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).

• 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

• Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet.

  PMID 41786602 · PMC13138013 · Genome research · 2026 · 7 claims · 5 setups

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  NNet uses PCA embedding followed by local KNN regression in PC space to construct cell-specific coexpression networks (CSNs), improving computational efficiency and estimate stability versus pairwise approaches.

  pbmc thp-1 lin small scrna-seq perturb-seq

• Genomic biomarkers of immunotherapy plus chemotherapy in patients with advanced NSCLC: Insights from the phase 3 ORIENT-11 study.

  PMID 41660271 · PMC12876322 · iScience · 2026 · 8 claims · 8 setups

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  A 9-gene Immune-Chemotherapy Prediction Score (ICPscore), derived from ORIENT-11 via WGCNA and LASSO Cox regression, predicts survival benefit from ICI plus chemotherapy in advanced NSCLC

  orient-11 hub nsclc oak bulk pd-l1 wgcna

• A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

  PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

  Has reproduction · 95

  RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

  tcga er+ ccle computational spearman correlation gene

• ISG15-driven immune modulation and tumor progression in breast cancer metastasis: insights from single-cell and spatial transcriptomics.

  PMID 41639695 · PMC12958617 · BMC medicine · 2026 · 8 claims · 8 setups

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  CSC proportion is elevated in lymph node metastatic tumor tissue (BRCA_LNMT) compared to primary tumor (BRCA_PT)

  4t1 brca tcga-brca top single-cell spatial bulk

• Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

  PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 75

  Stage-stratified molecular subclassification (analyzing Ta and T1 separately) is more biologically and clinically informative than subtypes derived from all NMIBC combined, especially for T1 tumors.

  stage combined patients copy genome-wide targeted

• Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

  PMID 41484081 · PMC12858953 · Nature communications · 2026 · 8 claims · 8 setups

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  Combined low-dose CTX + anti-CSF-1R (SNDX-ms6352) is highly effective against aggressive metastatic Trp53-null TNBC models with high macrophage infiltration, producing complete tumor regression in claudin-low models.

  trp53-null complete t12 cell-deficient imaging survival tumor