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).

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• Analysis of the TGF beta functional pathway in epithelial ovarian carcinoma.

  PMID 11531253 · PMC2364123 · British journal of cancer · 2001 · 6 claims · 6 setups

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  IGFIIR, TGFβ1 and TGFβRII are proposed to function as a unit in the TGFβ growth inhibitory pathway

  epithelial tumor genomic ovarian sscp sequencing pcr

• LMO1 expression in neuroblastoma cells reprograms tumor-associated macrophages to promote metastasis.

  PMID 41858882 · PMC12997303 · iScience · 2026 · 8 claims · 8 setups

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  LMO1 overexpression in MYCN-driven neuroblastoma cells reprograms tumor-associated macrophages to promote metastasis

  tumors macrophage u937 zebrafish single-cell gsva conditioned

• Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.

  PMID 41877584 · PMC13103941 · Cancer research communications · 2026 · 8 claims · 6 setups

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  Skp2 KO improves survival, drives apoptosis, and induces antitumor immunity in Rb1/Trp53-deficient murine osteosarcoma

  tumors same osteosarcoma skp2 scrna-seq mutation copy-number

• Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk.

  PMID 42013848 · PMC13198233 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Consensus meta-program (MP) expression patterns stratify LUAD patients with rare and reference oncogenic mutations into ICI-MP-H and ICI-MP-L subgroups reflecting differential predicted ICI benefit

  luad matched tcga epithelial single-cell multiplex bulk

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

  PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 67

  An individualized Bayesian causal discovery framework can learn tumor-specific intercellular communication networks (ICNs) by combining single-cell gene expression module (GEM) discovery, bulk tumor deconvolution, and individualized causal network learning.

  hnscc cd45+ cd8+ tcga single-cell bulk pseudo-time

• Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

  PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

  Has reproduction · 84

  MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

  patient-derived tumor single paired single-nucleus infercnv aracne-ap

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

  PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 8 claims · 7 setups

  Has reproduction · 53

  A computational framework mapping single-cell Z-score expression to matched patient-level CNV data can identify recurrent, cross-cell-type copy-number-driven expression (dosage) events.

  tnbc independent cng-up breast single-cell gene network

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• Mutation analysis of genes that control the G1/S cell cycle in melanoma: TP53, CDKN1A, CDKN2A, and CDKN2B.

  PMID 15819981 · PMC1097717 · BMC cancer · 2005 · 7 claims · 4 setups

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  TP53 gene shows heterozygous defects in 8 of 39 (20.5%) melanoma tumors, including novel point mutations and novel SNPs in intronic sequences

  metastatic melanoma genomic pcr-sscp sequencing pcr

• Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

  PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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  Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

  hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna

• Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

  PMID 41771574 · PMC12951371 · Cancer genomics & proteomics · 2026 · 7 claims · 8 setups

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  Malignant cells from HCC tumors resolve into six transcriptionally distinct subpopulations, including a progenitor-like CSC subset expressing EPCAM, SOX9, and SOX4

  malignant tumor csc six single-cell spatial copy

• CEBPB-Regulated Gastric Cell Plasticity Promotes Liver Metastasis of Gastric Cancer.

  PMID 41836678 · PMC12981248 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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  GC cells undergoing liver metastasis transcriptionally reprogram into a high-plasticity cell state

  tumor lines nci-n87 balb single-cell epigenomics transwell

• Single-nucleus ATAC-seq analysis resolves chromatin and transcriptional features of fibrolamellar carcinoma.

  PMID 41865105 · PMC13144680 · Scientific reports · 2026 · 8 claims · 5 setups

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  snATAC-seq resolves cell-type specific chromatin accessibility, microRNA activity, transcription factor networks, and super enhancer usage in FLC tumors versus non-malignant liver (NML).

  flc bulk snatac-seq snrna-seq single-nucleus bulk motif

• Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

  PMID 41923630 · PMC13130666 · Cell reports. Medicine · 2026 · 8 claims · 4 setups

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  A malignant cell subset expressing IFN-response and MHC-II genes (IFN/MHC-II) increases in proportion after pembrolizumab treatment and is associated with response

  hnscc ffpe syngeneic independent single-cell multiplexed tumor

• 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

• A tumor-intrinsic WNT-inhibitory NOTUM program drives immune resistance in microsatellite stable colorectal cancer.

  PMID 42097145 · PMC13198260 · Cell reports. Medicine · 2026 · 8 claims · 7 setups

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  A distinct NOTUM/NKD1/APCDD1-high, WNT-inhibitory cancer cell population (WICC) emerges predominantly in advanced-stage MSS CRC

  crc patient-derived ibd mmr-proficient single-cell cell-cycle patient-level

• 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

• High incidence of p53 gene mutation in human ovarian cancer and its association with nuclear accumulation of p53 protein and tumor DNA aneuploidy.

  PMID 1429209 · PMC5918982 · Japanese journal of cancer research : Gann · 1992 · 7 claims · 4 setups

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  p53 gene mutations occur at high incidence in human ovarian carcinoma, especially common epithelial type

  ovarian pcr-single direct immunohistochemistry