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).

• Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

  PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups

  Has reproduction · 100

  Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.

  gbm glioma gbm-focused glioma-related transcriptomic differential gene-regulatory

• 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

• An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

  PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 7 setups

  Has reproduction · 67

  An individualized causal analysis framework can discover tumor-specific intercellular communication networks (ICNs) from transcriptomic data

  hnscc pooled cd45+ cd8+ single-cell nhdp celda

• 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

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• 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 · 4 setups

  Has reproduction · 40

  Adding PD-1 blockade to neoadjuvant chemotherapy (NAPC) increases tumor infiltration of CD20+ B cells, CD4+ T cells, CD4+CD127+ T cells, CD8+ T cells, CD8+CD127+ and CD8+KLRG1+ T cells, whereas NAC alone increases only CD20+ B cells.

  cd45+ ffpe nsclc scrna-seq single-cell multiplex geo

• PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

  PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 6 claims · 6 setups

  Has reproduction · 75

  The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival across three independent cohorts.

  pbmcs sorted skin multiparameter targeted tcr

• Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

  PMID 39682743 · PMC11640164 · Cells · 2024 · 7 claims · 4 setups

  Has reproduction

  Immune-activation-related T-cell populations (APA, TRM, stem-like, early/late dysfunctional T-cells) are more heavily infiltrated in ICI-responsive malignancies (melanoma, bladder) than in poorly responsive ones (ovarian, pancreatic).

  melanoma bulk survival auroc

• Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology.

  PMID 39941893 · PMC11817449 · Cancers · 2025 · 8 claims · 7 setups

  Has reproduction · 50

  A standardized, reproducible protocol can establish meningioma organoids (MEN-Os) from patient-resected tumor tissue without mechanical/enzymatic dissociation, using serum-free medium lacking growth factors or exogenous ECM.

  patient-resected men-os parent oct-embedded organoid brightfield h&e

• Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

  PMID 37081150 · PMC10154250 · Nature immunology · 2023 · 8 claims · 6 setups

  Has reproduction · 37

  Orthogonal engineering of CD8+ T cells to co-secrete IL-2v and IL-33 (with PD-1 decoy) drives a novel synthetic effector state (C5 T_SE) that deviates from canonical PD-1+TOX+ exhaustion.

  ot1 b16-ova facs-sorted engineered adoptive flow single-cell