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).

• Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

  PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

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  The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

  chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus

• 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

• Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

  PMID 19788831 · PMC2819849 · Emerging infectious diseases · 2009 · 8 claims · 5 setups

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  NA gene sequences of oseltamivir-resistant viruses (ORVs) form a distinct phylogenetic cluster separate from oseltamivir-sensitive viruses (OSVs)

  influenza clinical partial sanger pyrosequencing molecular

• 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

• 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

• G, N, and P gene-based analysis of Chandipura viruses, India.

  PMID 15705335 · PMC3294343 · Emerging infectious diseases · 2005 · 8 claims · 4 setups

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  The 2003 epidemic CHPV isolates are closely related to, and not very divergent from, the 1965 isolate, indicating the outbreak was not associated with extensive mutations in the G, N, and P genes.

  chpv partial rt-pcr sequence phylogenetic

• Eighth major clade for hepatitis delta virus.

  PMID 17073101 · PMC3294742 · Emerging infectious diseases · 2006 · 7 claims · 7 setups

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  Three HDV isolates (dFr644, dFr2072, dFr2736) form a monophyletic group distinct from HDV-1 through HDV-7, constituting a new eighth major clade (HDV-8) of the Deltavirus genus.

  serum-derived complete same shd rt-pcr sequence phylogenetic

• Genomic signatures of human versus avian influenza A viruses.

  PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

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  52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

  throat clinical 401-genome avian rt-pcr immunofluorescent sequence

• Association of Escherichia coli O157:H7 tir polymorphisms with human infection.

  PMID 17718910 · PMC2063500 · BMC infectious diseases · 2007 · 8 claims · 6 setups

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  tir polymorphisms 255 T>A and RR1-RU3 (presence/absence) associate strongly with human vs bovine isolate source

  stec pcr multiplex elisa

• 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

• 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

• 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

• Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand.

  PMID 19643205 · PMC2790030 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2009 · 8 claims · 6 setups

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  The domain II loop of PvAMA-1 is almost completely conserved at the amino acid level, consistent with strong purifying selection.

  plasmodium pvama-1 vivax pcr molecular merozoite

• A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

  PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

  Has reproduction · 76

  58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

  asfv b602l porcine sardinian whole-genome sanger haemoadsorption

• 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

• Genetic diversity of vaccine candidate antigens in Plasmodium falciparum isolates from the Amazon basin of Peru.

  PMID 18505558 · PMC2432069 · Malaria journal · 2008 · 8 claims · 7 setups

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  CSP (Th2R/Th3R region) is polymorphic in Peruvian isolates, with four distinct alleles identified, none identical to the 3D7 vaccine strain

  pfcsp pfmsp-1 pfama-1 pflsa-1 pcr polymorphism multilocus

• 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

• 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

• Evaluation of the intra- and inter-specific genetic variability of Plasmodium lactate dehydrogenase.

  PMID 17961215 · PMC2194689 · Malaria journal · 2007 · 8 claims · 8 setups

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  No nucleotide variation was found among 49 P. falciparum pLDH isolates (100% homology)

  falciparum vivax ovale malariae nested-pcr