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).

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

  PMID 41699006 · PMC13002898 · Scientific reports · 2026 · 8 claims · 8 setups

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  CDC20, PLK1, BUB1, CDC45, and CDCA5 are concordantly identified as hub genes across seven NCBI-GEO datasets and the Pakistani RNA-seq dataset

  pakistani pdac overlapping tcga-paad bulk functional protein-protein

• Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.

  PMID 41579861 · PMC12923976 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  oncRNA binary presence-absence patterns constitute digital molecular barcodes that capture cancer type and subtype identity

  tcga exrna cptac mda-mb-231 small machine atac-seq

• Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

  PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 74

  540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

  breast colorectal lung common microarray kegg protein-protein

• SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

  PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

  user-submitted query genomes proteins domain profile-profile comparative

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime

• CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

  PMID 41686262 · PMC13136879 · Cancer immunology research · 2026 · 8 claims · 8 setups

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  CLK1 is markedly upregulated in immune-cold colorectal tumors and correlates with increased MDSC infiltration and CD8+ T-cell exclusion

  colorectal tcga-coad ct26 tumor scrna-seq bulk multiplex

• M6A-mediated molecular patterns and tumor microenvironment infiltration characterization in nasopharyngeal carcinoma.

  PMID 38532632 · PMC10978033 · Cancer biology & therapy · 2024 · 8 claims · 8 setups

  Has reproduction · 76

  NPC patients can be divided into two distinct m6A-related molecular subclasses based on prognostic m6A regulator expression

  npc gse102349 clinical expression ssgsea cibersort

• Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

  PMID 29783948 · PMC5963079 · BMC genomics · 2018 · 8 claims · 8 setups

  Has reproduction · 85

  Whole transcriptome sequencing with extensive TSS mapping identified 3078 transcription start sites and 629 ncRNAs in V. cholerae N16961

  cholerae lexa identified directional end rt-pcr