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).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: allelic ✕ Assay: phylogenetic ✕ Clear

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

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Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

proteins cdc candidate yersinia all-against-all computational cross-species
Identification of functional SNPs in the 5-prime flanking sequences of human genes.

PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

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7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

flanking synthetic genomic cloned comparative electrophoretic rflp
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

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Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

salmonella sequenced typhi whole-genome snp-based selection
MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome.

PMID 19702866 · PMC3985121 · Journal of applied microbiology · 2010 · 8 claims · 4 setups

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Danish C. jejuni isolates from gastroenteritis, RA and GBS patients are highly genetically diverse, comprising 51 STs within 18 clonal complexes among 122 isolates.

campylobacter concatenated clonal multilocus upgma clonalframe
Coxiella burnetii genotyping.

PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

coxiella burnetii matrix sequence pcr molecular pcr-based
Characterisation of the genetic diversity of Brucella by multilocus sequencing.

PMID 17448232 · PMC1877810 · BMC microbiology · 2007 · 8 claims · 5 setups

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Brucella isolates show low overall genetic diversity (1.5%) across nine sequenced loci, confirming the genus is genetically conserved.

brucella sequenced concatenated allelic multilocus ratio neighbour-joining
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

Has reproduction · 79

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

rhizobium strains genotype genome whole-genome orthologous snp
Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

PMID 33990625 · PMC8121833 · Scientific reports · 2021 · 8 claims · 6 setups

Has reproduction · 94

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

jejuni core whole-genome core k-mer
Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England.

PMID 15916705 · PMC1180443 · BMC microbiology · 2005 · 8 claims · 8 setups

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H. pylori strains from England are genetically distinct from strains obtained from other countries based on virulence gene analysis (cagT, cagE, cagA, vacA, iceA, oipA, babB)

pylori english pcr sequencing fluorescent
Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

PMID 18307777 · PMC2268939 · BMC microbiology · 2008 · 8 claims · 7 setups

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MLST of 26 C. trachomatis strains reveals three non-overlapping clonal complexes (groups I, II, III)

trachomatis pneumoniae chlamydiales mlst eburst upgma
Toward the use of genomics to study microevolutionary change in bacteria.

PMID 19855823 · PMC2756242 · PLoS genetics · 2009 · 7 claims · 5 setups

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The clonal population structure of bacteria, combined with occasional DNA import, provides a powerful context for identifying genetic bases of adaptive phenotypes via association studies.

neisseria campylobacter helicobacter sequence multilocus phylogeny-based
Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic
Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

genome-sequenced trachomatis same concatenated whole-genome multilocus ompa
Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups

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A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations

anthropi same candidate multi-locus pulsed-field antibiotyping
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population

Experiments

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

Identification of functional SNPs in the 5-prime flanking sequences of human genes.

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome.

Coxiella burnetii genotyping.

Characterisation of the genetic diversity of Brucella by multilocus sequencing.

Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England.

Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

Toward the use of genomics to study microevolutionary change in bacteria.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.