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 61

System / cell line: types ✕ Assay: sequence ✕ Clear

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
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
HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

PMID 15629059 · PMC5172246 · Genomics, proteomics & bioinformatics · 2003 · 7 claims · 5 setups

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HLA-A gene shows high polymorphism in the Northern Chinese Han population, with 74 gene types and 36 alleles detected in 161 individuals

genomic ihwg peripheral allele sequence-based pcr sbt
Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

PMID 12890320 · PMC3023423 · Emerging infectious diseases · 2003 · 8 claims · 4 setups

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Lateral gene transfer (LGT) produced roughly three times as many nucleotide changes as point mutation among the 96 O139 isolates.

vibrio same novel aligned multilocus pcr blast
Population genomics: diversity and virulence in the Neisseria.

PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

neisseria meningitidis meningococcal multi-locus microarray genome
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
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
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

genome transcriptome gene genes full-length genome cdna
Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

geographically cjd novel jejuni multilocus comparative phenotypic
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
Sys-BodyFluid: a systematical database for human body fluid proteome research.

PMID 18978022 · PMC2686600 · Nucleic acids research · 2009 · 6 claims · 4 setups

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Sys-BodyFluid is a web-based database integrating proteomic data from 11 human body fluids (plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, milk, amniotic fluid), containing over 10,000 proteins

body curated proteins literature sequence cross-body-fluid
Lineage specific recombination rates and microevolution in Listeria monocytogenes.

PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Recombination is more prevalent in lineage II than in lineage I

listeria allelic unique monocytogenes multilocus sawyer's genealogical
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
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
The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

PMID 19912342 · PMC2868947 · FEMS immunology and medical microbiology · 2010 · 7 claims · 5 setups

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The types of vaginal bacterial communities found in Japanese women closely resemble those previously found in White and Black North American women.

vaginal japanese t-rflp clone cluster
Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract.

PMID 31608047 · PMC6769089 · Frontiers in microbiology · 2019 · 7 claims · 5 setups

Has reproduction · 93

Five amplicon sequence variants (unclassified Flavobacteriales, Fusibacter, Planktotalea, Algicola, and Vibrio) were consistently enriched in disease lesions across three coral species (M. cavernosa, D. labyrinthiformis, D. stokesii)

coral cavernosa 16s differential principal
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

Has reproduction · 69

Sequenced GBS isolates from Saudi Arabia show high genetic diversity, with 28 sequence types and nine distinct serotypes including uncommon serotypes VII and VIII

gbs whole-genome multilocus capsular
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

subset drosophila ensembl lc-ms icat peptide-to-genome
Cataloging coding sequence variations in human genome databases.

PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

coding hapmap concurrent nssnps database hapmap amino
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

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SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

embryonic hesc small sequence adapter

Experiments

Coxiella burnetii genotyping.

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

HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

Population genomics: diversity and virulence in the Neisseria.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

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

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Sys-BodyFluid: a systematical database for human body fluid proteome research.

Lineage specific recombination rates and microevolution in Listeria monocytogenes.

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

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

The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract.

Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

Cataloging coding sequence variations in human genome databases.

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.