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 · 94
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.
PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups
Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power
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Has reproduction · 79
Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.
PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups
AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies
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Full-text index only
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.
PMID 37036103 · PMC10084500 · GigaScience · 2022 · 8 claims · 8 setups
GEN-ERA is a unified, publicly available toolbox of 13 Nextflow workflows supported by 14 Singularity containers for reproducible microbial genomic/phylogenomic analyses in both bacteria and small eukaryotes.
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Has reproduction · 86
Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.
PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 6 setups
Plasmid types II and III have more stable size, larger core genomes, and phylogenies that track the chromosome, indicating predominantly vertical transmission