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 · 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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Has reproduction · 99
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.
PMID 36513983 · PMC9749362 · BMC bioinformatics · 2022 · 8 claims · 7 setups
Long-read classifiers generally performed best among the 11 methods tested
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Has reproduction · 100
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups
nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.
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Has reproduction · 82
The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.
PMID 36196618 · PMC9720673 · Development (Cambridge, England) · 2022 · 8 claims · 8 setups
Can-elt-3 (and orthologues in C. portoensis and C. monodelphis) is expressed in the early E lineage prior to elt-2 orthologue expression
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Full-text index only
StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.
PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups
StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.