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).

• 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

  Has reproduction · 92

  cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

  jejuni same subset isolate cgmlst hqsnp genome

• Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

  PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 5 setups

  Has reproduction · 83

  CHCT, a hierarchical classification tool, splits classification of 30 cancer types into ten smaller subproblems using a two-tier architecture to classify primary cancer by methylation profile

  cancer clinical training independent methylation upgma random

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

  PMID 15498160 · PMC3320270 · Emerging infectious diseases · 2004 · 6 claims · 6 setups

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  Multiple spacer typing (MST), based on intergenic spacer sequencing, differentiates the three Y. pestis biovars

  pestis combined dental contemporary spacer phylogenetic pcr

• 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

  Full-text index only

  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

• InParanoid 6: eukaryotic ortholog clusters with inparalogs.

  PMID 18055500 · PMC2238924 · Nucleic acids research · 2008 · 8 claims · 3 setups

  Full-text index only

  InParanoid 6 is an updated eukaryotic ortholog database covering 35 species (34 eukaryotes plus E. coli as outgroup), providing pairwise ortholog clusters with inparalogs for all species pairs.

  eukaryotic pairwise average pairwise inparanoid upgma

• Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

  PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

  agaricia agaricites coral sites 2brad population hierarchical

• Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

  PMID 12194772 · PMC2732546 · Emerging infectious diseases · 2002 · 8 claims · 5 setups

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  Clonal complex, as defined by MLST, is an epidemiologically relevant unit for long- and short-term investigation of C. jejuni epidemiology.

  jejuni same clonal mlst multilocus heat-stable flaa

• InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

  PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

  Full-text index only

  InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

  eukaryotic homo sequence species pairwise algorithm low-complexity

• Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

  PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups

  Full-text index only

  560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space

  genodermatoses phenotype disease gene-phenotype manual correlation principal

• Coxiella burnetii genotyping.

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

  Full-text index only

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

  coxiella burnetii matrix sequence pcr molecular pcr-based

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

  PMID 18664269 · PMC2515158 · BMC microbiology · 2008 · 8 claims · 7 setups

  Full-text index only

  18 STR loci (1-5 base repeat units, copy number 4-26) were identified in the M. genitalium G37 genome via bioinformatics analysis.

  genitalium clinical selected 246-bp bioinformatics pcr plasmid

• 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

  Full-text index only

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

  trachomatis pneumoniae chlamydiales mlst eburst upgma

• 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

• Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

  PMID 19793394 · PMC2765450 · BMC genetics · 2009 · 8 claims · 4 setups

  Full-text index only

  The three-locus TaqI B-TaqI D-TaqI A haplotype at DRD2 constitutes a powerful genetic marker reflecting the most ancient dispersal of anatomically modern humans

  genomic genotype rflp haplotype pcr-rflp hardy-weinberg pairwise

• 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

• Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

  PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

  haploid mistral assembled masked whole-genome k-mer genome-wide

• Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

  PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

  Full-text index only

  Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

  gp41 hiv-1 recombination site-specific comparative