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
Using multiple alignments to improve seeded local alignment algorithms.
PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups
Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone
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Has reproduction · 57
Design considerations for workflow management systems use in production genomics research and the clinic.
PMID 34737383 · PMC8569008 · Scientific reports · 2021 · 8 claims · 2 setups
The choice of WfMS depends both on intrinsic language/engine features and on adoption, collaboration, and technical support within bioinformatics consortia.
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Full-text index only
Sequence similarity network reveals common ancestry of multidomain proteins.
PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups
Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.
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Has reproduction
Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.
PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 7 claims · 8 setups
Tabular ML classifiers (TabNet, XGBoost, LightGBM) trained on tumor-only-derived features achieve state-of-the-art somatic vs germline classification, with AUC>94% on TCGA holdout and AUC>85% on metastatic melanoma.