

  PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 86

  RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

  peripheral demrnas blood thp-1 rna-seq annotation wgcna

• Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

  PMID 41061199 · PMC12614327 · Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026 · 8 claims · 6 setups

  Has reproduction · 78

  Genomics can identify malignant transformation in MGUS and SMM, defining biologically distinct subsets termed genomic MM and genomic MGUS that are indistinguishable from or distinct from MM at the genomic level.

  cd138+ mgus bone whole-exome whole-genome cnv

• Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

  PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 63

  Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

  hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune

• Zebrafish functional xenograft vasculature platform identifies PF-502 as a durable vasculature normalization drug.

  PMID 37680473 · PMC10480778 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  The zebrafish functional xenograft vasculature platform (zFXVP) enables visualization and quantification of structurally and functionally realistic tumor vasculature formation.

  zebrafish endothelial tumor fluorescence edu dextran-tomato

• Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

  PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  CD39+CD8+ TILs are a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells within ccRCC tumors

  ccrcc tumor-reactive cd39 caix-specific single-cell bulk co-culture

• Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

  PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 74

  540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

  breast colorectal lung common microarray kegg protein-protein

• Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.

  PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups

  Has reproduction · 75

  sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample

  simulated adipose gastrocnemius dnb numerical microarray protein-protein

• A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

  PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

  coad consensus cibersort mcp-counter

• Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

  PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

  Has reproduction · 73

  FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

  peripheral white four gse75360 microarray gene weighted

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups

  Has reproduction · 59

  Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.

  metastatic tcga-brca homo gse40622 gene bulk rt-pcr