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).

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 6 setups

  Has reproduction · 87

  CoINcIDE is a methodological framework that discovers replicable patient subtypes (meta-clusters) across multiple datasets by finding consensus across dataset-specific clusterings, requiring no between-dataset transformations.

  breast ovarian simulated gene semi-supervised novo

• Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.

  PMID 18047719 · PMC2099488 · BMC bioinformatics · 2007 · 8 claims · 5 setups

  Full-text index only

  Deconvoluting gene expression variance into technical (Gaussian, ~6.5% relative SD) and biological components identifies hypervariable (HV) genes that reflect true biological response to infection without requiring replicates

  urothelial clustered genome-wide confocal k-means

• Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

  PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

  Has reproduction · 87

  NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

  lines bulk single-cell housekeeping bulk pca single-sample

• COVID-19 vaccination atlas using an integrative systems vaccinology approach.

  PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups

  Has reproduction · 69

  mRNA vaccines induce transient but strong immune responses after booster doses

  pbmcs immune pbmc bulk gene principal

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

• Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.

  PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 84

  TEPs from NSCLC patients show 111 upregulated and 108 downregulated genes compared to platelets from non-cancer donors

  platelets degs platelet-specific tep-specific transcriptome pathway k-means