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 · 90
Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.
PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups
Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified
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Full-text index only
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.
PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups
CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling
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Has reproduction · 64
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
PMID 34614189 · PMC8643649 · Nucleic acids research · 2021 · 8 claims · 8 setups
metaGEM enables end-to-end reconstruction of FBA-ready GEMs directly from metagenomes without relying on reference genomes
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Has reproduction · 64
A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.
PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups
Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).
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Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.
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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 · 69
High-resolution metagenomic reconstruction of the freshwater spring bloom.
PMID 36698172 · PMC9878933 · Microbiome · 2023 · 8 claims · 8 setups
High-frequency metagenomic sampling (57 samples, 3 filter sizes, 2 depths, 37 days) recovers thousands of prokaryotic, eukaryotic, and viral genomes tracking spring bloom succession in fine detail
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Has reproduction · 85
What defines a photosynthetic microbial mat in western Antarctica?
PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups
Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions
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Full-text index only
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.
PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups
Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.