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).

• Improving melanoma classification by integrating genetic and morphologic features.

  PMID 18532874 · PMC2408611 · PLoS medicine · 2008 · 7 claims · 5 setups

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  BRAF-mutant melanomas show distinct morphological features (upward migration and nesting of intraepidermal melanocytes, epidermal thickening, sharper lateral demarcation, larger/rounder/more pigmented tumor cells) compared to non-mutant melanomas

  archival same subset patients histopathological mutation quantitative

• Spatial single-cell analysis reveals tumor microenvironment signatures predictive of oral cavity cancer outcome.

  PMID 41707652 · PMC12923947 · Cell reports. Medicine · 2026 · 8 claims · 6 setups

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  Proliferating (KI67+) PROX1+ lymphatic endothelial cells (LECs) at the tumor invasive margin are a strong independent adverse prognostic factor for recurrence-free and overall survival in early-stage OSCC

  ffpe lymphatic representative oscc imaging ki67+prox1+ transcriptomic

• Different approaches to Imaging Mass Cytometry data analysis.

  PMID 37092034 · PMC10115470 · Bioinformatics advances · 2023 · 8 claims · 5 setups

  Has reproduction

  Imaging Mass Cytometry (IMC) is a high-multiplexing imaging platform capable of simultaneously detecting and visualizing up to 40 different protein targets in tissue sections.

  ffpe imc imaging raw channel

• Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.

  PMID 42062553 · PMC13259927 · Nature methods · 2026 · 8 claims · 6 setups

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  Xenium data show strong consistency across patients and technical replicates, with little technical variation between platforms

  ffpe matched xenium xenium single-nucleus immunohistochemistry

• Information extraction from full text scientific articles: where are the keywords?

  PMID 12775220 · PMC166134 · BMC bioinformatics · 2003 · 8 claims · 5 setups

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  The keyword content of the five article sections (A, I, M, R, D) is heterogeneous, i.e., different sections carry different kinds of information.

  corpus same articles keyword validation qualitative

• Immunoregulatory Roles of Tumor-Originated Pericytes Identified by Single-Cell Analysis in Glioblastoma.

  PMID 41001759 · PMC12713092 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025 · 8 claims · 8 setups

  Has reproduction

  CD146 (MCAM) is a superior surface marker for sorting GBM pericytes, labeling nearly all PDGFRβ+ pericytes with strong specificity, unlike NG2 which labels fewer vessel-associated pericytes.

  facs-sorted frozen dissociated scrna-seq scrna-seq immunofluorescence fluorescence-activated

• Dissecting the immunosuppressive microenvironment of LAMA3 + malignant cells and SPP1 + macrophages in esophageal squamous cell carcinoma using single-cell and spatial transcriptomics.

  PMID 41845425 · PMC13104401 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  A LAMA3+ epithelial subpopulation (C3) enriched at the invasive tumor front shows strong EMT signatures and is associated with poor prognosis

  escc epithelial scrna-seq tcga-escc scrna-seq spatial infercnv

• Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

  PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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  Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

  serum frozen ig-depleted clinical seldi-tof maldi lc-ms

• BRAF mutations in non-Hodgkin's lymphoma.

  PMID 14612909 · PMC2394455 · British journal of cancer · 2003 · 7 claims · 4 setups

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  BRAF is somatically mutated in a subset of NHLs (4/164, 2.4%)

  nhl reamplified haematoxylin-eosin-stained pcr-sscp sequencing microdissection

• Prevalence of von Hippel-Lindau gene mutations in sporadic renal cell carcinoma: results from The Netherlands cohort study.

  PMID 15932632 · PMC1177929 · BMC cancer · 2005 · 7 claims · 4 setups

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  VHL mutations were detected in 61% (114/187) of sporadic clear-cell RCC patients

  archival subset flanking paraffin-embedded pcr-sscp feasibility histopathological

• Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

  PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

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  BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

  colorectal colon patients bulk single-cell spatial bulk

• Decoding the heterogeneity of human undifferentiated spermatogonia reveals RAS-dependent regulation of stem cell fate.

  PMID 41579373 · PMC13003925 · Cell reports · 2026 · 8 claims · 7 setups

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  FSD1 is a cell-surface pan-uSPG marker that enables FACS purification of the entire uSPG population

  testis seminiferous testicular fsd1+ single-cell immunofluorescence whole-mount

• Beta-catenin nuclear labeling is a common feature of sessile serrated adenomas and correlates with early neoplastic progression after BRAF activation.

  PMID 19745699 · PMC2788075 · The American journal of surgical pathology · 2009 · 8 claims · 3 setups

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  Abnormal nuclear β-catenin labeling is common in SSAs but essentially absent in hyperplastic polyps (HPs)

  colorectal microdissected archival immunohistochemistry pcr histopathologic

• The liver as an immunological barrier redefined by single-cell analysis.

  PMID 32176810 · PMC7218664 · Immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 100

  Emerging single-cell technologies have advanced or redefined understanding of the liver's immunological barrier function

  liver c57bl sorted pdgfrb-gfp scrna-seq single-molecule

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 8 claims · 7 setups

  Has reproduction · 64

  Reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut-associated) and Deferribacteres (midgut-associated)

  rimicaris quality-filtered dereplicated deferribacteres shotgun ssu differential

• Heterogeneity of p53 mutational status in intramucosal carcinoma of the colorectum.

  PMID 11223545 · PMC5926696 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 4 setups

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  p53 gene mutations occur and diverge at the intramucosal carcinoma stage, before submucosal invasion

  endoscopically same pcr-based immunohistochemistry histologic

• Development of a fluorescent multiplex assay for detection of MSI-High tumors.

  PMID 15528789 · PMC3839403 · Disease markers · 2004 · 8 claims · 7 setups

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  Mononucleotide markers are the most sensitive and specific microsatellite marker type for detecting MSI-H tumors with MMR defects

  colorectal blood healthy non-msi-h microsatellite fluorescent immunohistochemistry

• Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

  PMID 18559093 · PMC2440550 · Molecular cancer · 2008 · 7 claims · 6 setups

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  Gain of chromosome 5p is the most frequent genomic alteration in invasive cervical cancer

  cervical tumors pap tumor snp fluorescence fish

• HCCaging: a liver physiological aging-related biomarker for hepatocellular carcinoma diagnosis based on transcriptome data.

  PMID 41942446 · PMC13230847 · npj aging · 2026 · 8 claims · 8 setups

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  A 16-gene HCCaging signature was derived via GSVA from genes overlapping age-associated upregulated genes in TCGA, scRNA-seq, and ICGC datasets

  tcga-lihc hcc icgc six bulk single-cell gsva-based

• A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

  PMID 42030938 · PMC13198283 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A multiomic (snRNA-seq, snATAC-seq, WGS, CODEX) atlas defines a core set of pHGG neoplastic cell states shared across molecular subtypes

  phgg neoplastic fetal single-nucleus whole-genome codex