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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Network inference and network response identification: moving genome-scale data to the next level of biological discovery.
PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups
Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability
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Has reproduction · 78
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.
PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups
Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely
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Has reproduction · 85
Single-Cell Differential Network Analysis with Sparse Bayesian Factor Models.
PMID 35186014 · PMC8855158 · Frontiers in genetics · 2021 · 8 claims · 2 setups
A hierarchical Bayesian factor model using treatment-dependent latent factor loadings can construct gene co-expression networks from scRNA-seq data and identify differences in network structure between two (or more) biological conditions.
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Quantitative phosphoproteomics by mass spectrometry: past, present, and future.
PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups
Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS