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).

• Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

  PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

  Full-text index only

  RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

  tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 8 claims · 6 setups

  Has reproduction · 69

  An ensemble feature selection strategy using consensus of feature relevance across 8 classifier types identifies a 100-miRNA signature from a 1046-feature TCGA dataset

  tcga geo mirnas mirna feature bibliographic

• 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

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• The relationship between PLOD1 expression level and glioma prognosis investigated using public databases.

  PMID 34040895 · PMC8127981 · PeerJ · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  PLOD1 mRNA expression is significantly higher in glioma tissue than in normal brain tissue

  glioma gbm cancer gene online genomic

• DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

  PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 84

  DeepProg is a novel ensemble framework of deep-learning and machine-learning approaches that robustly predicts patient survival subtypes using multi-omics data

  cancer breast hepatocarcinoma tcga multi-omics gene rna-seq