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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Full-text index only
The lords of the genomes.
PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups
Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them
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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 · 93
Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract.
PMID 31608047 · PMC6769089 · Frontiers in microbiology · 2019 · 7 claims · 5 setups
Five amplicon sequence variants (unclassified Flavobacteriales, Fusibacter, Planktotalea, Algicola, and Vibrio) were consistently enriched in disease lesions across three coral species (M. cavernosa, D. labyrinthiformis, D. stokesii)
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Has reproduction · 87
Machine learning reveals microbial interactions driving plastic degradation across plastisphere environments.
PMID 41657981 · PMC12876002 · Frontiers in microbiology · 2025 · 6 claims · 7 setups
Wastewater plastispheres harbor the most diverse and compositionally even microbial communities among the three habitats.
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Has reproduction · 84
Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group.
PMID 35883324 · PMC9312300 · Animals : an open access journal from MDPI · 2022 · 7 claims · 6 setups
Gut microbial diversity (alpha and beta) differs significantly among domestic males, domestic females, and wild male Datong yaks.
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Has reproduction · 77
Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.
PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups
Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.
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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 · 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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MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.
PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups
MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources
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Has reproduction · 70
Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility.
PMID 34021225 · PMC8140134 · Scientific reports · 2021 · 7 claims · 7 setups
Sulfate-reducing Desulfovibrio are the key microbial players responsible for H2S production in swine manure slurry despite being a minor community component
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Microbial genomics: from sequence to function.
PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups
Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.
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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 · 61
Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality.
PMID 41199168 · PMC12590650 · Genetics, selection, evolution : GSE · 2025 · 6 claims · 7 setups
39 heritable and 91 non-heritable bacterial genera were identified in the boar gut based on heritability of relative abundance
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Has reproduction · 55
Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).
PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups
The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation
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Has reproduction · 99
Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.
PMID 36242054 · PMC9563170 · Microbiome · 2022 · 8 claims · 8 setups
Three MAGs from a stratified salt crust represent a novel order, Nucleotidisoterales, within Ca. Nanohaloarchaeota
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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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SNP-VISTA: an interactive SNP visualization tool.
PMID 16336665 · PMC1325058 · BMC bioinformatics · 2005 · 7 claims · 3 setups
SNP-VISTA is an interactive Java-based visualization tool with two versions, GeneSNP-VISTA and EcoSNP-VISTA, for exploring large-scale SNP datasets
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Microbial metagenomics.
PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups
Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides
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Has reproduction · 57
Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.
PMID 32019831 · PMC7002113 · mSystems · 2020 · 8 claims · 7 setups
Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are diverse and abundant in the halite endolithic microbial community, with 1,538 total ncRNAs discovered across Archaea and Bacteria.
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Has reproduction · 63
Contrasting nutrient retention in alpine soils: the role of soil microbiome in phosphorus and nitrogen mobility in scree and meadow environments.
PMID 41632073 · PMC12883989 · FEMS microbiology ecology · 2026 · 6 claims · 8 setups
Scree soils have high mobile nitrate and phosphate, low phosphate sorption ability, and significantly greater phosphorus leaching despite lower organic matter and microbial biomass