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).

• An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

  PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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  A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

  lung known leukemia tumor paired-end computational snp

• Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

  PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 58

  PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA

  cancer tcga-stad stomach ges1 rna-seq pearson gsva

• Predicting position along a looping immune response trajectory.

  PMID 30296270 · PMC6175499 · PloS one · 2018 · 8 claims · 6 setups

  Has reproduction · 98

  Looper is a computational method that automatically identifies phase-shifted gene pairs (using SAX symbolic representation) that trace loops in longitudinal expression data.

  monocytes blood pbmcs montreal microarray qrt-pcr topological

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

  PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups

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  RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)

  u937 saos-2 chip-chip chip-on-chip gene

• Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.

  PMID 19893615 · PMC2764086 · PloS one · 2009 · 8 claims · 8 setups

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  Simultaneous analysis of 347 thyroid samples across 12 histological classes from six datasets improves definition of diagnostic markers compared to prior binary-class studies

  thyroid microarray gene real-time

• The Aging Microenvironment Is a Determinant of Immune Exclusion and Metastatic Fate in Pancreatic Cancer.

  PMID 41202211 · PMC12768431 · Cancer research · 2026 · 8 claims · 8 setups

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  Organismal aging accelerates PDAC progression and metastatic burden in an age-relevant syngeneic orthotopic mouse model

  kpc4662 orthotopic pdac pancreatic orthotopic heterochronic ultrasound