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).
-
Has reproduction · 92
Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.
PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups
cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.
-
Has reproduction · 94
Genome-wide insights into population structure and host specificity of Campylobacter jejuni.
PMID 33990625 · PMC8121833 · Scientific reports · 2021 · 8 claims · 6 setups
Both core and accessory genome characteristics show strong association with distinct host animal species, indicating multiple independent adaptive trajectories rather than a single common evolutionary path
-
Has reproduction · 95
A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.
PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups
ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids
-
Full-text index only
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.
PMID 19781061 · PMC2768977 · Genome biology · 2009 · 8 claims · 7 setups
The 027 genomes (CD196 and R20291) contain 234 additional genes compared to strain 630, spread across at least 50 regions of genetic difference, including a phage island, transposon genes, two-component response regulators, drug resistance genes and transporters
-
Has reproduction
Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.
PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups
SDSD is a distinct taxonomic entity, supported by a mean pairwise average nucleotide identity (ANI) of 99% among isolates
-
Has reproduction · 91
Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.
PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups
73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3
-
Has reproduction · 100
Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.
PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 8 claims · 7 setups
WGS typing of the S. Adjame outbreak showed marked sub-clustering and genetic heterogeneity atypical of a point-source Salmonella outbreak
-
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
-
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
-
Has reproduction · 69
Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.
PMID 38711928 · PMC11070470 · Frontiers in cellular and infection microbiology · 2024 · 8 claims · 8 setups
Sequenced GBS isolates from Saudi Arabia show high genetic diversity, with 28 sequence types and nine distinct serotypes including uncommon serotypes VII and VIII
-
Has reproduction · 85
Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.
PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups
18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.
-
Has reproduction · 89
Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.
PMID 36752777 · PMC9997745 · Microbial genomics · 2023 · 8 claims · 8 setups
Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types.
-
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
-
Has reproduction · 79
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups
196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions
-
Has reproduction · 82
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
An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis
-
Has reproduction · 95
A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.
PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups
P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)
-
Full-text index only
Insights into vertebrate evolution from the chicken genome sequence.
PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups
Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals
-
Full-text index only
Viruses take center stage in cellular evolution.
PMID 16787527 · PMC1779534 · Genome biology · 2006 · 8 claims · 6 setups
A large poxvirus-like dsDNA virus may have become the eukaryotic nucleus after being taken in by an ancestral cell (viral eukaryogenesis)
-
Has reproduction · 68
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.
PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups
The complete genome of L. plantarum ZLP001 was sequenced and compared with 18 other L. plantarum genomes to identify genomic features underlying its gut-health-promoting probiotic properties.
-
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.