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).

• Estrogen Production in Pancreatic Cancer Shapes a Tumor-Suppressive Stromal Microenvironment.

  PMID 41258799 · PMC12862343 · Cancer research · 2026 · 8 claims · 6 setups

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  Serum levels of stromal biomarkers associated with favorable outcomes were significantly higher in female patients with PDAC than in male patients

  pdac pdx magnetic bioinformatic single-nucleus

• TGFβ induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis.

  PMID 41492090 · PMC12858408 · Nature cancer · 2026 · 7 claims · 8 setups

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  TGFβ initially induces a full, typical EMT (stress fibers, loss of epithelial markers, motility) in dormancy-competent LUAD progenitors that subsequently transitions into an atypical spheroidal mesenchymal state lacking actin stress fibers.

  h2087-lcc m802t4-lcc reconstructed immunofluorescence antibody-mediated

• Deep-learning prediction of gene expression from personal genomes.

  PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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  Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

  gtex rosmap same monocyte paired mutagenesis chromhmm

• A cellular epigenetic classification system for glioblastoma.

  PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

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  ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

  gbm healthy pseudo-bulk tcga illumina single-cell deconvolution

• Tachykinin signaling defines distinct populations of glia in the enteric nervous system.

  PMID 41512855 · PMC12832054 · Neuron · 2026 · 8 claims · 8 setups

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  Mucosal and muscularis glia are transcriptionally distinct populations, with mucosal glia resembling microglia and muscularis glia resembling satellite glia/astrocytes

  ileum gfp+ intestinal intestine bulk scrna-seq bayesprism

• Integrating human plasma proteomes with genome-wide association data implicates novel proteins and drug targets for rheumatoid arthritis.

  PMID 41540382 · PMC12892679 · Clinical proteomics · 2026 · 8 claims · 8 setups

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  PWAS integrating RA GWAS with ARIC and INTERVAL plasma pQTL data identified 35 genetically regulated proteins (42 associations) significantly associated with RA risk.

  plasma shared gtex blood proteome-wide two-sample bayesian

• Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

  PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

  pancreatic kpc pdac tcga-paad rna-seq bulk proteomics

• pmid-41619969

  PMID 41619969 · PMC13051935 · 8 claims · 8 setups

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  POU2F3 ChIP-seq in isolated murine tuft cells identifies high-confidence POU2F3 binding sites/target genes enriched at gene promoters and the POU consensus motif

  facs-isolated pou2f3 duodenal non-small-cell chip-seq novo bulk

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• PDA: Pooled DNA analyzer.

  PMID 16643673 · PMC1539032 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  No software existed prior to PDA for complete pooled-DNA analysis including data standardization, allele frequency estimation, and single/multipoint association tests

  heterozygous pools ordered peak pooled single-point

• SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation.

  PMID 42026820 · PMC13106921 · Molecular ecology resources · 2026 · 7 claims · 5 setups

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  Naive diversity estimators applied directly to UCE alignments underestimate nucleotide diversity due to negative selection/conservation at the UCE core.

  honeybee finches sheep smelt whole-genome targeted

• Calculating expected DNA remnants from ancient founding events in human population genetics.

  PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

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  Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

  simulated forward-based size

• Comprehensive benchmarking of large language models for RNA secondary structure prediction.

  PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

  Has reproduction · 88

  Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

  archiveii bprna large-scale secondary cross-family self-supervised

• Protein co-evolution, co-adaptation and interactions.

  PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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  The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

  nuoe intra-protein coli interacting phylogenetic correlated domain-restricted

• A blood-based DNA damage signature in patients with Parkinson's disease is associated with disease progression.

  PMID 40913219 · PMC12443628 · Nature aging · 2025 · 8 claims · 2 setups

  Has reproduction · 69

  A blood-based DNA damage signature is present in PD patients and is associated with disease progression.

  blood gwas bulk genetic

• Using multiple alignments to improve seeded local alignment algorithms.

  PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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  Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

  alignment query leave-one-species-out seeded

• Bcipep: a database of B-cell epitopes.

  PMID 15921533 · PMC1173103 · BMC genomics · 2005 · 8 claims · 2 setups

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  Bcipep is a comprehensive database of experimentally determined linear B-cell epitopes compiled from literature and other public databases

  synthetic antigenic anti-peptide sequence

• Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

  PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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  Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

  pediatric same oligonucleotide quantitative

• An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations.

  PMID 32425511 · PMC7218276 · Bioinformatics and biology insights · 2020 · 8 claims · 6 setups

  Has reproduction · 84

  An integrated methodology combining nonnegative matrix factorization (NMF), the WebGestalt functional enrichment tool, and an ad hoc gene extraction procedure automatically identifies informative gene subsets from microarray data matrices that differ in number of genes (rows) and patients (columns)

  caf bone extracted microarray functional

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour