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).

• CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

  PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

  breast commercial vertebrate genes cdna activity computational

• Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.

  PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 7 claims · 7 setups

  Has reproduction · 100

  A distinct gene co-expression module with a prominent T cell signature is associated with unstable plaques.

  carotid calcified atherosclerotic cell-specific microarray single-cell immunohistochemistry

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

  PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups

  Has reproduction · 100

  Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.

  gbm glioma gbm-focused glioma-related transcriptomic differential gene-regulatory

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• TRED: a transcriptional regulatory element database, new entries and other development.

  PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

  Full-text index only

  TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

  cancer-related computational literature database

• A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

  PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

  Has reproduction · 95

  RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

  tcga er+ ccle computational spearman correlation gene