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).
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Full-text index only
Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.
PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups
Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1
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Has reproduction · 71
Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.
PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups
Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.
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Has reproduction · 85
NETISCE: a network-based tool for cell fate reprogramming.
PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups
NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.
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Has reproduction · 59
Nucleosome regulatory dynamics in response to TGFβ.
PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups
SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.