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 · 78
Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.
PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 7 setups
INVADE-seq simultaneously captures host and bacterial transcripts to map bacteria-host interactions across diverse testicular cell types at single-cell resolution
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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.
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Has reproduction · 50
Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.
PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups
BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes
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Has reproduction · 74
Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.
PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups
The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.
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Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.
PMID 17949499 · PMC2148065 · BMC genomics · 2007 · 8 claims · 8 setups
ECM-stimulated hMSC and OS-media-stimulated hMSC represent two distinct intermediate/transitional phenotypes en route to becoming osteoblasts
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Has reproduction · 90
The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.
PMID 41739249 · PMC12935840 · Archives of virology · 2026 · 7 claims · 7 setups
Phage Mimer is the first described single-stranded DNA phage targeting Pectobacterium and belongs to the family Microviridae, subfamily Bullavirinae.
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The genomics of probiotic intestinal microorganisms.
PMID 15998456 · PMC1175979 · Genome biology · 2005 · 8 claims · 8 setups
Genomic characterization of probiotic and commensal intestinal bacteria will deepen understanding of their beneficial effects on host health
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Has reproduction · 96
A bioinformatic pipeline for simulating viral integration data.
PMID 35496474 · PMC9046613 · Data in brief · 2022 · 7 claims · 3 setups
A snakemake-based pipeline was developed to simulate integration of a viral or vector genome into a host genome, including sub-genomic fragment integration, structural variation, and host-site deletions.
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Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups
About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain
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MODBASE, a database of annotated comparative protein structure models and associated resources.
PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups
MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.
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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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The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.
PMID 19914934 · PMC2808860 · Nucleic acids research · 2010 · 8 claims · 5 setups
GOLD is a comprehensive, centralized resource for tracking genome and metagenome sequencing projects and their associated metadata worldwide.
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Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.
PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups
966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome
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The genome of the simian and human malaria parasite Plasmodium knowlesi.
PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups
The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.
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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 · 8 setups
R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani', 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', and Wolbachia).
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Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.