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).

• The complement system contributes to the immunosuppressive microenvironment of uveal melanoma.

  PMID 41803879 · PMC13130498 · Journal of translational medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  Primary UM (pUM) preferentially expresses early complement pathway components over terminal membrane attack complex elements, with early factors showing prognostic significance.

  short-term metastatic normal pum bulk label-free single-cell

• Multiomic and functional validation of ACSL3, a regulator of fatty acid metabolism, as a lymph node metastasis-associated gene in lung adenocarcinoma.

  PMID 41998631 · PMC13261843 · Respiratory research · 2026 · 8 claims · 8 setups

  Full-text index only

  A five-gene FAM-related risk signature (ACSL3, MCAT, NDUFAB1, OLAH, ACSL4)-derived FScore stratifies LUAD prognosis across multiple independent cohorts

  tcga-luad luad a549 lymphatic bulk scrna-seq spatial

• Discovery and Evaluation of Biomarkers for Triple-Negative Breast Cancer Subtypes Uncovers Patient Stratification and Targeted Therapeutic Strategies.

  PMID 41671401 · PMC13176827 · Cancer research · 2026 · 7 claims · 8 setups

  Full-text index only

  A set of basal identity genes (SMA/ACTA2, TAGLN, TPM2) defined by scRNA-seq analysis enables subclassification of TNBC into a subgroup termed true basal TNBC (tB-TNBC)

  healthy ffpe tcga i-spy2 scrna-seq immunohistochemistry bulk

• SpaPheno: linking spatial transcriptomics to clinical phenotypes with interpretable machine learning.

  PMID 41975540 · PMC13185361 · Genome medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  SpaPheno integrates spatial transcriptomics with clinically annotated bulk RNA-seq to identify spatially resolved biomarkers predictive of patient outcomes including survival, tumor stage, and immunotherapy response

  cortex liver clear breast spatial elastic

• 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

• A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

  PMID 41833005 · PMC13248847 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

  Full-text index only

  LSTs exhibit a more malignant phenotype than PAs, with higher inferred CNV scores, stronger genetic correlation with colorectal cancer, and downregulation of adhesion molecules

  patients bulk colorectal epithelial clinical bulk single-cell

• 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

• COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

  PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).

  lung covid-19 interaction pre-clinical composite single-cell kaplan-meier

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

  PMID 41612476 · PMC12930642 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

  Full-text index only

  DHODH is markedly overexpressed in malignant prostate epithelial cells and abundant in tumors

  tcga-prad gse141445 22rv1 bulk single-cell lentiviral

• Histone methyl-transferase G9a inhibition boosts the efficacy of immune checkpoint inhibitors in experimental hepatocellular carcinoma.

  PMID 41923620 · PMC13130624 · Cell reports. Medicine · 2026 · 7 claims · 8 setups

  Full-text index only

  G9a expression inversely correlates with gene signatures predictive of favorable ICI response across multiple HCC patient cohorts

  tcga advanced nm53 plc bulk single-cell rt-qpcr

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

  meta-geo tcga-blca bca genomics unsupervised lasso weighted

• Single-cell mitophagy signature-based artificial intelligence model enhances prediction of prognosis and immunotherapy response in non-small-cell lung cancer.

  PMID 41851738 · PMC13112628 · Respiratory research · 2026 · 8 claims · 8 setups

  Full-text index only

  A six-gene MRG panel (FOS, CANX, EIF4G1, CALCOCO2, HSP90AB1, PRKAR1A) was selected via LASSO regression as prognostic markers in NSCLC.

  nsclc tcga external immunotherapy single-cell bulk transcriptomic

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• Trisomy 21 Drives ADARB1 Overexpression and Premature RNA Recoding in the Developing Fetal Brain.

  PMID 41917044 · PMC13039865 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  T21 causes widespread fetal brain gene expression dysregulation with significant enrichment for chromosome 21 genes and perturbation of neurodevelopmental, synaptic, and immune-related pathways

  fetal independent brain bulk editing type

• Identification of Molecular Subtypes of Clear-Cell Renal Cell Carcinoma in Patient-Derived Xenografts Using Multi-Omics.

  PMID 40282537 · PMC12026142 · Cancers · 2025 · 8 claims · 7 setups

  Full-text index only

  Each ccRCC PDX resembles one of the human molecular subtypes closely at both the transcript and protein levels.

  ccrcc differentially bulk lc-ms targeted

• scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.

  PMID 41877186 · PMC13134144 · Genome biology · 2026 · 8 claims · 7 setups

  Full-text index only

  scComm infers cell-cell communications at single-cell resolution using a data-adaptive L-R weighting module and supervised contrastive learning (SupCon loss) to distinguish significant CCC events from background noise

  simulated spatial liver single-cell simulated spatial scrna-seq

• PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.

  PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 5 setups

  Has reproduction · 40

  NAPC produces higher major pathological response (MPR) and pathological complete response (pCR) rates and longer DFS/OS than NAC alone

  cd45+ ffpe scrna-seq cd8+ single-cell multiplex gene