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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Has reproduction · 77
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.
PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 6 claims · 8 setups
PredTAD, a Gradient Boosting Machine model using epigenomic and genomic ChIP-seq-derived features plus neighboring-bin information, classifies 10 kb genomic bins as TAD boundary or non-boundary
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A simple and robust method for connecting small-molecule drugs using gene-expression signatures.
PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups
A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.
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Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.
PMID 12865921 · PMC2394238 · British journal of cancer · 2003 · 6 claims · 3 setups
Hierarchical cluster analysis of 2-DE proteome data can distinguish normal breast, benign breast, and breast cancer tissues based on protein expression profiles
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A qualitative assessment of direct-labeled cDNA products prior to microarray analysis.
PMID 15762992 · PMC1079821 · BMC genomics · 2005 · 5 claims · 5 setups
The Agilent 2100 Bioanalyzer can be used in a novel assay to assess the quality/quantity of direct-labeled Cy-dye cDNA prior to microarray hybridization