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).

• Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data.

  PMID 41916276 · PMC13261679 · Cell genomics · 2026 · 8 claims · 5 setups

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  BEAM jointly infers a full posterior distribution over cell-lineage phylogenies and tissue-migration graphs using a Bayesian model built on BEAST 2

  simulated orthotopic somatically simulated single-cell bulk

• IMIREG: a lineage-resolved regulon signature unveiling immune engagement archetypes and predicting immunotherapy response across diverse cancers.

  PMID 42092126 · PMC13234301 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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  IMIREG, a 14-regulon transcriptional signature, robustly predicts clinical benefit from ICB across 50 immunotherapy cohorts (52 treatment arms) spanning 16 cancer types with mean AUROC = 0.71

  imvigor210 matched gtex healthy bulk scrna-seq pathway

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• Targeting TPX2-dependent lineage plasticity by CDK4/6 inhibition reverses therapy resistance in neuroendocrine bladder carcinoma.

  PMID 41923619 · PMC13130694 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A 315-gene 'NE-like signature' (NE-like Sig), derived from the WGCNA MEmidnightblue module, marks a lineage-plasticity-associated transcriptional program distinct from canonical NE differentiation.

  cases in-house bladder nebc wgcna single-cell spatial

• Keratin 5 marks cancer-propagating cells sustained by an osteopontin-producing niche in high-grade serous ovarian carcinoma.

  PMID 42111394 · PMC13155427 · Cancer heterogeneity and plasticity · 2026 · 8 claims · 8 setups

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  KRT5+ cells represent bona fide cancer-propagating cells (CPCs) in HGSC

  hgsc skov3 facs-sorted nod immunohistochemistry lentiviral organoid

• Stemming cancer: functional genomics of cancer stem cells in solid tumors.

  PMID 18561035 · PMC2758383 · Stem cell reviews · 2008 · 8 claims · 8 setups

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  Cancer stem cells are a minority tumor subpopulation that alone can maintain indefinite tumor growth, as shown by serial transplantation experiments

  solid fetal cd133+ breast facs neurosphere genome-wide

• Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment.

  PMID 41817317 · PMC13223553 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 8 claims · 7 setups

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  High-grade histopathologic TIL infiltration is associated with significantly prolonged overall survival in breast and lung cancer BM.

  breast lung histopathologic sequencing tcr

• Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.

  PMID 41840060 · PMC13125306 · Scientific reports · 2026 · 8 claims · 7 setups

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  IDC exhibits significantly higher CNV burden than DCIS, supporting progressive genomic instability during tumor evolution

  her2-positive epithelial malignant tcga-brca single-cell spatial infercnv

• Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

  PMID 41933362 · PMC13173987 · BioData mining · 2026 · 8 claims · 7 setups

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  Single-cell analysis of integrated ovarian cancer datasets identifies 9 distinct mononuclear phagocyte clusters (MPC1-MPC9), of which MPC3, MPC5, and MPC7 are hypermetabolic

  ovarian mpc annotated tcga-oc single-cell gene pseudotime

• Single-cell omics data-driven decoding of tumor clonal evolution through reinforcement learning.

  PMID 41998716 · PMC13224513 · Genome medicine · 2026 · 8 claims · 3 setups

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  scRevol is an RL-based model that infers tumor clonal evolution from scRNA-seq-derived CNV profiles via a label assignment learning strategy.

  simulated lineage ovarian scrna-seq-derived

• Host-derived interleukin-1α drives tumor immunosuppression by reprogramming tumor-associated myeloid cells.

  PMID 41547846 · PMC12910057 · NPJ breast cancer · 2026 · 8 claims · 8 setups

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  Deletion of host Il1α causes rejection/regression of transplanted breast tumors

  h605 pymt tumor-infiltrating two-week orthotopic flow single-cell

• Critical role for a high-plasticity cell state in lung cancer.

  PMID 41565826 · PMC12960256 · Nature · 2026 · 8 claims · 8 setups

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  The HPCS is a transcriptionally distinct cancer cell state that functions as a hub for reciprocal transitions between other cancer cell states

  autochthonous kpfrt gfp+ sorted single-cell flow immunofluorescence

• FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

  PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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  FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

  prostate targeted single-nucleus scatac-seq

• 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

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

  PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

  mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq

• Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

  PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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  A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

  pca malignant tcga mda single-cell infercnv pseudotime

• Interpretable learning of temporal cellular dynamics from single-cell data.

  PMID 41875867 · PMC13030976 · Cell reports methods · 2026 · 7 claims · 7 setups

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  NeuroVelo couples a linear latent phase-space projection with a non-linear neural ODE, using RNA velocity as a physics-informed loss penalty, to jointly model cellular dynamics and enable gene-level interpretability

  gastrulation bone pancreatic cancer scrna-seq chip-seq computational

• Blood-based epigenetic instability linked to human aging and disease.

  PMID 41690920 · PMC13018287 · Nature communications · 2026 · 7 claims · 8 setups

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  31,744 unmethylated (and 6143 methylated) CpG loci in blood show highly consistent, stable methylation in young healthy individuals and are defined as Epigenetically Stable Loci (ESLs)

  blood normal paired aml illumina whole-genome methylation

• Divergent macrophage-regulated T cell states determine response to Bacillus Calmette-Guérin vaccine in high-risk bladder cancer.

  PMID 42081487 · PMC13262731 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  BCG responders show an increase in Th17-like Th1 CD4+ T cells with greater proinflammatory cytokine expression

  bladder pbmcs cd4+ separate scrna-seq trajectory flow

• Understanding sex differences in environmental health: a thought leaders' roundtable.

  PMID 15064168 · PMC1241928 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  Dioxin and corticosteroids both cause thymic atrophy but via distinct mechanisms; dioxin's atrophy kinetics resemble those induced by estrogen despite acting through a different receptor.

  laboratory mice nzb c57bl thymus radiation autoimmune