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).

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

  PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 6 setups

  Has reproduction · 86

  Plasmid types II and III have more stable size, larger core genomes, and phylogenies that track the chromosome, indicating predominantly vertical transmission

  rhizobium extrachromosomal plasmidome gse long-read k-mer genome

• Segmented filamentous bacteria are worldwide human gut commensals.

  PMID 41786702 · PMC13153320 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Identification and morphological/genomic characterization of a novel human SFB species, Anisomitus miae (Human-SFB-ML), from Malian/Gambian/Kenyan fecal samples, displaying SFB-specific morphology including the attachment tip structure

  fecal sfb human-sfb-ml publicly pacbio maximum gram

• Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

  PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

  Full-text index only

  MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

  mip diagnostic is900-specific pgg

• Microbial metagenomics.

  PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  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

  gastrointestinal acid ocean group metagenomic shotgun comparative

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• From Pasteur to genomics: progress and challenges in infectious diseases.

  PMID 15516917 · PMC7096024 · Nature medicine · 2004 · 8 claims · 8 setups

  Full-text index only

  Genomic sequencing has revealed the blueprint of most pathogens, enabling new diagnostics, therapeutics and vaccines including for previously uncultivable agents.

  bacterial neisseria sars hiv-infected whole-genome reverse nucleic

• Analysis of recent segmental duplications in the bovine genome.

  PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

  bos bovine genes cattle genome fluorescent repeat

• Genomic analysis of bacteria in the Acute Oak Decline pathobiome.

  PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens

  gibbsiella lonsdalea brenneria miseq genome novo comparative

• Comparative genomics and understanding of microbial biology.

  PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

  Full-text index only

  GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

  completed same sequenced mycobacterium whole-genome comparative phylogenomic

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

  Full-text index only

  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

  PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups

  Has reproduction · 89

  Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa

  aureus reduced genome cgmlst comparative

• 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

  Has reproduction · 74

  The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.

  cupriavidus stm taiwanensis genome 16s average

• Patterns and rates of intron divergence between humans and chimpanzees.

  PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Intron divergence (Ki) is strongly positively correlated with intron length

  orthologous genome whole-genome cpg recombination

• The genome of Brugia malayi - all worms are not created equal.

  PMID 18952001 · PMC2668601 · Parasitology international · 2009 · 8 claims · 8 setups

  Full-text index only

  Comparative genome analysis shows conserved long-range synteny but divergent local gene order between B. malayi and C. elegans, reflecting distinct evolutionary trajectories of parasitic and free-living lineages.

  malayi elegans wbm-infected filarial whole-genome genome-wide comparative

• NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis.

  PMID 19818133 · PMC2784325 · Genome biology · 2009 · 8 claims · 5 setups

  Full-text index only

  Determined and manually annotated the complete genome sequence of N. meningitidis clinical isolate strain 8013

  meningitidis archived strain neisseria whole-genome transposon targeted

• Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-Leaved Eriobotrya seguinii (Maleae, Rosaceae).

  PMID 41595526 · PMC12841229 · Genes · 2026 · 8 claims · 7 setups

  Full-text index only

  The E. seguinii mitogenome is the smallest and has the highest GC content of any known Eriobotrya species

  seguinii protein-coding mitogenomes whole-genome mitogenome repeat

• Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

  PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups

  Has reproduction · 72

  Phylogenomic analysis (370,877 amino acids) placed H. duospinosa within the family Neanuridae

  holacanthella duospinosa genome transcriptome phylogenomics

• Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

  PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 8 claims · 8 setups

  Has reproduction · 82

  An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis

  michiganensis a55848 african assembled whole-genome novo genome-based

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD is a distinct taxonomic entity, supported by a mean pairwise average nucleotide identity (ANI) of 99% among isolates

  sdsd sdse isolates genomes genome core-genome multilocus

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq