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 14

System / cell line: isolate ✕ Assay: type ✕ Clear

Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

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A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

novel hpv gene h5n1 whole-genome intrinsic statistical
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 · 6 claims · 8 setups

Has reproduction · 82

Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis

klebsiella isolate a55848 assembled short-read phenotypic genome-based
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

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

meningitidis archived strain neisseria whole-genome transposon targeted
SARS-CoV genome polymorphism: a bioinformatics study.

PMID 16144519 · PMC5172477 · Genomics, proteomics & bioinformatics · 2005 · 8 claims · 6 setups

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SARS-CoV isolates can be classified into groups/subgroups based on the number and distribution of SNVs and INDELs relative to a 'profile' sequence, and this classification aligns with phylogenetic tree relationships and epidemiological spread.

sars-cov annotated spike whole-genome positional codon
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
How bacterial communities expand functional repertoires.

PMID 17238278 · PMC1750926 · PLoS biology · 2006 · 8 claims · 7 setups

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The human microbiome contains roughly 100 times as many genes as does the human genome

bacteroides distal interleukin-10-deficient macrophages transcriptional metagenomic microbiota
Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.

PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups

Has reproduction · 92

bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B

sonnei same shigella assembled illumina oxford novo
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

Has reproduction · 91

73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3

monocytogenes isolate whole-genome core minimum
Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.

PMID 36560952 · PMC9763275 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

Has reproduction · 54

Inoculation with SAICEUPSM^T significantly reduces the oxidative stress enzymatic response (CAT, APX, SOD, GR) in Lupinus albus grown under mercury stress

lupinus saiceupsm^t greenhouse enzymatic mercury
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
Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

minimally-passaged pylori coli arginase urease heterologous
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

PMID 19922616 · PMC2784454 · BMC biology · 2009 · 8 claims · 7 setups

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The ratio of homologous recombination to mutation in B. pseudomallei is over two times higher than in Streptococcus pneumoniae, the highest yet reported in bacteria.

isolates genome snp snps multilocus genome bayesian
Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

PMID 19656662 · PMC2744841 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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Pyrosequencing™ can substitute for traditional sequencing methods, providing rapid (<1 h) and reliable detection of antibiotic resistance mutations in P. aeruginosa

clinical extracted pcr fluoroquinolone-resistant kirby–bauer multiplex sanger
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

Experiments

Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

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.

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

SARS-CoV genome polymorphism: a bioinformatics study.

Coxiella burnetii genotyping.

How bacterial communities expand functional repertoires.

Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.

Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.

Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.

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

Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.