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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TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.
PMID 42277027 · PMC13260335 · Nature communications · 2026 · 8 claims · 5 setups
TOFU-MAaPO yields significantly more high-quality MAGs than metaFun, nf-core/mag, and ATLAS due to integration of multiple complementary binning tools with unified MAGScoT refinement
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Has reproduction · 68
Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.
PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups
Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla
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Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.
PMID 19046425 · PMC2625370 · BMC genomics · 2008 · 6 claims · 7 setups
Identified a 12-bp Bacteroidetes DNA barcode and a 26-bp degenerate Firmicutes DNA barcode within the 16S rRNA gene
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Has reproduction · 58
MZPAQ: a FASTQ data compression tool.
PMID 31171931 · PMC6547476 · Source code for biology and medicine · 2019 · 7 claims · 3 setups
MZPAQ, a hybrid of MFCompress and ZPAQ, outperforms state-of-the-art and general-purpose compression tools on all benchmark datasets in terms of compression ratio