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).
-
Full-text index only
Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.
PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups
The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.
-
Has reproduction · 50
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.
PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups
MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.
-
Has reproduction · 83
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.
PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 7 claims · 8 setups
Phylogenomic analysis of the MAG clarified the taxonomic position of D. lemmermannii within the genus Dolichospermum and the ADA (Anabaena/Dolichospermum/Aphanizomenon) group
-
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
-
Has reproduction · 24
MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.
PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups
MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics
-
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).
-
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
-
Has reproduction · 84
Pharokka: a fast scalable bacteriophage annotation tool.
PMID 36453861 · PMC9805569 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 5 setups
Pharokka is a one-line, fast, scalable bacteriophage annotation tool producing standards-compliant outputs, installable via a two-line bioconda command
-
Has reproduction · 59
Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.
PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups
Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes
-
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
-
Has reproduction · 78
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups
METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.
-
Has reproduction · 66
Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.
PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups
Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient
-
Has reproduction · 71
Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.
PMID 41826827 · PMC13202766 · BMC microbiology · 2026 · 8 claims · 7 setups
R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', Wolbachia)