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).

• Single-cell multi-omic analysis of mitochondrial mutational mosaicism and dynamics.

  PMID 41839886 · PMC12996611 · Nature communications · 2026 · 7 claims · 7 setups

  Full-text index only

  mtscATAC-seq combined with POLG D274A hypermutator HEK293 lines reveals a substantially larger single-cell mtDNA mutational burden than previously appreciated by bulk sequencing

  hek293 pbmcs mitochondrial mtdna mutational

• Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

  PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 88

  APOBEC family genes are differentially expressed across cancer types and tissues, with APOBEC3B being the most aberrantly upregulated gene in most cancers including LUAD

  tcga tcga-luad beas-2b rna-seq somatic gene

• Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

  PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  CD39+CD8+ TILs constitute a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells

  memory sorted caix-specific cd39+pd-1bright scrna-seq bulk mhc

• Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

  PMID 41532847 · PMC13056296 · Cancer discovery · 2026 · 8 claims · 8 setups

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  High-depth targeted sequencing of >1,500 IM samples from six countries identified 47 significantly mutated driver genes, including ARID1A, KRAS/MAPK pathway genes, and PIGR

  subset matched saliva hek293t high-depth whole-genome genome-wide

• Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.

  PMID 41505106 · PMC12781890 · Nucleic acids research · 2026 · 6 claims · 8 setups

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  RNA-MosaicHunter accurately detects sSNVs from bulk RNA-seq with high precision (94.7% in TCGA, 99.3% in cell-line mixture) in default mode

  tcga cell-line same gtex bulk whole-exome whole-genome

• Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.

  PMID 41540108 · PMC13004696 · Nature medicine · 2026 · 7 claims · 7 setups

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  GPRC5D antigenic drift/mutational events occurred in 68.4% of relapsed cases following anti-GPRC5D TCE therapy (13/19 evaluable patients)

  cd138+ pbmcs cohort bulk single-cell targeted

• Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

  PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

  fresh tcga gbm bulk rna-seq consensus

• RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia.

  PMID 39820365 · PMC11739599 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  RSK1 is a conserved, exploitable therapeutic dependency across MPN and secondary AML

  sorted mpn cd34+ aml bulk targeted mass

• Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

  PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

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  HERV expression differs between primary and metastatic cutaneous melanoma

  tcga-skcm metastatic normal selected bulk consensus orf

• Single-cell resolution of an open chromatin signature in persister tumor cells.

  PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

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  Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

  non-malignant same epithelial tumor single-nucleus mitochondrial copy-number

• Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

  PMID 41674979 · PMC12885896 · Translational cancer research · 2026 · 8 claims · 8 setups

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  A FAM-related gene prognostic model (FAMGM) built using CoxBoost and random survival forest was identified as the optimal model among 101 machine learning combinations, based on highest average C-index across TCGA-BRCA and GSE96058 cohorts

  tcga-brca gse96058 brca breast bulk single-cell spatial

• Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

  PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups

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  SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival

  pdac bulk ssgsea differential

• 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

• Genomic and Immune Landscape of Recurrent and/or Metastatic Squamous Cell Carcinoma of the Head and Neck Progressing on Anti-PD-1 Treatment.

  PMID 41666253 · PMC13044521 · Cancer immunology research · 2026 · 6 claims · 8 setups

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  Tumor biopsies from anti-PD-1-resistant SCCHN show significantly more EGFR and MYCL amplifications and increased MYC pathway alterations compared with anti-PD-1-naive tumors

  ffpe blood tumor whole-exome bulk multiplex

• Repurposing public sarcoma multi-omics for neoantigen discovery.

  PMID 42012689 · PMC13100081 · Cancer immunology, immunotherapy : CII · 2026 · 8 claims · 7 setups

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  Reanalysis of legacy CKS multi-omic data shows that standard genome-wide metrics frequently underestimate the true immunogenic potential of these tumors.

  paired cks peptides whole-exome rna-seq hla

• Aging-associated differences in mammary tumor-initiating populations and immune evasion pathways in breast cancer.

  PMID 41719331 · PMC12933083 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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  Age at NMU exposure critically influences tumor incidence, mutational burden, molecular subtype, and the tumor immune microenvironment

  virgin mammary tcga-brca carcinogen-induced immunofluorescence bulk

• Bacillus Calmette-Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer.

  PMID 35311085 · PMC8930202 · Frontiers in oncology · 2022 · 8 claims · 8 setups

  Has reproduction · 30

  BCG therapy has bidirectional effects on tumor evolution and immune checkpoint landscape, with a significant reduction in neoantigen burden percentage in relapsed tumors

  tur matched nmibc relapsed whole-exome sequencing immune

• Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.

  PMID 41691315 · PMC12927254 · Genome medicine · 2026 · 8 claims · 8 setups

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  Tumor purity-adjusted DNA methylation profiling of 95 primary LUAD samples identifies four distinct epigenetic subtypes (epitypes M1-M4)

  luad methylation sequencing targeted

• Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

  PMID 41794040 · PMC13006398 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  CSF exhibits distinct, disease-specific immune landscapes across CNSL, BrMs, and GB-associated LMD

  csf peripheral brain cell-free single-cell deep spatial

• Molecular profiling of breast cancer in native American women reveals distinct genomic and transcriptomic features.

  PMID 41844957 · PMC13144316 · NPJ precision oncology · 2026 · 8 claims · 6 setups

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  This is the first multi-omics (mutation, CNV, RNA-seq) characterization of breast tumors from Native American women, providing a resource for future studies

  breast degs targeted panel-derived whole-transcriptome