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 · 87
Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.
PMID 41419779 · PMC12858935 · Scientific data · 2025 · 7 claims · 8 setups
A standardized assembly, binning, and dereplication pipeline was used to reconstruct 2,965 non-redundant MAGs from 38 mangrove sediment samples across six sites in Guangxi
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Has reproduction · 84
Towards reliable whole genome sequencing for outbreak preparedness and response.
PMID 35945497 · PMC9361258 · BMC genomics · 2022 · 7 claims · 4 setups
Amplicon-based Nanopore sequencing can rapidly generate whole genome sequences in samples with viral load up to Ct 33.
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A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.
PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups
Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis
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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)
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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 · 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 · 88
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.
PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups
Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life
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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
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Has reproduction · 66
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups
RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.
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Has reproduction · 76
What the Phage: a scalable workflow for the identification and analysis of phage sequences.
PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups
WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow
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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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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
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Has reproduction · 79
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.
PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups
Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses
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Has reproduction · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.
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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
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Has reproduction · 95
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.
PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups
Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns
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Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.
PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups
VLU infections are polymicrobial with no single bacterium colonizing the wounds
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Has reproduction · 91
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.
PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups
SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes
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Has reproduction · 90
Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.
PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.
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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.