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).

• Absence of the TAP2 human recombination hotspot in chimpanzees.

  PMID 15208713 · PMC423135 · PLoS biology · 2004 · 6 claims · 7 setups

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  The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees.

  western haplotype males simulated resequencing ld-based sperm

• 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

• New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.

  PMID 18673538 · PMC2553414 · Retrovirology · 2008 · 7 claims · 5 setups

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  04FR-KZS clusters with two previously described DRC viruses and represents CRF27_cpx, a complex recombinant involving A/E/G/H/J/K/U subtypes.

  pbmcs v3-v5 full-length undetermined v3-v5 full-length phylogenetic

• Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

  PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

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  PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

  cerevisiae genome chimpanzee hot computational microarray comparative

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage

• Mice and more.

  PMID 14519193 · PMC328447 · Genome biology · 2003 · 8 claims · 7 setups

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  A multispecies weighted conservation score, which accounts for each species' divergence rate, can identify conserved non-coding sequences (multispecies conserved sequences, MCSs) likely to be biologically significant

  cftr ciona embryonic chromosome comparative genome bac-based

• Recombinant vaccine-derived poliovirus in Madagascar.

  PMID 12899139 · PMC3023450 · Emerging infectious diseases · 2003 · 7 claims · 4 setups

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  Five acute flaccid paralysis cases in southern Madagascar were associated with vaccine-derived poliovirus (VDPV) type 2 isolates

  poliovirus genbank rflp partial sequence

• High genetic variability of HIV-1 in female sex workers from Argentina.

  PMID 17697319 · PMC1971708 · Retrovirology · 2007 · 7 claims · 6 setups

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  HIV-1 genetic diversity among Argentine FSWs is extensive, with BF recombinants predominating over subtypes B and C

  pbmc-derived aligned near pro heteroduplex pcr near

• Assisted large fragment insertion by Red/ET-recombination (ALFIRE)--an alternative and enhanced method for large fragment recombineering.

  PMID 17517785 · PMC1904275 · Nucleic acids research · 2007 · 6 claims · 7 setups

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  ALFIRE allows insertion of any fragment into small or large episomes without requiring an antibiotic selection gene in the final construct

  coli psc101badγβαa[hygro] psc101badγβαa-i-scei[amp] i-scei-cs-hmlhcgr-bac bacterial restriction pcr

• Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

  PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

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  HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

  plasma proviral cloned pbmc hiv-1 nested clonal

• 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

• A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

  PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

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  A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

  family k4425 embryonic scn9a-n641y linkage copy deletion

• Patterns and rates of intron divergence between humans and chimpanzees.

  PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups

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  Intron divergence (Ki) is strongly positively correlated with intron length

  orthologous genome whole-genome cpg recombination

• A genome search for primary vesicoureteral reflux shows further evidence for genetic heterogeneity.

  PMID 18197425 · PMC2259258 · Pediatric nephrology (Berlin, Germany) · 2008 · 8 claims · 7 setups

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  Genome-wide linkage analysis identifies several novel loci for primary VUR on chromosomes 1, 3, 4, and 22, supporting genetic heterogeneity.

  patients multiplex index pedigree genome-wide fine-mapping haplotype

• Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

  PMID 10081673 · PMC2627691 · Emerging infectious diseases · 1999 · 8 claims · 8 setups

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  Among 79 HIV-1 infected patients, 3 (3.8%) had dual infections, 6 (7.6%) had recombinant infections, and 70 (88.6%) had single-subtype infections

  pbmc uncultured pcr-amplified aligned rflp heteroduplex nested

• Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

  PMID 18832376 · PMC2577333 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  A novel enhancer trap method retrofitting BACs with Tn10-based transposons enables nontargeted, functional mapping of noncontiguous cis-regulatory elements as zebrafish transgenes.

  zebrafish bac genomic transgenic field bac

• 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