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 28

System / cell line: strains ✕ Assay: sanger ✕ Clear

SNPdetector: a software tool for sensitive and accurate SNP detection.

PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

inbred unrelated zebra same pcr manual comparative
Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.

PMID 19906940 · PMC2885759 · The Journal of general virology · 2010 · 8 claims · 5 setups

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Both PCR sequencing and IGA sequencing (via de novo assembly guiding reference-dependent assembly plus PCR finishing) can successfully generate complete HCMV genome sequences from infected cell cultures and clinical specimens

hcmv six pcr illumina reference-dependent
Global genetic diversity of human metapneumovirus fusion gene.

PMID 15207075 · PMC3323143 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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Phylogenetic analysis of the HMPV F gene identifies two main groups (A and B, 93%-96% amino acid identity) further divided into four subgroups (A1, A2, B1, B2)

hmpv llc-mk2 clinical rt-pcr sequence phylogenetic
Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand.

PMID 19453423 · PMC4941901 · Influenza and other respiratory viruses · 2008 · 8 claims · 6 setups

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Phylogenetic analysis revealed nine distinct genotypes among the 12 Thai SIVs examined.

swine nasal infectious embryonated rt-pcr subtype-specific viral
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

PMID 18258114 · PMC2600181 · Emerging infectious diseases · 2008 · 8 claims · 7 setups

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The nonstructural genes, especially NS5, are the most variable regions between highly and less neuroinvasive lineage 2 WNV strains

lineage mice patients complete phylogenetic nucleotide
Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

tlr4 mus chimpanzee baboon genomic coding sequence
In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

strains genomic celera blast-based targeted phred
First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

PMID 16959032 · PMC1570496 · Retrovirology · 2006 · 8 claims · 6 setups

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Nearly full-length sequencing of 10 HIV-1 seroincident MSM samples revealed 6 subtype B, 3 unique BF recombinants, and 1 novel B/C/F triple recombinant

pbmcs assembled hiv-1 triple nearly phylogenetic bootscan
Genetic variation of St. Louis encephalitis virus.

PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

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Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

slev rt-pcr phylogenetic recombination
A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species.

PMID 18618024 · PMC2453075 · PLoS neglected tropical diseases · 2008 · 7 claims · 8 setups

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ETR-D sequencing allows accurate, single-step identification of MTC species, circumventing the expensive polyphasic approach.

mtc tuberculosis phenotypic pcr mptr
Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

hcv 5'ncr serum maximum sequence recombination
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
TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

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tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

clinical pcr-negative representative whole-cell conventional colony locus-specific
Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

clinical concatenated cereus isolates multilocus phylogenetic pcr
Diversity of the parB and repA genes of the Burkholderia cepacia complex and their utility for rapid identification of Burkholderia cenocepacia.

PMID 18328098 · PMC2324101 · BMC microbiology · 2008 · 8 claims · 7 setups

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repA sequences show distinct clustering of B. cenocepacia relative to other Bcc species, enabling design of a species-specific multiplex PCR

burkholderia six bcc panel pcr phylogenetic multilocus
The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

coli hep-2 pslm862 eaec colony hep-2 pcr
More biology from the sequence.

PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

schizosaccharomyces chromosome genome cervical whole-genome sequence genome
Endemic Venezuelan equine encephalitis in northern Peru.

PMID 15200823 · PMC3323213 · Emerging infectious diseases · 2004 · 8 claims · 8 setups

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Four VEE complex lineages cocirculate in the Peruvian Amazon region: subtype ID (Panama genotype and Colombia/Venezuela genotype), subtype IIIC, and a newly proposed subtype IIID

veev pe2 subtype cotton sscp pcr phylogenetic
Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

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The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

cloned clinical hominis pcr culture sanger

Experiments

SNPdetector: a software tool for sensitive and accurate SNP detection.

Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.

Global genetic diversity of human metapneumovirus fusion gene.

Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

Genetic variation of St. Louis encephalitis virus.

A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species.

Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

Diversity of the parB and repA genes of the Burkholderia cepacia complex and their utility for rapid identification of Burkholderia cenocepacia.

The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

More biology from the sequence.

Endemic Venezuelan equine encephalitis in northern Peru.

Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.